******************************************************************************** MAST - Motif Alignment and Search Tool ******************************************************************************** MAST version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MAST software please access http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(48-54), 1998. ******************************************************************************** ******************************************************************************** DATABASE AND MOTIFS ******************************************************************************** DATABASE NC_014318.fasta (nucleotide) Last updated on Mon May 18 13:49:22 2015 Database contains 666 sequences, 23310 residues Scores for positive and reverse complement strands are combined. MOTIFS meme.xml (nucleotide) MOTIF WIDTH BEST POSSIBLE MATCH ----- ----- ------------------- 1 6 GAAGGA Random model letter frequencies (from non-redundant database): A 0.274 C 0.225 G 0.225 T 0.274 ******************************************************************************** ******************************************************************************** SECTION I: HIGH-SCORING SEQUENCES ******************************************************************************** - Each of the following 55 sequences has E-value less than 10. - The E-value of a sequence is the expected number of sequences in a random database of the same size that would match the motifs as well as the sequence does and is equal to the combined p-value of the sequence times the number of sequences in the database. - The combined p-value of a sequence measures the strength of the match of the sequence to all the motifs and is calculated by o finding the score of the single best match of each motif to the sequence (best matches may overlap), o calculating the sequence p-value of each score, o forming the product of the p-values, o taking the p-value of the product. - The sequence p-value of a score is defined as the probability of a random sequence of the same length containing some match with as good or better a score. - The score for the match of a position in a sequence to a motif is computed by by summing the appropriate entry from each column of the position-dependent scoring matrix that represents the motif. - Sequences shorter than one or more of the motifs are skipped. - The table is sorted by increasing E-value. ******************************************************************************** SEQUENCE NAME DESCRIPTION E-VALUE LENGTH ------------- ----------- -------- ------ complement(5677612..5678895) NC_014318 Amycolatopsis m... 9.4 35 complement(5874164..5875915) NC_014318 Amycolatopsis m... 9.4 35 complement(5880230..5880985) NC_014318 Amycolatopsis m... 9.4 35 complement(6026538..6027758) NC_014318 Amycolatopsis m... 9.4 35 complement(6068580..6069665) NC_014318 Amycolatopsis m... 9.4 35 complement(6992189..6992929) NC_014318 Amycolatopsis m... 9.4 35 complement(6996886..6997155) NC_014318 Amycolatopsis m... 9.4 35 complement(7056050..7057252) NC_014318 Amycolatopsis m... 9.4 35 complement(695965..697272) NC_014318 Amycolatopsis m... 9.4 35 complement(7309644..7310669) NC_014318 Amycolatopsis m... 9.4 35 complement(7359419..7361269) NC_014318 Amycolatopsis m... 9.4 35 complement(7503077..7504645) NC_014318 Amycolatopsis m... 9.4 35 complement(8193196..8194368) NC_014318 Amycolatopsis m... 9.4 35 complement(8273983..8274804) NC_014318 Amycolatopsis m... 9.4 35 complement(8549687..8551114) NC_014318 Amycolatopsis m... 9.4 35 complement(8561549..8562415) NC_014318 Amycolatopsis m... 9.4 35 complement(8565685..8566755) NC_014318 Amycolatopsis m... 9.4 35 complement(8569664..8570548) NC_014318 Amycolatopsis m... 9.4 35 complement(8887008..8888381) NC_014318 Amycolatopsis m... 9.4 35 complement(8898827..8899747) NC_014318 Amycolatopsis m... 9.4 35 complement(9210049..9211029) NC_014318 Amycolatopsis m... 9.4 35 complement(9468248..9468547) NC_014318 Amycolatopsis m... 9.4 35 complement(936860..938080) NC_014318 Amycolatopsis m... 9.4 35 complement(9883648..9885174) NC_014318 Amycolatopsis m... 9.4 35 complement(10088561..10089895) NC_014318 Amycolatopsis m... 9.4 35 complement(10187287..10190127) NC_014318 Amycolatopsis m... 9.4 35 complement(10191964..10192536) NC_014318 Amycolatopsis m... 9.4 35 complement(1283775..1285496) NC_014318 Amycolatopsis m... 9.4 35 complement(1381679..1383730) NC_014318 Amycolatopsis m... 9.4 35 complement(1698562..1700286) NC_014318 Amycolatopsis m... 9.4 35 complement(2498501..2499529) NC_014318 Amycolatopsis m... 9.4 35 complement(2516530..2517390) NC_014318 Amycolatopsis m... 9.4 35 complement(2637111..2638721) NC_014318 Amycolatopsis m... 9.4 35 complement(2735643..2736674) NC_014318 Amycolatopsis m... 9.4 35 complement(3225101..3226732) NC_014318 Amycolatopsis m... 9.4 35 complement(3253636..3254784) NC_014318 Amycolatopsis m... 9.4 35 complement(3260959..3261396) NC_014318 Amycolatopsis m... 9.4 35 complement(3262514..3264286) NC_014318 Amycolatopsis m... 9.4 35 complement(3601681..3602511) NC_014318 Amycolatopsis m... 9.4 35 complement(3619935..3621239) NC_014318 Amycolatopsis m... 9.4 35 complement(3879756..3880943) NC_014318 Amycolatopsis m... 9.4 35 complement(3909246..3909650) NC_014318 Amycolatopsis m... 9.4 35 complement(3917450..3918403) NC_014318 Amycolatopsis m... 9.4 35 complement(4166767..4167939) NC_014318 Amycolatopsis m... 9.4 35 complement(4250365..4251672) NC_014318 Amycolatopsis m... 9.4 35 complement(4276131..4278806) NC_014318 Amycolatopsis m... 9.4 35 complement(4360006..4361052) NC_014318 Amycolatopsis m... 9.4 35 complement(4522213..4524810) NC_014318 Amycolatopsis m... 9.4 35 complement(4700096..4701226) NC_014318 Amycolatopsis m... 9.4 35 complement(4701816..4702910) NC_014318 Amycolatopsis m... 9.4 35 complement(4750901..4751716) NC_014318 Amycolatopsis m... 9.4 35 complement(4833027..4834250) NC_014318 Amycolatopsis m... 9.4 35 complement(5379654..5381369) NC_014318 Amycolatopsis m... 9.4 35 complement(5435166..5435651) NC_014318 Amycolatopsis m... 9.4 35 complement(5509494..5512379) NC_014318 Amycolatopsis m... 9.4 35 ******************************************************************************** ******************************************************************************** SECTION II: MOTIF DIAGRAMS ******************************************************************************** - The ordering and spacing of all non-overlapping motif occurrences are shown for each high-scoring sequence listed in Section I. - A motif occurrence is defined as a position in the sequence whose match to the motif has POSITION p-value less than 0.0001. - The POSITION p-value of a match is the probability of a single random subsequence of the length of the motif scoring at least as well as the observed match. - For each sequence, all motif occurrences are shown unless there are overlaps. In that case, a motif occurrence is shown only if its p-value is less than the product of the p-values of the other (lower-numbered) motif occurrences that it overlaps. - The table also shows the E-value of each sequence. - Spacers and motif occurences are indicated by o -d- `d' residues separate the end of the preceding motif occurrence and the start of the following motif occurrence o [sn] occurrence of motif `n' with p-value less than 0.0001. A minus sign indicates that the occurrence is on the reverse complement strand. ******************************************************************************** SEQUENCE NAME E-VALUE MOTIF DIAGRAM ------------- -------- ------------- complement(5677612..5678895) 9.4 35 complement(5874164..5875915) 9.4 35 complement(5880230..5880985) 9.4 35 complement(6026538..6027758) 9.4 35 complement(6068580..6069665) 9.4 35 complement(6992189..6992929) 9.4 35 complement(6996886..6997155) 9.4 35 complement(7056050..7057252) 9.4 35 complement(695965..697272) 9.4 35 complement(7309644..7310669) 9.4 35 complement(7359419..7361269) 9.4 35 complement(7503077..7504645) 9.4 35 complement(8193196..8194368) 9.4 35 complement(8273983..8274804) 9.4 35 complement(8549687..8551114) 9.4 35 complement(8561549..8562415) 9.4 35 complement(8565685..8566755) 9.4 35 complement(8569664..8570548) 9.4 35 complement(8887008..8888381) 9.4 35 complement(8898827..8899747) 9.4 35 complement(9210049..9211029) 9.4 35 complement(9468248..9468547) 9.4 35 complement(936860..938080) 9.4 35 complement(9883648..9885174) 9.4 35 complement(10088561..10089895) 9.4 35 complement(10187287..10190127) 9.4 35 complement(10191964..10192536) 9.4 35 complement(1283775..1285496) 9.4 35 complement(1381679..1383730) 9.4 35 complement(1698562..1700286) 9.4 35 complement(2498501..2499529) 9.4 35 complement(2516530..2517390) 9.4 35 complement(2637111..2638721) 9.4 35 complement(2735643..2736674) 9.4 35 complement(3225101..3226732) 9.4 35 complement(3253636..3254784) 9.4 35 complement(3260959..3261396) 9.4 35 complement(3262514..3264286) 9.4 35 complement(3601681..3602511) 9.4 35 complement(3619935..3621239) 9.4 35 complement(3879756..3880943) 9.4 35 complement(3909246..3909650) 9.4 35 complement(3917450..3918403) 9.4 35 complement(4166767..4167939) 9.4 35 complement(4250365..4251672) 9.4 35 complement(4276131..4278806) 9.4 35 complement(4360006..4361052) 9.4 35 complement(4522213..4524810) 9.4 35 complement(4700096..4701226) 9.4 35 complement(4701816..4702910) 9.4 35 complement(4750901..4751716) 9.4 35 complement(4833027..4834250) 9.4 35 complement(5379654..5381369) 9.4 35 complement(5435166..5435651) 9.4 35 complement(5509494..5512379) 9.4 35 ******************************************************************************** ******************************************************************************** SECTION III: ANNOTATED SEQUENCES ******************************************************************************** - The positions and p-values of the non-overlapping motif occurrences are shown above the actual sequence for each of the high-scoring sequences from Section I. - A motif occurrence is defined as a position in the sequence whose match to the motif has POSITION p-value less than 0.0001 as defined in Section II. - For each sequence, the first line specifies the name of the sequence. - The second (and possibly more) lines give a description of the sequence. - Following the description line(s) is a line giving the length, combined p-value, and E-value of the sequence as defined in Section I. - The next line reproduces the motif diagram from Section II. - The entire sequence is printed on the following lines. - Motif occurrences are indicated directly above their positions in the sequence on lines showing o the motif number of the occurrence (a minus sign indicates that the occurrence is on the reverse complement strand), o the position p-value of the occurrence, o the best possible match to the motif (or its reverse complement), and o columns whose match to the motif has a positive score (indicated by a plus sign). ******************************************************************************** complement(5677612..5678895) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(5874164..5875915) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(5880230..5880985) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(6026538..6027758) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(6068580..6069665) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(6992189..6992929) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(6996886..6997155) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(7056050..7057252) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(695965..697272) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(7309644..7310669) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(7359419..7361269) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(7503077..7504645) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8193196..8194368) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8273983..8274804) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8549687..8551114) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8561549..8562415) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8565685..8566755) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8569664..8570548) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8887008..8888381) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(8898827..8899747) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(9210049..9211029) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(9468248..9468547) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(936860..938080) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(9883648..9885174) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(10088561..10089895) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(10187287..10190127) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(10191964..10192536) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(1283775..1285496) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(1381679..1383730) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(1698562..1700286) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(2498501..2499529) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(2516530..2517390) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(2637111..2638721) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(2735643..2736674) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3225101..3226732) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3253636..3254784) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3260959..3261396) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3262514..3264286) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3601681..3602511) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3619935..3621239) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3879756..3880943) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3909246..3909650) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(3917450..3918403) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4166767..4167939) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4250365..4251672) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4276131..4278806) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4360006..4361052) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4522213..4524810) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4700096..4701226) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4701816..4702910) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4750901..4751716) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(4833027..4834250) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(5379654..5381369) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(5435166..5435651) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 complement(5509494..5512379) NC_014318 Amycolatopsis mediterranei U32 chromosome, complete genome. LENGTH = 35 COMBINED P-VALUE = 1.40e-02 E-VALUE = 9.4 DIAGRAM: 35 ******************************************************************************** CPU: compute-0-1.local Time 0.082000 secs. mast meme.xml NC_014318.fasta -oc . -nostatus