Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010242.1 Corchorus capsularis cultivar CVL-1 contig10263, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 130719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6373 original size:13 final size:13
Alignment explanation
Indices: 6355--6382 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6345 GTCTTAGCAC
6355 AAAAAAAATGCAA
1 AAAAAAAATGCAA
6368 AAAAAAAATGCAA
1 AAAAAAAATGCAA
6381 AA
1 AA
6383 CTGACCCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAAAAATGCAA
Found at i:6909 original size:336 final size:330
Alignment explanation
Indices: 5766--6936 Score: 1089
Period size: 333 Copynumber: 3.5 Consensus size: 330
5756 CAAAAAACCG
* * * * *
5766 TACATGATTTCGACTAATATTTTGCAAAAATTG-CCTGAAATATTTTTCCTTAATTTTTTTTGTC
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAA--TTTTTTGTC
* * * ** *
5830 TAAAATACTCATGAAATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCATTCTTTTAA
64 TAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAA
* ** *
5895 AATCGTTTTTCATATTTTTCTAAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTA
129 TATCGTTTTTCATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* **
5960 AAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGTTGT
194 AAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATAAATATAAATATTTCAAGGAGT
* * *
6025 CTTGACGCCAAAAATCATGCAAAACTGAGCC-GGGACTCCGAAATGCATTTTTAG-CAAAAAAAA
259 CTTGACGCCAAAAATCATGCAAAACTG-CCCAGGGACCCCGAAATAC-TTTTTAGCCAAAAAAAA
6088 CTGTGATGGTT
322 CTGTGAT-G-T
* * * * * *
6099 AGTACACGATTTTGGCTAAAATTTTTCAAAAAATGACCAAAAAAATTATTCCTCAATTTTTTG-C
1 --TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTTGTC
* * * * * * ** * *
6163 TAAAATACTCATGAAATATATGTAATTTAATGCCAAAAAGATTGGAGGACTTTTCGCATTTTTCA
64 TAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAA
*
6228 TATCGTTTTTCATATTTTT-----TT-A-----AATTAAATCGAAACAAGATTCAGATGCTCATA
129 TATCGTTTTTCATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * * * *
6282 AAAACAAATCCTTAAAGGCAATGTGGCTTAGATTTGATTAGATGAATATGGAA-ATCTGAAGGAG
194 AAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATAAATAT-AAATATTTCAAGGAG
** * ** ** * *
6346 TCTT-A-GCACAAAAAAAATGCAAAAAAAAAATGCAAAACTGACCCCCGGAACCTA-TTTTTAAC
258 TCTTGACGC-CAAAAATCATGC-----AAAACTGC-CCAGGGA-CCCC-GAA-ATACTTTTTAGC
* *
6408 C--AAAAACCGTGATGATTAT
313 CAAAAAAAAC-TG-TGA-TGT
* * * * **
6427 TACACGATTTCGGCTAAAATTTTGCAAAAATTGTCCGGAAAGATAATTT-CTCAA-TTTTTGGAT
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATAT-TTTTCCTCAATTTTTTGTCT
* * * *
6490 AAAATACTCAT-AAATAACATATAATTCAACGCCAAAAATAATGAAGGGCTTTT-ACGCTTCTAA
65 AAAATACTCATAAAAT-ATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAA
** * * *
6553 TATAATTTTTCCTATTTTTCCGAATTAATTTCTAAGTAAATCGAAACAAGATTTAGATGCTCGTA
129 TATCGTTTTTCATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
6618 AAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATAAATATAAATATTTCAAGGAGT
194 AAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATAAATATAAATATTTCAAGGAGT
* *
6683 CTTGACGCCAAAAATCATGCAAAACTGCCCAGGGGCCCCGTAATACGTTTTTAGCCAAAAAAAAA
259 CTTGACGCCAAAAATCATGCAAAACTGCCCAGGGACCCCGAAATAC-TTTTTAGCC---AAAAAA
6748 AACTTGTGATGT
320 AAC-TGTGATGT
* * * * *
6760 TACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAATCTTTTTCCTCAATTTTTAGTC-A
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTTGTCTA
* * * * * *
6824 CAATACTCATAAAACATATATAATTGAACACAAAAAAGATTGAAGGGCTTTTCACGCTTCTAATA
66 AAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATA
* *
6889 TCGTTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAAACGAAACA
131 TCG-TTTTTCATA-TTTTTCCGAATTAATTTCTAATTAAATCGAAACA
6937 TAATTCAAAT
Statistics
Matches: 669, Mismatches: 120, Indels: 93
0.76 0.14 0.11
Matches are distributed among these distances:
320 2 0.00
321 11 0.02
322 86 0.13
323 1 0.00
325 31 0.05
326 89 0.13
327 11 0.02
328 16 0.02
329 9 0.01
330 16 0.02
331 3 0.00
332 10 0.01
333 161 0.24
334 31 0.05
335 46 0.07
336 133 0.20
337 11 0.02
338 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (330 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTTGTCTA
AAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATA
TCGTTTTTCATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
AACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATAAATATAAATATTTCAAGGAGTCT
TGACGCCAAAAATCATGCAAAACTGCCCAGGGACCCCGAAATACTTTTTAGCCAAAAAAAACTGT
GATGT
Found at i:7537 original size:308 final size:309
Alignment explanation
Indices: 7133--7714 Score: 870
Period size: 308 Copynumber: 1.9 Consensus size: 309
7123 GTAAAAAAAT
* * *
7133 ATATAATTTTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTATTATTT
1 ATATAATTTTCAACGCCAAAAAGATTGAAGGACCTTTCATGCTTCTAATATCGTTTTTATTATTT
*
7198 TCTCAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAACAAATACTTAAATT
66 TCTCAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAACAAATACTGAAATT
*
7263 CAATGTGGCA-GAAATTTGT-TTAGATGAATATAGATATTTCATGGAGTCTCGGCGCCAAAAATC
131 CAATGT-GAATGAAATTT-TATTAGATGAATATAGATATTTCATGGAGTCTCGGCGCCAAAAATC
* * *
7326 ATGCAAAACTAAGTCGAGGTTCCGAAACGCGTTTTTAGCAAAAAACCATGATGGTTAGTACACGA
194 ATGCAAAACTAAGTCGAGGCTCCGAAACGCCTTTTTAGCAAAAAACCATGATGGTTAGCACACGA
7391 TTTCGGCTAAAATTTTCCTGGCAATTTTTGGCTAAAATACTCATAAAATAC
259 TTTCGGCTAAAATTTTCCTGGCAATTTTTGGCTAAAATACTCATAAAATAC
* *
7442 ATATAA-TTT-AACGCCAAAAAGATTGGAGGACCTTTCATGCTTTTAATATCGTTTTTCA-TATT
1 ATATAATTTTCAACGCCAAAAAGATTGAAGGACCTTTCATGCTTCTAATATCGTTTTT-ATTATT
* * * *
7504 TT-TCGGATTTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAA
65 TTCTC--AATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAACAAATACTGAA
* *
7568 ATTCAATGTGAATGATATTTTATTAGATGAATATAGATATTTCATGGAGTCTCGGTGCCAAAAAT
128 ATTCAATGTGAATGAAATTTTATTAGATGAATATAGATATTTCATGGAGTCTCGGCGCCAAAAAT
* * * * * * *
7633 TATGCAAAACTAAGTTGGGGCTCTGAAACGCCTTTTTAGCCAAAAACCGTGATGGTTAGCATACG
193 CATGCAAAACTAAGTCGAGGCTCCGAAACGCCTTTTTAGCAAAAAACCATGATGGTTAGCACACG
7698 ATTTCGGCTAAAATTTT
258 ATTTCGGCTAAAATTTT
7715 GCAAAAAAAA
Statistics
Matches: 245, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
306 2 0.01
307 51 0.21
308 186 0.76
309 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (309 bp):
ATATAATTTTCAACGCCAAAAAGATTGAAGGACCTTTCATGCTTCTAATATCGTTTTTATTATTT
TCTCAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAACAAATACTGAAATT
CAATGTGAATGAAATTTTATTAGATGAATATAGATATTTCATGGAGTCTCGGCGCCAAAAATCAT
GCAAAACTAAGTCGAGGCTCCGAAACGCCTTTTTAGCAAAAAACCATGATGGTTAGCACACGATT
TCGGCTAAAATTTTCCTGGCAATTTTTGGCTAAAATACTCATAAAATAC
Found at i:8017 original size:340 final size:333
Alignment explanation
Indices: 7399--9666 Score: 1818
Period size: 340 Copynumber: 6.7 Consensus size: 333
7389 GATTTCGGCT
* *
7399 AAAA-TTTTCCTGGCAATTTTTGGCTAAAATACTCATAAAATACATATAATTTAACG-CCAAAAA
1 AAAATTTTTCCT--CAATTTTTAGCTAAAATACTCATAAAATAAATATAATTTAACGTCCAAAAA
* * * * *
7462 GATTGGAGGACCTTTCATGCTTTTAATATCGTTTTTCATATTTTTCGGATTTAATTTCTAATTAA
64 GATTGGAGTACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
* * * *
7527 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATTCAATGTGAATGATATTTTATT
129 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGATTTGATT
* * * *
7592 AGATGAATATAGATATTTCATGGAGTCTCGGTGCCAAAAATTATGCAAAACTAAGTTGGGG-CTC
194 AGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGTCGGGGAC-C
** * * *
7656 TGAAACGCCTTTTTAGCCAAAAACCGTGATGGTTAGCATACGATTTCGGCTAAAATTTTGCAAAA
258 CAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG-----
*
7721 AAAAAAATTGACCCAA
318 AAAAAAATTGACCCGA
* *
7737 AAAATTTTTCCGTCAATTTTTTGCTAAAATACTCATAAAATAAATATAATTTAACGTCAAAAAAA
1 AAAATTTTTCC-TCAATTTTTAGCTAAAATACTCATAAAATAAATATAATTTAACGTC-CAAAAA
* * * *
7802 GATTGGAGTATTTTTCACGCTTTTAATTTCGTTTTTCATATTTTTGTG-TTATAATTTCTAATTA
64 GATTGGAGTACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAT-TAATTTCTAATTA
* * * **
7866 AATCTAAATAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTGAT
128 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGATTTGAT
* * *
7931 TAGATGAATATAGATATTTCATGGAGTCTCGGCACCTAAAATCATGCAAAACTAAGTCGGGGACC
193 TAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGTCGGGGACC
* * * *
7996 CAAAACGCGTTGTTAGCCAAAAACTGTGATGGTTAGTACACGATTACGTCTAAAATTTT-ACAAA
258 CAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGA-AAA
*
8060 AAA-GGACCCGA
322 AAATTGACCCGA
*
8071 AAAATTTTTCCGTCTATTTTTAGCTAAAATACTCATAATATATATATATATGTGTGTATAATTTA
1 AAAATTTTTCC-TCAATTTTTAGCTAAAATACTCAT-A-A-A-ATA-A-A------TATAATTTA
* * *
8136 ACGT-GAAAAAAATTGGAGTACTTTTCACGCTTTTAATATCGCTTTTTCATTTTTTTCTGAATTA
53 ACGTCCAAAAAGATTGGAGTACTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTCTGAATTA
* * * * * *
8200 ATTTCTAATTAAATCGAAACAAGGTTTAAATGCTTGTAAAAACAAATTCTTAAATCCAATGT-AG
117 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGA-
* * * *
8264 CTTAGATTTGATTAGATGAATAT-GAATATCTCAAAGA-TACTTGGCGCCAAAAATCATGCAAAA
181 CTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGT-CTCGGCGCCAAAAATCATGCAAAA
* * * * ** * ** ** * *
8327 TTTAGTCGAGG-CCCAGAACGTATTTTGAGCCAAAAAATTGTGATTGAATATTACACAATTTCGG
244 CTAAGTCGGGGACCCAAAACGCGTTTTTAGCC-AAAAACCGTGA-TGGTTAGTACACGATTTCGG
* * **
8391 CTAGAATTTTG-CAAAAATTGACTTG-
307 CTAAAATTTTGAAAAAAATTGACCCGA
* * * * * * * * **
8416 AAAGTTATTTACTCAGTTTTTAGCCACAATTCTCATAAAAATATATATAATTTTCATTTCCAAAA
1 AAAATT-TTTCCTCAATTTTTAGCTAAAATACTCAT-AAAATAAATATAA-TTTAACGTCCAAAA
** * * ** *
8481 AGATT-GATGGT-CTTTTCATACTTCTAATATCGTTTTTCCTATTATTTTCCAAATTAATTTCAA
63 AGATTGGA--GTACTTTTCACGCTTTTAATATCGTTTTTCATA-T-TTTTCTGAATTAATTTCTA
* * ** * *** * *
8544 AGTAAATCGAAACAAAATTCAGATATTTGT-TTTACAAATCCTTAAATTCTATGTGACTGAGATC
124 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGATT
* * * ** ** * * *
8608 TGGTTAGATGAATATAGATATTTCAAGGAGTTTCTGCAACAAAAAAAATACAACACTGAA--CTG
189 TGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT-AAGTCGG
*** ** * ** * * *
8671 GGATCCTGGAACGATTTTTTGGTTAAAAACCGTGACTTCGACTAACGTACACGATTTCGGCTAAT
253 GGA-CCCAAAACGCGTTTTTAGCCAAAAACCGTGA--T-G-GTTA-GTACACGATTTCGGCTAAA
* *
8736 ATTTT-ACAAAAATTGACCAGA
312 ATTTTGAAAAAAATTGACCCGA
* * * ** * ** * *
8757 GATATTTTTCTTCTGTTTTTTGTCTAAAATACTCATAGCATATATATAATTCAAC-TCCAAAAAG
1 AAAATTTTTCCTCAATTTTTAG-CTAAAATACTCATAAAATAAATATAATTTAACGTCCAAAAAG
* ** *
8821 ATTGGAGGACTTTTCACAATTTTAAAATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAA
65 ATTGGAGTACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAA
* *
8886 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATGCAATGTGACTGAGATTTGATTA
130 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGATTTGATTA
* * * **
8951 GATGAATATAGATA---CAAGGAGTCTCGACGCCAAAAGTCATGCAAAACTGAG-CCCGGACCGC
195 GATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGTCGGGGACC-C
* * * * * * *
9012 AAAAGGCGTTTTTAGCAAAAAAAAAACTGTGATGGTTTGTACACTATATCAGCTAAAATTTTGGA
259 AAAACGCGTTTTTAGC----CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT-GA
* * *
9077 AAAAAAATGAACTGA
319 AAAAAATTGACCCGA
* * * * *
9092 AAAATTTTTCCTCAATTCTTAGCTAAAATACTCTTGAAATATATATAATTTAACG-CCAACAAGA
1 AAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATAAATATAATTTAACGTCCAAAAAGA
** * * * *
9156 TAAGAGGACTTCTCACGCTTTTCATATCGTTTTTTCATATTTTTTTCTAAATTAATTTCTAATTA
66 TTGGAGTACTTTTCACGCTTTTAATATCG-TTTTTCATA--TTTTTCTGAATTAATTTCTAATTA
* * * * * **
9221 AAT--AAAAAAAATTCAGATTCTTGTAAAAACAAATCCTTAAATGCAATGCAACTGAGATCTT-A
128 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGAT-TTGA
* * ** * * * * * * *
9283 TTAGATGAATA-CGAATATCTCAAGGAGTCTTAGCACCAAAAATAAAGTAAAACTGA-CCTGGGA
192 TTAGATGAATATAG-ATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGTCGGGGA
*** * * * ** * * * *
9346 TCCTGTAATGTGATTTTATTCAAAAACCGTGATGATTATTACACGATTTCGGTTAAAATTTTG-C
256 -CCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAA
*
9410 AAAAATTGACCTGA
320 AAAAATTGACCCGA
* * * *
9424 AAGATATTTCCTCAA-TTTTCGACTAAAATACTCATAAAA-AATATATAATTCAACG-CCAAAAA
1 AAAATTTTTCCTCAATTTTTAG-CTAAAATACTCATAAAATAA-ATATAATTTAACGTCCAAAAA
* * * * * * * *
9486 TATTGAACGGT--TTTTTACGCTTCTAATATCGTTTTTCCTACTTTTTCTGTATTAATTTATAAG
64 GATTGGA--GTACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAAT
* * *
9549 TAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTG
126 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGATTTG
* *
9614 ATTAGATCAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
191 ATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
9667 AACTGAATTG
Statistics
Matches: 1530, Mismatches: 322, Indels: 162
0.76 0.16 0.08
Matches are distributed among these distances:
330 23 0.02
331 15 0.01
332 167 0.11
333 25 0.02
334 176 0.12
335 124 0.08
336 145 0.09
337 134 0.09
338 137 0.09
339 18 0.01
340 282 0.18
341 14 0.01
342 3 0.00
343 1 0.00
344 51 0.03
345 170 0.11
346 45 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (333 bp):
AAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATAAATATAATTTAACGTCCAAAAAGA
TTGGAGTACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAAT
CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGACTGAGATTTGATTAG
ATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGTCGGGGACCCAA
AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAAAT
TGACCCGA
Found at i:8951 original size:673 final size:664
Alignment explanation
Indices: 7412--9666 Score: 1753
Period size: 673 Copynumber: 3.3 Consensus size: 664
7402 ATTTTCCTGG
* * * * * * *
7412 CAATTTTTGGCTAAAATACTCATAAAATACATATAATTTAACGCCAAAAAGATTGGAGGACCTTT
1 CAATTTTCGACTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGGAGGACTTTT
* * * *
7477 CATGCTTTTAATATCGTTTTTCATATTTTTCGGATTTAATTTCTAATTAAATCGAAACAAGATTC
66 CACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
* * * * * *
7542 AGATGCTCGTAAAAACAAATCCTGAAATTCAATGTGAATGATATTTTATTAGATGAATATAGATA
131 AGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTTGATTAGATGAATATAGATA
* * * * * *** * * *
7607 TTTCATGGAGTCTCGGTGCCAAAAATTATGCAAAACTAAGTTGGGGCTCTG-AAACGCCTTTTTA
196 -TTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCCGGAC-C-GCAAAAGCGTTTTTA
* * * * * * * * * *
7671 GC--CAAAAACCGTGATGGT-TAGCATACGATTTCGGCTAAAATTTTGCAAAAAAAAAAATTGAC
258 GCAAAAAAAACTGTGATGATAT-GTACACAATATCAGCTAAAATTTTG---GAAAAAAAA-TGAA
** * * * * * *
7733 CCAAAAAATTTTTCCGTCAATTTTTTGCTAAAATACTC-ATAAAATAAATATAATTTAACGTCAA
318 CTGAAAAATTTTTAC-TCAATTCTTAGCCAAAATACTCTA-AAAATATATATAATTTAACG-C-C
** * * * * * * ***
7797 AAAAAGATTGGAGTATTTTTCACGCTTTTAATTTCG-TTTTTCATATT-TTTGT-GTTA-TAATT
379 AAAAAGATAAGAGGACTTCTCACACTTCTAATATCGTTTTTTCATATTATTT-TCCAAATTAATT
* * * * * * ****
7858 TCTAATTAAATCTAAATAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGA
443 TCAAAGTAAA--TAAAAAAAATTCAGATTCTTGTAAAAACAAATCCTTAAATGCAATGCAACTGA
* * * ** * * * * *
7923 GATTTGATTAGATGAATATAG-ATATTTCATGGAGTCTCGGCACCTAAAATCATGCAAAACT-AA
506 GATCTGATTAGATGAATA-AGAATATCTCAAGGAGTCTTAGCAACAAAAATAAAGTAAAACTGAA
* *** ** * * * * *
7986 GTCGGGGA-CCCAAAACGCG-TTGTTAGCCAAAAACTGTGATGGTTAGTACACGATTACGTCTAA
570 --CTGGGATCCTGGAA-GCGATT-TTATTCAAAAACCGTGATGATAAGTACACGATTTCGGCTAA
** * * *
8049 AATTTTACAAAAAAGGACCCGAAAAATTTTTCCGT
631 AATTTTACAAAAATTGACCAGAAAGATATTTCC-T
* * * **
8084 CTATTTT-TAGCTAAAATACTCATAATATATATATATATGTGTGTATAATTTAACGTGAAAAAAA
1 CAATTTTCGA-CTAAAATACTCAT-A-A-A-A-A-ATA------TATAATTCAACGCCAAAAAAA
* *
8148 TTGGAGTACTTTTCACGCTTTTAATATCGCTTTTTCATTTTTTTCTGAATTAATTTCTAATTAAA
53 TTGGAGGACTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTCTGAATTAATTTCTAATTAAA
* * * *
8213 TCGAAACAAGGTTTAAATGCTTGTAAAAACAAAT-TCTTAAATCCAATGT-AGCTTAGATTTGAT
117 TCGAAACAAGATTTAGATGCTCGTAAAAACAAATCT-TTAAATCCAATGTGA-CTGAGATTTGAT
* * * * *
8276 TAGATGAATAT-GAATATCTCAAAGA-TACTTGGCGCCAAAAATCATGCAAAATTTAG-TCGAGG
180 TAGATGAATATAG-ATAT-TCAAGGAGT-CTTGGCGCCAAAAATCATGCAAAACTGAGCCCG-GA
* * * * * *
8338 CC-CAGAA-CGTATTTTGAGC-CAAAAAATTGTGATTGAATAT-TACACAATTTCGGCTAGAATT
241 CCGCAAAAGCGT-TTTT-AGCAAAAAAAACTGTGA-TG-ATATGTACACAATATCAGCTAAAATT
* * * * * * *
8399 TT-G-CAAAAATTG-ACTTG-AAAGTTATTTACTCAGTTTTTAGCCACAATTCTCATAAAAATAT
302 TTGGAAAAAAAATGAAC-TGAAAAATT-TTTACTCAATTCTTAGCCAAAATACTC-TAAAAATAT
*** * * * * *
8460 ATATAATTTTCATTTCCAAAAAGAT-TGATGGTCTTTTCATACTTCTAATATCG-TTTTTCCTAT
364 ATATAA-TTT-AACGCCAAAAAGATAAGA-GGACTTCTCACACTTCTAATATCGTTTTTTCATAT
* ***
8523 TATTTTCCAAATTAATTTCAAAGTAAATCGAAACAAAATTCAGATAT-TTGT-TTTACAAATCCT
426 TATTTTCCAAATTAATTTCAAAGTAAAT--AAAAAAAATTCAGAT-TCTTGTAAAAACAAATCCT
* * ** * * *
8586 TAAATTCTATGTGACTGAGATCTGGTTAGATGAATATAG-ATATTTCAAGGAGT-TTCTGCAACA
488 TAAATGCAATGCAACTGAGATCTGATTAGATGAATA-AGAATATCTCAAGGAGTCTT-AGCAACA
* *
8649 AAAA-AAA-TACAACACTGAACTGGGATCCTGGAA-CGATTTTTTGGTTAAAAACCGTGACTTCG
551 AAAATAAAGTA-AA-ACTGAACTGGGATCCTGGAAGCGATTTTAT--TCAAAAACCGTGA--T-G
* * * * *
8711 ACTAACGTACACGATTTCGGCTAATATTTTACAAAAATTGACCAGAGATATTTTTCTT
609 A-TAA-GTACACGATTTCGGCTAAAATTTTACAAAAATTGACCAGAAAGATATTTCCT
** * * ** * * *
8769 CTGTTTTTTGTCTAAAATACTCATAGCATATATATAATTCAACTCCAAAAAGATTGGAGGACTTT
1 C-AATTTTCGACTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGGAGGACTTT
** *
8834 TCACAATTTTAAAATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
65 TCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT
* *
8899 CAGATGCTCGTAAAAACAAATCTTTAAATGCAATGTGACTGAGATTTGATTAGATGAATATAGAT
130 TAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTTGATTAGATGAATATAGAT
* * *
8964 A--CAAGGAGTCTCGACGCCAAAAGTCATGCAAAACTGAGCCCGGACCGCAAAAGGCGTTTTTAG
195 ATTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCCGGACCGCAAAA-GCGTTTTTAG
* * *
9027 CAAAAAAAAAACTGTGATGGTTTGTACACTATATCAGCTAAAATTTTGGAAAAAAAATGAACTGA
259 C--AAAAAAAACTGTGATGATATGTACACAATATCAGCTAAAATTTTGGAAAAAAAATGAACTGA
* * ** *
9092 AAAATTTTTCCTCAATTCTTAGCTAAAATACTCTTGAAATATATATAATTTAACGCCAACAAGAT
322 AAAATTTTTACTCAATTCTTAGCCAAAATACTCTAAAAATATATATAATTTAACGCCAAAAAGAT
* * * * * * *
9157 AAGAGGACTTCTCACGCTTTTCATATCGTTTTTTCATATTTTTTTCTAAATTAATTTCTAATTAA
387 AAGAGGACTTCTCACACTTCTAATATCGTTTTTTCATATTATTTTCCAAATTAATTTCAAAGTAA
*
9222 ATAAAAAAAATTCAGATTCTTGTAAAAACAAATCCTTAAATGCAATGCAACTGAGATCTTATTAG
452 ATAAAAAAAATTCAGATTCTTGTAAAAACAAATCCTTAAATGCAATGCAACTGAGATCTGATTAG
* * * *
9287 ATGAATACGAATATCTCAAGGAGTCTTAGCACCAAAAATAAAGTAAAACTGACCTGGGATCCTGT
517 ATGAATAAGAATATCTCAAGGAGTCTTAGCAACAAAAATAAAGTAAAACTGAACTGGGATCCTGG
* * * * *
9352 AATGTGATTTTATTCAAAAACCGTGATGATTATTACACGATTTCGGTTAAAATTTTGCAAAAATT
582 AA-GCGATTTTATTCAAAAACCGTGATGATAAGTACACGATTTCGGCTAAAATTTTACAAAAATT
*
9417 GACCTGAAAGATATTTCCT
646 GACCAGAAAGATATTTCCT
* * *
9436 CAATTTTCGACTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAACGG-TTTT
1 CAATTTTCGACTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGGA-GGACTTT
* * * * * * *
9500 TTACGCTTCTAATATCGTTTTTCCTACTTTTTCTGTATTAATTTATAAGTAAATCAAAACAAGAT
65 TCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAT
* *
9565 TTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAGATCAATATAGA
129 TTAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTTGATTAGATGAATATAGA
9630 TATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
194 TA-TTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
9667 AACTGAATTG
Statistics
Matches: 1258, Mismatches: 239, Indels: 174
0.75 0.14 0.10
Matches are distributed among these distances:
666 69 0.05
667 143 0.11
668 2 0.00
669 2 0.00
670 63 0.05
671 29 0.02
672 144 0.11
673 171 0.14
674 79 0.06
675 31 0.02
676 8 0.01
678 2 0.00
679 30 0.02
680 69 0.05
681 95 0.08
682 36 0.03
683 7 0.01
684 55 0.04
685 141 0.11
686 80 0.06
687 1 0.00
688 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (664 bp):
CAATTTTCGACTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGGAGGACTTTT
CACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
AGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTTGATTAGATGAATATAGATA
TTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCCGGACCGCAAAAGCGTTTTTAGCA
AAAAAAACTGTGATGATATGTACACAATATCAGCTAAAATTTTGGAAAAAAAATGAACTGAAAAA
TTTTTACTCAATTCTTAGCCAAAATACTCTAAAAATATATATAATTTAACGCCAAAAAGATAAGA
GGACTTCTCACACTTCTAATATCGTTTTTTCATATTATTTTCCAAATTAATTTCAAAGTAAATAA
AAAAAATTCAGATTCTTGTAAAAACAAATCCTTAAATGCAATGCAACTGAGATCTGATTAGATGA
ATAAGAATATCTCAAGGAGTCTTAGCAACAAAAATAAAGTAAAACTGAACTGGGATCCTGGAAGC
GATTTTATTCAAAAACCGTGATGATAAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCA
GAAAGATATTTCCT
Found at i:11148 original size:337 final size:332
Alignment explanation
Indices: 9938--11154 Score: 1313
Period size: 331 Copynumber: 3.6 Consensus size: 332
9928 TGATAATTAT
** * * * * *
9938 TACACAATTTCGGCTAAAATTTTTTAAAAGTTGACCCCAAAGATATTTCCTCAATTTTTAGCCAT
1 TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAA
* *
10003 AATACTCATCAAAAATATATGATTCAACGCC-AAAAGCATTGAAGGTCTTTTTCACGCTTTTAAT
66 AATACTCAT-AAAAATATATAATTCAACGCCAAAAAG-ATTGAGGGT-TTTTT-ACGCTTTTAAT
* * * *
10067 ATCGTTTTTCGTATTTTTCTGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATACTCGTTA
127 ATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
* * * *
10132 AAACAAATCCTTAAATGCAATGTGGCT-AAGATTTATT-GAATGAATATAGATATTTTAAGGAGT
192 AAACAAATTCTTAAATCCAATGTGGCTGGA-ATTGATTAG-ATGAATATAGATATTTTAAGGAGT
* * **
10195 TTCGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAACT-CGTTTTTAGCCAAAAA-AA
255 CTCGGCGCCAAAAATCATGCAAAACTGAGTCG-GGCCCCG-AA-TGCGTTTTTAGCCAAAAACTG
** * *
10258 AAATTG-TGATGGTTAG
317 TGATGGTTAAT-GTTAG
* * * * * * ***
10274 TACATAATTTTGGCTAAAATTTTACAAAAAAATGACCCAAAAAATTTTTCCTCAATTTTACACTA
1 TACACAATTTCGGCTAAAATTTTGC-AAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTA
* * * * * *
10339 AAATACTCATAAAATTTATAAAATTTAAAGCCAAAAAGATTGA----ATTTCACGCTTTTAATAT
65 AAATACTCATAAAA-ATATATAATTCAACGCCAAAAAGATTGAGGGTTTTTTACGCTTTTAATAT
* * ** *
10400 CGTTTTTCATATTTTTCTAAAGTAAATTCTAATTAAATCGAAACAAGATTCAGATGTTTGTAAAA
129 CGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGT-AAA
* * * *
10465 AAGAAATACTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATGGATATTTTAAGGAGTCT
193 AACAAATTCTTAAATCCAATGTGGCTGGAA-TTGATTAGATGAATATAGATATTTTAAGGAGTCT
* * * * * *
10530 TGGCGCCAAAAATCATACAAAACTGAGTCAGGGCCCAAGAACGCTTTTTTAGTCAAAAACTGTGA
257 CGGCGCCAAAAATCATGCAAAACTGAGTC-GGGCCC-CGAATGCGTTTTTAGCCAAAAACTGTGA
10595 TGG-TAA----A-
320 TGGTTAATGTTAG
* * * *
10602 TACACGATTTCAGCTAAAATTTTGTAAAAATTGACTCAAAAGATATTTCCTCAATTTTTGGCTAA
1 TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAA
* * * *
10667 AATACTCATAAAAAGTATATAATTCAACACCAAAAAGATTGAAGAGCTTTTGACG-TTTCTAATA
66 AATACTCATAAAAA-TATATAATTCAACGCCAAAAAGATTG-AGGGTTTTTTACGCTTT-TAATA
* * * *
10731 TCGTTTTTCCTATTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGTAAA
128 TCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
* * *
10796 AACAAA-TCTTTAAATCCAATGTGGCTGGGAATTGATTAGATGACTATAGATATTTCAAGTAGTC
193 AACAAATTC-TTAAATCCAATGTGGCT-GGAATTGATTAGATGAATATAGATATTTTAAGGAGTC
* *
10860 TCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCCCTCGAATGCGTTTTTAGCCAAAAACTGTG
256 TCGGCGCCAAAAATCATGCAAAACTGAGTCGGG-CCC-CGAATGCGTTTTTAGCCAAAAACTGTG
10925 ATGGTTTAACTGTTAG
319 ATGG-TTAA-TGTTAG
* * ***
10941 TACACAATTTCGGCGAAAATTTTGCAAAAATTAACGGGAAAGAT-TTCTCCTCAATTTTTGGCTA
1 TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGATATT-TCCTCAATTTTTGGCTA
* *
11005 AAATACTCATAAAAATATATAATTCAATGTCAAAAAGATTAGAGGGTTTTTTACGC-TTTAATAT
65 AAATACTCATAAAAATATATAATTCAACGCCAAAAAGATT-GAGGGTTTTTTACGCTTTTAATAT
* * *
11069 CGTATTTCTTATTTTTCTAAATTAATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAA
129 CGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
11134 ACAAATTCTTAAATCCAATGT
194 ACAAATTCTTAAATCCAATGT
11155 TGCCGAGATT
Statistics
Matches: 736, Mismatches: 112, Indels: 65
0.81 0.12 0.07
Matches are distributed among these distances:
327 68 0.09
328 20 0.03
329 1 0.00
330 4 0.01
331 179 0.24
332 98 0.13
333 81 0.11
334 8 0.01
336 25 0.03
337 139 0.19
338 44 0.06
339 69 0.09
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (332 bp):
TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAA
AATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAGGGTTTTTTACGCTTTTAATATCG
TTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAC
AAATTCTTAAATCCAATGTGGCTGGAATTGATTAGATGAATATAGATATTTTAAGGAGTCTCGGC
GCCAAAAATCATGCAAAACTGAGTCGGGCCCCGAATGCGTTTTTAGCCAAAAACTGTGATGGTTA
ATGTTAG
Found at i:11831 original size:2 final size:2
Alignment explanation
Indices: 11826--11929 Score: 60
Period size: 2 Copynumber: 53.5 Consensus size: 2
11816 GTAAGATAAG
* * * * * *
11826 AT AT AT AT GT AT AT GT GT AT AT AT AT GT AC GT AT ACT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
11868 ACT AT AT ACT AT -T AT AT -T AT AT ACT AT AT AT AT -T AC AT -T
1 A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
11907 AT AT -T AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11930 ATCACGAACT
Statistics
Matches: 79, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
1 7 0.09
2 65 0.82
3 7 0.09
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11877 original size:15 final size:13
Alignment explanation
Indices: 11857--11927 Score: 67
Period size: 15 Copynumber: 5.3 Consensus size: 13
11847 TATATGTACG
11857 TATACTTATATACTA
1 TATAC-TATATA-TA
11872 TATACTATTATATTA
1 TATACTA-TATA-TA
11887 TATACTATATATA
1 TATACTATATATA
11900 T-TAC-AT-TATA
1 TATACTATATATA
*
11910 TTATATTATATATA
1 -TATACTATATATA
11924 TATA
1 TATA
11928 TAATCACGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
10 4 0.08
11 3 0.06
12 5 0.10
13 9 0.18
14 10 0.20
15 18 0.37
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (13 bp):
TATACTATATATA
Found at i:11885 original size:5 final size:5
Alignment explanation
Indices: 11877--11926 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
11867 TACTATATAC
*
11877 TATTA TATTA TA-TA CTATATA TATTA CATTA TATTA TATTA TATATA
1 TATTA TATTA TATTA -TAT-TA TATTA TATTA TATTA TATTA TAT-TA
11924 TAT
1 TAT
11927 ATAATCACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
4 2 0.05
5 27 0.69
6 8 0.21
7 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (5 bp):
TATTA
Found at i:11907 original size:26 final size:28
Alignment explanation
Indices: 11857--11929 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 28
11847 TATATGTACG
11857 TATACTTATATACTATATACTATTATATTA
1 TATAC-TATATA-TATATACTATTATATTA
11887 TATACTATATATAT-TAC-ATTATATTA
1 TATACTATATATATATACTATTATATTA
11913 TATTA-TATATATATATA
1 TA-TACTATATATATATA
11930 ATCACGAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
26 20 0.49
27 7 0.17
28 3 0.07
29 6 0.15
30 5 0.12
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
TATACTATATATATATACTATTATATTA
Found at i:12496 original size:14 final size:14
Alignment explanation
Indices: 12451--12488 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
12441 GCCCTAGCCG
*
12451 CTCCTCTCTCCCCTT
1 CTCC-CTCTCCCATT
12466 CTCCCTCTCCCATT
1 CTCCCTCTCCCATT
12480 CTCCCTCTC
1 CTCCCTCTC
12489 TAGTTCTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.03, C:0.61, G:0.00, T:0.37
Consensus pattern (14 bp):
CTCCCTCTCCCATT
Found at i:15109 original size:44 final size:43
Alignment explanation
Indices: 15009--15122 Score: 135
Period size: 44 Copynumber: 2.7 Consensus size: 43
14999 GATTTTGGTG
* *
15009 ACTTGATCTTGAATTGACAATAATTTAATTCAAGGGTCTTAGCG
1 ACTTGATCTTGAATTGAC-ATAATTTGATTCAAGGGTCTTAGCA
* *
15053 ACTTCATCTTGAATTGACGATAATTTGATTCAAGGGT-TTTGACA
1 ACTTGATCTTGAATTGAC-ATAATTTGATTCAAGGGTCTTAG-CA
*
15097 ACTTGATGTTGAATT-A-ATAATTTGAT
1 ACTTGATCTTGAATTGACATAATTTGAT
15123 GACCTGGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 10 0.16
43 4 0.06
44 48 0.77
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (43 bp):
ACTTGATCTTGAATTGACATAATTTGATTCAAGGGTCTTAGCA
Found at i:16357 original size:12 final size:13
Alignment explanation
Indices: 16335--16359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16325 TCTTTCTTTC
16335 TTTTCCTTTTTTT
1 TTTTCCTTTTTTT
16348 TTTTCCTTTTTT
1 TTTTCCTTTTTT
16360 CTCCGAGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCCTTTTTTT
Found at i:17443 original size:3 final size:3
Alignment explanation
Indices: 17435--17487 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
17425 CGATAGCAAC
17435 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17483 ATT AT
1 ATT AT
17488 CATCATCTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17652 original size:105 final size:104
Alignment explanation
Indices: 17471--17678 Score: 366
Period size: 105 Copynumber: 2.0 Consensus size: 104
17461 TATTATTATT
*
17471 ATTATTATTATTATTATCATCATCTTCTTTTAGAGTGCTTAATTATTATCGGGATTCAATGTTAT
1 ATTATTATTATTATTATCATCATCTTCTTTTAGAGTGCTTAATTATTATCCGGATTCAATGTTAT
17536 ATTCTCATGGAACAAATTAGCATAAATAAGATTAGCAAC
66 ATTCTCATGGAACAAATTAGCATAAATAAGATTAGCAAC
17575 ATTATTATTATTATTAT-AT-ATTGCTATCTTTTAGAGTGCTTAATTATTATCCGGATTCAATGT
1 ATTATTATTATTATTATCATCA-T-CT-TCTTTTAGAGTGCTTAATTATTATCCGGATTCAATGT
17638 TATATTCTCATGGAACAAATTAGCATAAATAAGATTAGCAA
63 TATATTCTCATGGAACAAATTAGCATAAATAAGATTAGCAA
17679 GATAAAATTT
Statistics
Matches: 100, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
102 1 0.01
103 3 0.03
104 19 0.19
105 77 0.77
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (104 bp):
ATTATTATTATTATTATCATCATCTTCTTTTAGAGTGCTTAATTATTATCCGGATTCAATGTTAT
ATTCTCATGGAACAAATTAGCATAAATAAGATTAGCAAC
Found at i:18757 original size:15 final size:15
Alignment explanation
Indices: 18737--18765 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18727 AACCCACGCA
18737 AACACAATATATATT
1 AACACAATATATATT
18752 AACACAATATATAT
1 AACACAATATATAT
18766 ATAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (15 bp):
AACACAATATATATT
Found at i:22788 original size:16 final size:16
Alignment explanation
Indices: 22739--22794 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
22729 CAGCACTTTT
*
22739 TTTTTCCTTAAATGCC
1 TTTTTGCTTAAATGCC
* *** *
22755 CTTTTGCTTTTTTACC
1 TTTTTGCTTAAATGCC
22771 TTTTTGCTTAAATGCC
1 TTTTTGCTTAAATGCC
22787 -TTTTGCTT
1 TTTTTGCTT
22795 CTTTATTTTT
Statistics
Matches: 29, Mismatches: 11, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.12, C:0.21, G:0.09, T:0.57
Consensus pattern (16 bp):
TTTTTGCTTAAATGCC
Found at i:22806 original size:31 final size:32
Alignment explanation
Indices: 22737--22806 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
22727 AGCAGCACTT
*
22737 TTTTTTTCCTTAAATGCCCTTTTGCTTTTTTA
1 TTTTTTTCCTTAAATGCCCTTTTGCTTCTTTA
** *
22769 CCTTTTTGCTTAAATG-CCTTTTGCTTCTTTA
1 TTTTTTTCCTTAAATGCCCTTTTGCTTCTTTA
22800 TTTTTTT
1 TTTTTTT
22807 AGAAATGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.11, C:0.19, G:0.07, T:0.63
Consensus pattern (32 bp):
TTTTTTTCCTTAAATGCCCTTTTGCTTCTTTA
Found at i:26008 original size:2 final size:2
Alignment explanation
Indices: 26001--26036 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25991 CCCAAAACAG
26001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26037 CTGAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29822 original size:30 final size:30
Alignment explanation
Indices: 29774--29830 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
29764 CTGCAACAAT
* * *
29774 TTTGGACGTCCATGATAGAGGATATTGCAC
1 TTTGGAAGTCCATAATAGAGGAAATTGCAC
*
29804 TTTGGAAGTCTATAATAGAGGAAATTG
1 TTTGGAAGTCCATAATAGAGGAAATTG
29831 TCTATGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (30 bp):
TTTGGAAGTCCATAATAGAGGAAATTGCAC
Found at i:30319 original size:1 final size:1
Alignment explanation
Indices: 30313--30339 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
30303 AGGTTTTAGG
30313 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
30340 GCCACAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:53579 original size:1 final size:1
Alignment explanation
Indices: 53573--53602 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
53563 TAAAATTTGG
53573 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53603 CTAAATCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:57256 original size:6 final size:7
Alignment explanation
Indices: 57239--57268 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
57229 TCTATAGTAT
57239 TTTTTTA
1 TTTTTTA
57246 TTTTTTA
1 TTTTTTA
57253 -TTTTTA
1 TTTTTTA
57259 TTTTTTA
1 TTTTTTA
57266 TTT
1 TTT
57269 CTTTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:57275 original size:13 final size:13
Alignment explanation
Indices: 57240--57268 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57230 CTATAGTATT
57240 TTTTTATTTTTTA
1 TTTTTATTTTTTA
57253 TTTTTATTTTTTA
1 TTTTTATTTTTTA
57266 TTT
1 TTT
57269 CTTTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:63499 original size:31 final size:31
Alignment explanation
Indices: 63461--63673 Score: 236
Period size: 31 Copynumber: 7.0 Consensus size: 31
63451 TATCACGGTG
* * *
63461 TGTACCAAAAAGTGACATGTGGCACACTACA
1 TGTACCAAAAAGTGACATGTGACACGCCACA
*** * *
63492 TGTACCAAAAAGTGACACACGTCACGCCACG
1 TGTACCAAAAAGTGACATGTGACACGCCACA
63523 TGTACCAAAAAGTGACATGTGACACGCCACA
1 TGTACCAAAAAGTGACATGTGACACGCCACA
*
63554 TGCACCAAAAAGTGACATGTGACACGCCACA
1 TGTACCAAAAAGTGACATGTGACACGCCACA
*
63585 TGTACCAAAAAGTGACATGT--CACGCCACG
1 TGTACCAAAAAGTGACATGTGACACGCCACA
* *
63614 TGTACCAAAAAGTGACACGT-AGCATGCCACA
1 TGTACCAAAAAGTGACATGTGA-CACGCCACA
** * * *
63645 TGTTTC-AAAAGTGGCATGTGGCATGCCAC
1 TGTACCAAAAAGTGACATGTGACACGCCAC
63674 GTGCACAAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
29 27 0.17
30 19 0.12
31 110 0.71
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (31 bp):
TGTACCAAAAAGTGACATGTGACACGCCACA
Found at i:63654 original size:91 final size:92
Alignment explanation
Indices: 63464--63673 Score: 282
Period size: 91 Copynumber: 2.3 Consensus size: 92
63454 CACGGTGTGT
* *
63464 ACCAAAAAGTGACATGTGGCACACTACATGTACCAAAAAGTGACACACGTCACGCCACGTGTACC
1 ACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGA-ACACGTCACGCCACGTGTACC
*
63529 AAAAAGTGACATGTGACACGCCACATGC
65 AAAAAGTGACACGTGACACGCCACATGC
* *
63557 ACCAAAAAGTGACATGTGACACGCCACATGTACCAAAAAGTG-ACATGTCACGCCACGTGTACCA
1 ACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGAACACGTCACGCCACGTGTACCA
* *
63621 AAAAGTGACACGT-AGCATGCCACATGT
66 AAAAGTGACACGTGA-CACGCCACATGC
** * *
63648 TTC-AAAAGTGGCATGTGGCATGCCAC
1 ACCAAAAAGTGACATGTGGCACGCCAC
63674 GTGCACAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
90 21 0.20
91 44 0.42
93 39 0.38
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (92 bp):
ACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTGAACACGTCACGCCACGTGTACCA
AAAAGTGACACGTGACACGCCACATGC
Found at i:64984 original size:29 final size:29
Alignment explanation
Indices: 64947--65004 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
64937 TAACTATTCA
* * *
64947 TTTTAGGATTAATTGATCCTTTAACTTTT
1 TTTTAGGATAAATTGACCCCTTAACTTTT
* *
64976 TTTTGGGATAAATTGGCCCCTTAACTTTT
1 TTTTAGGATAAATTGACCCCTTAACTTTT
65005 AAAAAGGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTTAGGATAAATTGACCCCTTAACTTTT
Found at i:65643 original size:27 final size:28
Alignment explanation
Indices: 65587--65643 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
65577 TCTCATTTTT
*
65587 AAAAGTTAAGGGGCCAACTTATCCCAAA
1 AAAAATTAAGGGGCCAACTTATCCCAAA
* *
65615 AAAAATTAAGGGGCCAATTTGTCCCAAA
1 AAAAATTAAGGGGCCAACTTATCCCAAA
65643 A
1 A
65644 TGGATAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (28 bp):
AAAAATTAAGGGGCCAACTTATCCCAAA
Found at i:77807 original size:1 final size:1
Alignment explanation
Indices: 77767--77795 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
77757 TTCGTTCATG
77767 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
77796 AACTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:79177 original size:3 final size:3
Alignment explanation
Indices: 79169--79245 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
79159 GAGGCATGCT
* * *
79169 CAG CAG CAG CAG CAG CAG CAG CAA CAG CAG CAA CAA CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
79217 CAA CAG CAG CAA CAA CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
79246 ACAACAACAG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.42, C:0.34, G:0.25, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:79199 original size:27 final size:27
Alignment explanation
Indices: 79169--79281 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 27
79159 GAGGCATGCT
*
79169 CAGCAGCAGCAGCAGCAGCAGCAACAG
1 CAGCAGCAACAGCAGCAGCAGCAACAG
*
79196 CAGCAACAACAGCAGCAGCAGCAACAG
1 CAGCAGCAACAGCAGCAGCAGCAACAG
* *
79223 CAGCAACAACAGCAGCAGCAGCAACAA
1 CAGCAGCAACAGCAGCAGCAGCAACAG
* *
79250 CAACAGCAAC--CACCA-CAGCAACAG
1 CAGCAGCAACAGCAGCAGCAGCAACAG
*
79274 CCGCAGCA
1 CAGCAGCA
79282 GCGAAGAGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.18
25 4 0.05
27 59 0.77
ACGTcount: A:0.42, C:0.36, G:0.21, T:0.00
Consensus pattern (27 bp):
CAGCAGCAACAGCAGCAGCAGCAACAG
Found at i:79246 original size:18 final size:18
Alignment explanation
Indices: 79178--79257 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
79168 TCAGCAGCAG
*
79178 CAGCAGCAGCAGCAACAG
1 CAGCAGCAGCAGCAACAA
* * * *
79196 CAGCAACAACAGCAGCAG
1 CAGCAGCAGCAGCAACAA
*
79214 CAGCAACAGCAGCAACAA
1 CAGCAGCAGCAGCAACAA
79232 CAGCAGCAGCAGCAACAA
1 CAGCAGCAGCAGCAACAA
*
79250 CAACAGCA
1 CAGCAGCA
79258 ACCACCACAG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.45, C:0.34, G:0.21, T:0.00
Consensus pattern (18 bp):
CAGCAGCAGCAGCAACAA
Found at i:79256 original size:12 final size:12
Alignment explanation
Indices: 79184--79272 Score: 67
Period size: 12 Copynumber: 7.7 Consensus size: 12
79174 GCAGCAGCAG
* *
79184 CAGCAGCAACAG
1 CAGCAACAACAA
*
79196 CAGCAACAACAG
1 CAGCAACAACAA
* *
79208 CAGCAGCAGCAA
1 CAGCAACAACAA
*
79220 CAGCAGCAACAA
1 CAGCAACAACAA
* *
79232 CAG---CAGCAG
1 CAGCAACAACAA
79241 CAGCAACAACAA
1 CAGCAACAACAA
* *
79253 CAGCAACCACCA
1 CAGCAACAACAA
79265 CAGCAACA
1 CAGCAACA
79273 GCCGCAGCAG
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 7 0.11
12 55 0.89
ACGTcount: A:0.46, C:0.36, G:0.18, T:0.00
Consensus pattern (12 bp):
CAGCAACAACAA
Found at i:79281 original size:12 final size:12
Alignment explanation
Indices: 79169--79257 Score: 106
Period size: 12 Copynumber: 7.4 Consensus size: 12
79159 GAGGCATGCT
*
79169 CAGCAGCAGCAG
1 CAGCAGCAGCAA
79181 CAGCAGCAGCAA
1 CAGCAGCAGCAA
*
79193 CAGCAGCAACAA
1 CAGCAGCAGCAA
*
79205 CAGCAGCAGCAG
1 CAGCAGCAGCAA
*
79217 CAACAGCAGCAA
1 CAGCAGCAGCAA
* *
79229 CAACAGCAGCAG
1 CAGCAGCAGCAA
* *
79241 CAGCAACAACAA
1 CAGCAGCAGCAA
79253 CAGCA
1 CAGCA
79258 ACCACCACAG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.44, C:0.34, G:0.22, T:0.00
Consensus pattern (12 bp):
CAGCAGCAGCAA
Found at i:89892 original size:86 final size:87
Alignment explanation
Indices: 89747--89919 Score: 323
Period size: 86 Copynumber: 2.0 Consensus size: 87
89737 TGGCCAATCC
89747 AGATGGAAGGATTAAGGTACATGCATTATTGGCTTGGCCTTAGTTTTATTGATTATGGGTTTGAG
1 AGATGGAAGGATTAAGGTACATGCATTATTGGCTTGGCCTTAGTTTTATTGATTATGGGTTTGAG
89812 TTTGAATTTTAGTTT-GGTTCA
66 TTTGAATTTTAGTTTAGGTTCA
89833 AGATGGAAGGATTAAGGTACATGCATTATTGGCTTGGCCTTAGTTATT-TTGATTATGGGTTTGA
1 AGATGGAAGGATTAAGGTACATGCATTATTGGCTTGGCCTTAGTT-TTATTGATTATGGGTTTGA
89897 GTTTGAATTTTAGTTTAGGTTCA
65 GTTTGAATTTTAGTTTAGGTTCA
89920 TCATTTTTCT
Statistics
Matches: 85, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
86 77 0.91
87 8 0.09
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.43
Consensus pattern (87 bp):
AGATGGAAGGATTAAGGTACATGCATTATTGGCTTGGCCTTAGTTTTATTGATTATGGGTTTGAG
TTTGAATTTTAGTTTAGGTTCA
Found at i:91352 original size:7 final size:7
Alignment explanation
Indices: 91342--91375 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
91332 ATTGCCATGC
91342 CCACAGG
1 CCACAGG
91349 CCACAGG
1 CCACAGG
91356 CCACAGG
1 CCACAGG
*
91363 CCAAAGG
1 CCACAGG
91370 CCACAG
1 CCACAG
91376 TTGCATCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.32, C:0.41, G:0.26, T:0.00
Consensus pattern (7 bp):
CCACAGG
Found at i:100774 original size:14 final size:15
Alignment explanation
Indices: 100745--100778 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
100735 TATATGCATG
*
100745 TATATAAGTTAAATT
1 TATATAAGTCAAATT
100760 TATATAA-TCAAATT
1 TATATAAGTCAAATT
100774 TATAT
1 TATAT
100779 GATAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
TATATAAGTCAAATT
Found at i:108488 original size:21 final size:21
Alignment explanation
Indices: 108462--108503 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
108452 CTTTGTCGCG
108462 AATCAAAATATTAAAGTATTA
1 AATCAAAATATTAAAGTATTA
108483 AATCAAAATATTAAAGTATTA
1 AATCAAAATATTAAAGTATTA
108504 TTCCAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AATCAAAATATTAAAGTATTA
Found at i:108866 original size:21 final size:22
Alignment explanation
Indices: 108826--108867 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
108816 AATCGACGAG
**
108826 TCGGTTCCATCGGGTTCTCGGA
1 TCGGTTCCATCGAATTCTCGGA
108848 TCGGTTCC-TCGAATTCTCGG
1 TCGGTTCCATCGAATTCTCGG
108868 GTCGAGTCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.10, C:0.29, G:0.29, T:0.33
Consensus pattern (22 bp):
TCGGTTCCATCGAATTCTCGGA
Found at i:108946 original size:15 final size:15
Alignment explanation
Indices: 108916--109041 Score: 72
Period size: 15 Copynumber: 8.5 Consensus size: 15
108906 TTATAAAAGT
*
108916 ATATATATTTATTATA
1 ATATATA-TAATTATA
108932 ATATATATAATTATA
1 ATATATATAATTATA
* *
108947 ATTATAATTTATATAATGA
1 A-TAT-ATATA-ATTAT-A
108966 ATATATATAA--AGTA
1 ATATATATAATTA-TA
108980 A-ATATATAATTACT-
1 ATATATATAATTA-TA
108994 -T-TATAT-A-TATA
1 ATATATATAATTATA
*
109005 ATATATATAAAGTA-A
1 ATATATAT-AATTATA
*
109020 ATACATATAATTATA
1 ATATATATAATTATA
109035 ATATATA
1 ATATATA
109042 ATTTATATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 31
0.69 0.06 0.25
Matches are distributed among these distances:
10 1 0.01
11 2 0.02
12 2 0.02
13 18 0.21
14 7 0.08
15 27 0.31
16 13 0.15
17 8 0.09
18 7 0.08
19 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATATAATTATA
Found at i:108954 original size:21 final size:19
Alignment explanation
Indices: 108915--108963 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
108905 GTTATAAAAG
108915 TATATAT-ATTTATTATAA
1 TATATATAATTTATTATAA
108933 TATATATAATTATAATTATAA
1 TATATATAATT-T-ATTATAA
*
108954 TTTATATAAT
1 TATATATAAT
108964 GAATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 1 0.04
21 16 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATAATTTATTATAA
Found at i:108988 original size:41 final size:42
Alignment explanation
Indices: 108938--109041 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 42
108928 TATAATATAT
108938 ATAATTATAATTATAATTTATATA-ATGAATATATATAAAGTAA
1 ATAA-TATAATTATAATTTATATATAT-AATATATATAAAGTAA
*
108981 AT-ATATAA-T-TACTTTATATATATAATATATATAAAGTAA
1 ATAATATAATTATAATTTATATATATAATATATATAAAGTAA
*
109020 ATACATATAATTATAATATATA
1 ATA-ATATAATTATAATTTATA
109042 ATTTATATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
39 28 0.53
40 3 0.06
41 11 0.21
42 2 0.04
43 9 0.17
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (42 bp):
ATAATATAATTATAATTTATATATATAATATATATAAAGTAA
Found at i:109042 original size:13 final size:13
Alignment explanation
Indices: 108934--109044 Score: 55
Period size: 13 Copynumber: 8.8 Consensus size: 13
108924 TTATTATAAT
108934 ATATATAATTATA
1 ATATATAATTATA
108947 AT-TATAATT-T-
1 ATATATAATTATA
108957 ATATAATGAA-TAT-
1 ATAT-AT-AATTATA
*
108970 ATATA-AAGTA-A
1 ATATATAATTATA
108981 ATATATAATTACTTTA
1 ATATATAATTA---TA
108997 TATATATAA-TAT-
1 -ATATATAATTATA
*
109009 ATATA-AAGTA-A
1 ATATATAATTATA
109020 ATACATATAATTATA
1 AT--ATATAATTATA
109035 ATATATAATT
1 ATATATAATT
109045 TATATTTATT
Statistics
Matches: 78, Mismatches: 2, Indels: 36
0.67 0.02 0.31
Matches are distributed among these distances:
10 6 0.08
11 18 0.23
12 15 0.19
13 21 0.27
14 4 0.05
15 3 0.04
16 3 0.04
17 8 0.10
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:109049 original size:39 final size:36
Alignment explanation
Indices: 108943--109049 Score: 101
Period size: 41 Copynumber: 2.7 Consensus size: 36
108933 TATATATAAT
108943 TATAATTATAATTTATATAATGAATATATATAAAGTAAATA
1 TATAATTATAA--TATATAAT---TATATATAAAGTAAATA
108984 TATAATTACTTTATATATATAA-TATATATAAAGTAAATACA
1 TATAATTA---TA-ATATATAATTATATATAAAGTAAAT--A
109025 TATAATTATAATATATAATT-TATAT
1 TATAATTATAATATATAATTATATAT
109050 TTATTATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
37 13 0.22
38 3 0.05
39 16 0.27
41 17 0.29
43 7 0.12
44 2 0.03
45 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (36 bp):
TATAATTATAATATATAATTATATATAAAGTAAATA
Found at i:115712 original size:105 final size:105
Alignment explanation
Indices: 115517--115720 Score: 232
Period size: 105 Copynumber: 1.9 Consensus size: 105
115507 TTAATATTAA
* * * * * * **
115517 ATTAAATATTTAGTTAAATATGAAATGTGATACGTGTCAATATTTTAATCCGTTTGTGGAGTCCA
1 ATTAAATATTTAATCAAATATGAAATGTGATACATATCAATATTTTAACCCCTTTGTAAAGTCCA
* * * *
115582 AAAACTCCACTGACGTTGTACCAAATAATAACTCATAAAT
66 AAAACTCCACTAACGGTATAACAAATAATAACTCATAAAT
*
115622 ATTAAATATTTAATCAATTATGAAAT-TGGATACATATCAATATTTTAACCCACTTTGTAAAGTC
1 ATTAAATATTTAATCAAATATGAAATGT-GATACATATCAATATTTTAACCC-CTTTGTAAAGTC
* * *
115686 CAACAACTTCAC-AACGGTATAACAAATGATAACTC
64 CAAAAACTCCACTAACGGTATAACAAATAATAACTC
115721 TCAATGAATT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
104 1 0.01
105 61 0.75
106 19 0.23
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (105 bp):
ATTAAATATTTAATCAAATATGAAATGTGATACATATCAATATTTTAACCCCTTTGTAAAGTCCA
AAAACTCCACTAACGGTATAACAAATAATAACTCATAAAT
Found at i:119228 original size:2 final size:2
Alignment explanation
Indices: 119223--119248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
119213 CAAAAAAAAG
119223 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
119249 ATTAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121041 original size:25 final size:27
Alignment explanation
Indices: 121013--121068 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
121003 TTTAATTTTT
*
121013 ATTTTTTTGG-C-TACAAGAAGGTTTA
1 ATTTTTTTGGCCAAACAAGAAGGTTTA
121038 ATTTTTTTTGGCCAAACAAGAAGGTTTA
1 A-TTTTTTTGGCCAAACAAGAAGGTTTA
121066 ATT
1 ATT
121069 GATAGCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 1 0.04
26 9 0.33
27 3 0.11
28 14 0.52
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTTTTGGCCAAACAAGAAGGTTTA
Found at i:122925 original size:23 final size:21
Alignment explanation
Indices: 122890--122932 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
122880 GGTAGTGGAG
122890 GAGGAGAACAAATATTGGAGAAT
1 GAGGAGAA-AAA-ATTGGAGAAT
*
122913 GAGGATAAAAAATTGGAGAA
1 GAGGAGAAAAAATTGGAGAA
122933 CAACAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.30, T:0.16
Consensus pattern (21 bp):
GAGGAGAAAAAATTGGAGAAT
Found at i:124846 original size:2 final size:2
Alignment explanation
Indices: 124839--124865 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
124829 AGTCCCTAGA
124839 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
124866 GTCCCTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:125913 original size:2 final size:2
Alignment explanation
Indices: 125906--125941 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
125896 TACAAGTAAT
* *
125906 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
125942 ATAACTAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:125924 original size:16 final size:16
Alignment explanation
Indices: 125905--125941 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
125895 ATACAAGTAA
125905 TTATATATATATATAT
1 TTATATATATATATAT
125921 TTATATATATATATAT
1 TTATATATATATATAT
125937 TTATA
1 TTATA
125942 ATAACTAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATATATATATAT
Found at i:126648 original size:205 final size:204
Alignment explanation
Indices: 126296--126674 Score: 749
Period size: 205 Copynumber: 1.9 Consensus size: 204
126286 CTCAAACCTG
126296 AAATCATTTGAACCATATGAACCGACACTTAAAAAGACTAAAACCAGAATTGACCCAAACCCAAA
1 AAATCATTTGAACCATATGAACCGACACTTAAAAAGACTAAAACCAGAATTGACCCAAACCCAAA
126361 TGACCCGACATTTGAGTGATCCGAGCCCAACCCAACCTGAAACTGAAAATTAACCGAACTCGTAT
66 TGACCCGACATTTGAGTGATCCGAGCCCAACCCAACCTGAAACTGAAAATTAACCGAACTCGTAT
126426 GATACGAAATTACCTTAATTCGAAAATGAACTAACCCAAATAACCAAACCCAAAACCAGAATTGA
131 GATACGAAATTACCTTAATTCGAAAATGAACTAACCCAAA-AACCAAACCCAAAACCAGAATTGA
126491 CCCAAACCCA
195 CCCAAACCCA
126501 AAATCATTTGAACCATATGAACCGACACTTAAAAAGACTAAAACCAGAATTGACCCAAACCCAAA
1 AAATCATTTGAACCATATGAACCGACACTTAAAAAGACTAAAACCAGAATTGACCCAAACCCAAA
126566 TGACCCGACATTTGAGTGATCCGAGCCCAACCCAACCTGAAACTGAAAATTAACCGAACTCGTAT
66 TGACCCGACATTTGAGTGATCCGAGCCCAACCCAACCTGAAACTGAAAATTAACCGAACTCGTAT
126631 GATACGAAATTACCTTAATTCGAAAATGAACTAACCCAAAAACC
131 GATACGAAATTACCTTAATTCGAAAATGAACTAACCCAAAAACC
126675 CGACTCGTCC
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
204 4 0.02
205 170 0.98
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.18
Consensus pattern (204 bp):
AAATCATTTGAACCATATGAACCGACACTTAAAAAGACTAAAACCAGAATTGACCCAAACCCAAA
TGACCCGACATTTGAGTGATCCGAGCCCAACCCAACCTGAAACTGAAAATTAACCGAACTCGTAT
GATACGAAATTACCTTAATTCGAAAATGAACTAACCCAAAAACCAAACCCAAAACCAGAATTGAC
CCAAACCCA
Found at i:127090 original size:156 final size:151
Alignment explanation
Indices: 126918--127369 Score: 694
Period size: 149 Copynumber: 3.0 Consensus size: 151
126908 CACAATAATA
* * *
126918 TTTTAAATTAAAATGGTAAAAACAAAATAATTATAAAAATATTAAATTTAATTAAATTAAAATAG
1 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
*
126983 AGTTTTTAGTAGAATCAAACTATATA-TAAAAAATTTTAATACTCCTATATCTAAGTTTTTAATG
66 AGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTT-A-A----TATATCCAAGTTTTTAATG
*
127047 AAAAATAGTAAAATGGTAAAAGTAAAC
125 AAAAATAGTAAAATGGTAAAAATAAAC
* *
127074 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGCAAATTG
1 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
* * *
127139 AGTTTTTAGTAGAATCAAAATATATATTAAAAAGTTTTAATATATCCAAGTTTTTAATGAATAAT
66 AGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
127204 AGT--AATGGTAAAAATAAAC
131 AGTAAAATGGTAAAAATAAAC
* * *
127223 TTTTAAATTAAAATGATAAAAATAAAATAGTCATAAAAATATTGAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
* *
127288 AGTTTTTAGTAGAATCAAACTAGATATTAAGAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
66 AGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
127353 AGTAAAATGGTAAAAAT
131 AGTAAAATGGTAAAAAT
127370 GAAGTAATTA
Statistics
Matches: 273, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
149 138 0.51
151 38 0.14
155 1 0.00
156 86 0.32
157 10 0.04
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (151 bp):
TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
AGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
AGTAAAATGGTAAAAATAAAC
Found at i:127486 original size:17 final size:17
Alignment explanation
Indices: 127447--127479 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
127437 GGGGGTAATC
*
127447 CAAGATCACCTGTGATG
1 CAAGATCACCGGTGATG
127464 CAAGATCACCGGTGAT
1 CAAGATCACCGGTGAT
127480 CAAAGATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (17 bp):
CAAGATCACCGGTGATG
Found at i:128659 original size:35 final size:35
Alignment explanation
Indices: 128608--128693 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
128598 ATCTTTTGAG
*
128608 CACCAAATTTGCTGCTGTTGGAATAAAATTAAAAA
1 CACCAAATTTGATGCTGTTGGAATAAAATTAAAAA
* *
128643 CACCAAATTTGTTGCTGTTGGAATAAAATTACAAA
1 CACCAAATTTGATGCTGTTGGAATAAAATTAAAAA
128678 CACCAAATTTGATGCT
1 CACCAAATTTGATGCT
128694 CGCCAAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (35 bp):
CACCAAATTTGATGCTGTTGGAATAAAATTAAAAA
Found at i:128703 original size:35 final size:35
Alignment explanation
Indices: 128608--128706 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
128598 ATCTTTTGAG
* ***
128608 CACCAAATTTGCTGCTGTTGGAATAAAATTAAAAA
1 CACCAAATTTGATGCTGTCCAAATAAAATTAAAAA
* *** *
128643 CACCAAATTTGTTGCTGTTGGAATAAAATTACAAA
1 CACCAAATTTGATGCTGTCCAAATAAAATTAAAAA
128678 CACCAAATTTGATGCTCG-CCAAATAAAAT
1 CACCAAATTTGATGCT-GTCCAAATAAAAT
128707 ACTCCTTGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 56 0.98
36 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (35 bp):
CACCAAATTTGATGCTGTCCAAATAAAATTAAAAA
Found at i:129318 original size:21 final size:23
Alignment explanation
Indices: 129281--129336 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
129271 AGAAGGAGAA
129281 GGAAAAAGAAAAGGAAAGAAAAAAAAG
1 GGAAAAAG-AAA-G-AAG-AAAAAAAG
129308 GGAAAAAGAAAGAAGAAAAAAAG
1 GGAAAAAGAAAGAAGAAAAAAAG
129331 GGAAAA
1 GGAAAA
129337 GTCGAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.48
24 3 0.10
25 1 0.03
26 3 0.10
27 8 0.28
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (23 bp):
GGAAAAAGAAAGAAGAAAAAAAG
Found at i:129337 original size:22 final size:20
Alignment explanation
Indices: 129288--129337 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 20
129278 GAAGGAAAAA
129288 GAAAAGGAAAGAAAAAAAAGG
1 GAAAA-GAAAGAAAAAAAAGG
129309 GAAAAAGAAAGAAGAAAAAAAGG
1 G-AAAAGAAAG-A-AAAAAAAGG
129332 GAAAAG
1 GAAAAG
129338 TCGAAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.23
22 10 0.38
23 10 0.38
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
GAAAAGAAAGAAAAAAAAGG
Done.