Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014435.1 Corchorus capsularis cultivar CVL-1 contig14456, 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: 25549
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1495 original size:330 final size:330
Alignment explanation
Indices: 4--2073 Score: 2223
Period size: 331 Copynumber: 6.3 Consensus size: 330
1 AGC
* * * *
4 GTACTAACCATCACAGTATTTGGCTAAAAACGCGATCCGGGCATCGACTCAGTTTTGCATGATTT
1 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCCTCAACTCAGTTTTGCATGA-TT
** * * * *
69 TTTG-CTCCAAGACTCATTGAAATTTCTATATTCATCTAACAAAATCTCAGCCACAGTGGATTTC
65 TTTGACGACAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
* * * * *
133 AGGATTTGTTTTTTCGAACATCGGAATCTTGTTTTGATTTTAATAAAAATTAATTCAT-AAAAAT
130 AGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAAAT
* * * * *
197 AGGAAAAATGATTTTAGAAGCGTGAAAAGCCATTCAATCTTTTTGGCATTCAATTATGTATTTTT
195 AGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTATATATTTTT
* * * * **
262 AACGAGTATTGTTTCCAAAAATT-GAGGAAAAAAATTTTCGGGTCAGTTTTCACAAAATTTTAGC
259 TACAAGTATTGTGTCCAAAAATTAGA-G-AAAAAATTTTCGGGTAAGTTTTTGCAAAATTTTAGC
326 CGAAATCGT
322 CGAAATCGT
* * *
335 GTACTAACCATCACAG-TTTTGAGCTAAAAACGCGTTCCGGGCTTCAGCTCAGTTTTGAATGATT
1 GTACTAACCATCACAGTTTTTG-GCTAAAAACGCGTTCCGGGCCTCAACTCAGTTTTGCATGATT
399 TTTGAC-ACCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCA-ATTTGGATT
65 TTTGACGA-CAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA-TTGGATT
* *
462 TAAGGATTTCTTTTTACGAGCATCAGAATCTTGTTTCGAATTTAATAGAAATTAATTCATAAAAA
128 TAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAA
* * * * * *
527 GTAGGAAAAACGATTTTAGAAGCGTGAAAAG-CCTTCAATGTTCTGACATTAAATTATATA-TTT
193 ATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTGGCATTGAATTATATATTTT
* *
590 TTACTAGTATTGTGTCCAAAAATT-GAGGAAAAAATTTTCGGGTTAGTTTTTGCAAAATTTTAGC
258 TTACAAGTATTGTGTCCAAAAATTAGA-GAAAAAATTTTCGGGTAAGTTTTTGCAAAATTTTAGC
*
654 TGAAATCGT
322 CGAAATCGT
* * **
663 GTACTAACTATCACAGCTTTTT-GCTAAAAACGCGTTCCCGATCTCAGA-TCAGTTTTGCATGAT
1 GTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTCCGGGCCTCA-ACTCAGTTTTGCATGAT
* * * * *
726 TTTTTAC-ACAAAGACTCATTGAAATATCTATATTTATTTAAGCAAATCTCAGACACATTGGATT
64 TTTTGACGAC-AAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
* * *
790 TAAGGATTTATTTTTACGAGCATCAGAATCTTGTTTCCATTTTATTAGAAATTAATTC-TAAAAA
128 TAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAA
* * * *
854 ATAGGAAAAACAATATTAGAAGCATGAAAAGCCCCTCAATATTTTTGGCATTG--TCCA-A-A--
193 ATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGGCATTGAAT-TATATATT
** * * *
913 AATTA-AGAGGATT-TGTCCAAAAATTAAAG-AAAAATCTTTAGGGCT-AGTTTTTGCAAAATTT
256 TTTTACA-AGTATTGTGTCCAAAAATTAGAGAAAAAAT-TTTCGGG-TAAGTTTTTGCAAAATTT
*
974 TAACCGAAATCGT
318 TAGCCGAAATCGT
* * * ** *** *
987 GTATTAACCATCACAGTTTTTGACTAAAAACACGTTCCAAGCCTTGGCTCAGTTTTGCATGTTTT
1 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCCTCAACTCAGTTTTGCATG-ATT
* * ** * * ** * *
1052 TTTGGCGCCAAGACTCAGAGAAATATCTATATTCTTCTAACCGAATCTCATACATATTAGATTTA
65 TTTGACGACAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
* * ** *
1117 AGGATTTGTTTTTACGAGCTTCAGAATCTTGTTTCCATTTTTTTAGAAATTAATTCAGAAAAAAT
130 AGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAAAT
* * *
1182 AGGAAAAACAATATTACAATCGTGAAAAGCCCTTCAATCATTTTT-GCATTGAATTATATATTTT
195 AGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT--TTTTTGGCATTGAATTATATATTTT
* * *
1246 TTACAAGTATTGTG-CACAAAAATT-GAGGAAAATTTTTCCGGGTAAGTTTTTGCAAAATTTTAA
258 TTACAAGTATTGTGTC-CAAAAATTAGAGAAAAAATTTT-CGGGTAAGTTTTTGCAAAATTTTAG
*
1309 CCGAAATCAT
321 CCGAAATCGT
* * * * *
1319 GTACTAACCATCACCGTTTTTGGCTAAAAACGTGTTTCGGGCCTCAACACCA-TTATGCATGATT
1 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCCTCAAC-TCAGTTTTGCATGATT
* * * *
1383 TTTGAC-ACAAGGCTAAGTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTA
65 TTTGACGACAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
* *
1447 AGGATTTGTTTTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCATAAAAAAT
130 AGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAAAT
* *
1512 AGGAAACACGATATTAGAAGCATGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTT
195 AGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTATATA--TTT
* ** * *
1577 TTTACGAGTA-TGATGTTTAGAAATTTAGGAGAAAAAATTTTCGGGTAAGTTTTCGCAAAATTTT
257 TTTACAAGTATTG-TGTCCA-AAAATTA-GAGAAAAAATTTTCGGGTAAGTTTTTGCAAAATTTT
1641 AGCCGAAATCGT
319 AGCCGAAATCGT
* * * * * ** * * *
1653 TTACTAACCATCACATTTTTTTAGCTAAAAATGTGTTTTGGGCCACGAA-TCATATTTTGAATGA
1 GTACTAACCATCACA-GTTTTTGGCTAAAAACGCGTTCCGGGCCTC-AACTCA-GTTTTGCATGA
* * * *
1717 TTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCTATCCAAATCTCAGCAACATTGGATT
63 TTTTTGACGACAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
* *
1782 TAAGGATTTGTTTTTACGAGCACCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCAGAAAAA
128 TAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAA
* * *** *
1847 ATAGG-AAAACGAT-TTTGAAAGCGTAAAAAGCCCTTCAATATTTTTAAAATTTAATTATAT-TT
193 ATAGGAAAAACGATATTAG-AAGCGTGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTATATATT
* * * * * * * *
1909 TCTTACTAGAATTGTGTCCAAAAATTAAAGAAAAATTTTTCGAGTTAGTTTTTGTAAAATTTTAG
256 TTTTACAAGTATTGTGTCCAAAAATTAGAGAAAAAATTTTCGGGTAAGTTTTTGCAAAATTTTAG
*
1974 TCGAAATCGT
321 CCGAAATCGT
* * * * **
1984 GTACTAACCATCACAGTTTTTGGCTAAAAACGTGTTTCAGGCC-CTTACTTTGTTTTGCATGATT
1 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCCTC-AACTCAGTTTTGCATGATT
*
2048 TTTGGTGCGA-AA-ACTCATTGAAATAT
65 TTT-G-ACGACAAGACTCATTGAAATAT
2074 TAATCGTTCG
Statistics
Matches: 1474, Mismatches: 211, Indels: 110
0.82 0.12 0.06
Matches are distributed among these distances:
323 11 0.01
324 89 0.06
325 115 0.08
326 49 0.03
327 43 0.03
328 209 0.14
329 73 0.05
330 213 0.14
331 243 0.16
332 146 0.10
333 21 0.01
334 49 0.03
335 39 0.03
336 59 0.04
337 115 0.08
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (330 bp):
GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGCCTCAACTCAGTTTTGCATGATTT
TTGACGACAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA
GGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCATAAAAAATA
GGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTGGCATTGAATTATATATTTTTTA
CAAGTATTGTGTCCAAAAATTAGAGAAAAAATTTTCGGGTAAGTTTTTGCAAAATTTTAGCCGAA
ATCGT
Found at i:5204 original size:329 final size:329
Alignment explanation
Indices: 4153--5302 Score: 1427
Period size: 329 Copynumber: 3.5 Consensus size: 329
4143 TGGTCTGATC
* * * *
4153 AAATATCTATATTCATCTAACCAAATCTTAGCCACATTTGATTTAAGGA--TGTTTTTACTAGTA
1 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * * * * *
4216 TAAGAATCTTTTTTCTATTTTATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATTTTAGAAG
66 TCAGAATATTGTTTCCATTTTATTAAAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAG
* * *
4281 CGTGAAAAACCCATCAA-CGTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGCCCAAA
131 CGTGAAAAACCCTTCAATC-TTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAA
* *
4345 AATTGAGGAAAAAATTTTCGGGGCAGTTTTCGCAAAATTTTAGCCGAAATCATGTACTAACCATC
195 AATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACT-A-CATC
* * * * * *
4410 ACTGTTTTTGGCTAAAAACACGTTTTGGGTCTCGACTTAGTTTTGCATGATTTTTGACATCAAGA
258 ACAGTTTTTGGTTAAAAACACGTTTCGGGTCTCGGCTCAGTTTTGCATGATTTTTGACACCAAGA
4475 CTCATTG
323 CTCATTG
* *
4482 AAATATCTATATTCTTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCA
1 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
** *
4547 TCAGAATATTGTTTCCATTTTAAAAGAGAAATTAATTCAGAAAAAAATAGGAAAAACGATATTAA
66 TCAGAATATTGTTTCCATTTTATTA-A-AAATTAATTCAG-AAAAAATAGGAAAAACGATATTAG
* * * *
4612 AAGCGTGAAAATCCCTTAAATCTTTTTGGCATTCAATTATATATTGTTTACGAGTATTGTGTCCA
128 AAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCA
* * *
4677 AAACTTGAGGAAAAAGTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGT--TACATC
193 AAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTACATC
* * * * * *
4740 ACAATTTTTTGTTAAAAACGCGTTACGGGTCTCAGCTCAGTATTGCATGATTTTTGACACCAAGA
258 ACAGTTTTTGGTTAAAAACACGTTTCGGGTCTCGGCTCAGTTTTGCATGATTTTTGACACCAAGA
4805 CTCATTG
323 CTCATTG
* * * *
4812 AAATATTTATATATTCATTTAACCAAATTTCAGCCACATTGGATTTAAGGACTTGTTTTTACGAG
1 AAATA--TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* *
4877 CATCAGAATCTTGTTTCCATTTTATTAAAAATTAATTCAGAAAAAATAGG-AAAATGATATTAGA
64 CATCAGAATATTGTTTCCATTTTATTAAAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGA
* * *
4941 ATCGTGAAAAACCCTTCAATCTTCTTGGCATTGAATTATATATTTTTTACGAGGA-TGTGTCCAA
129 AGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAA
* * * * * * * **
5005 AAATTAAAGACAAATTTTTAGGATCAGTTTTTGAAAAATTTTAGTTGAAATCGA-GTACTCACAA
194 AAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATC-ATGTACT-AC-A
* * * * *
5069 TCACAGTTTTTGGTTAAAAACACGTTTCAGGCCTCGGCTCAGTTTTGCTTGATTTTTGGCGCCAA
256 TCACAGTTTTTGGTTAAAAACACGTTTCGGGTCTCGGCTCAGTTTTGCATGATTTTTGACACCAA
**
5134 GACTCATAA
321 GACTCATTG
* * ** * * * *
5143 AAATATCTTTATTCATCTAACTAAATCTCAGAAATATTGGATTTAAGAATTTATTTTTACGAGCT
1 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * * * *
5208 TCAGAATATTGTTTCGATTTTATTAGAATTTAATTCATAAAAAATAGTAAATAA-GATATTAGAA
66 TCAGAATATTGTTTCCATTTTATTAAAAATTAATTCAGAAAAAATAGGAAA-AACGATATTAGAA
*
5272 GCGTGAAAAACCCTTCAATCTTTTTGTCATT
130 GCGTGAAAAACCCTTCAATCTTTTTGGCATT
5303 CTATTTACGA
Statistics
Matches: 705, Mismatches: 101, Indels: 29
0.84 0.12 0.03
Matches are distributed among these distances:
327 52 0.07
328 61 0.09
329 147 0.21
330 123 0.17
331 102 0.14
332 77 0.11
333 12 0.02
334 130 0.18
335 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (329 bp):
AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
TCAGAATATTGTTTCCATTTTATTAAAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAG
CGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAA
ATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTACATCACA
GTTTTTGGTTAAAAACACGTTTCGGGTCTCGGCTCAGTTTTGCATGATTTTTGACACCAAGACTC
ATTG
Found at i:5416 original size:108 final size:106
Alignment explanation
Indices: 5190--5398 Score: 248
Period size: 108 Copynumber: 2.0 Consensus size: 106
5180 TGGATTTAAG
* * * *
5190 AATTTATTTTTACGAGCTTCAGAATATTGTTTCGATTTTATTAGAATTTAATTCATAAAAAATAG
1 AATTTATATTTACGAGCATCAGAATATTGTTTCGATTTTAATAGAAATTAATTC--AAAAAATAG
*
5255 TAAATAAGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGT
64 -AAATAAGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGT
* * * *
5299 CA-TTCTATTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTC-AGAAA-A-AA
1 AATTTATATTTACGAGCATCAGAATATTGTTTCGATTTTAATAGAAATTAATTCAAAAAATAGAA
* * *
5360 A-ACGATTTTAGAAGCGTGAAAAGCCCTTCAATATTTTTG
66 ATAAGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTG
5399 ACATTAAATT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
101 34 0.39
102 3 0.03
104 1 0.01
105 4 0.05
108 45 0.51
109 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (106 bp):
AATTTATATTTACGAGCATCAGAATATTGTTTCGATTTTAATAGAAATTAATTCAAAAAATAGAA
ATAAGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGT
Found at i:5706 original size:434 final size:434
Alignment explanation
Indices: 4869--5736 Score: 1041
Period size: 434 Copynumber: 2.0 Consensus size: 434
4859 AGGACTTGTT
* *
4869 TTTACGAGCATCAGAATCTTGTTTCCATTTTATTAAAAATTAATTCAGAAAAAATAGGAAAATGA
1 TTTACGAGCATCAGAATCTTGTTTCCATTTTAATAAAAATTAATTCAG--AAAATA-GAAAACGA
* * * *
4934 TATTAGAATCGTGAAAAACCCTTCAATCTTCTTGGCATTGAATTATATATTTTTTACGAGGATGT
63 TATTAGAAGCGTGAAAAACCCTTCAATATTCTTGACATTAAATTATATATTTTTTACGAGGATGT
* **
4999 GTCCAAAAATTAAAGACAAATTTTTAGGATCAGTTTTTGAAAAATTTTAGTTGAAATCGAGTACT
128 GTCCAAAAATTAAAGACAAATTTTTAGGACCAGTTTTTGAAAAATTTTAGCCGAAATCGAGTACT
* * * * *
5064 CACAATCACAGTTTTTGGTTAAAAACACGTTTCAGGCCTCGGCTCAGTTTTGCTTGATTTTTGGC
193 AACAATCACAGTTTTTGGTTAAAAACACGTTTCAGACCCCGGCTCAGTTTTGCTTGATTTCTGAC
* * * * *
5129 GCCAAGACTCATAAAAATATCTTTATTCATCTAACTAAATCTCAGAAATATTGGATTTAAGAATT
258 ACCAAAACTCATAAAAATATCTATATTCATCTAACCAAATCTCAGAAACATTGGATTTAAGAATT
* * * * * * *
5194 TATTTTTACGAGCTTCAGAATATTGTTTCGATTTTATTAGAATTTAATTCATAAAAAATAGTAAA
323 TATTTTTACAAGCATCAGAATATTGTTTCGAATTTAATAGAAATTAATTCAGAAAAAATAGGAAA
* *
5259 TAAGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGTCATTCTA
388 TAAGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGACATTCTA
* * *
5306 TTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTCAG-AAA-A-AAAACGATTT
1 TTTACGAGCATCAGAATCTTGTTTCCATTTTAATAAAAATTAATTCAGAAAATAGAAAACGATAT
* * * *
5368 TAGAAGCGTGAAAAGCCCTTCAATATTTTTGACATTAAATTATATATTTTTTACTAGTATTGTGT
66 TAGAAGCGTGAAAAACCCTTCAATATTCTTGACATTAAATTATATATTTTTTACGAGGA-TGTGT
* * ** *
5433 CC-AAAATCTAAAGGA-AAATTTTTCGGGCCAGTTTTTGCTAAATTTTCA-CCGAAATCGTGTAC
130 CCAAAAAT-TAAA-GACAAATTTTTAGGACCAGTTTTTGAAAAATTTT-AGCCGAAATCGAGTAC
* * ** * *
5495 TAACCATGACAGTTTTTTTTTGCTAAAAC-CGTGTTTAGACCCCGGCTCAGTTTTGCTTGATTTC
192 TAACAATCACAGTTTTTGGTT--AAAAACACGT-TTCAGACCCCGGCTCAGTTTTGCTTGATTTC
** * ** * *
5559 TGACACCAAAACTCATTGAAATATCTATATTCATCTAACCATATCTCAGCCACCTTGGATTTGAG
254 TGACACCAAAACTCATAAAAATATCTATATTCATCTAACCAAATCTCAGAAACATTGGATTTAAG
* * * *
5624 GATTTGTTTTTACAAGCATCAGAATCTTGTTTCGAATTTAATAGAAATTAATTCAGAAATAATAG
319 AATTTATTTTTACAAGCATCAGAATATTGTTTCGAATTTAATAGAAATTAATTCAGAAAAAATAG
* **
5689 GAAA-AACGATTTTAGAAGCGTGAAAAGTCCTTCAATATTTTTGACATT
384 GAAATAA-GATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGACATT
5737 TAATTATATA
Statistics
Matches: 363, Mismatches: 60, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
431 64 0.18
432 64 0.18
433 9 0.02
434 181 0.50
437 45 0.12
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (434 bp):
TTTACGAGCATCAGAATCTTGTTTCCATTTTAATAAAAATTAATTCAGAAAATAGAAAACGATAT
TAGAAGCGTGAAAAACCCTTCAATATTCTTGACATTAAATTATATATTTTTTACGAGGATGTGTC
CAAAAATTAAAGACAAATTTTTAGGACCAGTTTTTGAAAAATTTTAGCCGAAATCGAGTACTAAC
AATCACAGTTTTTGGTTAAAAACACGTTTCAGACCCCGGCTCAGTTTTGCTTGATTTCTGACACC
AAAACTCATAAAAATATCTATATTCATCTAACCAAATCTCAGAAACATTGGATTTAAGAATTTAT
TTTTACAAGCATCAGAATATTGTTTCGAATTTAATAGAAATTAATTCAGAAAAAATAGGAAATAA
GATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGACATTCTA
Found at i:7896 original size:333 final size:329
Alignment explanation
Indices: 5306--8753 Score: 2856
Period size: 322 Copynumber: 10.5 Consensus size: 329
5296 TGTCATTCTA
* * *
5306 TTTACGAGCATCAGAATCTTGTTTCGATTTTAATAGAAATTAATTC---AGAA-A--AAAAACGA
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCAAAAAAATAGGAAAAACGA
* * *
5365 TTTTAGAAGCGTGAAAAGCCCTTCAATATTTTTGACATTAAATTATATATTTTTTACTAGTATTG
66 TATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACTAGTATTG
* * * * *
5430 TGTCCAAAATCTAAAGGAAAATTTTTCGGGCCAGTTTTTGCTAAATTTTCA-CCGAAATCGTGTA
131 TGTCAAAAAT-TAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTT-AGCCGAAATCGTGTA
* * * * * * *
5494 CTAACCATGACAGTTTTTTTTTGCTAAAACCGTGTTT-AGACCCCGGCTCAGTTTTGCTTGATTT
194 CTAACCATCACAG---TTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTT
* * * * * *
5558 CTGACACCAAAACTCATTGAAATATCTATATTCATCTAACCATATCTCAGCCACCTTGGATTTGA
256 TTGGCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA
5623 GGATTTGTT
321 GGATTTGTT
* * * * *
5632 TTTACAAGCATCAGAATCTTGTTTCGAATTTAATAGAAATTAATTCAGAAATAATAGGAAAAACG
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCA-AAAAAATAGGAAAAACG
* * * * *
5697 ATTTTAGAAGCGTGAAAAGTCCTTCAATATTTTTGACATTTAATTATATAGTTTTTACTAGTATT
65 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACTAGTATT
* * * * *
5762 GTGTCCAAAATTTAAAGAAAAATTTTTCGAGTCAGTTTTTGCAAAATTTTTGCTGAAATCGTGTA
130 GTGT-CAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
* ** * * * ** *
5827 CTAACCATCATAGTTTTTTTTTACTAAAAACGCGTTTTGGGCCCCGACTCAATTTTGCAAAACTT
194 CTAACCATCACAG---TTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTT
* * * * ** * *
5892 TTCGCGCCAAGACTCATTTAAATATCTATATTCAACTAACCAAATCTTGGCTACATTAGATTTAA
256 TTGGCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA
5957 GGATTTGTT
321 GGATTTGTT
* * * * *
5966 TTTACGAGCATCGGAATCATGTTTCGATTTTATTTGAAATTAATTTATAAAAAATAGGGAAAATG
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCA-AAAAAATAGGAAAAACG
* * * * * *
6031 ATATTAGAAGCATGAAAATCTCTTCAATCTTTTTTGCATTGAATTATATA-TTTTTA-TGAGAAT
65 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACT-AGTAT
* * *** * ** * *
6094 TCTGTATAAAAATTGGGGAAAAA-ATTTTCGGTTCAGTTTTCACAAAATTTTAGCTGAAATCATG
129 TGTGT-CAAAAATTAAAGAAAAATA-TTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
*** * * * * * *
6158 TACGT---CA-CATTTTTTTTGGATAAAAACGTGTTTCAGTCCTCGGCTCATATTTTGCATGA-T
192 TAC-TAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCA-GTTTTGCATGATT
* * * * *
6218 TTTGGCGACAACAGTCATTGAAATATCTATATTCATCTAACCTAATCTCAGGCACATTGGATTTA
255 TTTGGCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
6283 AGGATTTGTT
320 AGGATTTGTT
* * * * *
6293 TTTACGAGCACCAGAATCTTGCTTCGATTTTAATAGAAATTAATTCAAAAAAAT----AAAATGA
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCAAAAAAATAGGAAAAACGA
* * * * *** *
6354 TTTTA-ACAACGTGAAATGTCCTTCAATATTTTTAAAATTGAATTATATATTTTTTACTAGAATT
66 TATTAGA-AGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACTAGTATT
* *
6418 GTGTCTAAAAATTAAAG-AAAATATTTCGAGTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
130 GTGTC-AAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
* ** ****
6482 CTAACCATCACAGTTTTTGACTAAAAACGCGTTTCATGCATTTGCTCAGTTTTGCATGATTTTTG
194 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTG
* * * ** *
6547 GCGCCAAAACTCATTGACATATTTATATTCATCTAACCAAATCTTAGGTACATTGGATTGAAGGA
259 GCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA
*
6612 TTTGGT
324 TTTGTT
* * *
6618 TTTACGAGCACCAGAATCTTGTTTCTATTTTATTAGAAATTAATTC-AAAAAATAGGAAAAACGA
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCAAAAAAATAGGAAAAACGA
* * * * *
6682 TTTTAGAAGCATGAAAAACCCTTTAATATTTTTGGCATTGAATTATATATTTTTTA-TAATATTG
66 TATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACTAGTATTG
* * * * *
6746 TTTCCAAAAATTAAAGAAATATTTTTCGGGTTAGTTTTTGCAAAATTTTAGCCGGAATC-T-TA-
131 TGT-CAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * * * * *
6808 T---CACCACAGTTTCTT-GCGAAATACACGTTTCGGGTCCCTGCTCAGTTTTACATGATTTTTG
195 TAACCATCACAGTTT-TTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTG
* * * * * *
6869 GCGCCAAAACTTATTGGAATATCTTTATTCATCTAACCAAATCTAATCGACATTGGATTTAAGGA
259 GCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA
6934 TTTGTT
324 TTTGTT
* * * * * * * *
6940 TTTACGAGGATCTGATTCATATTTCGATTTAATCAGAAATTAATTTAAAATAAAT-GG-AAAATG
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCAAAA-AAATAGGAAAAACG
* * * * * * *
7003 AAATTAGAACCATGAAAAGCCCTCCAATATTTTTGGCTTTCAATTATAGATTTTTTA-TGAGTAT
65 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACT-AGTAT
* * * * * *
7067 TGTGGTC-AAAATTGAGGAAAAATATTTCGGGTTAATTTTTGCAAAAATTTTAGCCGAAATCTTT
129 TGT-GTCAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGC-AAAATTTTAGCCGAAATCGTG
** * * * ** *
7131 TACT-ATTATTCACAATTTTTTTGGCTAAAAACGCGTTTTGGGGTCGTGGCTAAGTTTTGCATGA
192 TACTAACCA-TCAC-A-GTTTTTGGCTAAAAACGCG-TTTCGGGCCCCGGCTCAGTTTTGCATGA
* * * * * * *
7195 TTTTTGGCACCAAAACTAATTGAAATATCTATATTCATCTAACAAAATCTAATCGACGTTGGATT
253 TTTTTGGCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
7260 TAAGGATTTGTT
318 TAAGGATTTGTT
* * * * * * * * ** *
7272 TTCACGAGAATCTGAATGATATTTCGATTTAATCAGAAATTACTTCATAAAAAATATAAAAAAAA
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCA-AAAAAATA-GGAAAAAC
* * * *
7337 AATATTAGAAGCGTGAAAAGCTCTTCAATCTTTTTGGCATTTAATTATATATTTTTTA-TGAGTA
64 GATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACT-AGTA
* * * ** * * *
7401 TTGTGGTCAAAAATTAAGGAAAAATCTTTCTGGTCAAATTATCCAAAATTTTAGCTGAAATCGTG
128 TTGT-GTCAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
* ** * * * *
7466 ---T----AT---AG-TTTTGGCTACAATTGCGTTCTGGGGCACCGACTCAGTATTGCATGATTT
192 TACTAACCATCACAGTTTTTGGCTAAAAACGCGTT-TCGGGCCCCGGCTCAGTTTTGCATGATTT
** * * * * *
7520 TTTACGCCAAGACTC-TTAATAATACCTATATTCATCAAACCAAATCTCAGCCACATTGAATTTA
256 TTGGCGCCAAAACTCATTGA-AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
7584 AGG-TTCT-TT
320 AGGATT-TGTT
* * * * *
7593 TTTACGAGTATTAGAATCTTGTTTCGATTTTATTAAAAATTAATTCAGAAAAAACAGGAAAAACG
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCA-AAAAAATAGGAAAAACG
* * * * * *
7658 ATATTAGAAGTGGGAAAATCCCTTCAATCTTTTTGTCATTGAATTATATTTTTTTTAACTAGTAT
65 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTT-ACTAGTAT
* * * * * * *
7723 TGTATCAAAAAATTTGACGAAAAATATTTCAGGTCAGTTTTCGCAAAATTTTTAGCTGAAAACGT
129 TGTGTC-AAAAA-TTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAA-TTTTAGCCGAAATCGT
* * * *
7788 ATACTAACCATCACCGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTACATGATTT
191 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTT
* *
7853 TTGGCGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAA
256 TTGGCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA
7918 GGATTTGTT
321 GGATTTGTT
* *
7927 TTTACTAGCATCAGAATCATGTTTCGATTTTATTAGAAATTATTTCAGAAAAAATAGGAAAAACG
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCA-AAAAAATAGGAAAAACG
* * *
7992 ATATTACAAGCGTGAAAAGCCCTTTAATCA-TTTTGGCATTGAATTATATATTTTTTACAAGTAT
65 ATATTAGAAGCGTGAAAAGCCCTTCAAT-ATTTTTGGCATTGAATTATATATTTTTTACTAGTAT
* * * * * * *
8056 TGTGGCCAACAATT-GAGGAAAAT-TTTCGGGTAAGCTTTTGCAAAATTTTAGCCGAAATAGTGT
129 TGT-GTCAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * ** * * * *
8119 ACTAACCATCACTGTTTTTGGCTAAAAACGCATTCCATGCCCCGTCTAAATTTCGCATGATTTTT
193 ACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTT
* * * * * ** *
8184 GACGCCAAGACTTATTGAAATATCTATCTTCATCTAACCAAATCTCAACCATTTTGGATTTAATG
258 GGCGCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGG
8249 ATTTGTT
323 ATTTGTT
** * * * * * * * * *
8256 TTTACGAGTGTCTGAATCATATTTCAATTTCATCATAAAATAATTTAAAATAAA-CGG-AAAACG
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCAAAA-AAATAGGAAAAACG
* * * * *
8319 AAATTTGAAGCGTGAAAAGCCCTTCAATTTTTTTGGCTTTGAATTATAGATTTTTTA-TCAGTAT
65 ATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACT-AGTAT
* * * * * *
8383 TGTGGCCAAAAAATAAGGAAAAACATTTCGGGTCAGTCTTTGTAAAGATTTTAGCCGAAATCGTG
129 TGT-GTCAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAA-ATTTTAGCCGAAATCGTG
* * * *
8448 CACTATCCATCACAGTTTTTTATTGCTAAAAA--CG---C--G-CCCGGATCAGTTTTGCATGAT
192 TACTAACCATCACAG--TTTT-TGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGAT
* * *
8505 TTTT-GC-CTCAAACACTCCTTGTAATATATATATATATATATATATATATATATCCTTCTAACC
254 TTTTGGCGC-CAAA-ACT-C-------------AT-T-GA-A-ATATCTATAT-T-CATCTAACC
* * * *
8568 AAATCTCAACCACAATT-TATTTAAGAATTTGTA
297 AAATCTCAGCCAC-ATTGGATTTAAGGATTTGTT
* * *
8601 TTTACGATCATCAGAATCTTGTTTCGATTTTGTTAGAAATTAATTCAGAAAAAAAATAGGAAAAA
1 TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTC---AAAAAAATAGGAAAAA
* * * * * * * *
8666 CGATATTAGAAGTGTGAAAAGGCCTTCAATCTTTTTCGCGTTTAATTATATACTTTTTACGAGTA
63 CGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACTAGTA
** * *
8731 TTACGCCAAAAATTAAGGAAAAA
128 TTGTGTCAAAAATTAAAGAAAAA
8754 ACTTTCTTGT
Statistics
Matches: 2529, Mismatches: 479, Indels: 206
0.79 0.15 0.06
Matches are distributed among these distances:
320 56 0.02
321 68 0.03
322 420 0.17
323 72 0.03
324 31 0.01
325 164 0.06
326 56 0.02
327 222 0.09
328 112 0.04
329 194 0.08
330 58 0.02
331 22 0.01
332 146 0.06
333 320 0.13
334 309 0.12
335 84 0.03
336 28 0.01
339 2 0.00
340 1 0.00
341 1 0.00
342 1 0.00
343 8 0.00
344 1 0.00
345 65 0.03
346 2 0.00
347 3 0.00
348 24 0.01
349 59 0.02
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (329 bp):
TTTACGAGCATCAGAATCATGTTTCGATTTTATTAGAAATTAATTCAAAAAAATAGGAAAAACGA
TATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTTACTAGTATTG
TGTCAAAAATTAAAGAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT
AACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
GCCAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATT
TGTT
Found at i:8535 original size:2 final size:2
Alignment explanation
Indices: 8528--8557 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8518 ACTCCTTGTA
8528 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
8558 CCTTCTAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9622 original size:113 final size:113
Alignment explanation
Indices: 9419--9645 Score: 373
Period size: 113 Copynumber: 2.0 Consensus size: 113
9409 TGTGGTCTGC
* *
9419 ATTCGTCATGGGCCCACCGACGAATACATGGCGAACAGTATCCCACGTCAAGTCAACGGATGACG
1 ATTCATCATGGGCCCACCGACGAATACATGGCGAACAGTATCCCACGCCAAGTCAACGGATGACG
* *
9484 TGGCAGGTTGACTCGGTCAACGGTCAACAGTTAACTTATAACGTGGCA
66 TGGCAGGTTGACTCGGTCAACGGTCAACAGTCAACTGATAACGTGGCA
* * * *
9532 ATTCATCATGGGCTCACCGGCGAATACATGGTGAATAGTATCCCACGCCAAGTCAACGGATGACG
1 ATTCATCATGGGCCCACCGACGAATACATGGCGAACAGTATCCCACGCCAAGTCAACGGATGACG
*
9597 TGGCAGGTTGACTCGGTCAACGGTCAACAGTCAACTGATGACGTGGCA
66 TGGCAGGTTGACTCGGTCAACGGTCAACAGTCAACTGATAACGTGGCA
9645 A
1 A
9646 GCTAAAATAT
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 105 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.20
Consensus pattern (113 bp):
ATTCATCATGGGCCCACCGACGAATACATGGCGAACAGTATCCCACGCCAAGTCAACGGATGACG
TGGCAGGTTGACTCGGTCAACGGTCAACAGTCAACTGATAACGTGGCA
Found at i:10533 original size:113 final size:113
Alignment explanation
Indices: 10328--10554 Score: 373
Period size: 113 Copynumber: 2.0 Consensus size: 113
10318 TGTGGTCCAC
* * *
10328 ATTCGTCATGGGCCCACCGACGAATATATGGCGAATAGTATCCCACGCCAAGTCAATGGATGACG
1 ATTCATCATGGGCCCACCGACGAATACATGGCGAATAGTATCCCACGCCAAGTCAACGGATGACG
* *
10393 TGGCAGGTTGACTCGGTCAACGGTCAACAGTTAACTGATGACGTGGCA
66 TGGCAGGTTGACTCGGTCAACGATCAACAGTCAACTGATGACGTGGCA
* * **
10441 ATTCATCATGGGCCCACCGGCGAATACATGGCGAATTGTATCCCACGTTAAGTCAACGGATGACG
1 ATTCATCATGGGCCCACCGACGAATACATGGCGAATAGTATCCCACGCCAAGTCAACGGATGACG
10506 TGGCAGGTTGACTCGGTCAACGATCAACAGTCAACTGATGACGTGGCA
66 TGGCAGGTTGACTCGGTCAACGATCAACAGTCAACTGATGACGTGGCA
10554 A
1 A
10555 GTGGTTCGAC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 105 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (113 bp):
ATTCATCATGGGCCCACCGACGAATACATGGCGAATAGTATCCCACGCCAAGTCAACGGATGACG
TGGCAGGTTGACTCGGTCAACGATCAACAGTCAACTGATGACGTGGCA
Found at i:10983 original size:566 final size:564
Alignment explanation
Indices: 9913--11042 Score: 2035
Period size: 566 Copynumber: 2.0 Consensus size: 564
9903 TACGGGGAAA
* *
9913 TGTATCCCACGTTAAGTCAACAGATGACGTGGCAGGTTGACTCGGTCAACGGTCAACAGTCAATT
1 TGTATCCCACGTTAAGTCAACAGATGACGTGGCAGGTTGACTCGGTCAACGATCAACAGTCAACT
* * *
9978 GATGACGTGGCAAGTGGTTCGACCAATAGAAGATGTGTAAATACTGCCATCGAGACTCGAAGCCT
66 GATGACGTGGCAAGTGGTTCGACCAACAGAAGATGTGTAAATACTGCCATCGAGACTCCAAGCAT
10043 AGTTCTTGAAGATGTAAGGCAATCATCCAACCATCAGAAAAAGAGGAGAAATATATGGTATAATT
131 AGTTCTTGAAGATGTAAGGCAATCATCCAACCATCAGAAAAAGAGGAGAAATATATGGTATAATT
10108 TTATACTTTTTTTATTATTTTTTCCGGATAAAAACCAGTTGTAAATTCCGGTTTTTGTTTTGTCC
196 TTATACTTTTTTTATTATTTTTTCCGGATAAAAACCAGTTGTAAATTCCGGTTTTTGTTTTGTCC
10173 GGTGTAAATTATGGATATTCAAATGAATTGGGTTGGGGTAAAGTTAAACTTTTTATTCCTTAAAT
261 GGTGTAAATTATGGATATTCAAATGAATTGGGTTGGGGTAAAGTTAAACTTTTTATTCCTTAAAT
*
10238 ACCCTAACCGGTTTGACAAAGTTAACCAAAACACAAAAAGTCAACAAAACGGATGACTCTCCTTC
326 ACCCTAACCGGTTTGACAAAGTTAACCAAAACACAAAAAGTCAACAAAACGGATGACTATCCTTC
* * *
10303 CCCGGCGCCACAACGTGTGGTCCACATTCGTCATGGGCCCACCGACGAATATATGGCGAATAGTA
391 CCCGGCGCCACAACGTGTGGTCCACATTCGTCATAGGCCCACCGACGAATACATGGCGAATAGCA
* *
10368 TCCCACGCCAAGTCAATGGATGACGTGGCAGGTTGACTCGGTCAACGGTCAACAGTTAACTGATG
456 TCCCACGCCAAGTCAACGGATGACGTGGCAGGTTGACTCGGTCAACGGTCAACAGTTAAATGATG
* *
10433 ACGTGGCAATTCATCATGGGCCCACCGGCGAATACATGGCGAAT
521 ACCTGGCAATTCATCATAGGCCCACCGGCGAATACATGGCGAAT
*
10477 TGTATCCCACGTTAAGTCAACGGATGACGTGGCAGGTTGACTCGGTCAACGATCAACAGTCAACT
1 TGTATCCCACGTTAAGTCAACAGATGACGTGGCAGGTTGACTCGGTCAACGATCAACAGTCAACT
** *
10542 GATGACGTGGCAAGTGGTTCGACCGGCGGAAGATGTGTAAATACTGCCATCGAGACTCCAAGCAT
66 GATGACGTGGCAAGTGGTTCGACCAACAGAAGATGTGTAAATACTGCCATCGAGACTCCAAGCAT
*
10607 AGTTCTTGAAGATGTAAGGCAATCATCCAACCATTAGAAAAAAGAGGAGAAATATATGGTATAAT
131 AGTTCTTGAAGATGTAAGGCAATCATCCAACCATCAG-AAAAAGAGGAGAAATATATGGTATAAT
* *
10672 TTTATACTTTTTTTATTATTTTTTTCGGATAAAAACCTGTTGTAAATTCCGGTTTTTTGTTTTGT
195 TTTATACTTTTTTTATTATTTTTTCCGGATAAAAACCAGTTGTAAATTCCGG-TTTTTGTTTTGT
*
10737 CCGGTGTAAATTATGGATATTCAAATGAATTGGGTTGGGGTAAAGTTAAACTTTTTATTCTTTAA
259 CCGGTGTAAATTATGGATATTCAAATGAATTGGGTTGGGGTAAAGTTAAACTTTTTATTCCTTAA
10802 ATACCCTAACCGGTTTGACAAAGTTAACCAAAACACAAAAAGTCAACAAAACGGATGACTATCCT
324 ATACCCTAACCGGTTTGACAAAGTTAACCAAAACACAAAAAGTCAACAAAACGGATGACTATCCT
* *
10867 TCCCTGGCGCCACAACGTGTGGTCTACATTCGTCATAGGCCCACCGACGAATACATGGCGAATAG
389 TCCCCGGCGCCACAACGTGTGGTCCACATTCGTCATAGGCCCACCGACGAATACATGGCGAATAG
10932 CATCCCACGCCAAGTCAACGGATGACGTGGCAGGTTGACTCGGTCAACGGTCAACAGTTAAATGA
454 CATCCCACGCCAAGTCAACGGATGACGTGGCAGGTTGACTCGGTCAACGGTCAACAGTTAAATGA
10997 TGACCTGGCAATTCATCATAGGCCCACCGGCGAATACATGGCGAAT
519 TGACCTGGCAATTCATCATAGGCCCACCGGCGAATACATGGCGAAT
11043 AGAACTACGG
Statistics
Matches: 541, Mismatches: 23, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
564 157 0.29
565 77 0.14
566 307 0.57
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (564 bp):
TGTATCCCACGTTAAGTCAACAGATGACGTGGCAGGTTGACTCGGTCAACGATCAACAGTCAACT
GATGACGTGGCAAGTGGTTCGACCAACAGAAGATGTGTAAATACTGCCATCGAGACTCCAAGCAT
AGTTCTTGAAGATGTAAGGCAATCATCCAACCATCAGAAAAAGAGGAGAAATATATGGTATAATT
TTATACTTTTTTTATTATTTTTTCCGGATAAAAACCAGTTGTAAATTCCGGTTTTTGTTTTGTCC
GGTGTAAATTATGGATATTCAAATGAATTGGGTTGGGGTAAAGTTAAACTTTTTATTCCTTAAAT
ACCCTAACCGGTTTGACAAAGTTAACCAAAACACAAAAAGTCAACAAAACGGATGACTATCCTTC
CCCGGCGCCACAACGTGTGGTCCACATTCGTCATAGGCCCACCGACGAATACATGGCGAATAGCA
TCCCACGCCAAGTCAACGGATGACGTGGCAGGTTGACTCGGTCAACGGTCAACAGTTAAATGATG
ACCTGGCAATTCATCATAGGCCCACCGGCGAATACATGGCGAAT
Found at i:11342 original size:109 final size:111
Alignment explanation
Indices: 11138--11354 Score: 348
Period size: 109 Copynumber: 2.0 Consensus size: 111
11128 TCATAATGGG
* * * *
11138 CATGGGCCCACCGGTGAATACACGGTGAATAATATCCCACGCCAAGTCAACGAATGACATGGCAG
1 CATGGGCCCACCAGCGAACACACGGTGAATAATATCCCACGCCAAGT--ACGAATGAAATGGCAG
*
11203 GTTGACTCAGTCAACGGTCAACAGTTGACTGATGATGTGGCAATTCAT
64 GTTGACTCAGTCAACGGTCAACAGTCGACTGATGATGTGGCAATTCAT
*
11251 CATGGGCCCACCAGCGAACACACGGTGAATAGTATCCCACGCCAAGT-C-AATGAAATGGCAGGT
1 CATGGGCCCACCAGCGAACACACGGTGAATAATATCCCACGCCAAGTACGAATGAAATGGCAGGT
11314 TGACTCAGTCAACGGTCAACAGTCGACTGATGATGTGGCAA
66 TGACTCAGTCAACGGTCAACAGTCGACTGATGATGTGGCAA
11355 GCTAAAATAT
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
109 54 0.55
110 1 0.01
113 43 0.44
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.19
Consensus pattern (111 bp):
CATGGGCCCACCAGCGAACACACGGTGAATAATATCCCACGCCAAGTACGAATGAAATGGCAGGT
TGACTCAGTCAACGGTCAACAGTCGACTGATGATGTGGCAATTCAT
Found at i:12143 original size:12 final size:12
Alignment explanation
Indices: 12126--12153 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12116 ACACGTTTAT
12126 ACGACACGAAAC
1 ACGACACGAAAC
12138 ACGACACGAAAC
1 ACGACACGAAAC
12150 ACGA
1 ACGA
12154 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:12405 original size:113 final size:112
Alignment explanation
Indices: 12170--12723 Score: 551
Period size: 113 Copynumber: 5.0 Consensus size: 112
12160 AGGTACACCC
* * *
12170 ACCGGTGAATACACGGTGAATAATATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTCA
1 ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTTA
* ** ** * *
12235 GTGAACGGTCAATAGTTGACTGATGATGTGGCAATTCATCATGGTCCC
66 GTGAACGGTCAATAGTTGACTGATGATGTGGCAACT-AAAATATTTCA
*
12283 ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTGACTTA
1 ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTTA
* * *
12348 GTCAACGGTCAACAGTCGAC-GATGATGTGGCAAGCTAAAATATTTCA
66 GTGAACGGTCAATAGTTGACTGATGATGTGGCAA-CTAAAATATTTCA
* * * *
12395 A--GTC----A-AC---GAATAATATCCCACGCCAAGTCAACGAATGACATGACAGGTTAACTCA
1 ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTTA
* ** ***
12450 GTGAACGGTCAATAGTTGACTGATGATGTGGCAATTCATCATGGGCTC-
66 GTGAACGGTCAATAGTTGACTGATGATGTGGCAACT-AAAAT-ATTTCA
*
12498 ACCGGCGAATACACGGTGAATAGTATCCCACGCGAAGTCAACGAATGACATGGCAGGTTAACTTA
1 ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTTA
* ** * ** *
12563 ATGAACGGTCAATAGTTGACTGATGATGTGGCAA-TTCATTATGGGCCC
66 GTGAACGGTCAATAGTTGACTGATGATGTGGCAACTAAAATAT--TTCA
* * * * * * *
12611 ACCGGCGAATACACGGTGAATAGTATCCCACACTAGGTCAACGAATGACATTGCTGGTTGATTTA
1 ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTTA
* * * * *
12676 GTCAACGGTCAACAGTCGAC-GATGACGTGGAAAGCTAAAATATTTCA
66 GTGAACGGTCAATAGTTGACTGATGATGTGGCAA-CTAAAATATTTCA
12723 A
1 A
12724 GAAAAATCGA
Statistics
Matches: 361, Mismatches: 61, Indels: 39
0.78 0.13 0.08
Matches are distributed among these distances:
102 62 0.17
103 17 0.05
104 2 0.01
105 4 0.01
106 1 0.00
109 1 0.00
110 4 0.01
111 1 0.00
112 34 0.09
113 230 0.64
114 5 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (112 bp):
ACCGGCGAATACACGGTGAATAGTATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTTA
GTGAACGGTCAATAGTTGACTGATGATGTGGCAACTAAAATATTTCA
Found at i:12572 original size:215 final size:216
Alignment explanation
Indices: 12187--12596 Score: 732
Period size: 215 Copynumber: 1.9 Consensus size: 216
12177 AATACACGGT
*
12187 GAATAATATCCCACGCCAAGTCAACGAATGACATGGCAGGTTAACTCAGTGAACGGTCAATAGTT
1 GAATAATATCCCACGCCAAGTCAACGAATGACATGACAGGTTAACTCAGTGAACGGTCAATAGTT
*
12252 GACTGATGATGTGGCAATTCATCATGGTCCCACCGGCGAATACACGGTGAATAGTATCCCACGCC
66 GACTGATGATGTGGCAATTCATCATGGGCCCACCGGCGAATACACGGTGAATAGTATCCCACGCC
* *
12317 AAGTCAACGAATGACATGGCAGGTTGACTTAGTCAACGGTCAACAGTCGAC-GATGATGTGGCAA
131 AAGTCAACGAATGACATGGCAGGTTAACTTAATCAACGGTCAACAGTCGACTGATGATGTGGCAA
12381 GCTAAAATATTTCAAGTCAAC
196 GCTAAAATATTTCAAGTCAAC
12402 GAATAATATCCCACGCCAAGTCAACGAATGACATGACAGGTTAACTCAGTGAACGGTCAATAGTT
1 GAATAATATCCCACGCCAAGTCAACGAATGACATGACAGGTTAACTCAGTGAACGGTCAATAGTT
* *
12467 GACTGATGATGTGGCAATTCATCATGGGCTCACCGGCGAATACACGGTGAATAGTATCCCACGCG
66 GACTGATGATGTGGCAATTCATCATGGGCCCACCGGCGAATACACGGTGAATAGTATCCCACGCC
* * *
12532 AAGTCAACGAATGACATGGCAGGTTAACTTAATGAACGGTCAATAGTTGACTGATGATGTGGCAA
131 AAGTCAACGAATGACATGGCAGGTTAACTTAATCAACGGTCAACAGTCGACTGATGATGTGGCAA
12597 TTCATTATGG
Statistics
Matches: 185, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
215 172 0.93
216 13 0.07
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (216 bp):
GAATAATATCCCACGCCAAGTCAACGAATGACATGACAGGTTAACTCAGTGAACGGTCAATAGTT
GACTGATGATGTGGCAATTCATCATGGGCCCACCGGCGAATACACGGTGAATAGTATCCCACGCC
AAGTCAACGAATGACATGGCAGGTTAACTTAATCAACGGTCAACAGTCGACTGATGATGTGGCAA
GCTAAAATATTTCAAGTCAAC
Found at i:12847 original size:8 final size:8
Alignment explanation
Indices: 12834--12860 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12824 CTTAATGTGC
12834 TGTATAGA
1 TGTATAGA
12842 TGTATAGA
1 TGTATAGA
12850 TGTATAGA
1 TGTATAGA
12858 TGT
1 TGT
12861 GTTGTGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (8 bp):
TGTATAGA
Found at i:13018 original size:33 final size:33
Alignment explanation
Indices: 12981--13054 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
12971 TTCCCTCTTC
* *
12981 TTAATTTCTCTGTTTTCTCCCTTCCATTTCCTT
1 TTAATTTCTCTGTTTACTCCCTTCCATCTCCTT
*
13014 TTAATTTCTCTGTTTACTCCCTTCCATCTCTTT
1 TTAATTTCTCTGTTTACTCCCTTCCATCTCCTT
13047 TTAATTTC
1 TTAATTTC
13055 CCGATGCCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.12, C:0.28, G:0.03, T:0.57
Consensus pattern (33 bp):
TTAATTTCTCTGTTTACTCCCTTCCATCTCCTT
Done.