Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012411.1 Corchorus capsularis cultivar CVL-1 contig12432, 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: 15749
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1759 original size:33 final size:33
Alignment explanation
Indices: 1692--1797 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
1682 TTCTCGTCAC
* * *
1692 CCAAAACAGATTTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
1722 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
1755 CCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1788 CCAAAACAGA
1 CCAAAACAGA
1798 TTTGTTTTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 21 0.32
33 45 0.68
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.25
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:1860 original size:33 final size:33
Alignment explanation
Indices: 1822--1915 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
1812 AATTAGCATC
*
1822 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * * *
1855 TAAAACAGATTTAGTGTCATTGCTAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** * *
1888 CAAATTAGGTTTAGTATCACCGCAAACA
1 CAAAACAGATTTAGTATCATCGCAAACA
1916 TCATCTAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:5796 original size:336 final size:332
Alignment explanation
Indices: 4590--6516 Score: 2950
Period size: 336 Copynumber: 5.8 Consensus size: 332
4580 TTGACGCATC
* *
4590 AATAAATATATTATTTAACGCCAAAAATATTGGAGGGACTTTCACGGTTCTAATTTCATTTTTAC
1 AATAAATATATTATTAAACGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTAC
*
4655 TATTTTTTTCTGAATTAATTTCTAACTAATTTTCGAAAAAAGATTCAGATGCTCGTAAAAACAAA
66 TATTTTTTTCTGAATTAATTTCTAATTAA--TTCG-AAAAAGATTCAGATGCTCGTAAAAACAAA
*
4720 TCCTTAAATCCATAGTGGCTGAGATTTTGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGC
128 TCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGC
** *
4785 CAAAAATCATGCAAAACTGAGGTGGGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTA
193 CAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTTA
* *
4850 TTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCGAAAGATTTTTCCTCAATATTTGGCC
258 GTACACGATTTCGACTAAAATTTCGCAAAAATTGA-CCCAAAAGATTTTTCCTCAATATTTGGCC
4915 AAAATACTCAT
322 AAAATACTCAT
* *
4926 AATAAATATATTATTTAACGCCAAAAATATTGGAGGGACTTTCACGGTTCTAATTTCATTTTTAC
1 AATAAATATATTATTAAACGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTAC
* *
4991 TATTTTTTTCTGTATTAATTTCTATTTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCC
66 TATTTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCC
* * *
5056 TTAAATACAAAGTGGCTGAGATTTGGTTAGA-CGAATATAAATATTTCAAGGAGTCTTGGCGCCA
131 TTAAATCCATAGTGGCTGAGATTTGGTTAGATC-AATATAGATATTTCAAGGAGTCTTGGCGCCA
*
5120 AAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAAAACTGTGATGGTTA
195 AAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGC--AAAAAACTGTGATGGTTA
* * * * *
5185 TTACACAATTTCGACTAAAATTTCGCAAAAATTTACCCCAAA-ATATTTTCCTCAATAATTGGCC
258 GTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGAT-TTTTCCTCAATATTTGGCC
5249 AAAATACTCAT
322 AAAATACTCAT
* * * * * * *
5260 AAAAAATATATTATTAAA-GAACAAAATTATTGGTGGCATTTTCACGGTTTTAATGTCATTTTTA
1 AATAAATATATTATTAAACG-CCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTA
* *
5324 CTATTTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTCGTAAAAACAAATC
65 CTATTTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATC
* * * *
5389 CTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAGTCTTGGTGCCT
130 CTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGCCA
* * * * *
5454 AAAATCATGCAAAACTGAGCCGCGATCTTGGAACGCGTTTTTAGCAAAAAACTTTGATGGTTAGC
195 AAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGT
5519 ACACGATTTCGACTAAAATTTCGCAAAAATTTGACCCAAAAGATTTTTCCTCAATATTTGGCCAA
260 ACACGATTTCGACTAAAATTTCGCAAAAA-TTGACCCAAAAGATTTTTCCTCAATATTTGGCCAA
5584 AATACTCAT
324 AATACTCAT
* *
5593 AATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTACA
1 AATAAATATATTATTAAACGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTT-TA
* * *
5658 CTA-TTTTTTCTGAATTAATTTCTAATTAATTTTCGAAAAAAGATTTAGATGCTCGTTAAAGCAA
65 CTATTTTTTTCTGAATTAATTTCTAATTAA--TTCG-AAAAAGATTCAGATGCTCGTAAAAACAA
5722 ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCG
127 ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCG
* * * *
5787 CCAAAAATCATGCAAAACTGAGCTGGGACATCGGAACACGTTTTTAGCCAAAAACTGTGATGGTT
192 CCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTT
*
5852 AGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCCTCAATAAATT-G
257 AGTACACGATTTCGACTAAAATTTCGCAAAAATTGA-CCCAAAAGATTTTTCCTCAAT-ATTTGG
5916 CCAAAATACTCAT
320 CCAAAATACTCAT
* * ** * *
5929 AAAAAATATATTATAAAACAACAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTAC
1 AATAAATATATTATTAAACGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTAC
* * * *
5994 TA-TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTTGTAACAACAAATCC
66 TATTTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCC
* *
6058 TT-AATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAAGTCTTGGCGCCA
131 TTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGG-AGTCTTGGCGCCA
* * * *
6122 AAAATCATGCAAAACTGAGCCGCGATCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGC
195 AAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGT
*
6187 ACACGATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGATTTTTCCTTAATATTTGGCCAAA
260 ACACGATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGATTTTTCCTCAATATTTGGCCAAA
6252 ATACTCAT
325 ATACTCAT
*
6260 AATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTAC
1 AATAAATATATTATTAAACGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTAC
* * * *
6325 TATTTTTTTCTGAATTAATTTCTTATTACTTTTCAAAAAAAGATTCAGATGCTCGTAAAAGCAAA
66 TATTTTTTTCTGAATTAATTTCTAATTA--ATTC-GAAAAAGATTCAGATGCTCGTAAAAACAAA
* *
6390 TCCTTAAATCCATATTGGCTGATATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGC
128 TCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGC
*
6455 CAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAACTGTGATGG
193 CAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGG
6517 CTCATAAAAA
Statistics
Matches: 1454, Mismatches: 115, Indels: 45
0.90 0.07 0.03
Matches are distributed among these distances:
330 3 0.00
331 140 0.10
332 204 0.14
333 255 0.18
334 263 0.18
335 186 0.13
336 400 0.28
337 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (332 bp):
AATAAATATATTATTAAACGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTTTTAC
TATTTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAAATCC
TTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGCCAA
AAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTA
CACGATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGATTTTTCCTCAATATTTGGCCAAAA
TACTCAT
Found at i:6066 original size:667 final size:667
Alignment explanation
Indices: 4593--6516 Score: 3162
Period size: 667 Copynumber: 2.9 Consensus size: 667
4583 ACGCATCAAT
* ** * * *
4593 AAATATATTATTTAACGCCAAAAATATTGGAGGGACTTTCACGGTTCTAATTTCATTTTTACTAT
1 AAATATATTATTAAACAACAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTAT
** *
4658 TTTTTTCTGAATTAATTTCTAACTAATTTTCGAAAAAAGATTCAGATGCTCGTAAAAACAAATCC
66 TTTTTTCTGAATTAATTTCTATTTAA--TTCG-AAAAAGATTTAGATGCTCGTAAAAACAAATCC
* * *
4723 TTAAATCCATAGTGGCTGAGATTTTGTTAGATCAATATAGATATTTCAAGGAGTCTTGGCGCCAA
128 TTAAATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAGTCTTGGCGCCAA
** * * **
4788 AAATCATGCAAAACTGAGGTGGGACCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTATTA
193 AAATCATGCAAAACTGAGCCGCGATCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGCA
*
4853 CACGATTTCGACTAAAATTTCGCAAAAATTGACCCCGAAAGATTTTTCCTCAATATTTGGCCAAA
258 CACGATTTCGACTAAAATTTCGCAAAAATTGA-CCCAAAAGATTTTTCCTCAATATTTGGCCAAA
* * *
4918 ATACTCATAATAAATATATTATTTAACGCCAAAAATATTGGAGGGACTTTCACGGTTCTAATTTC
322 ATACTCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTC
* *
4983 ATTTTTACTATTTTTTTCTGTATTAATTTCTATTTAA--TTCG-AAAAAGATTCAGATGCTCGTA
387 ATTTTTACTATTTTTTTCTGAATTAATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGTA
* * * *
5045 AAAACAAATCCTTAAATACAAAGTGGCTGAGATTTGGTTAGA-CGAATATAAATATTTCAAGGAG
452 AAAGCAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATC-AATATAGATATTTCAAGGAG
5109 TCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAAAAC
516 TCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAAC--AAAAAAC
* * *
5174 TGTGATGGTTATTACACAATTTCGACTAAAATTTCGCAAAAATTTACCCCAAAATATTTTCCTCA
579 TGTGATGGTTAGTACACAATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTCCTCA
5239 ATAATTGGCCAAAATACTCATAAA
644 ATAATTGGCCAAAATACTCATAAA
* * * *
5263 AAATATATTATTAAAGAACAAAATTATTGGTGGCATTTTCACGGTTTTAATGTCATTTTTACTAT
1 AAATATATTATTAAACAACAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTAT
5328 TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTCGTAAAAACAAATCCTTA
66 TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTCGTAAAAACAAATCCTTA
* *
5393 AATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAGTCTTGGTGCCTAAAA
131 AATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAGTCTTGGCGCCAAAAA
* * *
5458 TCATGCAAAACTGAGCCGCGATCTTGGAACGCGTTTTTAGCAAAAAACTTTGATGGTTAGCACAC
196 TCATGCAAAACTGAGCCGCGATCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGCACAC
5523 GATTTCGACTAAAATTTCGCAAAAATTTGACCCAAAAGATTTTTCCTCAATATTTGGCCAAAATA
261 GATTTCGACTAAAATTTCGCAAAAA-TTGACCCAAAAGATTTTTCCTCAATATTTGGCCAAAATA
5588 CTCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATT
325 CTCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATT
* * *
5653 TTACACTA-TTTTTTCTGAATTAATTTCTAATTAATTTTCGAAAAAAGATTTAGATGCTCGTTAA
390 TT-TACTATTTTTTTCTGAATTAATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGTAAA
5717 AGCAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCT
454 AGCAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCT
* * * * *
5782 TGGCGCCAAAAATCATGCAAAACTGAGCTGGGACATCGGAACACGTTTTTAGCCAAAAACTGTGA
519 TGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAACTGTGA
*
5847 TGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCCTCAATAA
584 TGGTTAGTACACAATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGA-TTTTCCTCAAT-A
5912 ATT-GCCAAAATACTCATAAA
647 ATTGGCCAAAATACTCATAAA
*
5932 AAATATATTATAAAACAACAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTA-
1 AAATATATTATTAAACAACAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTAT
* *
5996 TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTTGTAACAACAAATCCTT-
66 TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTCGTAAAAACAAATCCTTA
6060 AATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAAGTCTTGGCGCCAAAA
131 AATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGG-AGTCTTGGCGCCAAAA
6125 ATCATGCAAAACTGAGCCGCGATCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGCACA
195 ATCATGCAAAACTGAGCCGCGATCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGCACA
*
6190 CGATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGATTTTTCCTTAATATTTGGCCAAAATA
260 CGATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGATTTTTCCTCAATATTTGGCCAAAATA
6255 CTCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATT
325 CTCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATT
* * *
6320 TTTACTATTTTTTTCTGAATTAATTTCTTATTACTTTTCAAAAAAAGATTCAGATGCTCGTAAAA
390 TTTACTATTTTTTTCTGAATTAATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGTAAAA
* *
6385 GCAAATCCTTAAATCCATATTGGCTGATATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTT
455 GCAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTT
6450 GGCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAACTGTGAT
520 GGCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAACTGTGAT
6515 GG
585 GG
6517 CTCATAAAAA
Statistics
Matches: 1169, Mismatches: 75, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
666 4 0.00
667 627 0.54
668 234 0.20
669 91 0.08
670 212 0.18
671 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (667 bp):
AAATATATTATTAAACAACAAAAATATTGGAGGGATTTTCACGGTTTTAATGTCATTTTTACTAT
TTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTTAGATGCTCGTAAAAACAAATCCTTA
AATCCATAGTGGCTGAGATTTGGTTAGATGAACATAGATATTTCAAGGAGTCTTGGCGCCAAAAA
TCATGCAAAACTGAGCCGCGATCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGCACAC
GATTTCGACTAAAATTTCGCAAAAATTGACCCAAAAGATTTTTCCTCAATATTTGGCCAAAATAC
TCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATTT
TTACTATTTTTTTCTGAATTAATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGTAAAAG
CAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTG
GCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAACTGTGATG
GTTAGTACACAATTTCGACTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTCCTCAATAATTG
GCCAAAATACTCATAAA
Found at i:6718 original size:258 final size:261
Alignment explanation
Indices: 6255--6774 Score: 816
Period size: 258 Copynumber: 2.0 Consensus size: 261
6245 GGCCAAAATA
* * *
6255 CTCATAATAAATATATTATTAAATGCCAAAAATATTGGAGGGACTTTCACGGTTTTAATTTCATT
1 CTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGACGGACTTTCACGGTTTTAATTTCATT
*
6320 TTTACTATTTTTTTCTGAATTAATTTCTTATTACTTTTCAAAAAAAGATTCAGATGCTCGTAAAA
66 TTTACTATTTTTTTCTGAATTAATTTCTTATTAC-ATTCAAAAAAAGATTCAGATGCTCGTAAAA
* * * *
6385 GCAAATCCTTAAATCCATATTGGCTGATATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTT
130 ACAAATCCTTAAATCCATAGTGGCTGAGATTTAGTTAGATCAATATAGATATTTCAAGGAGTCTT
* *
6450 GGCGCCAAAAATCATGCAAAACTGAGCCGGGACCTCGGAACGCGTTTTTAACAAAAAACTGTGAT
195 GGCACCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTTAACAAAAAACTGTGAT
6515 GG
260 GG
*
6517 CTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGACGGATTTTCACGGTTTT-ATTGTCAT
1 CTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGACGGACTTTCACGGTTTTAATT-TCAT
* * *
6581 TTTTACTA-TTTTTTCTGAATTAATTTC-TATTTA-ATTC-GAAAAAGATTCGGGTGCTCGTAAA
65 TTTTACTATTTTTTTCTGAATTAATTTCTTA-TTACATTCAAAAAAAGATTCAGATGCTCGTAAA
*
6642 AACAAATCCTTAAATCCATAGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCT
129 AACAAATCCTTAAATCCATAGTGGCTGAGATTTAGTTAGATCAATATAGATATTTCAAGGAGTCT
* * *
6707 TGGCACCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGTGTTTTTAGCCAAAAACTGTGA
194 TGGCACCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTTAACAAAAAACTGTGA
6772 TGG
259 TGG
6775 TTAGTACACG
Statistics
Matches: 238, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
258 144 0.61
259 3 0.01
260 2 0.01
261 25 0.11
262 64 0.27
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (261 bp):
CTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGACGGACTTTCACGGTTTTAATTTCATT
TTTACTATTTTTTTCTGAATTAATTTCTTATTACATTCAAAAAAAGATTCAGATGCTCGTAAAAA
CAAATCCTTAAATCCATAGTGGCTGAGATTTAGTTAGATCAATATAGATATTTCAAGGAGTCTTG
GCACCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGCGTTTTTAACAAAAAACTGTGATG
G
Found at i:9029 original size:333 final size:331
Alignment explanation
Indices: 6517--9571 Score: 3334
Period size: 332 Copynumber: 9.2 Consensus size: 331
6507 ACTGTGATGG
** * * * * *
6517 CTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGACGGATTTTCACGGTTTTATTGTCATT
1 CTCATAAAAAATATATTATTAATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCATT
* * *
6582 TTTAC-TATTTTTTCTGAATTAATTTCTATTTAATTCGAAAAAGATTCGGGTGCTCGTAAAAACA
66 TTT-CTTATTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACA
*
6646 AATCCTTAAATCCATAGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC
130 AATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC
* * * * *
6711 ACCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGTGTTTTTAGCCAAAAACTGTGATGGT
195 GCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGT
* *
6776 TAGTACACGATTTCGATTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCCTCAATATTTGG
260 TAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGATTTTT-CTCAATATTTGG
6841 CCAAAATA
324 CCAAAATA
* * * *
6849 CTCATAATAAATATATTATTAAAT-GCCAAAAATATTGGAGGGATTTTCTACGGTTTTAATTTCA
1 CTCATAAAAAATATATTATT-AATCGCCAAAAATATTGGAGGGCTTTTC-ACGCTTTTAATATCA
*
6913 TTTTT-TACTATTTTTTTTCGAATTAATTTCTAATTAATTTTCGAAAAAAGATTCAGATGCTCGT
64 TTTTTCT--TATTTTTTCT-GAATTAATTTCTAATTAA--TTCG-AAAAAGATTCAGATGCTCGT
* *
6977 AAAAGCAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAG
123 AAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * **
7042 TCTTGGCGCAAAAAATCATGCAAAACTAAGCAGGGACCCCTAAACGCGTTTTTAGCCAAAATA-T
188 TCTTGGCGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAA-ACT
* * * *
7106 GTGATGATTAGTACACGATTTCGACTAAAATTTCGCAAAAAAATG-CTCCCAAAAGATTTCTCCT
252 GTGATGGTTAGTACACGATTTCGACTAAAATTTCGC-AAAAATTGAC-CCCCAAAGATTT-TTCT
*
7170 CAATATTTGGCCAAAACA
314 CAATATTTGGCCAAAATA
* * * * *
7188 CTCATAAAAAATATATTATTGAA-CACCAATAATATTGGAAGGCTTTTCTCGCTATTAATATCAT
1 CTCATAAAAAATATATTATT-AATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCAT
* * * *
7252 TTTTATTATTTTTT-TAGAACTAATTTCTAATTTATTAGAAAAAGATTCAGATGCTCGTAAAAAC
65 TTTTCTTATTTTTTCT-GAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAAC
* * ** * * *
7316 ACATCCTTAAATCCATAGTAGCTGAGATTTGGTTTTATGAATATAAATATTTCAAGGAGTTTTGA
129 AAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGG
* ***
7381 CGCAAAAAAATCATGCAAAA-TAGAGCCGGGACCCCAGAACGCGTTTTTAGGTGAAAACTGTG--
194 CGC-AAAAAATCATGCAAAACT-GAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGAT
* * * * *
7443 CG-TA-T--ACGATTTCAACTAAAATTTCGCAAAAATTGACCCCCAAGGACTTTTCCTCAGTATT
257 GGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGA-TTTTTCTCAATATT
*
7504 TGGCCAAAGTA
321 TGGCCAAAATA
* * * * * *
7515 ATCATAACAAATATGTTATTAAGCGCCAAAAATATTGAAGGGCTTTTCACGCTTTTAATTTCATT
1 CTCATAAAAAATATATTATTAATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCATT
* * * *
7580 TTTCTTATTTTTTTTCTGAATTAATTTCTAGTTAATTCAAAAAAAGATTTAGATGATCGT-AAAA
66 TTTCTTA--TTTTTTCTGAATTAATTTCTAATTAATTC-GAAAAAGATTCAGATGCTCGTAAAAA
* * * *
7644 GAAATCCTTAAATCCTTAGTGGCTGAGATTTGGTTAGATGAATATAGATAATTCAAGGATTCTTG
128 CAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
* * * * *
7709 GCGC-AAAAATCATGCAAAACTGAGCCGAGACCCCGTAACGCGTTTTAATCCAAAAACAGTGATG
193 GCGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATG
* * *
7773 GTTAGTACACGATTTCGACTAAAATTTCACAAAAAAAAAATGACCCCAAAAGATTTTTCTCAATA
258 GTTAGTACACGATTTCGACTAAAATTTCGC----AAAAATTGACCCCCAAAGATTTTTCTCAATA
* *
7838 TTTAGCTAAAATA
319 TTTGGCCAAAATA
* **
7851 CTCATATAAAATATATTATTAAAT-GCCAGTAATATTGGAGGGCTTTTCACGC--TT--T-T-A-
1 CTCATAAAAAATATATTATT-AATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCAT
* *
7908 -----TT-TTTTTTCTAAATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAAACA
65 TTTTCTTATTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACA
* *
7967 AATCCTTAAATCCATAGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTCTTGGC
130 AATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC
* * * *
8032 GCAAAAAATCGTGCAAAACTGAGCCGAGA-CCCGGAACG-GTTTTTAGCCAAAAACTATGATAGT
195 GCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGT
* * * * * * *
8095 TAGTACATGCACGATTTTGACTAAAATTACTCATAAATTGACCCCAAAATATTTATCCTCAATAT
260 TAGT--A--CACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGATTT-TTCTCAATAT
8160 TTGGCCAAAATA
320 TTGGCCAAAATA
* * * * * *
8172 CTCATAAAAAATATATTATTAAACGCCAAAAATATTGAATGGCTTTTGAAGCTTTTAATGTCATT
1 CTCATAAAAAATATATTATTAATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCATT
* * *
8237 GTTATTATTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAAGATTCTGATGCTCGTAAAAACA
66 TTTCTTATTTTTTCTGAATTAATTTCTAATTAATTCG-AAAAAGATTCAGATGCTCGTAAAAACA
* * *
8302 AATCCTTAAATCCATAGTGGCTAAGATTTGTTTAGATGAATATAAATATTTCAAGGAGTCTTGGC
130 AATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC
* * * * * * *
8367 TCAAAAAAGTCATACAAAACTGAGCCGGAACCTCGGAACGTGTTTTTAGCCAAAATCTATGATGG
195 GCAAAAAA-TCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGG
* * * *
8432 TTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGAACCCAAAAGATTTCTCCGCAATATTTG
259 TTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGATTT-TTCTCAATATTTG
* *
8497 GCCGAAATT
323 GCCAAAATA
* * * **
8506 CTAATAAAAAATTTATTATTAATCGCC-AAAATATTGGAGGGTTTTTCACGCCATTAATATCATT
1 CTCATAAAAAATATATTATTAATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCATT
* * * * *
8570 ATTATTATTTTTTCTGTATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAATCAA
66 TTTCTTATTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAA
* * * * *
8635 ATCCTTAAATACATAGTGGCTGAGATTTTGTTAGATAAATATAGATATTTGAAGAAGTCTTGGCG
131 ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
* * *
8700 CAAAAAATCATACAAAACTGAGTCGGGACCTCGGAACGCG-TTTTAGCCAAAAACTGTGATGGTT
196 CAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTT
* ** * * * * * *
8764 AGTACACGATTTCGGCTAAAATTTTTC-AAAACTGACCCCCGATGATAATTTTCACAATTTTTTG
261 AGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGAT--TTTTCTCAATATTTGG
*
8828 CCACAATA
324 CCAAAATA
* ** * * * * *
8836 CTCATAAAAAATATATAATTTGTCTCCAAAAAACATTTGAGGGCTTTTCACACTTCTAATATCAT
1 CTCATAAAAAATATATTATTAATCGCC-AAAAATATTGGAGGGCTTTTCACGCTTTTAATATCAT
* * * *
8901 TTTTCTTATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTTAGATGCTCGTAAAACC
65 TTTTCTTATTTTTTCTGAATTAATTTCTAATTAATTCGAAA-AAGATTCAGATGCTCGTAAAAAC
* *
8966 AAATCCTTAAATCCA-ATGTTGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
129 AAATCCTTAAATCCATA-GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
* ** * * * *
9030 GCGCTAAAAATCATGCAAAACTGAGTAGGGGCCTCTGAACGCGTTTTTAGCCAAAAACCGTGATG
193 GCGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATG
* * * * * * * * *
9095 GTCAGTACACGATTTTGGCTAAAATTTTGGAAAAATTGA-TCCCAATGATTTTTCCTTAATTTTT
258 GTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGATTTTT-CTCAATATTT
*
9159 GGCTAAAATA
322 GGCCAAAATA
* * * * * *
9169 CTCAT-AAAAATATATAATTAAACACCAAAAAGATTGGAGAGCTTTTCACGGTTTTAATATCATT
1 CTCATAAAAAATATATTATTAATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCATT
* * * *
9233 TTTCTTAGTTTTTCTGAATTTAACTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAC
66 TTTCTTATTTTTTCTGAA-TTAATTTCTAATTAATTCGAAA-AAGATTCAGATGCTCGTAAAAAC
* * * * *
9298 AAATCATTAAATCCA-ATGTTGTTGAGATTTGGTAAGATGAATATAGATATGTCAAGGAGTCTTG
129 AAATCCTTAAATCCATA-GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
* * * ** *
9362 GCGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGTTTAAAAAAATGTGA
193 GCGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAG--CCAAAAACTGTGA
* * * ** *
9427 TGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAACCGA-CCCCAAAGATTTCTCCTCAAT-T
256 TGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGATTT-TTCTCAATAT
*** *
9490 TTTTACATTAATA
320 TTGGCCA-AAATA
* * * * * * * *
9503 ATCATAGAAAATATATAATTCAA-CGTCAAAAAAATT-GATAGGCTTTTCACGTTTTTAATATCG
1 CTCATAAAAAATATATTATT-AATCGCCAAAAATATTGGA-GGGCTTTTCACGCTTTTAATATCA
9566 TTTTTC
64 TTTTTC
9572 CTACAATTTT
Statistics
Matches: 2318, Mismatches: 326, Indels: 155
0.83 0.12 0.06
Matches are distributed among these distances:
320 63 0.03
321 161 0.07
322 26 0.01
323 2 0.00
324 22 0.01
325 1 0.00
326 3 0.00
327 138 0.06
328 26 0.01
329 100 0.04
330 105 0.05
331 85 0.04
332 366 0.16
333 330 0.14
334 294 0.13
335 167 0.07
336 98 0.04
337 38 0.02
338 211 0.09
339 81 0.03
340 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (331 bp):
CTCATAAAAAATATATTATTAATCGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATATCATT
TTTCTTATTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
CAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTT
AGTACACGATTTCGACTAAAATTTCGCAAAAATTGACCCCCAAAGATTTTTCTCAATATTTGGCC
AAAATA
Found at i:9326 original size:665 final size:664
Alignment explanation
Indices: 6517--9571 Score: 3400
Period size: 665 Copynumber: 4.6 Consensus size: 664
6507 ACTGTGATGG
* * * * *
6517 CTCATAAAAAATATATTATTAAAGGCCAAAAATATTGGACG-GATTTTCACGGTTTTATTGTCAT
1 CTCATAAAAAATATATTATTAAACGCCAAAAATATTGGA-GAGCTTTTCACGGTATTAATATCAT
* * *
6581 TTTTACTATTTTTTCTGAATTAATTTCT-ATTTAATTCGAAAAAGATTCGGGTGCTCGTAAAAAC
65 TTTTATTA-TTTTTCTGAATTAATTTCTAATTT-ATTCGAAAAAGATTCAGATGCTCGTAAAAAC
*
6645 AAATCCTTAAATCCATAGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTGG
128 AAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGG
* * * * *
6710 CACCAAAAATCATGCAAAACTGAGCCGAGACCTCGGAACGTGTTTTTAGCCAAAAACTGTGATGG
193 CGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGG
* * *
6775 TTAGTACACGATTTCGATTAAAATTTCGCAAAAATTGACCCCAAAAGATTTTTCCTCAATATTTG
258 TTAGTACACGATTTCGACTAAAATTTCTCAAAAATTGACCCCCAAAGATTTTTCCTCAATATTTG
* * * **
6840 GCCAAAATACTCATAATAAATATATTATTAAAT-GCCAAAAATATTGGAGGGATTTTCTACGGTT
323 GCCAAAATACTCATAAAAAATATATTATTAAATCGCCAAAAATATTGAAGGGCTTTTC-ACACTT
* * *
6904 TTAATTTCATTTTT-TACTATTTTTTTTCGAATTAATTTCTAATTAATTTTCGAAAAAAGATTCA
387 TTAATTTCATTTTTCT--TATTTTTTCT-GAATTAATTTCTAA-TAA-ATTCGAAAAAAGATTTA
*
6968 GATGCTCGTAAAAGCAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGACTATAGATAT
447 GATGCTCGTAAAA-CAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATAT
* * *
7033 TTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTAAGCAGGGACCCCTAAACGCGTTTTTAGC
511 TTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCAGGGACCTCTGAACGCGTTTTTAGC
* *
7098 CAAAATA-TGTGATGATTAGTACACGATTTCGACTAAAATTTCGCAAAAAAATGCTCCCAAAAGA
576 CAAAA-ACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCG-AAAAAAATGATCCCAAAAGA
*
7162 TTTCTCCTCAATATTTGGCCAAAACA
639 TTTCTCCTCAATATTTGGCCAAAATA
* * * * *
7188 CTCATAAAAAATATATTATTGAACACCAATAATATTGGA-AGGCTTTTCTCGCTATTAATATCAT
1 CTCATAAAAAATATATTATTAAACGCCAAAAATATTGGAGA-GCTTTTCACGGTATTAATATCAT
* * *
7252 TTTTATTATTTTTTTAGAACTAATTTCTAATTTATTAGAAAAAGATTCAGATGCTCGTAAAAACA
65 TTTTATTATTTTTCT-GAATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAAACA
* * ** * * *
7317 CATCCTTAAATCCATAGTAGCTGAGATTTGGTTTTATGAATATAAATATTTCAAGGAGTTTTGAC
129 AATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC
* *** *
7382 GCAAAAAAATCATGCAAAA-TAGAGCCGGGACCCCAGAACGCGTTTTTAGGTGAAAACTGTG--C
194 GC-AAAAAATCATGCAAAACT-GAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATG
* * * * *
7444 G-TA-T--ACGATTTCAACTAAAATTTCGCAAAAATTGACCCCCAAGGACTTTTCCTCAGTATTT
257 GTTAGTACACGATTTCGACTAAAATTTCTCAAAAATTGACCCCCAAAGATTTTTCCTCAATATTT
* * * * * *
7505 GGCCAAAGTAATCATAACAAATATGTTATT-AAGCGCCAAAAATATTGAAGGGCTTTTCACGCTT
322 GGCCAAAATACTCATAAAAAATATATTATTAAATCGCCAAAAATATTGAAGGGCTTTTCACACTT
* * *
7569 TTAATTTCATTTTTCTTATTTTTTTTCTGAATTAATTTCTAGTTAATTCAAAAAAAGATTTAGAT
387 TTAATTTCATTTTTCTTA--TTTTTTCTGAATTAATTTCTAATAAATTCGAAAAAAGATTTAGAT
* * * *
7634 GATCGTAAAAGAAATCCTTAAATCCTTAGTGGCTGAGATTTGGTTAGATGAATATAGATAATTCA
450 GCTCGTAAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCA
* * * * * *
7699 AGGATTCTTGGCGC-AAAAATCATGCAAAACTGAGCCGAGACC-CCGTAACGCGTTTTAATCCAA
515 AGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCAGGGACCTCTG-AACGCGTTTTTAGCCAA
* * *
7762 AAACAGTGATGGTTAGTACACGATTTCGACTAAAATTTCACAAAAAAAAAATGACCCCAAAAGAT
579 AAACTGTGATGGTTAGTACACGATTTCGACTAAAATTT--C--GAAAAAAATGATCCCAAAAGAT
* * *
7827 TT-TTCTCAATATTTAGCTAAAATA
640 TTCTCCTCAATATTTGGCCAAAATA
* * ** *
7851 CTCATATAAAATATATTATTAAATGCCAGTAATATTGGAGGGCTTTTCAC-G---------C--T
1 CTCATAAAAAATATATTATTAAACGCCAAAAATATTGGAGAGCTTTTCACGGTATTAATATCATT
* *
7904 TTTATTTTTTTTCTAAATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAAACAAA
66 TTTATTATTTTTCTGAATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAAACAAA
* *
7969 TCCTTAAATCCATAGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAGGGAGTCTTGGCGC
131 TCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGC
* * * *
8034 AAAAAATCGTGCAAAACTGAGCCGAGA-CCCGGAACG-GTTTTTAGCCAAAAACTATGATAGTTA
196 AAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTA
* * * * * *
8097 GTACATGCACGATTTTGACTAAAATTACTCATAAATTGACCCCAAAATATTTATCCTCAATATTT
261 GT--A--CACGATTTCGACTAAAATTTCTCAAAAATTGACCCCCAAAGATTTTTCCTCAATATTT
* *
8162 GGCCAAAATACTCATAAAAAATATATTATTAAA-CGCCAAAAATATTGAATGGCTTTTGA-AGCT
322 GGCCAAAATACTCATAAAAAATATATTATTAAATCGCCAAAAATATTGAAGGGCTTTTCACA-CT
* * * *
8225 TTTAATGTCATTGTTATTATTTTTTCTGAATTAATTTCTAATTAATTCGAAAAAAGATTCT-GAT
386 TTTAATTTCATTTTTCTTATTTTTTCTGAATTAATTTCTAATAAATTCGAAAAAAGATT-TAGAT
* * *
8289 GCTCGTAAAAACAAATCCTTAAATCCATAGTGGCTAAGATTTGTTTAGATGAATATAAATATTTC
450 GCTCGT-AAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
* * * * * *
8354 AAGGAGTCTTGGCTCAAAAAAGTCATACAAAACTGAGCCGGAACCTCGGAACGTGTTTTTAGCCA
514 AAGGAGTCTTGGCGCAAAAAA-TCATGCAAAACTGAGCAGGGACCTCTGAACGCGTTTTTAGCCA
* * * * *
8419 AAATCTATGATGGTTAGTACACGATTTCGACTAAAATTTCGCAAAAATTGAACCCAAAAGATTTC
578 AAAACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGAAAAAAATGATCCCAAAAGATTTC
* * *
8484 TCCGCAATATTTGGCCGAAATT
643 TCCTCAATATTTGGCCAAAATA
* * * * * **
8506 CTAATAAAAAATTTATTATTAATCGCC-AAAATATTGGAGGGTTTTTCACGCCATTAATATCATT
1 CTCATAAAAAATATATTATTAAACGCCAAAAATATTGGAGAGCTTTTCACGGTATTAATATCATT
* * *
8570 ATTATTATTTTTTCTGTATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAATCAA
66 TTTATTA-TTTTTCTGAATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAAACAA
* * * * *
8635 ATCCTTAAATACATAGTGGCTGAGATTTTGTTAGATAAATATAGATATTTGAAGAAGTCTTGGCG
130 ATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
* * *
8700 CAAAAAATCATACAAAACTGAGTCGGGACCTCGGAACGCG-TTTTAGCCAAAAACTGTGATGGTT
195 CAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTT
* * * * * * * *
8764 AGTACACGATTTCGGCTAAAATTTTTC-AAAACTGACCCCCGATGATAATTTT-CACAATTTTTT
260 AGTACACGATTTCGACTAAAATTTCTCAAAAATTGACCCCCAAAGAT--TTTTCCTCAATATTTG
* * ** * *
8827 GCCACAATACTCATAAAAAATATATAATT-TGTCTCCAAAAAACATTTG-AGGGCTTTTCACACT
323 GCCAAAATACTCATAAAAAATATATTATTAAATCGCC-AAAAATA-TTGAAGGGCTTTTCACACT
* * * *
8890 TCTAATATCATTTTTCTTATTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTTAGATG
386 TTTAATTTCATTTTTCTTATTTTTTCTGAATTAATTTCTAATAAATTCGAAAAAAGATTTAGATG
* *
8955 CTCGTAAAACCAAATCCTTAAATCCA-ATGTTGTTGAGATTTGGTTAGATGAATATAGATATTTC
451 CTCGTAAAA-CAAATCCTTAAATCCATA-GTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
* * *
9019 AAGGAGTCTTGGCGCTAAAAATCATGCAAAACTGAGTAGGGGCCTCTGAACGCGTTTTTAGCCAA
514 AAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGCAGGGACCTCTGAACGCGTTTTTAGCCAA
* * * * * * * * *
9084 AAACCGTGATGGTCAGTACACGATTTTGGCTAAAATTTTGGAAAAATTGATCCC-AATGATTTTT
579 AAACTGTGATGGTTAGTACACGATTTCGACTAAAATTTCGAAAAAAATGATCCCAAAAGATTTCT
* * *
9148 CCTTAATTTTTGGCTAAAATA
644 CCTCAATATTTGGCCAAAATA
* * * *
9169 CTCAT-AAAAATATATAATTAAACACCAAAAAGATTGGAGAGCTTTTCACGGTTTTAATATCATT
1 CTCATAAAAAATATATTATTAAACGCCAAAAATATTGGAGAGCTTTTCACGGTATTAATATCATT
* * * * *
9233 TTTCTTAGTTTTTCTGAATTTAACTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAC
66 TTTATTA-TTTTTCTGAA-TTAATTTCTAATTTATTCGAAA-AAGATTCAGATGCTCGTAAAAAC
* * * * *
9298 AAATCATTAAATCCA-ATGTTGTTGAGATTTGGTAAGATGAATATAGATATGTCAAGGAGTCTTG
128 AAATCCTTAAATCCATA-GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG
* * * ** *
9362 GCGCCAAAAATAATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGTTTAAAAAAATGTGA
192 GCGCAAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAG--CCAAAAACTGTGA
* * ** *
9427 TGGTTAGTACACGATTTCGGCT-AAATTTTTGCAAAAACCGA-CCCCAAAGATTTCTCCTCAAT-
255 TGGTTAGTACACGATTTCGACTAAAATTTCT-CAAAAATTGACCCCCAAAGATTTTTCCTCAATA
*** * * * * * * *
9489 TTTTTACATTAATAATCATAGAAAATATATAATTCAA-CGTCAAAAAAATTGATA-GGCTTTTCA
319 TTTGGCCA-AAATACTCATAAAAAATATATTATTAAATCGCCAAAAATATTGA-AGGGCTTTTCA
** * *
9552 CGTTTTTAATATCGTTTTTC
382 CACTTTTAATTTCATTTTTC
9572 CTACAATTTT
Statistics
Matches: 2006, Mismatches: 304, Indels: 153
0.81 0.12 0.06
Matches are distributed among these distances:
647 16 0.01
648 8 0.00
649 24 0.01
650 107 0.05
651 14 0.01
653 1 0.00
654 39 0.02
655 84 0.04
656 67 0.03
657 119 0.06
658 71 0.04
659 2 0.00
660 2 0.00
661 74 0.04
662 81 0.04
663 172 0.09
664 191 0.10
665 294 0.15
666 164 0.08
667 174 0.09
668 75 0.04
669 10 0.00
670 7 0.00
671 158 0.08
672 52 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (664 bp):
CTCATAAAAAATATATTATTAAACGCCAAAAATATTGGAGAGCTTTTCACGGTATTAATATCATT
TTTATTATTTTTCTGAATTAATTTCTAATTTATTCGAAAAAGATTCAGATGCTCGTAAAAACAAA
TCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGC
AAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTA
GTACACGATTTCGACTAAAATTTCTCAAAAATTGACCCCCAAAGATTTTTCCTCAATATTTGGCC
AAAATACTCATAAAAAATATATTATTAAATCGCCAAAAATATTGAAGGGCTTTTCACACTTTTAA
TTTCATTTTTCTTATTTTTTCTGAATTAATTTCTAATAAATTCGAAAAAAGATTTAGATGCTCGT
AAAACAAATCCTTAAATCCATAGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
CTTGGCGCAAAAAATCATGCAAAACTGAGCAGGGACCTCTGAACGCGTTTTTAGCCAAAAACTGT
GATGGTTAGTACACGATTTCGACTAAAATTTCGAAAAAAATGATCCCAAAAGATTTCTCCTCAAT
ATTTGGCCAAAATA
Found at i:10162 original size:31 final size:30
Alignment explanation
Indices: 10124--10228 Score: 131
Period size: 31 Copynumber: 3.5 Consensus size: 30
10114 TATACTGGCT
* * *
10124 AAATGCTCAATTTGGTACCAAACCTTTGACG
1 AAATGCTCAATTTGATACTAAACCTTTCA-G
*
10155 AAATGCTCAATTTGATACTAAACC-TTCAA
1 AAATGCTCAATTTGATACTAAACCTTTCAG
10184 AAATGCTCAATTTGATACTAAACCTTTCAGG
1 AAATGCTCAATTTGATACTAAACCTTTCA-G
**
10215 ATTTGCTCAATTTG
1 AAATGCTCAATTTG
10229 GTACGATTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
29 24 0.37
30 7 0.11
31 34 0.52
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTTCAG
Found at i:10197 original size:29 final size:30
Alignment explanation
Indices: 10124--10209 Score: 120
Period size: 29 Copynumber: 2.9 Consensus size: 30
10114 TATACTGGCT
* * * *
10124 AAATGCTCAATTTGGTACCAAACCTTTGACG
1 AAATGCTCAATTTGATACTAAACC-TTCACA
10155 AAATGCTCAATTTGATACTAAACCTTCA-A
1 AAATGCTCAATTTGATACTAAACCTTCACA
10184 AAATGCTCAATTTGATACTAAACCTT
1 AAATGCTCAATTTGATACTAAACCTT
10210 TCAGGATTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.51
30 3 0.06
31 22 0.43
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTCACA
Found at i:10750 original size:27 final size:27
Alignment explanation
Indices: 10710--10787 Score: 75
Period size: 32 Copynumber: 2.6 Consensus size: 27
10700 AAAAATGTGG
*
10710 CTCTTTCGACTTGAAAAATAATTTTTCTT
1 CTCTTT-GA-TTGAAAAATAATTTTCCTT
10739 CTCTTTGATTGAAAAATCTGATAATTTTCCTT
1 CTCTTTGATTG-AAAA----ATAATTTTCCTT
*
10771 CTCTTTGATTAAAAAAT
1 CTCTTTGATTGAAAAAT
10788 CTGTGGGGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
27 5 0.12
28 6 0.14
29 6 0.14
31 4 0.10
32 21 0.50
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (27 bp):
CTCTTTGATTGAAAAATAATTTTCCTT
Found at i:10785 original size:31 final size:32
Alignment explanation
Indices: 10727--10790 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
10717 GACTTGAAAA
* *
10727 ATAATTTTTCTTCTCTTTGATTGAAAAATCTG
1 ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
10759 ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
1 ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
10791 TGGGGGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (32 bp):
ATAATTTTCCTTCTCTTTGATTAAAAAATCTG
Found at i:11606 original size:78 final size:78
Alignment explanation
Indices: 11475--11629 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 78
11465 ATGTTGAAAT
*
11475 CATTAGTTAAGTATTGCTATTATAAATAAAAGCTGAATTTTAATGACATCTTGTGTCTCCATTCT
1 CATTAGTTAAGTATTGCTATTATAAATAAAAGCTGAATTTTAATGACAACTTGTGTCTCCATTCT
11540 GCTAATTTTAAAG
66 GCTAATTTTAAAG
* * * *
11553 CATTAGTTAAGTATTGTTGTTATAAGTAAAAGCTGAATTTTAATGACAACTTGTGTCTTCATTCT
1 CATTAGTTAAGTATTGCTATTATAAATAAAAGCTGAATTTTAATGACAACTTGTGTCTCCATTCT
11618 GCTAATTTTAAA
66 GCTAATTTTAAA
11630 CAGATTAAGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (78 bp):
CATTAGTTAAGTATTGCTATTATAAATAAAAGCTGAATTTTAATGACAACTTGTGTCTCCATTCT
GCTAATTTTAAAG
Found at i:11880 original size:98 final size:97
Alignment explanation
Indices: 11707--11907 Score: 350
Period size: 98 Copynumber: 2.1 Consensus size: 97
11697 TTGCCATTAC
* *
11707 ATATCCTAATGGTTAAAATGTCAGCAACCCATTTAAAGAACAAAAGCTACATAAATAGCAATATC
1 ATATTCTAATGGGTAAAATGTCAGCAACCCATTTAAAGAACAAAAGCTACATAAATAGCAATATC
*
11772 CAAGGCTTAAACC-AGTTGTTACAAACACCAAA
66 CAAGGCTTAAACCTA-TTGTTACAAACACAAAA
11804 ATATTCTAATGGGTAAAATGTCAGCAACCCCATTTAAAGAACAAAAGCTACATAAATAGCAATAT
1 ATATTCTAATGGGTAAAATGTCAGCAA-CCCATTTAAAGAACAAAAGCTACATAAATAGCAATAT
11869 CCAAGGCTTAAACCTATTGTTACAAACACAAAA
65 CCAAGGCTTAAACCTATTGTTACAAACACAAAA
11902 ATATTC
1 ATATTC
11908 CAGTCAATGT
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 25 0.25
98 73 0.74
99 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (97 bp):
ATATTCTAATGGGTAAAATGTCAGCAACCCATTTAAAGAACAAAAGCTACATAAATAGCAATATC
CAAGGCTTAAACCTATTGTTACAAACACAAAA
Found at i:15140 original size:24 final size:24
Alignment explanation
Indices: 15108--15159 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
15098 TGAACAGCAG
**
15108 CTCCTAAATCTTCATTATGGTGAC
1 CTCCTAAATCTTCATTATCCTGAC
15132 CTCCTAAATCTTCATTATCCTGAC
1 CTCCTAAATCTTCATTATCCTGAC
15156 CTCC
1 CTCC
15160 ATCTTGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.37
Consensus pattern (24 bp):
CTCCTAAATCTTCATTATCCTGAC
Found at i:15653 original size:2 final size:2
Alignment explanation
Indices: 15646--15678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15636 TTTCCTCAAG
15646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15679 TCATAGCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.