Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008075.1 Corchorus capsularis cultivar CVL-1 contig08096, 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: 114108
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:308 original size:1 final size:1
Alignment explanation
Indices: 304--338 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
294 TTTTTTTAGG
304 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
339 ATTACGAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1792 original size:669 final size:653
Alignment explanation
Indices: 340--1950 Score: 1746
Period size: 669 Copynumber: 2.4 Consensus size: 653
330 TTTTTTTTTA
* * * * * * *
340 TTACGAGTATTAGAATCTTGTTTCAATTTAATAAGAAATTAATTTGGAAAACAAATAGAAAAACG
1 TTACGAGCATCAGAATCATGTTTCGATTTAATTAGAAATTAATTTAGAAAA-AAAAAGAAAAACG
* * * *
405 ATATTAGAAGCCTGAAAAGCCATT-CA-TTTTTCTGGCGTTAAGTTATATATTTTATTTGAGTAT
65 ATATTAGAAGCATGAAAAGCCCTTCCACTTTTT-T-GCGTTAAGTTATATATTTTATATGATTAT
* * * * *
468 TGTGGCCAAAAATTAAGGAAAAAGATTTT-GCGTCAATTTTTGCAAAATTTTAACCGAAATCGTG
128 TGTGACAAAAAATTAATG-AAAA-ATTTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTA
*
532 TACTAACCATCAC-ATTTTTTGGATAAAAAAGCGTTTCGGGGCCTCGGCTCAGTTTTGCATGATT
191 TACTAACCATCACGA-TTTTTGGATAAAAAAGCGTTAC-GGGCCTCGGCTCAGTTTTGCATGATT
* * * *
596 TTTGACAGCAAGACTCATTGAAATATCTATATTCATCTAACCAAATATCAGCCACATTGGATTTA
254 TTTG-CACCAAGACTCCTTGAAATATCCATATTCATCTAACCAAATATCAGCCACATTGGATTGA
* * * *
661 AGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGGTTTAATTAAAAATTAATTTAGAAAAAAA
318 AGGATTTATTTTTACAAGCATCTCAATCATGTTTCGATTTAATTAAAAATTAATTCAGAAAAAAA
* * * * * *
726 GGAAAAACGATATTAATATCGTGAAAAGCACTTCCACCTTTTTTGTGTTAAATTATATATTTTTT
383 AGAAAAACGATATTAATAGCCTGAAAACCACTTCCACCTTTTTGGCGTTAAATTATATATTTTTT
* * *
791 ATGAGTATCGTGACTAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCGAAATTTTGACCG
448 ATGAGTATCGTGACCAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCAAAATTTTAACCG
* ** * *
856 AAATCGTGTATCACAGTTTTTGGCTTAAAACGCGTTCCGGGGCTCCGGCTCAATTTTGCATGATT
513 AAATCGTATATCACAGTTTTTGGCCAAAAACGCGTTCCGGGACCCCGGCTCAATTTTGCATGATT
* * *
921 TTTTGTGTCAAGACTCCTTGTAATATCAATATTCATCTAACAAAATCTCAGCCATAGTGGATATA
578 TTTGGTGTCAAGACTCATTGAAATATCAATATTCATCTAACAAAATCTCAGCCATAGTGGATATA
*
986 AGGATTTGTTT
643 AAGATTTGTTT
* * *
997 TTACGAGCATCAGAATCAAGTTTTGATTTAATTAGAAATTAA-TTCGAAAAAGAAAAGAAAAACG
1 TTACGAGCATCAGAATCATGTTTCGATTTAATTAGAAATTAATTTAGAAAAA-AAAAGAAAAACG
* * * * * * * *
1061 ATATTATAAGCATGAAAATCCCTTCAATCTTTTTGGGGATGAGTTATATGTTTTATATGATTATT
65 ATATTAGAAGCATGAAAAGCCCTTCCA-CTTTTTTGCGTTAAGTTATATATTTTATATGATTATT
* *
1126 GTGACAAAAAATTAATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATA
129 GTGACAAAAAATTAATGAAAAAT-TTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTATA
** * *
1191 CTAACCATCACGATTTCCGGATAAAAATGCGTTCCAGGGCCTCGGCTCAGTTTTGCATGATTTTT
193 CTAACCATCACGATTTTTGGATAAAAAAGCGTTAC-GGGCCTCGGCTCAGTTTTGCATGA-TTTT
* * * * *
1256 TGCACCAAGACTCCTTGAAATATCCATATTTATCTAGCCAAATCTCATCCACCTTGGATTGAAGG
256 TGCACCAAGACTCCTTGAAATATCCATATTCATCTAACCAAATATCAGCCACATTGGATTGAAGG
* * * * *
1321 TTTTTTTAATTTTTAACTAGTAT-TACAATCTTGTTTCGATTTAA-TAACAAATTAATTCGGAAA
321 ---ATTT-ATTTTT-ACAAGCATCT-CAATCATGTTTCGATTTAATTAA-AAATTAATTCAG-AA
* *
1384 ACAAAAAGAAAAACGATATT-ATAAGCCTGAAAAACCA-TT-CATTCTTTTTGGCGTTAAGTTAT
378 A-AAAAAGAAAAACGATATTAAT-AGCCTG-AAAACCACTTCCA-CCTTTTTGGCGTTAAATTAT
* * * * * *
1446 ATATTTTATT-TGAGTATTGTGGCCAAAAATT-AGG-GAAAAATCTTTGGGTCAATTTTTGCAAA
439 ATATTTT-TTATGAGTATCGTGACCAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCAAA
* ***
1508 ATTTTAACCGAAATCGTATACTAACCATCACGGTTTTTGGCCAAAAATGCGTTTTTGGACCCCGG
503 ATTTTAACCGAAATCGTATA-T---CA-CA--GTTTTTGGCCAAAAACGCGTTCCGGGACCCCGG
* * * *
1573 CTCAGTTTTGCATGATTTTTGGCTG-CAAGACTTATTGAAATATCTATATTCATCTAACCAAATC
561 CTCAATTTTGCATGATTTTTGG-TGTCAAGACTCATTGAAATATCAATATTCATCTAACAAAATC
*
1637 TCAG-CA-ACGTTGGATTTAAAGATTTGTTT
625 TCAGCCATA-G-TGGATATAAAGATTTGTTT
* * *
1666 TTATGAGCATCTGAATCATGTTTCGGTTTAATTAGAAATTAATTTAGAAAAAAAAAGAAAAACGA
1 TTACGAGCATCAGAATCATGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAAAAGAAAAACGA
* * * * *
1731 TATTAGAAGCGTGAAAAGCCCTTCCACCTTTTTTGTGTTAAATTATATATTTTACATGATTATCG
66 TATTAGAAGCATGAAAAGCCCTTCCA-CTTTTTTGCGTTAAGTTATATATTTTATATGATTATTG
* * * * * *
1796 TGACTAAAAATT-GTGGAAAAAAATTTTGGGGTCAAGTTTTGCGAAATTTTAACCGAAATCATAT
130 TGACAAAAAATTAAT-G--AAAAATTTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTAT
* * * *
1860 ACTAACCATCACAGTTTTTTGGCTTAAAACGCGTTACGGGTCCTCGGCTCAGTTTTGCATGATTT
192 ACTAACCATCAC-GATTTTTGGATAAAAAAGCGTTACGGG-CCTCGGCTCAGTTTTGCATGATTT
*
1925 TTG-ACTTCAAGACTCCTTGTAATATC
255 TTGCAC--CAAGACTCCTTGAAATATC
1951 ATTTTAATTA
Statistics
Matches: 794, Mismatches: 121, Indels: 64
0.81 0.12 0.07
Matches are distributed among these distances:
655 3 0.00
656 45 0.06
657 214 0.27
658 7 0.01
659 5 0.01
660 3 0.00
661 9 0.01
662 73 0.09
663 11 0.01
664 64 0.08
665 8 0.01
666 2 0.00
667 3 0.00
668 4 0.01
669 216 0.27
670 65 0.08
671 62 0.08
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (653 bp):
TTACGAGCATCAGAATCATGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAAAAGAAAAACGA
TATTAGAAGCATGAAAAGCCCTTCCACTTTTTTGCGTTAAGTTATATATTTTATATGATTATTGT
GACAAAAAATTAATGAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTATACTA
ACCATCACGATTTTTGGATAAAAAAGCGTTACGGGCCTCGGCTCAGTTTTGCATGATTTTTGCAC
CAAGACTCCTTGAAATATCCATATTCATCTAACCAAATATCAGCCACATTGGATTGAAGGATTTA
TTTTTACAAGCATCTCAATCATGTTTCGATTTAATTAAAAATTAATTCAGAAAAAAAAGAAAAAC
GATATTAATAGCCTGAAAACCACTTCCACCTTTTTGGCGTTAAATTATATATTTTTTATGAGTAT
CGTGACCAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCAAAATTTTAACCGAAATCGTA
TATCACAGTTTTTGGCCAAAAACGCGTTCCGGGACCCCGGCTCAATTTTGCATGATTTTTGGTGT
CAAGACTCATTGAAATATCAATATTCATCTAACAAAATCTCAGCCATAGTGGATATAAAGATTTG
TTT
Found at i:4067 original size:665 final size:659
Alignment explanation
Indices: 1953--4890 Score: 2987
Period size: 665 Copynumber: 4.4 Consensus size: 659
1943 GTAATATCAT
* * *
1953 TTTAATTAGAAATTATTTCGTAAAAAAAAAACGAAAGACGATATTAGAA-AAGTGAAAAGCCC-T
1 TTTAATTAGAAATTAATTCG--AAAAAAAAA-GAAAAACGATATTAGAAGCA-TGAAAAGCCCTT
* * * * * * *
2016 CAAATC-TCTTGTGTTAAATTATATATTTT-TATGACTATTGTAACTAAAAATTGAGGAAAAAAA
62 C-AATCTTTTTGGGTTAAGTTATATATTTTATATGAGTATTGTGACCAAAAATTAAGG--AAAAA
* * * * *
2079 T-TTTAGGGTCAAGTTATGCGAAATTTTAACCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
124 TCTTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAATCACAGTTTTTGGCT
* * * *
2143 TCAAACGCGTTATGGGACCCCGGCTCCGTTTTGCATGATTTTTGGC-GTCAAGACTCCTTGTAAT
189 TAAAACGCGTTCTGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGCAG-CAAGACTCATTGTAAT
* *
2207 ATCAATATTCATCTAACGAAATCTCAACCATAGTGGATATAAGGATTTGTTTTTACGAGCATCAG
252 ATCAATATTCATCTAACGAAATCTCAACAACAGTGGATATAAGGATTTGTTTTTACGAGCATCAG
* * * * *
2272 AATCAAGTTTTGATTTAATTAGAAATTAATTCAAAAAAGAAAAAGAAAAATGATATTAGAAGCAC
317 AATCATGTTTCGATTTAATTAGAAATTAATT-GAAAAAGAAAAAGAAAAACGATATTAGAAGCAT
* * * *
2337 GAAAATCCCTTCAATCTTTTTGGTGATGAGTTATATATTTTATATGATTATTGTGACAAAAAATT
381 GAAAATCCCTTCAATCTTTTTGGCGATAAGTTATATATTTTATATGAGTATTGTGACTAAAAATT
**
2402 AAGG-AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGTCAAAATCGTATACT-A-A-CA-A-
446 AAGGAAAAAAT-TTTCGGGTCAATTTTTGCAAAATTTTAACCAAAATCGTATACTAATATCACAG
***** * * *
2461 TTTTTGGCTAAAAATGCGTTCTGGGATTTTGGCTCAGTTTTGCTTGATTTTCGGCACCAAAACTC
510 TTTTTGGCTAAAAATGCGTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTC
** *
2526 CTTGAAATATCCATATTCATCTAACCAAAT-TACATCCACATTGGATTGGAGGATTTTTTTTTTA
574 CTTGAAATATCCATATTCATCTAACCAAATCT-CATCCACATTGGATTAAAGGA-TTTGTTTTTA
** * * * *
2590 TGATCATTAGAGTCTTGTTTCGA
637 CAAGCATCAGAATCATGTTTCGA
* ** *
2613 TTTAA-TATGAAATTAATTGAGAAAAAAAAAGAAAAACGATATTAGAAGTTTGAAAAGCCTTTCA
1 TTTAATTA-GAAATTAATT-CGAAAAAAAAAGAAAAACGATATTAGAAGCATGAAAAGCCCTTCA
* * *
2677 ATATTTTAGGCGTTAAGTTATATATTTTATATGAGTATTGTGGCCAAAAATTAAGGAAAAATCTT
64 ATCTTTTTGG-GTTAAGTTATATATTTTATATGAGTATTGTGACCAAAAATTAAGGAAAAATCTT
*
2742 TTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAAT--CAGTTTTTGGCTTAAA
128 TCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAATCACAGTTTTTGGCTTAAA
* *
2805 ACGCGTTAC-GGGACCCCGGCTCCA-TTTTGCATGATTTTTGG-TGTCAAGACTCCA-TGTATTA
193 ACGCGTT-CTGGG-CCCCGGCT-CAGTTTTGCATGATTTTTGGCAG-CAAGACT-CATTGTAATA
* * * *
2866 TCAATATTCATCTAATGAAATCTCAACCATAGTGAATATAAGGATTTGTTTTTACGAGCATCAGA
253 TCAATATTCATCTAACGAAATCTCAACAACAGTGGATATAAGGATTTGTTTTTACGAGCATCAGA
* * *
2931 ATCACGTTAT-GATTTAATTAGAAATTAATT--------AAAA-AAAAACGGTTTTAGAAGCATG
318 ATCATGTT-TCGATTTAATTAGAAATTAATTGAAAAAGAAAAAGAAAAACGATATTAGAAGCATG
* * * * *
2986 AAAATCCCTTCAATCTTTTTGGGGATGAGTTATATATTTTATATGATTATTGTTACCAAAAATTA
382 AAAATCCCTTCAATCTTTTTGGCGATAAGTTATATATTTTATATGAGTATTGTGACTAAAAATTA
* * * * *
3051 ACGAAAAATTTTTGGGGTCAATTTTTGCAAAATTTTAGCAAAAATCGTATACTAATCATCAC-GA
447 AGGAAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAACCAAAATCGTATACTAAT-ATCACAG-
* * * *
3115 TTTATGGCTAAAAATGTGTTCCGGGGCCTCGGCTCAGTTTTGCTTGATTTTTGGCACCAAGACTC
510 TTTTTGGCTAAAAATGCGTT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTC
* * *
3180 CTTGAAATATCCATATTAATCTAACCAAATCTCATCCACCTTTGATTAAAGGA-TT-TTTTTACA
574 CTTGAAATATCCATATTCATCTAACCAAATCTCATCCACATTGGATTAAAGGATTTGTTTTTACA
* *
3243 AGCATTAGAATCTTGTTTCGA
639 AGCATCAGAATCATGTTTCGA
* * *
3264 TTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCATTCA
1 TTTAATTAGAAATTAATTC-GAAAA-AAAAAGAAAAACGATATTAGAAGCATGAAAAGCCCTTCA
* * * * *
3329 ATCTTTTTGGCATTAAGTTATATATTTTATTTGAGTATTCTGGCCGAAAATTAAGGAAAAATCTT
64 ATCTTTTTGG-GTTAAGTTATATATTTTATATGAGTATTGTGACCAAAAATTAAGGAAAAATCTT
* * * *
3394 TTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTGACAATCACGGTTTTTGGCTAAAA
128 TCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAATCACAGTTTTTGGCTTAAA
* * * *
3459 ATGCGTTCTGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACTCATTGAAATATCTAT
193 ACGCGTTCTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGCAAGACTCATTGTAATATCAAT
* * * * * *
3524 ATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCAT
258 ATTCATCTAACGAAATCTCAACAACAGTGGATATAAGGATTTGTTTTTACGAGCATCAGAATCAT
**
3589 GTTTCGATTTAATTAGAAATTAATTTAGAAAAAAGAAAAAGAAAAACGATATTAGAAGTGTGAAA
323 GTTTCGATTTAATTAGAAATTAA-TT-G-AAAAAGAAAAAGAAAAACGATATTAGAAGCATGAAA
* * * * * * * * *
3654 A-CCCTTCCACCTTTTTTGCGTTAAATTATATATTTT-TATGAGTATCGTGGCTAGAAATTGAGG
385 ATCCCTTCAATCTTTTTGGCGATAAGTTATATATTTTATATGAGTATTGTGACTAAAAATTAAGG
* * *
3717 AAAAAAATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTATACTAACTATCACAGTTT
450 -AAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAACCAAAATCGTATACTAA-TATCACAGTTT
* * * * * * ** *
3782 CTAGCTTAAAACGCGTTACGGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACTTCTT
513 TTGGCTAAAAATGCGTT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTT
* * * * * * *
3847 GTAATATCAATATTCATCTAACGAAATCTCAACCATAGTGGA-TATAAGGATTTGTTTTTACGAG
577 GAAATATCCATATTCATCTAACCAAATCTCATCCACATTGGATTA-AAGGATTTGTTTTTACAAG
* **
3911 CATCAGAATCAAGTTTTAA
641 CATCAGAATCATGTTTCGA
* * *
3930 TTTAATTAGAAATTAATTCGAAAAAGAAAAGAAAGACGATATTATAAGCATGAAAATCCCTTCAA
1 TTTAATTAGAAATTAATTCGAAAAA-AAAAGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAA
* * * * * *
3995 TCTTTTTGGGGATGAGTTATATGTTTTATATGATTATTGTGACAAAAAATTAATGAAAAATCTTT
65 TCTTTTT-GGGTTAAGTTATATATTTTATATGAGTATTGTGACCAAAAATTAAGGAAAAATCTTT
* * * * * *
4060 CGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCAC-GATTTTCGGCTAAAA
129 CGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAATCACAG-TTTTTGGCTTAAA
* * * * * * * * *
4124 ATGCGTTTCGGGGCCTCGGCTCAGTTTTGCCTGATTTTTTGCACCAAGACTCCTTGAAATATCCA
193 ACGCG-TTCTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGCAAGACTCATTGTAATATCAA
* * * * * * * *
4189 TATTCATCTAGCCAAATCTCATCCACCA-TGGAT-TGAAGGGGTTTTTTTTTACGAGTATTAGAA
257 TATTCATCTAACGAAATCTCA-ACAACAGTGGATAT-AA-GGATTTGTTTTTACGAGCATCAGAA
* * * * * * *
4252 TCTTGTTTCAATTTAATAAGAAATTAATTTGGAAAACAAATAGAAAAACGATATTAGAAGCCTGA
319 TCATGTTTCGATTTAATTAGAAATTAA-TTGAAAAAGAAAAAGAAAAACGATATTAGAAGCATGA
* * * * * * *
4317 AAAGCCATTC-ATTTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATG-GTCAAAAATTA
383 AAATCCCTTCAATCTTTTTGGCGATAAGTTATATATTTTATATGAGTATTGTGACT-AAAAATTA
* * * * *
4380 AGGAAAAAGATTTT-GCGTCAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACAG
447 AGGAAAAA-ATTTTCGGGTCAATTTTTGCAAAATTTTAACCAAAATCGTATACTAA-TATCACAG
* * * *
4444 TTTTTGGGTAAAAAAGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGCAAGACTC
510 TTTTTGGCTAAAAATGCG-TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTC
* * * *
4509 ATTGAAATATCTATATTCATCTAACCAAATATCAGT-CACATTGGATTTAAGGATTTGTTTTTAC
574 CTTGAAATATCCATATTCATCTAACCAAATCTCA-TCCACATTGGATTAAAGGATTTGTTTTTAC
* *
4573 AAGCATCTGAATCATGTTTCGG
638 AAGCATCAGAATCATGTTTCGA
* * * * * * * *
4595 TTAAATTAAAAATTAATTTAGAAAGAAAAAGGAAAAACAATATTA-ATATCTTGAAAAGCACTTC
1 TTTAATTAGAAATTAA-TTCGAAA-AAAAAAGAAAAACGATATTAGA-AGCATGAAAAGCCCTTC
* * * * * * * * **
4659 CACCTTTTTTGTGTTAAATTATATATTTTTTATGAGTATCGTGACTAAAAATTGAGGAAAAAAAT
63 AATC-TTTTTGGGTTAAGTTATATATTTTATATGAGTATTGTGACCAAAAATTAAGGAAAAATCT
* * *
4724 ATTCGGGTCAAGTTTTGCGAAATTTTGACCGAAATCGTGTACTAA-ACATCACAGTTTTTGGCTT
127 -TTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACA-ATCACAGTTTTTGGCTT
* * * **
4788 AAAACGCGTTACAGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACTCATTGTAATAT
190 AAAACGCGTT-CTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGCAAGACTCATTGTAATAT
* * *
4853 CAATATTCATCTAACGAAATCTCATCCATAGTGGATAT
254 CAATATTCATCTAACGAAATCTCAACAACAGTGGATAT
4891 TATAAGCATG
Statistics
Matches: 1916, Mismatches: 287, Indels: 142
0.82 0.12 0.06
Matches are distributed among these distances:
648 121 0.06
649 10 0.01
651 46 0.02
652 151 0.08
653 116 0.06
654 127 0.07
655 2 0.00
658 184 0.10
659 25 0.01
660 74 0.04
661 23 0.01
663 21 0.01
664 177 0.09
665 416 0.22
666 236 0.12
667 185 0.10
668 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (659 bp):
TTTAATTAGAAATTAATTCGAAAAAAAAAGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAAT
CTTTTTGGGTTAAGTTATATATTTTATATGAGTATTGTGACCAAAAATTAAGGAAAAATCTTTCG
GGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAATCACAGTTTTTGGCTTAAAACG
CGTTCTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGCAAGACTCATTGTAATATCAATATT
CATCTAACGAAATCTCAACAACAGTGGATATAAGGATTTGTTTTTACGAGCATCAGAATCATGTT
TCGATTTAATTAGAAATTAATTGAAAAAGAAAAAGAAAAACGATATTAGAAGCATGAAAATCCCT
TCAATCTTTTTGGCGATAAGTTATATATTTTATATGAGTATTGTGACTAAAAATTAAGGAAAAAA
TTTTCGGGTCAATTTTTGCAAAATTTTAACCAAAATCGTATACTAATATCACAGTTTTTGGCTAA
AAATGCGTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCC
ATATTCATCTAACCAAATCTCATCCACATTGGATTAAAGGATTTGTTTTTACAAGCATCAGAATC
ATGTTTCGA
Found at i:4411 original size:333 final size:331
Alignment explanation
Indices: 1953--4888 Score: 2813
Period size: 333 Copynumber: 8.9 Consensus size: 331
1943 GTAATATCAT
* * * ***
1953 TTTAATTAGAAATT-ATTTCGTAAAAAAAAAACGAAAGACGATATTAGAAAAGTGAAAAGCCC-T
1 TTTAATAAGAAATTAATTT-G-GAAAAAAAAA-GAAAAACGATATTAGAAGCCTGAAAAGCCCTT
* * * * * * *
2016 CAAATC-TCTT-GTGTTAAATTATATATTTT-TATGACTATTGT-AACTAAAAATTGAGGAAAAA
63 C-AATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAA
* * * *
2077 AATTTTAGGGTCAAGTTATGCGAAATTTTAACCGAAATCGTGTACTAACCATCACAGTTTTTGGC
127 TATTTT-GGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACA-TTTTTGGC
** * * * *
2142 TTCAAACGCGTTAT-GGGACCCCGGCTCCGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGTAA
190 TAAAAACGCGTT-TCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAA
* * * *
2206 TATCAATATTCATCTAACGAAATCTCAACCATAGTGGATATAAGGATTTGTTTTTACGAGCATCA
254 TATCAATATTCATCTAACCAAATCTCATCCACAGTGGAT-TAAGGATTTGTTTTTACGAGCATTA
* *
2271 GAATCAAGTTTTGA
318 GAATCATGTTTCGA
* *** * *
2285 TTTAATTAGAAATTAATTCAAAAAAGAAAAAGAAAAATGATATTAGAAGCAC-GAAAATCCCTTC
1 TTTAATAAGAAATTAATTTGGAAAA-AAAAAGAAAAACGATATTAGAAGC-CTGAAAAGCCCTTC
* * * * *
2349 AATCTTTTTGGTGATGAGTTATATATTTTATATGATTATTGT-GACAAAAAATTAAGGAAAAATC
64 AATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATA
* ** * *
2413 TTTCGGGTCAATTTTTGCAAAATTTTAGTCAAAATCGTATACT-A--A-CA-ATTTTTGGCTAAA
129 TTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACATTTTTGGCTAAA
* ***** * * * *
2473 AATGCG-TTCTGGGATTTTGGCTCAGTTTTGCTTGATTTTCGGCACCAAAACTCCTTGAAATATC
194 AACGCGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATC
* * * * * *
2537 CATATTCATCTAACCAAAT-TACATCCACATTGGATTGGAGGATTTTTTTTTTATGATCATTAGA
258 AATATTCATCTAACCAAATCT-CATCCACAGTGGATT-AAGGA-TTTGTTTTTACGAGCATTAGA
* *
2601 GTCTTGTTTCGA
320 ATCATGTTTCGA
* ** *
2613 TTTAATATGAAATTAA-TTGAGAAAAAAAAAGAAAAACGATATTAGAAGTTTGAAAAGCCTTTCA
1 TTTAATAAGAAATTAATTTG-GAAAAAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTTCA
* * * *
2677 ATATTTTAGGCGTTAAGTTATATATTTTATATGAGTATTGTGG-CCAAAAATTAAGGAAAAATCT
65 ATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATAT
* * *
2741 TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACAATCA-GTTTTTGGCTTAAA
130 TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACATTTTTGGCTAAAA
* * ** * * *
2805 ACGCGTTACGGGACCCCGGCTCCA-TTTTGCATGATTTTTGGTGTCAAGACTCCATGTATTATCA
195 ACGCGTTTCGGGGCCCCGGCT-CAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCA
** * * * *
2869 ATATTCATCTAATGAAATCTCAACCATAGTGAATATAAGGATTTGTTTTTACGAGCATCAGAATC
259 ATATTCATCTAACCAAATCTCATCCACAGTGGAT-TAAGGATTTGTTTTTACGAGCATTAGAATC
*
2934 ACGTTAT-GA
323 ATGTT-TCGA
* * * * *
2943 TTTAATTAGAAATTAA-TT-------AAAA-AAAAACGGTTTTAGAAGCATGAAAATCCCTTCAA
1 TTTAATAAGAAATTAATTTGGAAAAAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTTCAA
* * * * * * *
2999 TCTTTTTGGGGATGAGTTATATATTTTATATGATTATTGT-TACCAAAAATTAACGAAAAAT-TT
66 TCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATATT
* ** * * *
3062 TTGGGGTCAATTTTTGCAAAATTTTAGCAAAAATCGTATACTAATCATCACGATTTATGGCTAAA
131 TT-GGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCAC-ATTTTTGGCTAAA
* * * * * * *
3127 AATGTGTTCCGGGGCCTCGGCTCAGTTTTGCTTGATTTTTGGCACCAAGACTCCTTGAAATATCC
194 AACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCA
* ** * *
3192 ATATTAATCTAACCAAATCTCATCCACCTTTGATTAAAGGA-TT-TTTTTACAAGCATTAGAATC
259 ATATTCATCTAACCAAATCTCATCCACAGTGGATT-AAGGATTTGTTTTTACGAGCATTAGAATC
*
3255 TTGTTTCGA
323 ATGTTTCGA
** *
3264 TTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCATTCA
1 TTTAATAAGAAATTAATTTGGAAAA-AAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTTCA
* * * ** *
3329 ATCTTTTTGGCATTAAGTTATATATTTTATTTGAGTATTCTGG-CCGAAAATTAAGGAAAAATCT
65 ATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATAT
* * *
3393 TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTGACAATCACGGTTTTTGGCTAAA
130 TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCAC-ATTTTTGGCTAAA
* * * * * *
3458 AATGCG-TTCTGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACTCATTGAAATATCT
194 AACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCA
* * * *
3522 ATATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACAAGCATCT-GAAT
259 ATATTCATCTAACCAAATCTCATCCACAGTGGA-TTAAGGATTTGTTTTTACGAGCAT-TAGAAT
3586 CATGTTTCGA
322 CATGTTTCGA
* * **
3596 TTTAATTAGAAATTAATTTAGAAAAAAGAAAAAGAAAAACGATATTAGAAGTGTGAAAA-CCCTT
1 TTTAATAAGAAATTAATTT-G-GAAAA-AAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTT
* * * * * * * * *
3660 CCACCTTTTTTGCGTTAAATTATATATTTT-TATGAGTATCGTGG-CTAGAAATTGAGGAAAAAA
63 CAATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAAT
* * * * * *
3723 ATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTATACTAACTATCACAGTTTCTAGCT
128 ATTTT-GGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACA-TTTTTGGCT
* * * * * * *
3788 TAAAACGCGTTACGGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACTTCTTGTAATA
191 AAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATA
* * * *
3853 TCAATATTCATCTAACGAAATCTCAACCATAGTGGATATAAGGATTTGTTTTTACGAGCATCAGA
256 TCAATATTCATCTAACCAAATCTCATCCACAGTGGAT-TAAGGATTTGTTTTTACGAGCATTAGA
* **
3918 ATCAAGTTTTAA
320 ATCATGTTTCGA
* * * * * *
3930 TTTAATTAGAAATTAA-TTCGAAAAAGAAAAGAAAGACGATATTATAAGCATGAAAATCCCTTCA
1 TTTAATAAGAAATTAATTTGGAAAAA-AAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTTCA
* * * * * * *
3994 ATCTTTTTGGGGATGAGTTATATGTTTTATATGATTATTGT-GACAAAAAATTAATGAAAAATCT
65 ATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATAT
* * * * *
4058 TTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTCGGCTAAA
130 TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCAC-ATTTTTGGCTAAA
* * * * * *
4123 AATGCGTTTCGGGGCCTCGGCTCAGTTTTGCCTGATTTTTTGCACCAAGACTCCTTGAAATATCC
194 AACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCA
* * * *
4188 ATATTCATCTAGCCAAATCTCATCCACCA-TGGATTGAAGGGGTTTTTTTTTACGAGTATTAGAA
259 ATATTCATCTAACCAAATCTCATCCA-CAGTGGATT-AA-GGATTTGTTTTTACGAGCATTAGAA
* *
4252 TCTTGTTTCAA
321 TCATGTTTCGA
* *
4263 TTTAATAAGAAATTAATTTGGAAAACAAATAGAAAAACGATATTAGAAGCCTGAAAAGCCATTC-
1 TTTAATAAGAAATTAATTTGGAAAA-AAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTTCA
* * * * *
4327 ATTTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATGGTC-AAAAATTAAGGAAAAAGAT
65 ATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATAT
* * *
4391 TTTGCGTCAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACAGTTTTTGGGTAAA
130 TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACA-TTTTTGGCTAAA
* * * * *
4456 AAAGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGCAAGACTCATTGAAATATCT
194 AACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCA
* * *
4521 ATATTCATCTAACCAAATATCAGT-CACATTGGATTTAAGGATTTGTTTTTACAAGCATCT-GAA
259 ATATTCATCTAACCAAATCTCA-TCCACAGTGGA-TTAAGGATTTGTTTTTACGAGCAT-TAGAA
*
4584 TCATGTTTCGG
321 TCATGTTTCGA
* * * * * * *
4595 TTAAATTAA-AAATTAATTTAGAAAGAAAAAGGAAAAACAATATTA-ATATCTTGAAAAGCACTT
1 TTTAA-TAAGAAATTAATTTGGAAA-AAAAAAGAAAAACGATATTAGA-AGCCTGAAAAGCCCTT
* * * * * * * * * *
4658 CCACCTTTTTTGTGTTAAATTATATATTTTTTATGAGTATCGT-GACTAAAAATTGAGGAAAAAA
63 CAATCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAAT
* * * * *
4722 ATATTCGGGTCAAGTTTTGCGAAATTTTGACCGAAATCGTGTACTAAACATCACAGTTTTTGGCT
128 AT-TTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACA-TTTTTGGCT
* * * * * * * *
4787 TAAAACGCGTTACAGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACTCATTGTAATA
191 AAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATA
* *
4852 TCAATATTCATCTAACGAAATCTCATCCATAGTGGAT
256 TCAATATTCATCTAACCAAATCTCATCCACAGTGGAT
4889 ATTATAAGCA
Statistics
Matches: 2130, Mismatches: 397, Indels: 153
0.79 0.15 0.06
Matches are distributed among these distances:
320 5 0.00
321 159 0.07
322 10 0.00
323 89 0.04
325 1 0.00
326 3 0.00
327 216 0.10
328 46 0.02
329 2 0.00
330 130 0.06
331 292 0.14
332 348 0.16
333 459 0.22
334 369 0.17
335 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (331 bp):
TTTAATAAGAAATTAATTTGGAAAAAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCCTTCAA
TCTTTTTGGCGTTAAGTTATATATTTTATATGAGTATTGTGGACAAAAAATTAAGGAAAAATATT
TTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACATTTTTGGCTAAAAA
CGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCAAT
ATTCATCTAACCAAATCTCATCCACAGTGGATTAAGGATTTGTTTTTACGAGCATTAGAATCATG
TTTCGA
Found at i:4617 original size:999 final size:989
Alignment explanation
Indices: 1953--4890 Score: 3733
Period size: 999 Copynumber: 3.0 Consensus size: 989
1943 GTAATATCAT
* * *
1953 TTTAATTAGAAATTATTTCGTAAAAAAAAAACGAAAGACGATATTAGAA-AAGTGAAAAGCCC-T
1 TTTAATTAGAAATTAATTCG--AAAAAAAAA-GAAAGACGATATTAGAAGCA-TGAAAATCCCTT
* * * * * * * * *
2016 CAAATC-TCTT-GTGTTAAATTATATATTTT-TATGACTATTGTAACTAAAAATTGAGGAAAAAA
62 C-AATCTTTTTGGGGATGAGTTATATATTTTATATGATTATTGTAACAAAAAATTAACG--AAAA
* * * * * * *
2078 ATTTTAGGGTCAAGTTATGCGAAATTTTAACCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
124 ATTTTAGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCAC-GATTTTGGCT
** * * * * ** *
2143 TCAAACGCGTTAT-GGGACCCCGGCTCCGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGTAAT
188 AAAAATGCGTT-TCGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAAT
* * * * * * *
2207 ATCAATATTCATCTAACGAAATCTCAACCA-TAGTGGATATAAGGATTTGTTTTTACGAGCATCA
252 ATCCATATTCATCTAACCAAATCTCATCCACCA-TGGAT-TAAGGGTTTTTTTTTACGAGCATTA
** * * * * *
2271 GAATCAAGTTTTGATTTAATTAGAAATTAATTCAAAAAAGAAAAAGAAAAATGATATTAGAAGCA
315 GAATCTTGTTTCGATTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGC-
* * * * * * * *
2336 C-GAAAATCCCTTCAATCTTTTTGGTGATGAGTTATATATTTTATATGATTATTGT-GACAAAAA
379 CTGAAAAGCCATTCAATCTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATGGAC-AAAA
* ** * *
2399 ATTAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGTCAAAATC-GTA-TA-C-TAACA
443 ATTAAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCTGTACTACCATCACA
* ***** * * *
2460 ATTTTTGGCTAAAAATGCGTTCTGGGATTTTGGCTCAGTTTTGCTTGATTTTCGGCACCAAAACT
508 GTTTTTGGCTAAAAATGCGTTC-GGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACT
* * ** *
2525 CCTTGAAATATCCATATTCATCTAACCAAATTACA-TCCACATTGGATTGGAGGATTTTTTTTTT
572 CATTGAAATATCTATATTCATCTAACCAAATT-CAGT-CACATTGGATTTAAGGA-TTTGTTTTT
** * * * *
2589 ATGATCAT-TAGAGTCTTGTTTCGATTTAA-TATGAAATTAATTGAG-AAAA-AAAAAGAAAAAC
634 ACAAGCATCT-GAATCATGTTTCGATTTAATTA-GAAATTAATTTAGAAAAAGAAAAAGAAAAAC
* * * * *
2650 GATATTAGAAGTTTGAAAAGCCTTTCA-ATATTTTAGGCGTTAAGTTATATATTTTATATGAGTA
697 GATATTAGAAGTTTGAAAACCCTTCCACCT-TTTT-TGCGTTAAATTATATATTTT-TATGAGTA
* * * ** * *
2714 TTGTGGCCAAAAATTAAGGAAAAATCTTTT-GGGTCAATTTTTGCAAAATTTTAACCGAAATCGT
759 TCGTGGCTAAAAATTGAGGAAAAAAATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGT
* *
2778 GTACTAACA--ATCAGTTTTTGGCTTAAAACGCGTTACGGGACCCCGGCTCCA-TTTTGCATGAT
824 GTACTAACATCA-CAGTTTTTGGCTTAAAACGCGTTACGGGTCCCCAGCT-CAGTTTTGCATGAT
* * * * *
2840 TTTTGG-TGTCAAGACTCCATGTATTATCAATATTCATCTAATGAAATCTCAACCATAGTGAATA
887 TTTTGGCT-TCAAGACTTCTTGTAATATCAATATTCATCTAACGAAATCTCAACCATAGTGGATA
* *
2904 TAAGGATTTGTTTTTACGAGCATCAGAATCACGTTATGA
951 TAAGGATTTGTTTTTACGAGCATCAGAATCAAGTTATAA
* *
2943 TTTAATTAGAAATTAATT------AAAAA-AAA-ACGGTTTTAGAAGCATGAAAATCCCTTCAAT
1 TTTAATTAGAAATTAATTCGAAAAAAAAAGAAAGACGATATTAGAAGCATGAAAATCCCTTCAAT
* * *
3000 CTTTTTGGGGATGAGTTATATATTTTATATGATTATTGTTACCAAAAATTAACGAAAAATTTTTG
66 CTTTTTGGGGATGAGTTATATATTTTATATGATTATTGTAACAAAAAATTAACGAAAAA-TTTTA
* *
3065 GGGTCAATTTTTGCAAAATTTTAGCAAAAATCGTATACTAATCATCACGATTTATGGCTAAAAAT
130 GGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTT-TGGCTAAAAAT
* * *
3130 GTGTTCCGGGGCCTCGGCTCAGTTTTGCTTGATTTTTGGCACCAAGACTCCTTGAAATATCCATA
194 GCGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCCATA
* * * * * *
3195 TTAATCTAACCAAATCTCATCCACCTTTGATTAAAGG-ATTTTTTTACAAGCATTAGAATCTTGT
259 TTCATCTAACCAAATCTCATCCACCATGGATTAAGGGTTTTTTTTTACGAGCATTAGAATCTTGT
3259 TTCGATTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCC
324 TTCGATTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCC
* * * *
3324 ATTCAATCTTTTTGGCATTAAGTTATATATTTTATTTGAGTATTCTGGCCGAAAATTAAGGAAAA
389 ATTCAATCTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATGGACAAAAATTAAGGAAAA
* *
3389 ATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTGACAATCACGGTTTTTGGC
454 ATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATC-TGTACT-ACCATCACAGTTTTTGGC
*
3454 TAAAAATGCGTTCTGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACTCATTGAAATA
517 TAAAAATGCGTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACTCATTGAAATA
3519 TCTATATTCATCTAACCAAATCTCAG-CAACATTGGATTTAAGGATTTGTTTTTACAAGCATCTG
582 TCTATATTCATCTAACCAAAT-TCAGTC-ACATTGGATTTAAGGATTTGTTTTTACAAGCATCTG
3583 AATCATGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAGAAAAAGAAAAACGATATTAGAAGT
645 AATCATGTTTCGATTTAATTAGAAATTAATTTAG-AAAAAGAAAAAGAAAAACGATATTAGAAGT
* *
3648 GTGAAAACCCTTCCACCTTTTTTGCGTTAAATTATATATTTTTATGAGTATCGTGGCTAGAAATT
709 TTGAAAACCCTTCCACCTTTTTTGCGTTAAATTATATATTTTTATGAGTATCGTGGCTAAAAATT
*
3713 GAGGAAAAAAATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTATACTAACTATCACA
774 GAGGAAAAAAATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTGTACTAAC-ATCACA
* *
3778 GTTTCTAGCTTAAAACGCGTTACGGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACT
838 GTTTTTGGCTTAAAACGCGTTACGGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACT
3843 TCTTGTAATATCAATATTCATCTAACGAAATCTCAACCATAGTGGATATAAGGATTTGTTTTTAC
903 TCTTGTAATATCAATATTCATCTAACGAAATCTCAACCATAGTGGATATAAGGATTTGTTTTTAC
*
3908 GAGCATCAGAATCAAGTTTTAA
968 GAGCATCAGAATCAAGTTATAA
*
3930 TTTAATTAGAAATTAATTCGAAAAAGAAAAGAAAGACGATATTATAAGCATGAAAATCCCTTCAA
1 TTTAATTAGAAATTAATTCGAAAAA-AAAAGAAAGACGATATTAGAAGCATGAAAATCCCTTCAA
* * *
3995 TCTTTTTGGGGATGAGTTATATGTTTTATATGATTATTGTGACAAAAAATTAATGAAAAATCTTT
65 TCTTTTTGGGGATGAGTTATATATTTTATATGATTATTGTAACAAAAAATTAACGAAAAAT-TTT
*
4060 CGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTCGGCTAAAAA
129 AGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTT-GGCTAAAAA
* *
4125 TGCGTTTCGGGGCCTCGGCTCAGTTTTGCCTGATTTTTTGCACCAAGACTCCTTGAAATATCCAT
193 TGCGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCCAT
* *
4190 ATTCATCTAGCCAAATCTCATCCACCATGGATTGAAGGGGTTTTTTTTTACGAGTATTAGAATCT
258 ATTCATCTAACCAAATCTCATCCACCATGGATT-AA-GGGTTTTTTTTTACGAGCATTAGAATCT
* ** *
4255 TGTTTCAATTTAATAAGAAATTAATTTGGAAAACAAATAGAAAAACGATATTAGAAGCCTGAAAA
321 TGTTTCGATTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGCCTGAAAA
* *
4320 GCCATTC-ATTTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATGGTCAAAAATTAAGGA
386 GCCATTCAATCTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATGGACAAAAATTAAGGA
** *
4384 AAAAGATTTTGCGTCAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACAGTTTTT
451 AAAATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATC-TGTACT-ACCATCACAGTTTTT
* * * *
4449 GGGTAAAAAAGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGACAGCAAGACTCATTGA
514 GGCTAAAAATGCG-TTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACTCATTGA
4514 AATATCTATATTCATCTAACCAAATATCAGTCACATTGGATTTAAGGATTTGTTTTTACAAGCAT
578 AATATCTATATTCATCTAACCAAAT-TCAGTCACATTGGATTTAAGGATTTGTTTTTACAAGCAT
* * * *
4579 CTGAATCATGTTTCGGTTAAATTAAAAATTAATTTAG--AAAGAAAAAGGAAAAACAATATTA-A
642 CTGAATCATGTTTCGATTTAATTAGAAATTAATTTAGAAAAAGAAAAA-GAAAAACGATATTAGA
* * *
4641 TA-TCTTGAAAAGCACTTCCACCTTTTTTGTGTTAAATTATATATTTTTTATGAGTATCGTGACT
706 -AGT-TTGAAAA-CCCTTCCACCTTTTTTGCGTTAAATTATATA-TTTTTATGAGTATCGTGGCT
* *
4705 AAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCGAAATTTTGACCGAAATCGTGTACTAAA
767 AAAAATTGAGGAAAAAAATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTGTACT-AA
*
4770 CATCACAGTTTTTGGCTTAAAACGCGTTACAGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTT
831 CATCACAGTTTTTGGCTTAAAACGCGTTACGGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTT
*
4835 CAAGAC-TCATTGTAATATCAATATTCATCTAACGAAATCTCATCCATAGTGGATAT
896 CAAGACTTC-TTGTAATATCAATATTCATCTAACGAAATCTCAACCATAGTGGATAT
4891 TATAAGCATG
Statistics
Matches: 1710, Mismatches: 183, Indels: 101
0.86 0.09 0.05
Matches are distributed among these distances:
978 1 0.00
979 188 0.11
980 24 0.01
981 148 0.09
982 28 0.02
983 44 0.03
984 113 0.07
985 86 0.05
986 43 0.03
987 156 0.09
988 2 0.00
990 17 0.01
993 1 0.00
994 4 0.00
995 5 0.00
996 247 0.14
997 22 0.01
998 154 0.09
999 423 0.25
1000 4 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (989 bp):
TTTAATTAGAAATTAATTCGAAAAAAAAAGAAAGACGATATTAGAAGCATGAAAATCCCTTCAAT
CTTTTTGGGGATGAGTTATATATTTTATATGATTATTGTAACAAAAAATTAACGAAAAATTTTAG
GGTCAATTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTGGCTAAAAATGC
GTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCCATATT
CATCTAACCAAATCTCATCCACCATGGATTAAGGGTTTTTTTTTACGAGCATTAGAATCTTGTTT
CGATTTAATAAGAAATTAATTCAGAAAACAAAAAGAAAAACGATATTAGAAGCCTGAAAAGCCAT
TCAATCTTTTTGGCGTTAAGTTATATATTTTATTTGAGTATTATGGACAAAAATTAAGGAAAAAT
CTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCTGTACTACCATCACAGTTTTTGGCTAAA
AATGCGTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCAGCAAGACTCATTGAAATATCTA
TATTCATCTAACCAAATTCAGTCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCAT
GTTTCGATTTAATTAGAAATTAATTTAGAAAAAGAAAAAGAAAAACGATATTAGAAGTTTGAAAA
CCCTTCCACCTTTTTTGCGTTAAATTATATATTTTTATGAGTATCGTGGCTAAAAATTGAGGAAA
AAAATTTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTGTACTAACATCACAGTTTTTGG
CTTAAAACGCGTTACGGGTCCCCAGCTCAGTTTTGCATGATTTTTGGCTTCAAGACTTCTTGTAA
TATCAATATTCATCTAACGAAATCTCAACCATAGTGGATATAAGGATTTGTTTTTACGAGCATCA
GAATCAAGTTATAA
Found at i:5759 original size:933 final size:919
Alignment explanation
Indices: 3967--5823 Score: 3214
Period size: 933 Copynumber: 2.0 Consensus size: 919
3957 AAAGAAAGAC
*
3967 GATATTATAAGCATGAAAATCCCTTCAATCTTTTTGGGGATGAGTTATATGTTTTATATGATTAT
1 GATATTATAAGCATGAAAATCCCTTCAATCTTTTTGGGGATGAGTTATATATTTTATATGATTAT
4032 TGTGACAAAAAATTAATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTAT
66 TGTGACAAAAAATTAATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTAT
*
4097 ACTAACCATCACGATTTTCGGCTAAAAATGCGTTTCGGGGCCTCGGCTCAGTTTTGCCTGATTTT
131 ACTAACCATCACGATTTTCGGCTAAAAATGCGTTCCGGGGCCTCGGCTCAGTTTTGCCTGATTTT
4162 TTGCACCAAGACTCCTTGAAATATCCATATTCATCTAGCCAAATCTCATCCACCATGGATTGAAG
196 TTGCACCAAGACTCCTTGAAATATCCATATTCATCTAGCCAAATCTCATCCACCATGGATTGAAG
*
4227 GGGTTTTTTTTTACGAGTATTAGAATCTTGTTTCAATTTAATAAGAAATTAATTTGGAAAACAAA
261 GGGTTTTTTTTTACGAGTATTAGAATCTTGTTTAAATTTAATAAGAAATTAATTTGGAAAACAAA
*
4292 TAGAAAAACGATATTAGAAGCCTGAAAAGCCATTCATTTTTTTGGCGTTAAGTTATATATTTTAT
326 TAGAAAAACGATATTAGAAGCCAGAAAAGCCATTCATTTTTTTGGCGTTAAGTTATATATTTTAT
** *
4357 TTGAGTATTATGGTCAAAAATTAAGGAAAAAGATTTTGCGTCAATTTTTGCAAAATTTTAACCGA
391 TTGAGTATTATGACCAAAAATTAAGGAAAAAGATTTTGCGTCAATTTTCGCAAAATTTTAACCGA
* *
4422 AATCATGTACTAACCATCACAGTTTTTGGGTAAAAAAGCGTTTCGGGGCCCCGGCTCAGTTTTGC
456 AATCATGTACTAACCATCACAGTTTTTGGCTAAAAAAGCGTTCCGGGGCCCCGGCTCAGTTTTGC
* * *
4487 ATGATTTTTGACAGCAAGACTCATTGAAATATCTATATTCATCTAACCAAATATCAGTCACATTG
521 ATGATTTCTGACAGCAAGACTCATTGAAATATCTATAATCATCTAACCAAATACCAGTCACATTG
4552 GATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGGTTAAATTAAAAATTAATTTAGA
586 GATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGGTTAAATTAAAAATTAATTTAGA
* *
4617 AAGAAAAAGGAAAAACAATATTAATATCTTGAAAAGCACTTCCACCTTTTTTGTGTTAAATTATA
651 AAGAAAAAGGAAAAACAATATTAATATCGTGAAAAGCACTTCCACCTTTTTTGTGTTAAATTAAA
4682 TATTTTTTATGAGTATCGTGACTAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCGAAAT
716 TATTTTTTATGAGTATCGTGACTAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCGAAAT
*
4747 TTTGACCGAAATCGTGTACTAAACATCACAGTTTTTGGCTTAAAACGCGTTACAGGTCCCCAGCT
781 TTTGACCGAAATCGTGTACTAAACATCACAGTTTTTGGCTTAAAACGCGTTACAGGGCCCCAGCT
*
4812 CAGTTTTGCATGATTTTTGGCT-TCAAGACTCATTGTAATATCAATATTCATCTAACGAAATCTC
846 CAATTTTGCATGATTTTTGG-TGTCAAGACTCATTGTAATATCAATATTCATCTAACGAAATCTC
*
4876 ATCCATAGTG
910 AGCCATAGTG
*
4886 GATATTATAAGCATGAAAATCCCTTCAATCTTTTTGGGTATGAGTTATATATTTTATATGATTAT
1 GATATTATAAGCATGAAAATCCCTTCAATCTTTTTGGGGATGAGTTATATATTTTATATGATTAT
4951 TGTGACAAAAAATTAATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTAT
66 TGTGACAAAAAATTAATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTAT
5016 ACTAACCATCACGATTTTCGGCTAAAAATGCGTTCCGGGGCCTCGGCTCAGTTTTGCCTGATTTT
131 ACTAACCATCACGATTTTCGGCTAAAAATGCGTTCCGGGGCCTCGGCTCAGTTTTGCCTGATTTT
*
5081 TTGCACCAAGACTCCTTGAAATATCCATATTCATCTAGCCAAATCTCATCCACCTTGGATTGAAG
196 TTGCACCAAGACTCCTTGAAATATCCATATTCATCTAGCCAAATCTCATCCACCATGGATTGAAG
**
5146 GTTTTTTTTTATTTTTTTATTTTTTACGAGTATTAGAATCTTGTTTAAATTTAATAAGAAATTAA
261 G------------GGTTT-TTTTTTACGAGTATTAGAATCTTGTTTAAATTTAATAAGAAATTAA
5211 TTTGGAAAACAAATAGAAAAACGATATTAGAAGCCAGAAAAGCCATTCATTTTTTTTGGCGTTAA
313 TTTGGAAAACAAATAGAAAAACGATATTAGAAGCCAGAAAAGCCATTCA-TTTTTTTGGCGTTAA
* *
5276 GTTATATATTTTATTTGAGTATTGTGACCAAAAATTAAGGAAAAATATTTTGCGTCAATTTTCGC
377 GTTATATATTTTATTTGAGTATTATGACCAAAAATTAAGGAAAAAGATTTTGCGTCAATTTTCGC
* *
5341 AAAATTTTAACCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAAGCGTTCCGGGGCCC
442 AAAATTTTAACCGAAATCATGTACTAACCATCACAGTTTTTGGCTAAAAAAGCGTTCCGGGGCCC
*
5406 CGGCTCAGTTTTGCATGATTTCTGACAGCAAGACTCATTGAAATATCTATAATCATCTCACCAAA
507 CGGCTCAGTTTTGCATGATTTCTGACAGCAAGACTCATTGAAATATCTATAATCATCTAACCAAA
* *
5471 TACCAGTCACATTGGATTTATGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGGTTTAATTA
572 TACCAGTCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGGTTAAATTA
*
5536 AAAATTAATTTAGAAA-AAAAAGGAAAAACGATATTAATATCGTGAAAAGCACTTCCACCTTTTT
637 AAAATTAATTTAGAAAGAAAAAGGAAAAACAATATTAATATCGTGAAAAGCACTTCCACCTTTTT
* * *
5600 TGTGTTAAATTAAATATTTTTTATGAGTATTGTGGCTAAAAATTGTGGAAAAAAAATATTCGGGT
702 TGTGTTAAATTAAATATTTTTTATGAGTATCGTGACTAAAAATTGAGG-AAAAAAATATTCGGGT
5665 CAAGTTTTGCGAAATTTTGACCGAAATCGTGTACTAAACATCACAGTTTTTGGCTTAAAACGCGT
766 CAAGTTTTGCGAAATTTTGACCGAAATCGTGTACTAAACATCACAGTTTTTGGCTTAAAACGCGT
* * * * *
5730 TTCGGGGCTCCGGCTCAATTTTGCATGATTTTTGGTGTCAAGACTCCTTGTAATATCAATATTCA
831 TACAGGGCCCCAGCTCAATTTTGCATGATTTTTGGTGTCAAGACTCATTGTAATATCAATATTCA
*
5795 TCTAACGAAATCTCAGCCATGGTG
896 TCTAACGAAATCTCAGCCATAGTG
5819 GATAT
1 GATAT
5824 AAGGATTTGT
Statistics
Matches: 884, Mismatches: 38, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
919 257 0.29
931 3 0.00
932 184 0.21
933 440 0.50
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (919 bp):
GATATTATAAGCATGAAAATCCCTTCAATCTTTTTGGGGATGAGTTATATATTTTATATGATTAT
TGTGACAAAAAATTAATGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTAT
ACTAACCATCACGATTTTCGGCTAAAAATGCGTTCCGGGGCCTCGGCTCAGTTTTGCCTGATTTT
TTGCACCAAGACTCCTTGAAATATCCATATTCATCTAGCCAAATCTCATCCACCATGGATTGAAG
GGGTTTTTTTTTACGAGTATTAGAATCTTGTTTAAATTTAATAAGAAATTAATTTGGAAAACAAA
TAGAAAAACGATATTAGAAGCCAGAAAAGCCATTCATTTTTTTGGCGTTAAGTTATATATTTTAT
TTGAGTATTATGACCAAAAATTAAGGAAAAAGATTTTGCGTCAATTTTCGCAAAATTTTAACCGA
AATCATGTACTAACCATCACAGTTTTTGGCTAAAAAAGCGTTCCGGGGCCCCGGCTCAGTTTTGC
ATGATTTCTGACAGCAAGACTCATTGAAATATCTATAATCATCTAACCAAATACCAGTCACATTG
GATTTAAGGATTTGTTTTTACAAGCATCTGAATCATGTTTCGGTTAAATTAAAAATTAATTTAGA
AAGAAAAAGGAAAAACAATATTAATATCGTGAAAAGCACTTCCACCTTTTTTGTGTTAAATTAAA
TATTTTTTATGAGTATCGTGACTAAAAATTGAGGAAAAAAATATTCGGGTCAAGTTTTGCGAAAT
TTTGACCGAAATCGTGTACTAAACATCACAGTTTTTGGCTTAAAACGCGTTACAGGGCCCCAGCT
CAATTTTGCATGATTTTTGGTGTCAAGACTCATTGTAATATCAATATTCATCTAACGAAATCTCA
GCCATAGTG
Found at i:7107 original size:333 final size:330
Alignment explanation
Indices: 5166--10488 Score: 4701
Period size: 333 Copynumber: 16.0 Consensus size: 330
5156 ATTTTTTTAT
* * * ** * * *
5166 TTTTTACGAGTATTAGAATCTTGTTTAAATTTAATAAGAAATTAATTTGGAAAACAAATA-GAAA
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AAAAAGGAAA
** * * * * *
5230 AACGATATTAGAAGCCAGAAAAGCCATTCATTTTTTTTGGCGTTAAGTTATATATTTTATT-TGA
65 AACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTT-TTATGA
* * * * * *
5294 GTATTGTGACCAAAAATTAAGGAAAAATATTTTGCGTCAA-TTTTCGCAAAATTTTAACCGAAAT
128 GTATTGTGGCTAAAAATTGAGGAAAAA-ATTTCGGGTCAAGTTTT-GCGAAATTTTAACCGAAAT
* * *
5358 CGTGTACTAACCATCATAGTTTTTGGCTAAAAAAGCGTTCCGGGGCCCCGGCTCAGTTTTGCATG
191 CGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATG
* * * * * * * * *
5423 ATTTCTGACAG-CAAGACTCATTGAAATATCTATAATCATCTCACCAAATAC-CAGTCACATTGG
256 ATTTTTGGC-GTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAAT-CTCA-CCATAGTGG
* *
5486 ATTTATGGATTTG
318 ATATAAGGATTTG
* * * * **
5499 TTTTTACAAGCATCTGAATC-ATGTTTCGGTTTAATTAAAAATTAATTTAG-AAAAAAAAGGAAA
1 TTTTTACGAGCATCAGAATCTA-GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAA
* * * * *
5562 AACGATATTA-ATATCGTGAAAAGCACTTCC-ACCTTTTTTGTGTTAAATTAAATATTTTTTATG
65 AACGATATTAGA-AGCGTGAAAAGC-CCTCCAATC-TTTTTGCGTTAAATTATATATTTTTTATG
* *
5625 AGTATTGTGGCTAAAAATTGTGGAAAAAAAATATTCGGGTCAAGTTTTGCGAAATTTTGACCGAA
127 AGTATTGTGGCTAAAAATTGAGG--AAAAAAT-TTCGGGTCAAGTTTTGCGAAATTTTAACCGAA
* * * * *
5690 ATCGTGTACTAAACATCACAGTTTTTGGCTTAAAACGCGTTTCGGGGCTCCGGCTCAATTTTGCA
189 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCA
* * * *
5755 TGATTTTTGGTGTCAAGACTCCTTGTAATATCAATATTCATCTAACGAAATCTCAGCCATGGTGG
254 TGATTTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGG
5820 ATATAAGGATTTG
318 ATATAAGGATTTG
* * *
5833 TTTTTACGAGCATCAGAATCAAGTTTTGATTTAATTAGAAATTAATTC-GAAAAAAAAA-GTAAA
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAA
* ** * * * * * * * * *
5896 ACGATATTATAAGTATGAAAATCCCTTCAATCTTTTTGGGGATGAGTTATATGTTTTATATGATT
66 ACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTTTTATGAGT
* * * * * * * * * * *
5961 ATTGTGACCAAAACTTAACGAAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCAAAATCGT
130 ATTGTGGCTAAAAATTGAGGAAAAA-ATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGT
* * * * * * *
6026 ATACTAACCATCAC-GATTTTTGGCTAAAAATGTGTTCCGGGGCCTCGACTCAGTTTTGCTTGAT
194 GTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATGAT
** * * * * ***
6090 TTTTGGCACCAAGACTCCTTGAAATATCCATATTTATCTAGCCAAATATCATCCACCTTGGAT-T
258 TTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGGATAT
6154 GAAGGATTT-
322 -AAGGATTTG
* * * * * * *
6163 TTTTTAAACTAGTATTACAATCTTGTTTCGATTTAATAAGAAATTAATTCGGAAAACAAAAGGAA
1 TTTTT--ACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAA
* *
6228 AAACGATATTAGAAGCCTGAAAAGCCATCCAATCTTTTTGGCGTTAAATTATATATTTTATT-TG
64 AAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTT-TTATG
* * * * *
6292 AGTATTGTGGCCAAAAATT-AGGGAAAAATCTTTGGGTCAATTTTTG-AAAATTTTAACCGAAAT
127 AGTATTGTGGCTAAAAATTGAGGAAAAAAT-TTCGGGTCAAGTTTTGCGAAATTTTAACCGAAAT
** * * * * ** *
6355 CGTGTACTAACCATCATGGTTTTTGGCCAAAAATGCGTTTCTGGATCCCGGCTTAGTTTTGCATG
191 CGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATG
* * *
6420 ATTTTTGGCAG-CAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCA-ACGTTGG
256 ATTTTTGGC-GTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCACCATA-G-TGG
6483 AT-TAAAGGATTTG
318 ATAT-AAGGATTTG
* * * * *
6496 TTTTTATGAGCATCTGAATCATA-TTTCGGTTTAATTAGAAATTAATTTAGTAAAAAAAAAGGAA
1 TTTTTACGAGCATCAGAATC-TAGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAAAAAGGAA
* * * * *
6560 AAACGACATTAGAAGCGTGAAAATCCCTGCC-ACCTTTTTTGTGTTAAATTATATATTTTATATG
64 AAACGATATTAGAAGCGTGAAAAGCCCT-CCAATC-TTTTTGCGTTAAATTATATATTTTTTATG
* * ** * *
6624 -GTTATCGTTGCTAAAAATTGAGGACAAAAAAATTTTAAGGTCAAGGTTTGCGAAATTTTAACTG
127 AG-TATTGTGGCTAAAAATTGAGG---AAAAAA-TTTCGGGTCAAGTTTTGCGAAATTTTAACCG
* * * * *
6688 AAATCGTGTATTAACCATTAGAGTTTTTGGCTTAAAACGCGTTACGGGTCCCCGGCTCAGTTTTG
187 AAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTG
* * * * * *
6753 CATGGTTTTAGGC-TACAAGACTCCTTGTAATATCAATATTCATCTTACTAAATCCCGACCATAG
252 CATGATTTTTGGCGT-CAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC-ACCATAG
6817 TGGATATAAGGATTTG
315 TGGATATAAGGATTTG
* *
6833 TTTTTACGAGCATCAGAATCTAGTTTCGTTTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAG
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAA
** * * *
6898 ACGATATTAGAAAAGTAAAAAGCCCTCCAATCCCTTTTGCGTTAAATTATATATTTTTTATGACT
66 ACGATATTAGAAGCGTGAAAAGCCCTCCAAT-CTTTTTGCGTTAAATTATATATTTTTTATGAGT
* * * * *
6963 ATTGTAGCTAATAATTGAGGAAAAAATTTCCAGGTCGAGTTTGGCGAAATTTTAACCGAAATCGT
130 ATTGTGGCTAAAAATTGAGGAAAAAATTT-CGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGT
* * * * * * *
7028 GTACTAACAATCACAGTTTTTTGCTTAAAACGTGTTACGGGTCCCCGGCTCAATTTTACATGATT
194 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATGATT
* *
7093 TTTGGCGTCAAGACTCCTTGTAATATCAATATTCATCTAACGAAATCTCAACCATAGTGGATATA
259 TTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC-ACCATAGTGGATATA
**
7158 AGCCTTTG
323 AGGATTTG
* * *
7166 TTTTTACGAGCATCAGAATCAAGTTAT-GATTTAATTAGAAATTAATT-GAAAAAAGAAAAAGAA
1 TTTTTACGAGCATCAGAATCTAGTT-TCGATTTAATTAGAAATTAATTCGGAAAAA-AAAAGGAA
* * ** * * *
7229 AAACGATATTAGAAGCATGAAAATCCCGT-CAATCTTTTTGGCAATGAGTTATATATTTTATATG
64 AAACGATATTAGAAGCGTGAAAAGCCC-TCCAATCTTTTT-GCGTTAAATTATATATTTTTTATG
* * * * * * * * * *
7293 ATTATTGTGACAAAAAATTAACGAAAAATATTTTGGGTCAATTTTTGCAAAATTTTAGCCAAAAT
127 AGTATTGTGGCTAAAAATTGAGGAAAAA-ATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAAT
* ** * ** * *
7358 CGTATACTAACCATCAC-GATTTTTGGCTAAAAATACGTTCCGGGGCGTCGACTCAGTTTTGCTT
191 CGTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCAT
** * * ***
7422 GATTTTTGGCACCAATACTCCTTGAAATATCCATATTCATCTAAACCAAATCTCATCCACCTTGG
255 GATTTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCT-AACCAAATCTCA-CCATAGTGG
* *
7487 AT-TGAAGGTTTTTT
318 ATAT-AAGG-ATTTG
* * * * *
7501 TTTGTTAGGAGCATTAGAATCTTGTTTCGATATAATAAGAAATTAATTCGGAAAAGAAAAA-GAA
1 TTT-TTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AAAAAGGAA
* ** * **
7565 AAAAGATATTAGAAGCCCGAAAAGCCATTGAATCTTTTTGACGTTAAATTATATATTTTATT-TG
64 AAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTG-CGTTAAATTATATATTTT-TTATG
* * * * *
7629 AGTATTTTGGCCAAAAATT-AGGGAAAAATCTTTGGGTCAATTTTTGCGAAATTTTAACCGAAAT
127 AGTATTGTGGCTAAAAATTGAGGAAAAAAT-TTCGGGTCAAGTTTTGCGAAATTTTAACCGAAAT
* * * * *
7693 TGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCTGGGCCCCGGCTCAGTTTTGCATG
191 CGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATG
* * * * * *
7758 ATTTTTGGTAG-CAAAACTCATTGAAATATCTATATTCATCCAACCAAATCTCAGCA-ACGTTGG
256 ATTTTTGG-CGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCACCATA-G-TGG
* *
7821 ATTTAGGGATTTG
318 ATATAAGGATTTG
* * * **
7834 TTTTTATGAGCATCTGAATC-ATGTTTCGGTTTAATTAGAAATTAATTTAG-AAAAAAAAGGAAA
1 TTTTTACGAGCATCAGAATCTA-GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAA
* * *
7897 GAA-GATATTAGAATCGTGAAAAGCCCTTCC--TCCTTTTTTGTGTTAAATTATATATTTTATAT
65 -AACGATATTAGAAGCGTGAAAAGCCC-TCCAAT-C-TTTTTGCGTTAAATTATATATTTTTTAT
* * * * *
7959 GATTATCGTGGCTAAAAATTGTGGAAAAAAAATTTTAGGGTCATGTTTTGCGAAATTTTAACCGA
126 GAGTATTGTGGCTAAAAATTGAGG--AAAAAA-TTTCGGGTCAAGTTTTGCGAAATTTTAACCGA
* * *
8024 AATCGTGTATTAACCATCACAGTTTTTTGGCTTAAAACGCGTTACGGGTCCCCGGCTCAGTTTTG
188 AATCGTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTG
* * * * * *
8089 CATGGTTTTTGGCTTGAAGACTCCTTGTAATATCAATATTCATCTAACTAAATCCCAGCCATAGT
252 CATGATTTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGT
8154 GGATATAAGGATTTG
316 GGATATAAGGATTTG
*
8169 TTTTTACGAGCATCAGAAT-TCAGTTTCGTTTTAAGTT-GAAATTAATTCGG-AAAAAAAAGGAA
1 TTTTTACGAGCATCAGAATCT-AGTTTCGATTTAA-TTAGAAATTAATTCGGAAAAAAAAAGGAA
* * * * * *
8231 AGACGATATTAGAAGAGTGAAAAACCGTCCAATCTCTTTTGCATTGAATTATATATTTTTTATGA
64 AAACGATATTAGAAGCGTGAAAAGCCCTCCAATCT-TTTTGCGTTAAATTATATATTTTTTATGA
* * * * * *
8296 CTATTGTAGCTAAAAACTGTGGAAAAAATTTCCGGATCAAGTTTTACGAAATTTTAACCGAAATC
128 GTATTGTGGCTAAAAATTGAGGAAAAAATTT-CGGGTCAAGTTTTGCGAAATTTTAACCGAAATC
* * * *
8361 GTGTACTAACCATCACAGTTTTTTTGCTTAAAACGCGTTACGGGACCCCGACTCAGTTTTGCATG
192 GTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATG
* * * *
8426 ATTTTTGGTGTCAAGACTCCTTGTAATATCAATATTCATCTAGCAAAATCTCAACCATAGTGGAT
256 ATTTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC-ACCATAGTGGAT
8491 ATAAGGATTTG
320 ATAAGGATTTG
* * * *
8502 TTTTTATGAGCATCAGAATCAAATTTTGATTTAATTAGAAATTAATTC-GAAAAAGAAAA-GAAA
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAA-AAAAGGAAA
* * * * * * * * *
8565 AACGATATTAGAAGCATGAAAATCCCTTCAATTTTTTTGGCGATGAGTTATATATTTTATATGAT
65 AACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTTTTATGAG
* * * * * * *** *
8630 TATTGTGACCAAAAATT-ATTGAAAAATCTTTCGGGTCGATTTTTAAAAAATTTTAGCC-AAA--
129 TATTGTGGCTAAAAATTGA-GGAAAAA-ATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATC
* * * * * * * * * * *
8691 ----AC--ATCAT--GA-TTTTTAGCAAAAAATGCGTTCCGGAGTCTCGGCTCAGTTTTCCTTGA
192 GTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATGA
* * * * * * * *
8747 TTTTTAGC-ACAAAGACTCCTTGAAATATCTATATTTATCTTATCAAATCTCATCCACATTGGAT
257 TTTTTGGCGTC-AAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGGAT
*
8811 TTAAGGATTT-
320 ATAAGGATTTG
* * * * * * *
8821 TTTTTA-GAGCATTAAAATCTTGTTTCAATTTAATAAGAAATTAATTTGGAGGAAAAAAAAAGAA
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGA--AAAAAAAAGGAA
* * * * * *
8885 AAACGATATTAGAAGCCTGAAAAGTCATTCAATATTTTTGGCGTTAAGTTATATATTTTATT-TG
64 AAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTT-TTATG
* * * * * * *
8949 AGTATTGTGGCCAAAAATTAAGGAAAAATCTTTTGGGTTAA-TCTTTTCAAAATTTTAACCGAAA
127 AGTATTGTGGCTAAAAATTGAGGAAAAA-ATTTCGGGTCAAGT-TTTGCGAAATTTTAACCGAAA
* *** * *
9013 TCGTCTACTAACCATCTTGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCTGTTTTGCAT
190 TCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCAT
* * * ** * * * *
9078 GATTTTTTGCGGCAAGACTCATTGAAATATTTATATTCATCTAACCAAATCTCAGTCACATTGCA
255 GATTTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGGA
*
9143 TTTAAGGATTTG
319 TATAAGGATTTG
* * * ** * **
9155 TTTTAATGAGTATCTCAATC-ATGTTT-GGTTTAATTAGAAATTAATTTAG-AAAAAAAA-GAAA
1 TTTTTACGAGCATCAGAATCTA-GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAA
* *
9216 AACGATATTAGAAGCGTGAAAAGCCCTTCCACCTTTTTTTGCGTTAAATTATATATTTTTTATGA
65 AACGATATTAGAAGCGTGAAAAGCCC-TCCA-ATCTTTTTGCGTTAAATTATATATTTTTTATGA
**
9281 GTATCATGGCTAAAAATTGAGGAAAAAAAAATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAA
128 GTATTGTGGCTAAAAATTGAGG---AAAAAATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAA
*
9346 TCGTGTACTAACCATCACGGTTTTTGGCT-AAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCAT
190 TCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCAT
* * * * ** * *
9410 GATTCTTAGCTTCAAGACTCCTTGTAATATCAATATTCATCTAATGAAATTTCAGGCATAGTGGA
255 GATTTTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGGA
9475 TATAAGGATTTG
319 TATAAGGATTTG
* * * * *
9487 TTTTTACGAGCATCAGAATCCAGTTTCGTTTTAATTAAAAATTAATTC-GAAAAAAAAAAGAAAG
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAA
* * * *
9551 ACGATATTAGATGAGTGAAAAGCACTCCAATCTCTTTTGCGTTAAATTATATATTTTTTATGACT
66 ACGATATTAGAAGCGTGAAAAGCCCTCCAATCT-TTTTGCGTTAAATTATATATTTTTTATGAGT
* * * *
9616 ATTGTAGCTAAAAACTGTGGAAAAAATTTCCGGGTCAAGTTTTACGAAATTTTAACCGAAATCGT
130 ATTGTGGCTAAAAATTGAGGAAAAAATTT-CGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGT
* * * *
9681 GTACTAACCATCACAGTTTTTTGCTTAAAACGCGTTACGGGACCCCGACTCAGTTTTGCATGATT
194 GTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATGATT
* * * *
9746 TTTGGTGTCAAGACTCCTTGTAATATCAATATTCATCTAACAAAATCTCAACAATAGTGGATATA
259 TTTGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC-ACCATAGTGGATATA
9811 AGGATTTG
323 AGGATTTG
* * * * *
9819 TTTTTACGAGAATCATAATCAAATTTTGATTTAATTAGAAATTAATTC-GAAAAAGAAAA-GAAA
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAA-AAAAGGAAA
** * * * * * * * *
9882 AACGATATTAGAAGTATGAAAATCCCTTCAATATTTTTGGGGATGAGTTATATATTTTTTATGAT
65 AACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTTTTATGAG
* * * * * ** * * *
9947 TATTGTGACAAAAAATT-ATTGAAAAATCTTTCGGGTCAATTTTTGTAAAAATTTAGCCAAAATC
129 TATTGTGGCTAAAAATTGA-GGAAAAA-ATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATC
* * * * * *
10011 --CTA-T-ACTATCAC-GATTTTTGGCTAAAAATGCGTT-CTGGGGTCTCGGCTCAGTTTTGCTT
192 GTGTACTAACCATCACAG-TTTTTGGCTAAAAACGCGTTAC-GGGGCCCCGGCTCAGTTTTGCAT
* * * * * * *
10070 GATTTTTGGC-ACTAAGACTCCTTGAAATATCTATATTTATCTTATCAAATCTCATCCACATTGG
255 GATTTTTGGCGTC-AAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGG
*
10134 ATTTAAGGATTT-
318 ATATAAGGATTTG
* * * * * *
10146 TTTTTA-AAGCATTAGAATCTTGTTTCGATTTAATAAGAAATTAAGTTGGGAAAATAAAAAAGAA
1 TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAA-TTCGGAAAA-AAAAAGGAA
* * * * *
10210 AAACGATATTAGAAACCTGAAAAGCCATTCAATCTTTTTGGCGTTAAGTTATATA--TTTTATGA
64 AAACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTT-GCGTTAAATTATATATTTTTTATGA
* * * * ** *
10273 GTATTGTGACCAAATATTAAGGAAAAATATTTTAGGTCAA-TCTTTGCAAAATTTTAACCGAAAT
128 GTATTGTGGCTAAAAATTGAGGAAAAA-ATTTCGGGTCAAGT-TTTGCGAAATTTTAACCGAAAT
* * ** **
10337 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTTGAAGCCCCGGCTCAGTTTTGCATG
191 CGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATG
* * * * ** * *
10402 ATTTTTTGCGGCAAGACTCATTTTTAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGG
256 ATTTTTGGCGTCAAGACTC--CTTGAAATATCAATATTCATCTAACCAAATCTCA-CCATAGTGG
* *
10467 ATTTGAGGATTTG
318 ATATAAGGATTTG
*
10480 TTTTCACGA
1 TTTTTACGA
10489 TCATTTAAAT
Statistics
Matches: 4080, Mismatches: 737, Indels: 344
0.79 0.14 0.07
Matches are distributed among these distances:
318 32 0.01
319 10 0.00
320 97 0.02
321 108 0.03
322 6 0.00
324 4 0.00
326 32 0.01
327 70 0.02
328 114 0.03
329 53 0.01
330 59 0.01
331 416 0.10
332 752 0.18
333 1125 0.28
334 439 0.11
335 369 0.09
336 211 0.05
337 176 0.04
338 6 0.00
339 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (330 bp):
TTTTTACGAGCATCAGAATCTAGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAA
ACGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGCGTTAAATTATATATTTTTTATGAGTA
TTGTGGCTAAAAATTGAGGAAAAAATTTCGGGTCAAGTTTTGCGAAATTTTAACCGAAATCGTGT
ACTAACCATCACAGTTTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAGTTTTGCATGATTTT
TGGCGTCAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCACCATAGTGGATATAAGG
ATTTG
Found at i:10683 original size:43 final size:43
Alignment explanation
Indices: 10636--10742 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
10626 GCCTACGTAT
**
10636 GGCCCAACTTGGGCCCAAATAATG-AGACACCTGGCCCAATTAA
1 GGCCCAACTTGGGCCCAAATAATGTA-ACACCAAGCCCAATTAA
* * * ***
10679 GGCCCAACTTGGTCCAAAATTATGTAATGTCAAGCCCAATTAA
1 GGCCCAACTTGGGCCCAAATAATGTAACACCAAGCCCAATTAA
10722 GGCCCAACTTGGGCCCAAATA
1 GGCCCAACTTGGGCCCAAATA
10743 TAGCACTCCT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (43 bp):
GGCCCAACTTGGGCCCAAATAATGTAACACCAAGCCCAATTAA
Found at i:12258 original size:32 final size:32
Alignment explanation
Indices: 12222--12568 Score: 633
Period size: 32 Copynumber: 10.9 Consensus size: 32
12212 TTCAACTTTC
12222 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
12254 CCAAATGACATTGAACTTGCCTTAA-TCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
12285 CCAAATGACATTGAACTTGCCTTAATCCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
12317 CCAAATGACATTGAACTTGCCTTAATCCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
12349 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
12381 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
12413 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
12445 CCAAATAACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
* *
12477 CAAAATCACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
12509 CCAAATCACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
12541 CCAAATGACATTGAACTTGCCTTAATTC
1 CCAAATGACATTGAACTTGCCTTAATTC
12569 GCATTGGCCC
Statistics
Matches: 307, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 31 0.10
32 276 0.90
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.31
Consensus pattern (32 bp):
CCAAATGACATTGAACTTGCCTTAATTCACAT
Found at i:12880 original size:121 final size:123
Alignment explanation
Indices: 12639--12881 Score: 319
Period size: 121 Copynumber: 2.0 Consensus size: 123
12629 TCGAGACAAT
* * * * *
12639 AAGGCAATCCTTGCTGCCACAAGGATATGCTCAGCTCCAATTGGGAAGACAACTGCAGAGGAGAA
1 AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATCGGGAAGACAACTGCAGAAGAGAA
** * * * * *
12704 GAAACGTTATCCATAAACCATCAGAGCAGACAAAGTAAACTTACAACAAACAAATCTG
66 GAAACACTATCAAGAAACCATCAGAGCAGACAAAGGAAAATCACAACAAACAAATCTG
12762 AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATCGGG-AGAC-ACTGCAGAAGAGAA
1 AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATCGGGAAGACAACTGCAGAAGAGAA
* * * * *
12825 GAAACACTATCAAGAAACCATCAGAGCATACTAAGGAAAATCAGAGCAAGCAAATCT
66 GAAACACTATCAAGAAACCATCAGAGCAGACAAAGGAAAATCACAACAAACAAATCT
12882 ATGCAATGGC
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
121 58 0.56
122 4 0.04
123 41 0.40
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (123 bp):
AAGGCAATCCTAGCTGCCACAAGGATACGCTCAGATCCAATCGGGAAGACAACTGCAGAAGAGAA
GAAACACTATCAAGAAACCATCAGAGCAGACAAAGGAAAATCACAACAAACAAATCTG
Found at i:16630 original size:26 final size:26
Alignment explanation
Indices: 16601--16668 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 26
16591 ATGATATCAA
16601 CACCTGTAGATAAAAGCTTAAGTTGC
1 CACCTGTAGATAAAAGCTTAAGTTGC
*
16627 CACCTGAAGATTAAATAAAAGCTTAAGTTGC
1 CACCT---G--TAGATAAAAGCTTAAGTTGC
*
16658 CACCTGAAGAT
1 CACCTGTAGAT
16669 TAAATAGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
26 8 0.24
28 1 0.03
29 1 0.03
31 24 0.71
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (26 bp):
CACCTGTAGATAAAAGCTTAAGTTGC
Found at i:16645 original size:31 final size:31
Alignment explanation
Indices: 16610--16687 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
16600 ACACCTGTAG
16610 ATAAAAGCTTAAGTTGCCACCTGAAGATTAA
1 ATAAAAGCTTAAGTTGCCACCTGAAGATTAA
16641 ATAAAAGCTTAAGTTGCCACCTGAAGATTAA
1 ATAAAAGCTTAAGTTGCCACCTGAAGATTAA
*
16672 ATAGAAGCTTAAGTTG
1 ATAAAAGCTTAAGTTG
16688 ATTCCAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (31 bp):
ATAAAAGCTTAAGTTGCCACCTGAAGATTAA
Found at i:18902 original size:20 final size:20
Alignment explanation
Indices: 18877--18916 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18867 AAGAGCAGAT
18877 ATAATGAACAAGAAGATACA
1 ATAATGAACAAGAAGATACA
*
18897 ATAATGTACAAGAAGATACA
1 ATAATGAACAAGAAGATACA
18917 TGTTACACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.17
Consensus pattern (20 bp):
ATAATGAACAAGAAGATACA
Found at i:23877 original size:19 final size:20
Alignment explanation
Indices: 23831--23878 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
23821 TGTGGCACGC
*
23831 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
23853 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
23872 CACATGT
1 CACATGT
23879 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:23883 original size:53 final size:53
Alignment explanation
Indices: 23798--23900 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
23788 GACGTGGCAC
* **
23798 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* *
23851 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
23901 GACACGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:23928 original size:31 final size:31
Alignment explanation
Indices: 23850--23948 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
23840 CAAAAAGTCG
* * *
23850 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
*
23881 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
** * *
23912 TGCCA-GATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACG-TGTACCAAAAAGTGACACGTGGCA
23943 TGCCAC
1 TGCCAC
23949 ATGCACAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.02
31 56 0.98
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18
Consensus pattern (31 bp):
TGCCACGTGTACCAAAAAGTGACACGTGGCA
Found at i:32328 original size:60 final size:60
Alignment explanation
Indices: 32230--32349 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
32220 TTTTGCTTAG
* *
32230 ACTTCTATAGAAAACATAATGGCGTTTCTTGATCAATCATCAACTATGCACTGGAATCTT
1 ACTTCTATACAAAACATAATGGCGTTTCTTGATAAATCATCAACTATGCACTGGAATCTT
*
32290 ACTTCTATACAAAACATAATGGTGTTTCTTGATAAATCATCAACTATGCACTGGAATCTT
1 ACTTCTATACAAAACATAATGGCGTTTCTTGATAAATCATCAACTATGCACTGGAATCTT
32350 CTGCAACTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (60 bp):
ACTTCTATACAAAACATAATGGCGTTTCTTGATAAATCATCAACTATGCACTGGAATCTT
Found at i:45705 original size:18 final size:18
Alignment explanation
Indices: 45681--45723 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
45671 AGGGAGGAGG
45681 AGAAGAAGAAAATGAAGA
1 AGAAGAAGAAAATGAAGA
* * *
45699 CGAAGAAGAAGATGAGGA
1 AGAAGAAGAAAATGAAGA
45717 AGAAGAA
1 AGAAGAA
45724 ATGGTCCCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.05
Consensus pattern (18 bp):
AGAAGAAGAAAATGAAGA
Found at i:50722 original size:18 final size:17
Alignment explanation
Indices: 50685--50741 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
50675 TCTGTTTTTG
*
50685 GAAAGAAAATGAAAAG-A
1 GAAAGAAAA-AAAAAGAA
50702 GAAAGAAAAAAAAGAGAA
1 GAAAGAAAAAAAA-AGAA
*
50720 GAAAAGAAAAGAAAAGAA
1 G-AAAGAAAAAAAAAGAA
50738 GAAA
1 GAAA
50742 AAACAGGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.09
17 14 0.40
18 7 0.20
19 11 0.31
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (17 bp):
GAAAGAAAAAAAAAGAA
Found at i:50726 original size:5 final size:5
Alignment explanation
Indices: 50686--50737 Score: 70
Period size: 5 Copynumber: 10.2 Consensus size: 5
50676 CTGTTTTTGG
*
50686 AAAGA AAATGA AAAGA GAAAGA AAA-A AAAGA GAAGA AAAGA AAAGA AAAGA
1 AAAGA AAA-GA AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
50737 A
1 A
50738 GAAAAAACAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 28 0.67
6 10 0.24
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:50732 original size:13 final size:12
Alignment explanation
Indices: 50686--50742 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
50676 CTGTTTTTGG
50686 AAAGAAAATGAAA
1 AAAGAAAA-GAAA
*
50699 AGAG-AAAGAAA
1 AAAGAAAAGAAA
*
50710 AAA-AAGAGAAGA
1 AAAGAAAAGAA-A
50722 AAAGAAAAGAAA
1 AAAGAAAAGAAA
50734 AGAAGAAAA
1 A-AAGAAAA
50743 AACAGGGGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 11 0.31
12 9 0.25
13 16 0.44
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:50742 original size:18 final size:18
Alignment explanation
Indices: 50686--50742 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
50676 CTGTTTTTGG
50686 AAAGAAAATGAAAAG-AG-
1 AAAGAAAA-GAAAAGAAGA
*
50703 AAAGAAAAAAAAGAGAAGA
1 AAAGAAAAGAAA-AGAAGA
50722 AAAGAAAAGAAAAGAAGA
1 AAAGAAAAGAAAAGAAGA
50740 AAA
1 AAA
50743 AACAGGGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 11 0.31
19 11 0.31
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAAGAAAAGAAAAGAAGA
Found at i:50744 original size:15 final size:14
Alignment explanation
Indices: 50686--50744 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
50676 CTGTTTTTGG
50686 AAAGAAAATGAAAAGA
1 AAAGAAAA--AAAAGA
50702 GAAAGAAAAAAAAGA
1 -AAAGAAAAAAAAGA
*
50717 GAAGAAAAGAAAAGA
1 AAAGAAAA-AAAAGA
50732 AAAGAAGAAAAAA
1 AAAGAA-AAAAAA
50745 CAGGGGAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.18
15 21 0.55
16 2 0.05
17 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAAAAGA
Found at i:52097 original size:22 final size:22
Alignment explanation
Indices: 52067--52108 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52057 TAATATCACA
* * *
52067 ATAATAATAATGATGATAAATG
1 ATAAAAATAATAATAATAAATG
52089 ATAAAAATAATAATAATAAA
1 ATAAAAATAATAATAATAAA
52109 AAACAAAACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (22 bp):
ATAAAAATAATAATAATAAATG
Found at i:69407 original size:3 final size:3
Alignment explanation
Indices: 69399--69430 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
69389 TAATAGAATG
69399 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
69431 TAAAGAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:81540 original size:2 final size:2
Alignment explanation
Indices: 81533--81563 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
81523 CTTGGAGTAC
81533 AT AT 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 AT AT A
81564 GTCAATGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82100 original size:19 final size:21
Alignment explanation
Indices: 82054--82101 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
82044 TGTGGCACGC
*
82054 CACATGTACCAAAAAATCGTGC
1 CACATGTACCAAAAAA-CGTGA
82076 CACATGTACC-AAAAA-GTGA
1 CACATGTACCAAAAAACGTGA
82095 CACATGT
1 CACATGT
82102 CACGTCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
21 5 0.20
22 10 0.40
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (21 bp):
CACATGTACCAAAAAACGTGA
Found at i:82115 original size:53 final size:53
Alignment explanation
Indices: 82020--82121 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
82010 CGACGTGGCA
**
82020 TGCCACATGGACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAATCG
1 TGCCACATGGACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAATCG
* * * *
82073 TGCCACATGTACCAAAAAGTGACACATGTCACGTCACGTGTACCAAAAA
1 TGCCACATGGACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAA
82122 GTGACACGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (53 bp):
TGCCACATGGACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAATCG
Found at i:84413 original size:34 final size:34
Alignment explanation
Indices: 84370--84439 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
84360 TGCAGCTGCT
84370 GCTGTTGGGAGACTCACCCACTATAACCAGGTGC
1 GCTGTTGGGAGACTCACCCACTATAACCAGGTGC
84404 GCTGTTGGGAGACTCACCCACTATAACCAGGTGC
1 GCTGTTGGGAGACTCACCCACTATAACCAGGTGC
84438 GC
1 GC
84440 GACATGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (34 bp):
GCTGTTGGGAGACTCACCCACTATAACCAGGTGC
Found at i:84468 original size:26 final size:26
Alignment explanation
Indices: 84438--84489 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
84428 AACCAGGTGC
84438 GCGACATGGGTCGGATCCAGATTAGT
1 GCGACATGGGTCGGATCCAGATTAGT
84464 GCGACATGGGTCGGATCCAGATTAGT
1 GCGACATGGGTCGGATCCAGATTAGT
84490 CAGGGCTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (26 bp):
GCGACATGGGTCGGATCCAGATTAGT
Found at i:99746 original size:17 final size:18
Alignment explanation
Indices: 99724--99759 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
99714 CAATATATGA
99724 TTAGAA-CCTCTTAAGAG
1 TTAGAATCCTCTTAAGAG
*
99741 TTAGAATCTTCTTAAGAG
1 TTAGAATCCTCTTAAGAG
99759 T
1 T
99760 CATAAAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (18 bp):
TTAGAATCCTCTTAAGAG
Found at i:113583 original size:2 final size:2
Alignment explanation
Indices: 113576--113609 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
113566 AAATATTTAG
113576 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
113610 TTAAGGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113897 original size:11 final size:11
Alignment explanation
Indices: 113881--113905 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
113871 CATATTCTCC
113881 TTTTTTTTCTT
1 TTTTTTTTCTT
113892 TTTTTTTTCTT
1 TTTTTTTTCTT
113903 TTT
1 TTT
113906 CGTTTCAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Done.