Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012662.1 Corchorus olitorius cultivar O-4 contig12695, 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: 91398
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:938 original size:333 final size:329
Alignment explanation
Indices: 4--2583 Score: 2905
Period size: 331 Copynumber: 7.8 Consensus size: 329
1 TTT
* * * *
4 CAATCTTTTTGGCACT-AATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAATAT
1 CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTA-TCAAAAAATTTAAGAAATAT
* *
68 TTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAATTTTTGGCTA
65 TTTTCGGGTCAATTTTC-CAAAATTTTAGCCAAAATCGTGT-ATAACCATCACAGTTTTTGGCTA
* * * * * *
133 AAAAAACG-TTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCATTGAGATA
128 AAAAAGCGTTTC-GGGGCACCGACTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAAATA
* *
197 TCCATATTCATCTAATCAAATCTCAGCCACATAAG-ATTTTAGAATTTGTTTTTACGAGCATCTG
192 TCCATATTCATCTAAACAAATCTCAGCCACAT-TGCATTTTAGAATTTGTTTTTACGAGCATCTG
** *
261 AATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCG-C
256 AATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATTAAAA-CGTC
*
325 GAAAAGTCCTC
320 -AAAAGCCCTC
* * * * * * *
336 CAATATTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAAATTGAGGAAATAT
1 CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTATC-AAAAAATTTAAGAAATAT
* * *
401 TTTTTGGGTGAATTTT-CAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGCTTTTTGGCTA
65 TTTTCGGGTCAATTTTCCAAAATTTTAGCCAAAATCGTGTA-TAACCATCACAG-TTTTTGGCTA
* * * * * *
465 GAAACGCGTTTCAGGGCCCCTACTCAGTTTTGCATGA-TTTTTG-ATGCCGAGACTCCTT-AAAT
128 AAAAAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTGCA--CCAAGACTCCTTGAAAT
* * * *
527 ATCCATATTCATGTAAACAAATCTAAGCCACATTGCAATTTAGAATTTGTTTTTACGAGCATTTG
191 ATCCATATTCATCTAAACAAATCTCAGCCACATTGCATTTTAGAATTTGTTTTTACGAGCATCTG
* * * *
592 AATATTCTTTCGATTTAATTAAAAATTAATTCGGAAAAAATAGGAAAAACGGTATTGAAAACGTC
256 AATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATT-AAAACGTC
*
657 AAAAGCCCTT
320 AAAAGCCCTC
* * * * * *
667 TAATCTTTTTGGCTACT-AATTATATAT-TGTTTACAAGTATTTTAGCATAAAATTTTAAGAAAC
1 CAATCTTTTTGG-TACTAAATTATAAATAT-TTTACGAGTATTTTATCA-AAAAATTTAAGAAAT
* * *
730 ATTTTTCGAGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTGATAACCATCACAGTTTTTAGC
63 ATTTTTCGGGTCAATTTTC-CAAAATTTTAGCCAAAATCGTGT-ATAACCATCACAGTTTTTGGC
* * * * * *
795 TAAAAAAGCATTTCGGGACACCGACTCAGTTTTGCCTGAGTTTTTGCACCAAGACTCCTGGAGAT
126 TAAAAAAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAAAT
* *
860 ATCCATATTCATCTAATCAAATCTCAGCCACATTAG-ATTTTAGAATTTGTTTTTATGAGCATCT
191 ATCCATATTCATCTAAACAAATCTCAGCCACATT-GCATTTTAGAATTTGTTTTTACGAGCATCT
* *
924 GAATCTTGTTTCGATTTAATTAAAAATTGATTCTGAAAAAATATGAAAAACGATATTAAAAGCGT
255 GAATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATTAAAA-CGT
* **
989 GAAAAGTACTC
319 CAAAAGCCCTC
** * * * * * *
1000 CAATC--TTTGGTGTTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAACTGAGGAAATATT
1 CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTATCAAAAAATTTAAGAAATATT
* * ** *
1063 TTTCGAGTCACTTTTTTTAAAATTTTAGCCAAAATCGTG--T-ACCATCACAGCTTTTTGGCTAG
66 TTTCGGGTCA-ATTTTCCAAAATTTTAGCCAAAATCGTGTATAACCATCACAG-TTTTTGGCTAA
* * * * * * * *
1125 AAACGCGTTTCAGGTCCCCTAGTCAGTTTTGCATGA-TTTTTGACGCCGAGACTCCTTGAAATAT
129 AAAAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTG-CACCAAGACTCCTTGAAATAT
* * * *
1189 CCATATTCATGTAAACAAATCTCAGCCACATTGTAATTTAGAATTTGTTTTTACGAGCATTTGAA
193 CCATATTCATCTAAACAAATCTCAGCCACATTGCATTTTAGAATTTGTTTTTACGAGCATCTGAA
* * * * *
1254 TATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTGAAAACGTCAA
258 TCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATT-AAAACGTCAA
*
1319 AAGCCCTT
322 AAGCCCTC
* * * *
1327 CAATCTTTTTGGCGACT-AATTATATATTTTTTACGAGTATTTTATCCCAAAAATTTAAGAAATA
1 CAATCTTTTTGG-TACTAAATTATAAATATTTTACGAGTATTTTAT-CAAAAAATTTAAGAAATA
*
1391 TTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCT
64 TTTTTCGGGTCAATTTTC-CAAAATTTTAGCCAAAATCGTGT-ATAACCATCACAGTTTTTGGCT
* * * * * * *
1456 AAAAAAGCGTTCCGGGGCACCGGCTCAGTTTTCCTTGATTTTTTGCACAAAGACTGCTTGAGATA
127 AAAAAAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAAATA
* *
1521 TCCATATTCATCTAATCAAATCTCAGCCACAATAG-ATTTTAGAATTTGTTTTTACGAGCATCTG
192 TCCATATTCATCTAAACAAATCTCAGCCAC-ATTGCATTTTAGAATTTGTTTTTACGAGCATCTG
** *
1585 AATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCG-C
256 AATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATTAAAA-CGTC
*
1649 GAAAAGTCCTC
320 -AAAAGCCCTC
* * * * * *
1660 CAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAATTGAGGAAATATT
1 CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTATCAAAAAATTTAAGAAATATT
* * *
1725 TTTCGGGTGAATTTT-CAAAATTTTAGCCAAAATCGTGTACTAACCATCACGACTTTTTGGCTAG
66 TTTCGGGTCAATTTTCCAAAATTTTAGCCAAAATCGTGTA-TAACCATCAC-AGTTTTTGGCTAA
* * * * * * * *
1789 AAACGCGATTCAGGTCCCCTACTCAGTTTTGCATGA-TTTTTGACGCCGAGACTCCTTGAAATAT
129 AAAAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTG-CACCAAGACTCCTTGAAATAT
* * * *
1853 CCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGTTTTTACGAGCATTTGAA
193 CCATATTCATCTAAACAAATCTCAGCCACATTGCATTTTAGAATTTGTTTTTACGAGCATCTGAA
* * * * *
1918 TATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTGAAAACGTCAA
258 TCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATT-AAAACGTCAA
* *
1983 AAGACCTT
322 AAGCCCTC
* * * *
1991 CAATCTTTTTGGCACT-AATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAATAT
1 CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTA-TCAAAAAATTTAAGAAATAT
*
2055 TTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTA
65 TTTTCGGGTCAATTTTC-CAAAATTTTAGCCAAAATCGTGT-ATAACCATCACAGTTTTTGGCTA
* * * *
2120 AAAAAGCG-TTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGAGATA
128 AAAAAGCGTTTC-GGGGCACCGACTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAAATA
* * *
2184 TCCATATTCATCTAATCAAATCTCAGCCACAATAG-ATTTTGGAATTTGTTTTTACGAGCATCTG
192 TCCATATTCATCTAAACAAATCTCAGCCAC-ATTGCATTTTAGAATTTGTTTTTACGAGCATCTG
* *
2248 AATCTTGTTTCGATTTAATTAAAAATTAATTC-AAAAAAATATGAAAAACGATATTAAAAAC-AC
256 AATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATT-AAAACGTC
2311 GAAAAGTCCC-C
320 -AAAAG-CCCTC
** * * * *
2322 CAATCTTTTTGGTGTTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAA-CTAAGGAAATAT
1 CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTATCAAAAAATTTAA-GAAATAT
* * * * *
2386 TTTTCAGGTTACTTTTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGACTTTTTGGCT
65 TTTTCGGGTCA-ATTTTCCAAAATTTTAGCCAAAATCGTGTA-TAACCATCAC-AGTTTTTGGCT
* * * * * * * * *
2451 AGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTTACGCCGAGACTCCTTGAAATA
127 AAAAAAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAAATA
* * * *
2516 TCCATATTCATGTAAAAAAAATCTCAGCCACATTGCATTATAGAATTTGTTTTTACGAGCATTTG
192 TCCATATTCATCT-AAACAAATCTCAGCCACATTGCATTTTAGAATTTGTTTTTACGAGCATCTG
2581 AAT
256 AAT
2584 ATTCTTAAAA
Statistics
Matches: 1875, Mismatches: 308, Indels: 129
0.81 0.13 0.06
Matches are distributed among these distances:
326 17 0.01
327 175 0.09
328 4 0.00
329 33 0.02
330 164 0.09
331 556 0.30
332 398 0.21
333 505 0.27
334 23 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (329 bp):
CAATCTTTTTGGTACTAAATTATAAATATTTTACGAGTATTTTATCAAAAAATTTAAGAAATATT
TTTCGGGTCAATTTTCCAAAATTTTAGCCAAAATCGTGTATAACCATCACAGTTTTTGGCTAAAA
AAGCGTTTCGGGGCACCGACTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAAATATCCA
TATTCATCTAAACAAATCTCAGCCACATTGCATTTTAGAATTTGTTTTTACGAGCATCTGAATCT
TGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATATGAAAAACGATATTAAAACGTCAAAAGC
CCTC
Found at i:2414 original size:664 final size:664
Alignment explanation
Indices: 2--2589 Score: 4384
Period size: 664 Copynumber: 3.9 Consensus size: 664
1 T
2 TTCAATCTTTTTGGC-ACTAATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAAT
1 TTCAATCTTTTTGGCGACTAATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAAT
* *
66 ATTTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAATTTTTGGC
66 ATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGC
* *
131 TAAAAAAACGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCATTGAGAT
131 TAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGAGAT
196 ATCCATATTCATCTAATCAAATCTCAGCCAC-ATAAGATTTTAGAATTTGTTTTTACGAGCATCT
196 ATCCATATTCATCTAATCAAATCTCAGCCACAAT-AGATTTTAGAATTTGTTTTTACGAGCATCT
260 GAATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCGC
260 GAATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCGC
* *
325 GAAAAGTCCTCCAATATTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAAAT
325 GAAAAGTCCTCCAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTC-AAAAAAC
* *
390 TGAGGAAATATTTTTTGGGTGAATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGC
389 TGAGGAAATATTTTTCGGGTGAATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGAC
* *
455 TTTTTGGCTAGAAACGCGTTTCAGGGCCCCTACTCAGTTTTGCATGATTTTTGATGCCGAGACTC
454 TTTTTGGCTAGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTGACGCCGAGACTC
* *
520 CTT-AAATATCCATATTCATGTAAACAAATCTAAGCCACATTGCAATTTAGAATTTGTTTTTACG
519 CTTGAAATATCCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGTTTTTACG
*
584 AGCATTTGAATATTCTTTCGATTTAATTAAAAATTAATTCGGAAAAAATAGGAAAAACGGTATTG
584 AGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTG
649 AAAACGTCAAAAGCCC
649 AAAACGTCAAAAGCCC
* * * *
665 TTTAATCTTTTTGGCTACTAATTATATATTGTTTACAAGTATTTTAG--CATAAAATTTTAAGAA
1 TTCAATCTTTTTGGCGACTAATTATATATTTTTTACGAGTATTTTAGTCCA-AAAA-TTTAAGAA
* * * *
728 ACATTTTTCGAGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTGATAACCATCACAGTTTTTA
64 ATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTG
* * * * * * *
793 GCTAAAAAAGCATT-TCGGGACACCGACTCAGTTTTGCCTGAGTTTTTGCACCAAGACTCCTGGA
129 GCTAAAAAAGCGTTCT-GGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGA
* *
857 GATATCCATATTCATCTAATCAAATCTCAGCCACATTAGATTTTAGAATTTGTTTTTATGAGCAT
193 GATATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTAGAATTTGTTTTTACGAGCAT
* *
922 CTGAATCTTGTTTCGATTTAATTAAAAATTGATTC-TGAAAAAATATGAAAAACGATATTAAAAG
258 CTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAT-AAAAAATATGAAAAACAATATTAAAAG
* * *
986 CGTGAAAAGTACTCCAATC--TTTGGTGTTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAA
322 CGCGAAAAGTCCTCCAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAA
* * * *
1049 ACTGAGGAAATATTTTTCGAGTCACTTTTTTTAAAATTTTAGCCAAAATCGTG---T-ACCATCA
387 ACTGAGGAAATATTTTTCGGGTGA--ATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCA
*
1110 C-AGCTTTTTGGCTAGAAACGCGTTTCAGGTCCCCTAGTCAGTTTTGCATGATTTTTGACGCCGA
450 CGA-CTTTTTGGCTAGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTGACGCCGA
* *
1174 GACTCCTTGAAATATCCATATTCATGTAAACAAATCTCAGCCACATTGTAATTTAGAATTTGTTT
514 GACTCCTTGAAATATCCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGTTT
1239 TTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGG
579 TTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGG
1304 TATTGAAAACGTCAAAAGCCC
644 TATTGAAAACGTCAAAAGCCC
1325 TTCAATCTTTTTGGCGACTAATTATATATTTTTTACGAGTATTTTA-TCCCAAAAATTTAAGAAA
1 TTCAATCTTTTTGGCGACTAATTATATATTTTTTACGAGTATTTTAGT-CCAAAAATTTAAGAAA
1389 TATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGG
65 TATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGG
* * *
1454 CTAAAAAAGCGTTCCGGGGCACCGGCTCAGTTTTCCTTGATTTTTTGCACAAAGACTGCTTGAGA
130 CTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGAGA
1519 TATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTAGAATTTGTTTTTACGAGCATCT
195 TATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTAGAATTTGTTTTTACGAGCATCT
1584 GAATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCGC
260 GAATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCGC
*
1649 GAAAAGTCCTCCAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAATT
325 GAAAAGTCCTCCAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAACT
1714 GAGGAAATATTTTTCGGGTGAATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGACT
390 GAGGAAATATTTTTCGGGTGAATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGACT
*
1779 TTTTGGCTAGAAACGCGATTCAGGTCCCCTACTCAGTTTTGCATGATTTTTGACGCCGAGACTCC
455 TTTTGGCTAGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTGACGCCGAGACTCC
1844 TTGAAATATCCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGTTTTTACGA
520 TTGAAATATCCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGTTTTTACGA
1909 GCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTGA
585 GCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTGA
*
1974 AAACGTCAAAAGACC
650 AAACGTCAAAAGCCC
1989 TTCAATCTTTTTGGC-ACTAATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAAT
1 TTCAATCTTTTTGGCGACTAATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAAT
*
2053 ATTTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGC
66 ATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGC
2118 TAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGAGAT
131 TAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGAGAT
*
2183 ATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTGGAATTTGTTTTTACGAGCATCTG
196 ATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTAGAATTTGTTTTTACGAGCATCTG
* * *
2248 AATCTTGTTTCGATTTAATTAAAAATTAATTCA-AAAAAATATGAAAAACGATATTAAAAACACG
261 AATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCGCG
* * *
2312 AAAAGTCCCCCAATCTTTTTGGTGTTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAACTA
326 AAAAGTCCTCCAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAACTG
* * *
2377 AGGAAATATTTTTCAGGTTACTTTTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGAC
391 AGGAAATATTTTTCGGGTGA--ATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGAC
*
2442 TTTTTGGCTAGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTTACGCCGAGACTC
454 TTTTTGGCTAGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTGACGCCGAGACTC
2507 CTTGAAATATCCATATTCATGTAAAAAAAATCTCAGCCACATTGC-ATTATAGAATTTGTTTTTA
519 CTTGAAATATCCATATTCATGT-AAAAAAATCTCAGCCACATTGCAATT-TAGAATTTGTTTTTA
2571 CGAGCATTTGAATATTCTT
582 CGAGCATTTGAATATTCTT
2590 AAAATTAATT
Statistics
Matches: 1807, Mismatches: 91, Indels: 52
0.93 0.05 0.03
Matches are distributed among these distances:
659 74 0.04
660 469 0.26
661 30 0.02
662 213 0.12
663 316 0.17
664 647 0.36
665 58 0.03
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (664 bp):
TTCAATCTTTTTGGCGACTAATTATATATTTTTTACGAGTATTTTAGTCCAAAAATTTAAGAAAT
ATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGC
TAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTTGAGAT
ATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTAGAATTTGTTTTTACGAGCATCTG
AATCTTGTTTCGATTTAATTAAAAATTAATTCATAAAAAATATGAAAAACAATATTAAAAGCGCG
AAAAGTCCTCCAATCTTTTTGGTATTAAATTGTAAATATTTTATGAGTATTTTCTCAAAAAACTG
AGGAAATATTTTTCGGGTGAATTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGACTT
TTTGGCTAGAAACGCGTTTCAGGTCCCCTACTCAGTTTTGCATGATTTTTGACGCCGAGACTCCT
TGAAATATCCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGTTTTTACGAG
CATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGGTATTGAA
AACGTCAAAAGCCC
Found at i:3647 original size:332 final size:329
Alignment explanation
Indices: 2652--3940 Score: 1435
Period size: 332 Copynumber: 3.9 Consensus size: 329
2642 TAGGGTTTAT
* * * * *
2652 AAAATTAAGGAAAAACTTTTCGACTCAGTTTTTGCAAAATTTTAACTGAAATCGTATACTATCCA
1 AAAATTGAGGAAAAATTTTTCGACTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCA
* * * * *
2717 TCACAGTTTTTAGCTAAAAAA-GTCTTCCAGGTCCCCGATTCAGCTTTGCATGATTTTTGACGCC
66 TCACAGTTTTTGGCTAAAAAACG--TTCC-GGACCCCGACTCAGTTTTGCATGATTTTTGGCGCC
* * * * *
2781 AACACTCCTTGAAATATCTATACTCCTGTATGAAAGCAAATCTCAGCCACATTTGATTTAAAGAC
128 AAGACTCCTTGAAATATCTATA-T--T-CATCAAACCAAATCTCAGCCACAATTGATTT-AAGAC
* * * *
2846 GTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTTTATTAGAAATTAATTTTAAAAAAAAATAT
188 TTGTTTTTACGAGCATCAGAATCTTATTTCGATTTTTATTAGAAATTAA--TT-AAAAAAAATAG
* * * * * * *
2911 GAAAAACGATATTAAAAGTGTGAAAAGCTTTTTCATCTTTTTGGCATTGAATTATATATTTTTTA
250 GAAAAACGATATTAGAAGCGTGAAAAGCCTTTTAATATTTTTGACATTGAATTATATAATTTTTA
*
2976 CGACTATTATGTCAA
315 CGACTATTGTGTCAA
* * * *
2991 AAAATTGAGGAAAAATATTTCGACTCAATTTTTGCAAAAATTTACCCGAAATCGTG-----T--A
1 AAAATTGAGGAAAAATTTTTCGACTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCA
* * * * * *
3049 -CACGGTTTTTTG-TAAAAAAAGGTGTTCTGGGGCCCCTG-CTCAATTTTGCATGATTTTTGGCG
66 TCACAGTTTTTGGCT-AAAAAA--CGTTC-CGGACCCC-GACTCAGTTTTGCATGATTTTTGGCG
* * ** *
3111 CCAAGAGTCCTTAAAATATCTATATTTTTCAAACCAAATCTCTGCCACAATTGATTTATAGACTT
126 CCAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTA-AGACTT
* * * *
3176 GTTTTTACGAGGATCAGAATCTTATTTCGATTTCTATTAGAAATTAATTCACAAAAATAGGAAAA
190 GTTTTTACGAGCATCAGAATCTTATTTCGATTTTTATTAGAAATTAATTAAAAAAAATAGGAAAA
*
3241 ACGATATTAGAAGCGTGAAAAGCCTTTTAATCATTTTGGA-ATTGAATTATATAATTTTTACGAC
255 ACGATATTAGAAGCGTGAAAAGCCTTTTAAT-ATTTTTGACATTGAATTATATAATTTTTACGAC
3305 TATTGTGTCAA
319 TATTGTGTCAA
* * *
3316 AAAACTGAGGAAAAATTTTTCGGCTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
1 AAAATTGAGGAAAAATTTTTCGACTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCA
* * * *
3381 TCACAGTTTTTGGCTAAAAACACGTTCCGGACCCTGACACAGTTTTGCATAATTTTTGGTGCCAA
66 TCACAGTTTTTGGCTAAAAA-ACGTTCCGGACCCCGACTCAGTTTTGCATGATTTTTGGCGCCAA
* * * * *
3446 GACTCGTTGAAATATATATATTCATCTAACCAAATCTCAGTCAC-ATTGAATTTAAGGATTTGTT
130 GACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTG-ATTTAA-GACTTGTT
*
3510 TTTACGAGCATCAGAATCTTGTTTCG-TTTTATATTAGAAATTAATTAAAAAAAAATAGGAAAAA
193 TTTACGAGCATCAGAATCTTATTTCGATTTT-TATTAGAAATTAATT-AAAAAAAATAGGAAAAA
* * * * *
3574 CAATTTTAGAAGCGTGAAAAGCCTTTTAATTTTTTTGACATTGAATTATATACTTTTTACGGCTA
256 CGATATTAGAAGCGTGAAAAGCCTTTTAATATTTTTGACATTGAATTATATAATTTTTACGACTA
3639 TTGTGTCAA
321 TTGTGTCAA
* * * * * *
3648 AAAATTGAGGAAAAATTTTTTGGCTCCGTATTTGCAAAATTTTAGCCGAAATCATGCACTATCCA
1 AAAATTGAGGAAAAATTTTTCGACTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCA
* * * * * *
3713 TCAC-GATTTTTGGCTAAAAAGGTCTTTCAGGGCCCCGGCTCAGTTTTGTATGATTTTTGGCGCC
66 TCACAG-TTTTTGGCTAAAAA--ACGTTCCGGACCCCGACTCAGTTTTGCATGATTTTTGGCGCC
* * *
3777 GAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTAATTTTAAGAC---A
128 AAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGA-TTTAAGACTTGT
* * *
3839 TTTTACTAGCATCAGAATCTTATTTCGATTTTTATTAGAAATTAATTTAAAAAAATAGAAAAAAC
192 TTTTACGAGCATCAGAATCTTATTTCGATTTTTATTAGAAATTAATTAAAAAAAATAGGAAAAAC
* * *
3904 GATATTAGAAGCGTAAAAAGCCTTTCAATGTTTTTGA
257 GATATTAGAAGCGTGAAAAGCCTTTTAATATTTTTGA
3941 ACCAATTAGG
Statistics
Matches: 807, Mismatches: 114, Indels: 68
0.82 0.12 0.07
Matches are distributed among these distances:
325 123 0.15
326 7 0.01
327 1 0.00
328 74 0.09
329 49 0.06
330 50 0.06
331 143 0.18
332 208 0.26
333 92 0.11
334 12 0.01
339 48 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (329 bp):
AAAATTGAGGAAAAATTTTTCGACTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCCA
TCACAGTTTTTGGCTAAAAAACGTTCCGGACCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAG
ACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACAATTGATTTAAGACTTGTTTTT
ACGAGCATCAGAATCTTATTTCGATTTTTATTAGAAATTAATTAAAAAAAATAGGAAAAACGATA
TTAGAAGCGTGAAAAGCCTTTTAATATTTTTGACATTGAATTATATAATTTTTACGACTATTGTG
TCAA
Found at i:4097 original size:39 final size:40
Alignment explanation
Indices: 4053--4134 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
4043 TCTATGATGG
* *
4053 AGCATAGCTACAGGGAAGC-AATTGTTTGGCTAATTGTCT
1 AGCATAGCTACAAGGAAGCAAACTGTTTGGCTAATTGTCT
*
4092 AGCATAGCTACAAGGAAGCAAACTGTTTGGCTGATTGTCT
1 AGCATAGCTACAAGGAAGCAAACTGTTTGGCTAATTGTCT
4132 AGC
1 AGC
4135 TAACTATGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 18 0.46
40 21 0.54
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (40 bp):
AGCATAGCTACAAGGAAGCAAACTGTTTGGCTAATTGTCT
Found at i:6406 original size:62 final size:62
Alignment explanation
Indices: 6325--6668 Score: 607
Period size: 62 Copynumber: 5.5 Consensus size: 62
6315 TGAAGGCACG
* *
6325 ACAGACACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
6387 ACAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
6449 ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
6511 GCAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
*
6573 GCAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
1 ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
* * * *
6635 GCAGGCACGAAAGTACAAGAGAAGACAGAGGAAG
1 ACAGGCACGAAGGTACACGAGAAGACACAGGAAG
6669 ACAGACACGA
Statistics
Matches: 276, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 276 1.00
ACGTcount: A:0.36, C:0.23, G:0.38, T:0.03
Consensus pattern (62 bp):
ACAGGCACGAAGGTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCA
Found at i:6685 original size:34 final size:34
Alignment explanation
Indices: 6640--6753 Score: 140
Period size: 34 Copynumber: 3.6 Consensus size: 34
6630 GGCCAGCAGG
* *
6640 CACGAAAGTACAAGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
6674 CACGAAGGT--AC------AC-GA-GAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
6698 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
6732 CACGAAGGTACACGAGAAGACA
1 CACGAAGGTACACGAGAAGACA
6754 CAGTGGTGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
24 18 0.26
25 2 0.03
26 4 0.06
32 3 0.04
33 2 0.03
34 39 0.57
ACGTcount: A:0.48, C:0.18, G:0.30, T:0.04
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:6692 original size:24 final size:24
Alignment explanation
Indices: 6665--6721 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
6655 GAAGACAGAG
6665 GAAGACAGACACGAAGGTACACGA
1 GAAGACAGACACGAAGGTACACGA
6689 GAAGACAGACACGAAGGTACACGA
1 GAAGACAGACACGAAGGTACACGA
6713 GAAGACAGA
1 GAAGACAGA
6722 GGAAGACAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.19, G:0.30, T:0.04
Consensus pattern (24 bp):
GAAGACAGACACGAAGGTACACGA
Found at i:6709 original size:58 final size:58
Alignment explanation
Indices: 6640--6753 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 58
6630 GGCCAGCAGG
6640 CACGAAAGTACAAGAGAAGACAGAGGAAGACAGACACGAAGGTACACGAGAAGACAGA
1 CACGAAAGTACAAGAGAAGACAGAGGAAGACAGACACGAAGGTACACGAGAAGACAGA
* *
6698 CACGAAGGTACACGAGAAGACAGAGGAAGACAGACACGAAGGTACACGAGAAGACA
1 CACGAAAGTACAAGAGAAGACAGAGGAAGACAGACACGAAGGTACACGAGAAGACA
6754 CAGTGGTGCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.48, C:0.18, G:0.30, T:0.04
Consensus pattern (58 bp):
CACGAAAGTACAAGAGAAGACAGAGGAAGACAGACACGAAGGTACACGAGAAGACAGA
Found at i:6857 original size:2 final size:2
Alignment explanation
Indices: 6852--6886 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6842 AAAAACAGAA
6852 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6887 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7669 original size:44 final size:45
Alignment explanation
Indices: 7619--7726 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
7609 GAAAACGTGC
* *
7619 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
* * ** *
7663 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
*
7708 AGGAGATCAAAGAGAGCTT
1 AGGAGATCAAAGAAAGCTT
7727 TGGCTCCATG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 14 0.25
45 42 0.75
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (45 bp):
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
Found at i:7698 original size:45 final size:45
Alignment explanation
Indices: 7642--7742 Score: 184
Period size: 45 Copynumber: 2.2 Consensus size: 45
7632 AAGTTAGAAT
*
7642 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
*
7687 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
7732 CCATGATTGCC
1 CCATGATTGCC
7743 GAGTGCACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
Found at i:13018 original size:25 final size:25
Alignment explanation
Indices: 12990--13038 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
12980 TGTTGGTTTG
*
12990 TAGAGACCGAGCGAGAGTGTTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
13015 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
13039 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:14554 original size:334 final size:333
Alignment explanation
Indices: 13555--17923 Score: 4062
Period size: 333 Copynumber: 13.1 Consensus size: 333
13545 AAAACCAACT
* * * * * * * **
13555 GAAATTGTGTACTAACTATCACG-GTTTTTTGGCTAGAAATGCATTTCAGGGCCCCTACTCAGTT
1 GAAATCGTGTAATAACCATCACGAG-TTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGTT
** * * * * *
13619 TTGCACGA-TTTTTGACGCCGAGACTCCATGAAATATCCATATTCATGTGAA--AATATCTCAGC
65 TTGCTTGATTTTTTG-CGACAAGACTCCTTGAGATATCCATATTCATCT-AATCAA-ATCTCAGC
* * * * * *
13681 CACATTGCAATTTAGAATTTGTTTTTACGAGCATTTGAATATTCTTTCGATTCAATTAGAAATTA
127 CACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTA
* **
13746 ATTCGGAAAAAATAGGAAAAACGATATT-GAAAACGTCAAAAGCCCTCCAATCTTTTTGGCAACT
192 ATTCGGAAAAAATAGGAAAAACGATATTAG-AAACGTCAAAAGCCCTTCAATCTTTTTGGC-GTT
* * * *
13810 AATTATATATTTTTTACGAGTATTTTAGCCCAAAAATTTAAGAAATA-TTTTCGGATCAATTTTC
255 AATTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTT
13874 ACAAAATTTTAGCC
320 ACAAAATTTTAGCC
* *
13888 GAAATCGTGTATATAACCAAT-AC-AGTTTTTGGCTAAAAAAACG-TTCTAGGGCACCAGCTCAG
1 GAAATCGTGTA-ATAACC-ATCACGAGTTTTTGGCTAAAAAAGCGTTTC-AGGGCACCGGCTCAG
13950 TTTTGCTTGATTTTTTGC-ACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGC
63 TTTTGCTTGATTTTTTGCGAC-AAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGC
* * * * *
14014 CACAATGGATTTTAGAATTTCTTTTTGCGAGCATCTGAATCTTGTTTCGATTTAATTAAAAACTA
127 CACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTA
* * * * * *
14079 ATTCAGAAAAAATATGAAAAATGATATTA-AAAGCG-CGAAAAGTCCTCCAATCTTTTTGGTGTT
192 ATTCGGAAAAAATAGGAAAAACGATATTAGAAA-CGTC-AAAAGCCCTTCAATCTTTTTGGCGTT
* * * * * * *
14142 AAATTGTAAATATTTTATGAGTATTTT--CTCAAAAAAATGAGGAAATATTTTTCGGGTAAATTT
255 -AATTATATATTTTTTATGAGTATTTTAGC-CCAAAAATTTAGGAAATATTTTTCGGGTCAA-TT
14205 TTTA-AAAATTTTAGCC
317 TTTACAAAATTTTAGCC
* * * * * **
14221 AAAATCGTGTAGT-ACCATCACGA-TTTTAATGGCTAAAAACGCGTTTCAAGGCTCCTACTCAGT
1 GAAATCGTGTAATAACCATCACGAGTTTT--TGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGT
* * * ** ** * * **
14284 TTTGCATGATTTTTTACGTCGGGACAACTTGAAATATCCATATTCATGTAAAAAAAATCTCAGCC
64 TTTGCTTGATTTTTTGCGACAAGACTCCTTGAGATATCCATATTCATCT-AATCAAATCTCAGCC
* * * * * *
14349 ACATTGCAGTATAGAATTTGTTTTTACAAGCATTTGAATATTCTTTCGATTTAATTAAAAATTAA
128 ACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAA
*
14414 TTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAA-CCCTTCAATCATTTTGGCGTCTAA
193 TTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCGT-TAA
* * * *
14478 TTATATATTTTTTACGAGTATTTTAGCCCAAAAATTTAAGAAATATTTTTCAGGTCAATTTTCAC
257 TTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTTAC
*
14543 AAAAATTTAGCC
322 AAAATTTTAGCC
* * *
14555 GAAATCGTGTAATAACCAT-ACCAGTTTTTGGCTAAAAAAGCGTTCCGGGGCACCGGCTCAGTTT
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGTTT
14619 TGCTTGATTTTTTGC-ACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCAC
66 TGCTTGATTTTTTGCGAC-AAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCAC
* ** * * * *
14683 AATAAATTTTAGAATTTTTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATT
130 ATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAATT
* * *
14748 CGGAAAAAATAGGGAAAACGATATT-GAAATCGTCAAAAGCCCTTTAATCTTTTTGGCATTTAAT
195 CGGAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAGCCCTTCAATCTTTTTGGC-GTTAAT
* ** * * * *
14812 CATATATTTTTTTACAAGTATTTTAGCCCAAAAATTTAGGAAGTATTTTTCGAGTCAACTTTCAC
258 TATATA-TTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTTAC
*
14877 AAAATTTTAGCT
322 AAAATTTTAGCC
* *
14889 GAAATCGTGTAATAATCAAT-AC-AGTTTTTGGCTAAAAAAGCGTTCCAGGGCACCGGCTCAGTT
1 GAAATCGTGTAATAA-CCATCACGAGTTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGTT
* *
14952 TTGCTTGATTTTTTGC-ACAAAGACTCCTTGAGATATCCATATTCATTTAATCAAATCTCAGCCG
65 TTGCTTGATTTTTTGCGAC-AAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCA
* * * * *
15016 CAATAGATTTTAGAATTTGTTTTTACGATCATCTGAATATTCTTTCGATTTAATTAGAAATTAAT
129 CATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAAT
*
15081 TCGGAAAAAAATTGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCGTATAA
194 TCGG-AAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCGT-TAA
* * *
15146 TTATATATTTTTTACGATTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCAC
257 TTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTTAC
15211 -AAATTTTAGCC
322 AAAATTTTAGCC
* * *
15222 GAAATCGTGTAATAACCATCA-TAGTTTTTGGCTAAAAAAGCG-TTCTGGGGCATCGGCTCAGTT
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTC-AGGGCACCGGCTCAGTT
15285 TTGCTTGATTATTTT-C-ACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCC
65 TTGCTTGATT-TTTTGCGAC-AAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCC
* * * * *
15348 ACAATAGATTTTAGAATTTTTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAAAAATTAA
128 ACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATT-A
* * * * * * **
15413 ATT-AGAAAAAATATGAAAAACGATATTA-AAATCGTGAAAAGTCCTCCAATATTTTTGGTATTA
192 ATTCGGAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAGCCCTTCAATCTTTTTGGCGTT-
* * * * * *
15476 AATTGTAAATATTTTATGAGTATTTT--CTCAAAAAATT-GAGAAATTATTTTTCGGGTCACTTT
255 AATTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAG-GAAA-TATTTTTCGGGTCAATTT
*
15538 TTTCAAAATTTTAGCC
318 TTACAAAATTTTAGCC
* * * * * **
15554 AAAATCGTGTATTAATCATCACG-GTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCCCAACTCAG
1 GAAATCGTGTAATAACCATCACGAG---TTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAG
* * * * * * **
15618 TTTTGCATGA-TTTTAGACGGCAAGACTGCTTGAAATATCCATATTCATGTAAAAAAATCTCAGC
63 TTTTGCTTGATTTTTTG-CGACAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGC
* * * * * **
15682 CACATTGCAATTTAGAATTTGTTTTTACGAGCATTTGAATATTCTTTCGATTTGATTTGAAATTA
127 CACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTA
* *
15747 ATTC---------A-GAAAAAAGATATTAGAAACGTCAAAA-CCTCTTCAATCTTTTTGGCATCT
192 ATTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCC-CTTCAATCTTTTTGGCGT-T
* * * *
15801 AATTATATATTTTTTACGAGTATTTTAGCCCAATAATTTAGGAAATA-TATTCGGGTCAATTTTC
255 AATTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTT
15865 ACAAAATTTTAGCC
320 ACAAAATTTTAGCC
* * *
15879 TAAATCGTGTAATAATCAT-AC-AGTTTTTGGCTAAAAAAGCG-TTCTGGGGCACCGGCTCAGTT
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTC-AGGGCACCGGCTCAGTT
15941 TTGCTTGATTTTTTGC-ACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCA
65 TTGCTTGATTTTTTGCGAC-AAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCA
** * *
16005 CATAAGACTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAAT
129 CATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAAT
* * * * * * *
16070 TCATGAAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCCTCCAATATTTTTGGCATTAA
194 TC-GGAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAGCCCTTCAATCTTTTTGGCGTTAA
* * * * *
16134 CTTGTATATATTTTATGAGTATTTTA-TCCAAAAATTGAGGAAATATTTTTCGGGTCATTTTTTT
257 -TTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCA-ATTTTT
* *
16198 GCAAAATTTTAG-A
320 ACAAAATTTTAGCC
* * * * * ** * *
16211 GAAAATCGTGTAACAATCATCACAGATTTTTTTTTTTTAGCTGAAATCGCATCTT-AAGGC-CTC
1 G-AAATCGTGTAATAACCATCAC-GA------GTTTTTGGCTAAAAAAGCGT-TTCAGGGCAC-C
* * * * * * * * **
16274 TGCTCAGTTTTGCATGATTTTTGGTGTCGAGACTCCTTGAAATATCCATATTCATGTAAAAAAAT
56 GGCTCAGTTTTGCTTGATTTTTTGCGACAAGACTCCTTGAGATATCCATATTCATCTAATCAAAT
* * * * * *
16339 CTCAGCTACATTGCAATTTAGAATTTGTTTTTACAAGCATTTGAATATTGTTTCGATTTAATTAG
121 CTCAGCCACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAA
* * * *
16404 AAATTAGTTCTGAAAAAATAGGAAAAGACGATATTTAGAAACGTTAAAAGCCCTTCAATCTTTGT
186 AAATTAATTCGGAAAAAATAGGAAAA-ACGATA-TTAGAAACGTCAAAAGCCCTTCAATCTTTTT
* * * *
16469 GGCATTGAATTAAATATTTTTTATGAGTATTTTAGCCAGAAAAAAATTTGAGAAAATATTTTTCG
249 GGCGTT-AATTATATATTTTTTATGAGTATTTTAGCC---CAAAAATTT-AGGAAATATTTTTCG
*
16534 GGTCAATTTTCACAAAATTTTAGCC
309 GGTCAATTTTTACAAAATTTTAGCC
* * * * * * * *
16559 AAAATCATTTAATAAACATCAC-AGTTTTTAGCTAAAAAAGTGTTGC-GGG-A---GCTCATTTT
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGTTT
*
16618 TGCTTGATTTTTTGCGCCAAGACT-CTTAGAGATATCCATATTCATCTAATCAAATCTCAGCCAC
66 TGCTTGATTTTTTGCGACAAGACTCCTT-GAGATATCCATATTCATCTAATCAAATCTCAGCCAC
* * * *
16682 ATTGGATTTAAGAATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAAAAATTAATT
130 ATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAATT
* * * ** *
16747 CAGAAAAAATATG-AAAACGATATTA-AAGGA-GTGAAAATTCCTTCAATCTTTTTGACGTTAAG
195 CGGAAAAAATAGGAAAAACGATATTAGAA--ACGTCAAAAGCCCTTCAATCTTTTTGGCGTTAA-
* * ** * ** * * * *
16809 TTATATA--TATTCTGAGTATTTTA-TAC-AAAATTT-GAGAAAAAAATTCCGAGTCATTTTTTG
257 TTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAG-GAAATATTTTTCGGGTCAATTTTTA
* *
16869 TAAAATTTTAGTC
321 CAAAATTTTAGCC
* * ** * * *
16882 GAAATCGTG---T-ACTATCATG-GTTTTCAGCTAAAAAACGCATTTC-GGGGATCCGGCTCAAT
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAA-GCGTTTCAGGGCA-CCGGCTCAGT
* ** * * * ***
16941 TTTGCATGATTTTTCAC-ACCGAGACTACTTGAAATATATGTATTCATCTAATCAAATCTCAGCC
64 TTTGCTTGATTTTTTGCGA-CAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCC
* * *
17005 ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAA
128 ACATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAA
* * * *
17070 TTCGGAAAAAATAGGGAAAACGATATTAGAAACGTCAAAAGCCCTTCAATATTTTTGACATTGAA
193 TTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCGTT-AA
* * * * *
17135 TTATATATTTTTTATAAGTATTTTTGCCAAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTAC
257 TTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTTAC
* *
17200 AAAATGTTAGCT
322 AAAATTTTAGCC
** * * * * * *
17212 GAAATCGTGTAATAATTATCAC-AGATTTTAGCTAAAAAAGCATTTTAGGGCCCCGGCTCAATTT
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGTTT
* * * *
17276 TGCTTGATTTTTTGCGCCAAGACT-TTTGGAGATATCCATATTCGTCTAATCAAATCTCAGTCAC
66 TGCTTGATTTTTTGCGACAAGACTCCTT-GAGATATCCATATTCATCTAATCAAATCTCAGCCAC
** * * * *
17340 ATTGGATTGAAGAATTTGTTTTTACGAGAATCTGAATTTTGTTTCGATTTAATTATAAACTAATT
130 ATTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAATT
* * * *
17405 CAG-AAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCCC--CAAAT-ATTTTGGCGTTAA
195 CGGAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAG-CCCTTC-AATCTTTTTGGCGTT-A
** * * * **
17465 ATTAT-TCATAGTTTATGAGTATTTTA-TCCAAAAATTGAGGAAAAAATTTTT-TAGTCAATTTT
256 ATTATAT-ATTTTTTATGAGTATTTTAGCCCAAAAATTTAGG-AAATATTTTTCGGGTCAA-TTT
*
17527 TTGCAAAATTTTAGCC
318 TTACAAAATTTTAGCC
* * * * * * * * *
17543 AAAATCTTGTACTAACAATCAC-AGGTTTTTTTTTTTTGCTAAAAACGCATTTTAAGGC-CTCGG
1 GAAATCGTGTAATAACCATCACGA-G------TTTTTGGCTAAAAAAGCGTTTCAGGGCAC-CGG
* ** ** * * ** *
17606 CTCAGTTTTG-TATCATTTTAAGCTCCGAGACT-CTCTGAAATATTTATATTCATCTAACCAAAT
58 CTCAGTTTTGCT-TGATTTTTTGCGACAAGACTCCT-TGAGATATCCATATTCATCTAATCAAAT
* * *
17669 CTCAGCCACATTGGA-TTTATGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA
121 CTCAGCCACATTGGATTTTA-GAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTA
* * ** *
17733 AAAATTAATTCGG-AAAAATAGGATAAACAATATTAGATGCGTTAAAAGCCCTTCAATCTTTTTG
185 AAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTG
** * * *
17797 AAGTCGAATTATATATTTTTTA--AGTATTTTAG-CCAAAAATTAAGGAAATATCTTTCGGGT-A
250 GCGT-TAATTATATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCA
*
17858 AGTTTTTGCAAAATTTTAGCC
314 A-TTTTTACAAAATTTTAGCC
* * *
17879 GAAATCGTGTACTAACCATCAC-AGTTTTT-GATAAAAACGCGTTTC
1 GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTC
17924 GAGGATATAT
Statistics
Matches: 3337, Mismatches: 533, Indels: 337
0.79 0.13 0.08
Matches are distributed among these distances:
319 20 0.01
320 12 0.00
321 136 0.04
322 6 0.00
323 33 0.01
324 11 0.00
325 231 0.07
326 53 0.02
327 16 0.00
328 26 0.01
329 20 0.01
330 79 0.02
331 168 0.05
332 341 0.10
333 777 0.23
334 634 0.19
335 204 0.06
336 58 0.02
337 30 0.01
338 170 0.05
339 36 0.01
340 1 0.00
341 16 0.00
342 141 0.04
343 51 0.02
344 8 0.00
345 1 0.00
347 39 0.01
348 19 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (333 bp):
GAAATCGTGTAATAACCATCACGAGTTTTTGGCTAAAAAAGCGTTTCAGGGCACCGGCTCAGTTT
TGCTTGATTTTTTGCGACAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACA
TTGGATTTTAGAATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATTAATTC
GGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCGTTAATTAT
ATATTTTTTATGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTTACAAAA
TTTTAGCC
Found at i:15341 original size:667 final size:665
Alignment explanation
Indices: 13572--17921 Score: 4941
Period size: 667 Copynumber: 6.5 Consensus size: 665
13562 TGTACTAACT
* * * * * ** * *
13572 ATCACGGTTTTTTGGCTAGAAATGCATTTCAGGGCCCCTACTCAGTTTTGCACGA-TTTTTGACG
1 ATCACAGTTTTTTGGCTAAAAACGCGTTTCAAGG-CCCGGCTCAGTTTTGCATGATTTTTTG-CA
* * * *
13636 CCGAGACTCCATGAAATATCCATATTCATGTGAAAATATCTCAGCCACATTGCAATTTAGAATTT
64 CCGAGACTCCTTGAAATATCCATATTCATTTAAAAAAATCTCAGCCACATTGCAATTTAGAATTT
*
13701 GTTTTTACGAGCATTTGAATATTCTTTCGATTCAATTAGAAATTAATTCGGAAAAAATAGGAAAA
129 GTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAA
* *
13766 ACGATATT-GAAAACGTCAAAAGCCCTCCAATCTTTTTGGCAACTAATTATATATTTTTTACGAG
194 ACGATATTAG-AAACGTCAAAAGCCCTTCAATCTTTTTGGCATCTAATTATATATTTTTTACGAG
* *
13830 TATTTTAGCCCAAAAATTTAAGAAATA-TTTTCGGATCAATTTTCACAAAATTTTAGCCGAAATC
258 TATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATC
* * *
13894 GTGTATATAACCAAT-ACAGTTTTTGGCTAAAAAAACGTTCTAGGGCACCAGCTCAGTTTTGCTT
323 GTGTA-ATAACC-ATCACAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTT
*
13958 GATTTTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATGGA
386 GATTTTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAGA
* * *
14023 TTTTAGAATTTCTTTTTGCGAGCATCTGAATCTTGTTTCGATTTAATTAAAAACTAATTCAGAAA
451 TTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAA
* * ** * *
14088 AAATATGAAAAATGATATTAAAAGCGCGAAAAGTCCTCCAATCTTTTTGGTGTTAAATTGTAAAT
516 AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATAT
* * * * **
14153 ATTTTATGAGTATTTT-CTCAAAAAAATGAGGAAATATTTTTCGGGTAAATTTTTTAAAAATTTT
581 ATTTTATGAGTATTTTAC-CCAAAAATTGAGGAAATATTTTTCGAGTCAATTTTTGCAAAATTTT
* *
14217 AGCCAAAATCGTGTAGT-ACC
645 AGCCAAAATCGTGTAATAATC
* ** *
14237 ATCAC-GATTTTAATGGCTAAAAACGCGTTTCAAGGCTCCTACTCAGTTTTGCATGATTTTTTAC
1 ATCACAG-TTTT-TTGGCTAAAAACGCGTTTCAAGGC-CCGGCTCAGTTTTGCATGATTTTTTGC
** * ** * * *
14301 GTCGGGACAACTTGAAATATCCATATTCATGTAAAAAAAATCTCAGCCACATTGCAGTATAGAAT
63 ACCGAGACTCCTTGAAATATCCATATTCAT-TTAAAAAAATCTCAGCCACATTGCAATTTAGAAT
* *
14366 TTGTTTTTACAAGCATTTGAATATTCTTTCGATTTAATTAAAAATTAATTCGGAAAAAATAGGAA
127 TTGTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAA
* *
14431 AAACGATATTAGAAACGTCAAAA-CCCTTCAATCATTTTGGCGTCTAATTATATATTTTTTACGA
192 AAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCATCTAATTATATATTTTTTACGA
* * *
14495 GTATTTTAGCCCAAAAATTTAAGAAATATTTTTCAGGTCAATTTTCACAAAAATTTAGCCGAAAT
257 GTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAAT
*
14560 CGTGTAATAACCAT-ACCAGTTTTTGGCTAAAAAAGCGTTCCGGGGCACCGGCTCAGTTTTGCTT
322 CGTGTAATAACCATCA-CAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTT
*
14624 GATTTTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAAA
386 GATTTTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAGA
* * * * * *
14689 TTTTAGAATTTTTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAA
451 TTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAA
* * * * * * ** * *
14754 AAATAGGGAAAACGATATTGAAATCGTCAAAAGCCCTTTAATCTTTTTGGCATTTAATCATATAT
516 AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATA-
* ** * * * **
14819 TTTTTTACAAGTATTTTAGCCCAAAAATTTAGGAAGTATTTTTCGAGTCAACTTTCACAAAATTT
580 TATTTTATGAGTATTTTA-CCCAAAAATTGAGGAAATATTTTTCGAGTCAATTTTTGCAAAATTT
**
14884 TAGCTGAAATCGTGTAATAATC
644 TAGCCAAAATCGTGTAATAATC
* * * *
14906 AAT-ACAG-TTTTTGGCTAAAAAAGCGTTCCAGGGCACCGGCTCAGTTTTGCTTGATTTTTTGCA
1 -ATCACAGTTTTTTGGCTAAAAACGCGTTTCAAGGC-CCGGCTCAGTTTTGCATGATTTTTTGCA
** * ** * * *
14969 CAAAGACTCCTTGAGATATCCATATTCATTTAATCAAATCTCAGCCGCAATAG-ATTTTAGAATT
64 CCGAGACTCCTTGAAATATCCATATTCATTTAAAAAAATCTCAGCCAC-ATTGCAATTTAGAATT
* * *
15033 TGTTTTTACGATCATCTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGAA
128 TGTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATAGGAA
* *
15098 AAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCGTATAATTATATATTTTTTACGA
192 AAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCATCTAATTATATATTTTTTACGA
*
15163 TTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCAC-AAATTTTAGCCGAAAT
257 GTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAAT
* *
15227 CGTGTAATAACCATCATAGTTTTTGGCTAAAAAAGCGTTCTGGGGCATCGGCTCAGTTTTGCTTG
322 CGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTG
15292 ATTATTTT-CACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAGA
387 ATT-TTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAGA
* *
15356 TTTTAGAATTTTTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAAAAATTAAATT-AGAA
451 TTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATT-AATTCAGAA
* * * * *
15420 AAAATATGAAAAACGATATTAAAATCGTGAAAAGTCCTCCAATATTTTTGGTATTAAATTGTAAA
515 AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATA
* * * *
15485 TATTTTATGAGTATTTT-CTCAAAAAATTGA-GAAATTATTTTTCGGGTCACTTTTTTCAAAATT
580 TATTTTATGAGTATTTTAC-CCAAAAATTGAGGAAA-TATTTTTCGAGTCAATTTTTGCAAAATT
*
15548 TTAGCCAAAATCGTGTATTAATC
643 TTAGCCAAAATCGTGTAATAATC
* * ** *
15571 ATCACGGTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCCCAACTCAGTTTTGCATGA-TTTTAG-
1 ATCACAG--TTTTTTGGCTAAAAACGCGTTTCAAGG-CCCGGCTCAGTTTTGCATGATTTTTTGC
* * *
15634 ACGGCAAGACTGCTTGAAATATCCATATTCATGTAAAAAAATCTCAGCCACATTGCAATTTAGAA
63 AC--CGAGACTCCTTGAAATATCCATATTCATTTAAAAAAATCTCAGCCACATTGCAATTTAGAA
* *
15699 TTTGTTTTTACGAGCATTTGAATATTCTTTCGATTTGATTTGAAATTAATTC---------A-GA
126 TTTGTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGA
*
15754 AAAAAGATATTAGAAACGTCAAAA-CCTCTTCAATCTTTTTGGCATCTAATTATATATTTTTTAC
191 AAAACGATATTAGAAACGTCAAAAGCC-CTTCAATCTTTTTGGCATCTAATTATATATTTTTTAC
* * *
15818 GAGTATTTTAGCCCAATAATTTAGGAAATA-TATTCGGGTCAATTTTCACAAAATTTTAGCCTAA
255 GAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAA
*
15882 ATCGTGTAATAATCAT-ACAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCT
320 ATCGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCT
15946 TGATTTTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCAC-ATAA
385 TGATTTTTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAAT-A
*
16010 GACTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCATG
449 GATTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCA-G
* * *
16075 AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCATTAACTTGTA
513 AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATA
* * *
16140 TATATTTTATGAGTATTTTATCCAAAAATTGAGGAAATATTTTTCGGGTCATTTTTTTGCAAAAT
578 TATATTTTATGAGTATTTTACCCAAAAATTGAGGAAATATTTTTCGAGTCA-ATTTTTGCAAAAT
** *
16205 TTTAGAGAAAATCGTGTAACAATC
642 TTTAGCCAAAATCGTGTAATAATC
* * * * *
16229 ATCACAGATTTTTTTTTTTTAGCTGAAATCGCATCTT-AAGGCCTCTGCTCAGTTTTGCATGATT
1 ATCACAG-------TTTTTTGGCTAAAAACGCGT-TTCAAGGCC-CGGCTCAGTTTTGCATGATT
* *** * *
16293 TTTGGTGTCGAGACTCCTTGAAATATCCATATTCATGTAAAAAAATCTCAGCTACATTGCAATTT
57 TTTTGCACCGAGACTCCTTGAAATATCCATATTCATTTAAAAAAATCTCAGCCACATTGCAATTT
* * * *
16358 AGAATTTGTTTTTACAAGCATTTGAATATTGTTTCGATTTAATTAGAAATTAGTTCTGAAAAAAT
122 AGAATTTGTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAAT
* * *
16423 AGGAAAAGACGATATTTAGAAACGTTAAAAGCCCTTCAATCTTTGTGGCAT-TGAATTAAATATT
187 AGGAAAA-ACGATA-TTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCATCT-AATTATATATT
* * *
16487 TTTTATGAGTATTTTAGCCAGAAAAAAATTTGAGAAAATATTTTTCGGGTCAATTTTCACAAAAT
249 TTTTACGAGTATTTTAGCC---CAAAAATTT-AGGAAATATTTTTCGGGTCAATTTTCACAAAAT
* * * * * *
16552 TTTAGCCAAAATCATTTAATAAACATCACAGTTTTTAGCTAAAAAAGTG-T-TGCGGG-A---GC
310 TTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTTCTG-GGGCACCGGC
* * *
16611 TCATTTTTGCTTGATTTTTTGCGCCAAGACT-CTTAGAGATATCCATATTCATCTAATCAAATCT
374 TCAGTTTTGCTTGATTTTTTGCACAAAGACTCCTT-GAGATATCCATATTCATCTAATCAAATCT
* * * * *
16675 CAGCCACATTGGATTTAAGAATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAAAA
438 CAGCCACAATAGATTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAA
* * * * * *
16740 ATTAATTCAGAAAAAATATG-AAAACGATATTAAAGGAGTGAAAATTCCTTCAATCTTTTTGACG
503 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCA
* * ** * * ** * *
16804 TTAAGTTATATATA--TTCTGAGTATTTTATACAAAATTTGA-GAAAAAAATTCCGAGTCATTTT
568 TTAAATTATATATATTTTATGAGTATTTTACCCAAAAATTGAGGAAATATTTTTCGAGTCAATTT
* * * *
16866 TTGTAAAATTTTAGTCGAAATCGTGTACT-ATC
633 TTGCAAAATTTTAGCCAAAATCGTGTAATAATC
* ** * ** * * **
16898 AT----GGTTTTCAGCTAAAAAACGCATTTCGGGGATCCGGCTCAATTTTGCATGATTTTTCACA
1 ATCACAGTTTTTTGGCT-AAAAACGCGTTTCAAGG-CCCGGCTCAGTTTTGCATGATTTTTTGCA
* *** * ** * *
16959 CCGAGACTACTTGAAATATATGTATTCATCTAATCAAATCTCAGCCACATTG-GATTTAAGGATT
64 CCGAGACTCCTTGAAATATCCATATTCATTTAAAAAAATCTCAGCCACATTGCAATTT-AGAATT
* * *
17023 TGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGGAA
128 TGTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAA
* * **
17088 AACGATATTAGAAACGTCAAAAGCCCTTCAATATTTTTGACAT-TGAATTATATATTTTTTATAA
193 AACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCATCT-AATTATATATTTTTTACGA
* * * * * * *
17152 GTATTTTTGCCAAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATGTTAGCTGAAAT
257 GTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAAT
** * * * * * * *
17217 CGTGTAATAATTATCACAGATTTTAGCTAAAAAAGCATTTTAGGGCCCCGGCTCAATTTTGCTTG
322 CGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTG
* * * * * * *
17282 ATTTTTTGCGCCAAGACT-TTTGGAGATATCCATATTCGTCTAATCAAATCTCAGTCACATTGGA
387 ATTTTTTGCACAAAGACTCCTT-GAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAGA
** * * * *
17346 TTGAAGAATTTGTTTTTACGAGAATCTGAATTTTGTTTCGATTTAATTATAAACTAATTCAG-AA
451 TTTTAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAA
* *
17410 AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC-CCAAAT-ATTTTGGCGTTAAATTAT-TC
516 AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC-AATCTTTTTGGCATTAAATTATAT-
* * * *
17472 ATAGTTTATGAGTATTTTATCCAAAAATTGAGGAAAAAATTTTT-TAGTCAATTTTTTGCAAAAT
579 ATATTTTATGAGTATTTTACCCAAAAATTGAGG-AAATATTTTTCGAGTCAA-TTTTTGCAAAAT
* *
17536 TTTAGCCAAAATCTTGTACTAA-C
642 TTTAGCCAAAATCGTGTAATAATC
* * * * *
17559 AATCACAGGTTTTTTTTTTTTGCTAAAAACGCATTTTAAGGCCTCGGCTCAGTTTTGTATCATTT
1 -ATCACA-G-----TTTTTTGGCTAAAAACGCGTTTCAAGGCC-CGGCTCAGTTTTGCATGATTT
** * ** * ** *
17624 TAAGCTCCGAGACT-CTCTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTG-GATTT
58 TTTGCACCGAGACTCCT-TGAAATATCCATATTCATTTAAAAAAATCTCAGCCACATTGCAATTT
* * * * * *
17687 ATGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCGG-AAAAA
122 A-GAATTTGTTTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* * ** * * *
17751 TAGGATAAACAATATTAGATGCGTTAAAAGCCCTTCAATCTTTTT-GAAGTCGAATTATATATTT
186 TAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCA-TCTAATTATATATTT
* * **
17815 TTTA--AGTATTTTAG-CCAAAAATTAAGGAAATATCTTTCGGGT-AAGTTTTTGCAAAATTTTA
250 TTTACGAGTATTTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAA-TTTTCACAAAATTTTA
* * *
17876 GCCGAAATCGTGTACTAACCATCACAGTTTTT-GATAAAAACGCGTT
314 GCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTT
17922 TCGAGGATAT
Statistics
Matches: 3194, Mismatches: 384, Indels: 213
0.84 0.10 0.06
Matches are distributed among these distances:
653 69 0.02
654 12 0.00
655 11 0.00
656 178 0.06
657 310 0.10
658 219 0.07
659 163 0.05
660 7 0.00
661 36 0.01
662 5 0.00
663 142 0.04
664 14 0.00
665 69 0.02
666 446 0.14
667 585 0.18
668 292 0.09
669 12 0.00
670 94 0.03
671 152 0.05
672 31 0.01
673 5 0.00
674 55 0.02
675 73 0.02
676 127 0.04
677 1 0.00
678 7 0.00
679 10 0.00
680 49 0.02
681 20 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (665 bp):
ATCACAGTTTTTTGGCTAAAAACGCGTTTCAAGGCCCGGCTCAGTTTTGCATGATTTTTTGCACC
GAGACTCCTTGAAATATCCATATTCATTTAAAAAAATCTCAGCCACATTGCAATTTAGAATTTGT
TTTTACGAGCATTTGAATATTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAAC
GATATTAGAAACGTCAAAAGCCCTTCAATCTTTTTGGCATCTAATTATATATTTTTTACGAGTAT
TTTAGCCCAAAAATTTAGGAAATATTTTTCGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTG
TAATAACCATCACAGTTTTTGGCTAAAAAAGCGTTCTGGGGCACCGGCTCAGTTTTGCTTGATTT
TTTGCACAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAATAGATTTTA
GAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATA
TGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTT
ATGAGTATTTTACCCAAAAATTGAGGAAATATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCAA
AATCGTGTAATAATC
Found at i:53801 original size:18 final size:18
Alignment explanation
Indices: 53780--53838 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
53770 TTACATACAT
53780 TTATTTGTAATCATAAAA
1 TTATTTGTAATCATAAAA
* * * *
53798 TTATTT-T-TTTACTACAT
1 TTATTTGTAATCA-TAAAA
53815 TTATTTGTAATCATAAAA
1 TTATTTGTAATCATAAAA
53833 TTATTT
1 TTATTT
53839 TTTTCTTCTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 2 0.07
17 10 0.33
18 16 0.53
19 2 0.07
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATTTGTAATCATAAAA
Found at i:53821 original size:35 final size:36
Alignment explanation
Indices: 53770--53842 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 36
53760 AAGCATTAGC
53770 TTACATACATTTATTTGTAATCATAAAATTATTTTT
1 TTACATACATTTATTTGTAATCATAAAATTATTTTT
53806 TTAC-TACATTTATTTGTAATCATAAAATTATTTTT
1 TTACATACATTTATTTGTAATCATAAAATTATTTTT
53841 TT
1 TT
53843 CTTCTTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 33 0.89
36 4 0.11
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (36 bp):
TTACATACATTTATTTGTAATCATAAAATTATTTTT
Found at i:72354 original size:20 final size:19
Alignment explanation
Indices: 72319--72358 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
72309 TAAAGATTTG
*
72319 ATTAGTTTAGTTTTAATTA
1 ATTAGTTTAGTATTAATTA
72338 ATTAGTATTAGTATTAATTA
1 ATTAGT-TTAGTATTAATTA
72358 A
1 A
72359 ACCCACTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (19 bp):
ATTAGTTTAGTATTAATTA
Found at i:80804 original size:13 final size:13
Alignment explanation
Indices: 80772--80800 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
80762 TGAATTAATG
80772 AATTAGTATAAAA
1 AATTAGTATAAAA
80785 AATTAGTA-AAAA
1 AATTAGTATAAAA
80797 AATT
1 AATT
80801 TAGTTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
AATTAGTATAAAA
Found at i:82154 original size:18 final size:18
Alignment explanation
Indices: 82133--82174 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
82123 TGTGTCACCG
82133 GTGAAATCTGTGGCAGCT
1 GTGAAATCTGTGGCAGCT
*
82151 GTGAAATCTGTGTCAGCT
1 GTGAAATCTGTGGCAGCT
82169 GTGAAA
1 GTGAAA
82175 GGAGCATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (18 bp):
GTGAAATCTGTGGCAGCT
Found at i:87226 original size:19 final size:19
Alignment explanation
Indices: 87204--87241 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
87194 GAATTTTATG
87204 TTGGCAAAACCTTTCTATA
1 TTGGCAAAACCTTTCTATA
87223 TTGGCAAAACCTTTCTATA
1 TTGGCAAAACCTTTCTATA
87242 ATCAACTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
TTGGCAAAACCTTTCTATA
Done.