Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015079.1 Corchorus capsularis cultivar CVL-1 contig15100, 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: 91956
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:14369 original size:21 final size:21
Alignment explanation
Indices: 14345--14388 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
14335 TTATTGGGGG
*
14345 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
14366 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
14387 TT
1 TT
14389 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:14483 original size:33 final size:33
Alignment explanation
Indices: 14436--14662 Score: 298
Period size: 33 Copynumber: 6.9 Consensus size: 33
14426 TTTGCCCTTA
14436 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* *
14469 GCCACGGCGAAGCCTCCCCACTAAGG-TGGCTCT
1 GCCACGGCGGAGCCTCCCCACT-AGGACGGCTCT
*
14502 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* * *
14535 GCCAGGGTGGAGCCTCCCCACTAGGGCGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* *
14568 GCCACGGCGGAGCCGCCCCATTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* *
14601 GCCACGGC-TAGCCGCCCCACTAGGACGGCT-T
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* * *
14632 AGCCACAGCGGAGCCGCCCCACTAGGGCGGC
1 -GCCACGGCGGAGCCTCCCCACTAGGACGGC
14663 AAGGCTTTTT
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
31 1 0.01
32 30 0.17
33 140 0.80
34 3 0.02
ACGTcount: A:0.15, C:0.41, G:0.32, T:0.12
Consensus pattern (33 bp):
GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
Found at i:14767 original size:32 final size:33
Alignment explanation
Indices: 14726--14787 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
14716 TTAGTACCGA
14726 TGCCGCCCCAGG-GGGCGGCCTGGCCATGGTAG
1 TGCCGCCCCAGGAGGGCGGCCTGGCCATGGTAG
*
14758 TGCCGCCCCAGGAGGGCGGCTTGGCCATGG
1 TGCCGCCCCAGGAGGGCGGCCTGGCCATGG
14788 CTCAGCCGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.10, C:0.34, G:0.44, T:0.13
Consensus pattern (33 bp):
TGCCGCCCCAGGAGGGCGGCCTGGCCATGGTAG
Found at i:15505 original size:11 final size:13
Alignment explanation
Indices: 15473--15511 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
15463 TAGATAATAT
15473 ATAATATAATTAA
1 ATAATATAATTAA
15486 ATAATATAATT-A
1 ATAATATAATTAA
*
15498 AT-ATATAATAAA
1 ATAATATAATTAA
15510 AT
1 AT
15512 TGAATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATTAA
Found at i:15612 original size:21 final size:22
Alignment explanation
Indices: 15574--15617 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
15564 AATCTTTTTA
15574 TCACAATTTGATTTCATTTAAT
1 TCACAATTTGATTTCATTTAAT
*
15596 TCACAATTTTA-TTCATTTAAT
1 TCACAATTTGATTTCATTTAAT
15617 T
1 T
15618 TTTATAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (22 bp):
TCACAATTTGATTTCATTTAAT
Found at i:38308 original size:22 final size:22
Alignment explanation
Indices: 38283--38831 Score: 187
Period size: 22 Copynumber: 25.2 Consensus size: 22
38273 ATGATTTCTT
38283 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
38305 TATGAAATTTTAATAACGTTAC
1 TATGAAATTTTGATAACCTTCC
* * * **
38327 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** **
38349 TAT--AATTTTTTTAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* *
38369 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
38391 TAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
38413 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
38435 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* ** *
38458 TATGAGATGCTGATAATC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * **
38479 ATATGATATATTGATAACCATGT
1 -TATGAAATTTTGATAACCTTCC
* * *
38502 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
38523 ATATG-AATTGTT-AGTAATCACATT--
1 -TATGAAATT-TTGA-TAA-C-C-TTCC
* *
38547 T-TGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
38568 TATGAAATTGTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
38590 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
38613 AATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
38636 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
*
38657 TTATGAAATCTTGATAA-----C
1 -TATGAAATTTTGATAACCTTCC
* *
38675 TA-CAAATTTTGATAATC-TCTC
1 TATGAAATTTTGATAACCTTC-C
** *
38696 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
38718 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * **
38740 TATGAAATCTTGATCTA-CATAG
1 TATGAAATTTTGAT-AACCTTCC
* * *
38762 TATGGAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
38784 TATGAAAATTTGA-AA-ATAAAC
1 TATGAAATTTTGATAACCT-TCC
*
38805 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
38827 TATGA
1 TATGA
38832 TCCTCCTTGA
Statistics
Matches: 385, Mismatches: 103, Indels: 78
0.68 0.18 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 17 0.04
21 30 0.08
22 255 0.66
23 65 0.17
24 3 0.01
26 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:38620 original size:23 final size:23
Alignment explanation
Indices: 38594--38656 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
38584 CCTCGTTATG
*
38594 AAATTTTGATAAACCTTCCAATA
1 AAATTTTGATAAACCTCCCAATA
*
38617 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCAATA
38640 AAATTTTGAT-AACCTCC
1 AAATTTTGATAAACCTCC
38657 TTATGAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 7 0.18
23 31 0.82
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCAATA
Found at i:38753 original size:44 final size:44
Alignment explanation
Indices: 38282--38823 Score: 270
Period size: 44 Copynumber: 12.5 Consensus size: 44
38272 TATGATTTCT
* * * *
38282 TTATGAAATTTTGATAACCTTCCTATGAAATTTTAATAACGTTA
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * * * *** ** **
38326 CTATGGAATTTCGAGAACCTTTTTAT--AATTTTTTTAACCTTT
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * *
38368 TTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA-AGACCTCA
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATA-ACCTCA
* * * *
38412 CTATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACA
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCA
* * ** * * * * *
38457 CTATGAGATGCTGATAATCTCCATATGATATATTGATAACCAT-G
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCA
* * * * * *
38501 TTATGAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCACA
1 TTATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAACCTCA
* * * * * *
38545 TTTTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCG
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * * *
38589 TTATGAAATTTTGATAAACCTTCCAATAAAATTTTGATAAACCTCC
1 TTATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACCTCA
* * * *
38635 CTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAA---C-
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * * **
38675 -TA-CAAATTTTGATAATCTCTCTATGATTTTTTGATAACCTCA
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
* * * * *
38717 TTATGAAATTTTGTTAATCTCCCTATGAAATCTTGATCTACAT-A
1 TTATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACCTCA
* * * * * *
38761 GTATGGAATTTTGATAACC-CTCTTATGAAAATTTGA-AA-ATAAA
1 TTATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACCT-CA
*
38804 CTATGAAATTTTGATAACCT
1 TTATGAAATTTTGATAACCT
38824 TCATATGATC
Statistics
Matches: 368, Mismatches: 107, Indels: 46
0.71 0.21 0.09
Matches are distributed among these distances:
38 28 0.08
39 2 0.01
41 4 0.01
42 30 0.08
43 25 0.07
44 184 0.50
45 76 0.21
46 19 0.05
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (44 bp):
TTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA
Found at i:41256 original size:22 final size:22
Alignment explanation
Indices: 41231--41416 Score: 155
Period size: 22 Copynumber: 8.5 Consensus size: 22
41221 AATCACATTT
* *
41231 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
41253 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
41275 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
41297 TGAAATTTTTATAACCTCACTT
1 TGAAATTTTGATAACCTCTCTA
*
41319 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
41341 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTCTA
* * *
41365 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
41387 TGAGA-TTTGATAACCT-TTTA
1 TGAAATTTTGATAACCTCTCTA
*
41407 TCAAATTTTG
1 TGAAATTTTG
41417 GTACTCTTTG
Statistics
Matches: 127, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
20 6 0.05
21 24 0.19
22 80 0.63
24 5 0.04
25 12 0.09
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:41806 original size:22 final size:22
Alignment explanation
Indices: 41605--41917 Score: 142
Period size: 22 Copynumber: 14.1 Consensus size: 22
41595 AGACTTTTAC
* *
41605 AACCTTCATATGAAATTTTGAT
1 AACCTTCCTATGAAATTTTAAT
* * *
41627 AACAC--ACTAAGAAATTTTGAT
1 AAC-CTTCCTATGAAATTTTAAT
* *
41648 AACC-TCCTCATGAAATATTAGT
1 AACCTTCCT-ATGAAATTTTAAT
**
41670 AACC-T-C-ATGAAATTTTGTT
1 AACCTTCCTATGAAATTTTAAT
*
41689 AACC-ACACTATGAAATTCTT-AT
1 AACCTTC-CTATGAAATT-TTAAT
* *
41711 AACCTTGCTATGACAATCTCTTTGAT
1 AACCTTCCTATGA-AA--T-TTTAAT
* * * *
41737 AACCTTTCTATAAAATTGTGAT
1 AACCTTCCTATGAAATTTTAAT
* * * * * *
41759 AATCATACTATGGAATTTCAAA
1 AACCTTCCTATGAAATTTTAAT
*
41781 AACCTTCCTAAGAAATTTTAAT
1 AACCTTCCTATGAAATTTTAAT
*
41803 AACCTAATCCTATGAAATTTTGAT
1 AACCT--TCCTATGAAATTTTAAT
**
41827 AA-CTTCCATATGAAATTTTGGT
1 AACCTTCC-TATGAAATTTTAAT
* * * *
41849 AACCATACTATGGAATTTTGAT
1 AACCTTCCTATGAAATTTTAAT
*
41871 AACC-TCCTCATGAAATTATAAT
1 AACCTTCCT-ATGAAATTTTAAT
* * *
41893 AACCATCTTATAAAATTTTAAT
1 AACCTTCCTATGAAATTTTAAT
41915 AAC
1 AAC
41918 GACACAGAGA
Statistics
Matches: 224, Mismatches: 48, Indels: 38
0.72 0.15 0.12
Matches are distributed among these distances:
19 14 0.06
20 1 0.00
21 26 0.12
22 133 0.59
23 14 0.06
24 17 0.08
25 5 0.02
26 14 0.06
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (22 bp):
AACCTTCCTATGAAATTTTAAT
Found at i:41856 original size:90 final size:87
Alignment explanation
Indices: 41731--41917 Score: 205
Period size: 90 Copynumber: 2.1 Consensus size: 87
41721 TGACAATCTC
* *
41731 TTTGATAACCTTTCTATAAAATTGTGATAATCATACTATGGAATTTCAAAAACCTTCCT-AAGAA
1 TTTGATAA-CTTCCTATAAAATTGTGATAACCATACTATGGAATTTCAAAAACC-TCCTCAAGAA
* *
41795 ATTTTAATAACCTAATCCTATGAAAT
64 ATTATAATAACC--ATCCTATAAAAT
* * * ** * *
41821 TTTGATAACTTCCATATGAAATTTTGGTAACCATACTATGGAATTTTGATAACCTCCTCATGAAA
1 TTTGATAACTTCC-TATAAAATTGTGATAACCATACTATGGAATTTCAAAAACCTCCTCAAGAAA
*
41886 TTATAATAACCATCTTATAAAAT
65 TTATAATAACCATCCTATAAAAT
*
41909 TTTAATAAC
1 TTTGATAAC
41918 GACACAGAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
88 18 0.22
89 8 0.10
90 56 0.68
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (87 bp):
TTTGATAACTTCCTATAAAATTGTGATAACCATACTATGGAATTTCAAAAACCTCCTCAAGAAAT
TATAATAACCATCCTATAAAAT
Found at i:41869 original size:44 final size:44
Alignment explanation
Indices: 41605--41898 Score: 185
Period size: 44 Copynumber: 6.6 Consensus size: 44
41595 AGACTTTTAC
* * * *
41605 AACCTTCATATGAAATTTTGATAA-CACACTAAGAAATTTTGAT
1 AACCTTCCTATGAAATTTTGATAACCATACTATGGAATTTTGAT
* * *
41648 AACC-TCCTCATGAAATATT-AGTAACC-T-C-ATGAAATTTTGTT
1 AACCTTCCT-ATGAAATTTTGA-TAACCATACTATGGAATTTTGAT
* * * *
41689 AACC-ACACTATGAAATTCTT-ATAACCTTGCTATGACAATCTCTTTGAT
1 AACCTTC-CTATGAAATT-TTGATAACCATACTATG-GAA--T-TTTGAT
* * * * ** *
41737 AACCTTTCTATAAAATTGTGATAATCATACTATGGAATTTCAAA
1 AACCTTCCTATGAAATTTTGATAACCATACTATGGAATTTTGAT
* * * *
41781 AACCTTCCTAAGAAATTTTAATAACCTAATCCTATGAAATTTTGAT
1 AACCTTCCTATGAAATTTTGATAACC--ATACTATGGAATTTTGAT
*
41827 AA-CTTCCATATGAAATTTTGGTAACCATACTATGGAATTTTGAT
1 AACCTTCC-TATGAAATTTTGATAACCATACTATGGAATTTTGAT
* *
41871 AACC-TCCTCATGAAATTATAATAACCAT
1 AACCTTCCT-ATGAAATTTTGATAACCAT
41899 CTTATAAAAT
Statistics
Matches: 193, Mismatches: 39, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
41 28 0.15
42 11 0.06
43 18 0.09
44 64 0.33
45 9 0.05
46 30 0.16
47 4 0.02
48 29 0.15
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (44 bp):
AACCTTCCTATGAAATTTTGATAACCATACTATGGAATTTTGAT
Found at i:42591 original size:17 final size:17
Alignment explanation
Indices: 42569--42615 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
42559 AAGAGATCAC
42569 AAATATTCAATTAAAAT-
1 AAATATT-AATTAAAATA
* *
42586 AAATATTTAAATAATATA
1 AAATA-TTAATTAAAATA
42604 AAATATTAATTA
1 AAATATTAATTA
42616 GAACTGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTAATTAAAATA
Found at i:44386 original size:40 final size:40
Alignment explanation
Indices: 44341--44416 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
44331 CAGGAATTGG
*
44341 GCTGTTTAATTCTAGAATTCAAGATACATAATATAGGTGA
1 GCTGTTTAATTCTACAATTCAAGATACATAATATAGGTGA
*
44381 GCTGTTTAATTCTACAATTCAAGATACATATTATAG
1 GCTGTTTAATTCTACAATTCAAGATACATAATATAG
44417 ATTAGCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (40 bp):
GCTGTTTAATTCTACAATTCAAGATACATAATATAGGTGA
Found at i:59490 original size:15 final size:16
Alignment explanation
Indices: 59461--59495 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
59451 AAATTCATTT
*
59461 ATTATGTTACTAATAA
1 ATTATGTTACAAATAA
59477 ATTAT-TTACAAATAA
1 ATTATGTTACAAATAA
59492 ATTA
1 ATTA
59496 GAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTATGTTACAAATAA
Found at i:61524 original size:103 final size:103
Alignment explanation
Indices: 61343--61542 Score: 339
Period size: 103 Copynumber: 1.9 Consensus size: 103
61333 AATTGTAGTC
* *
61343 TCACTCTTATTAGTATAAATAATAAACTATGAACAATGCCTGTAAGGGTAGGGCTTATGGATGGG
1 TCACTCTTATTAGTATAAATAATAAACTATGAACAAGGCCTGTAAGGGCAGGGCTTATGGATGGG
*
61408 CTAGTCAAGGTATATATTTTCGGTCTTTGGGGGTCGTA
66 CTAGTCAACGTATATATTTTCGGTCTTTGGGGGTCGTA
* *
61446 TCACTCTTATTAGTATAAATAATAAATTATGAACAAGGCCTGTAAGGGCAGGTG-TTTTGGATGG
1 TCACTCTTATTAGTATAAATAATAAACTATGAACAAGGCCTGTAAGGGCAGG-GCTTATGGATGG
61510 GCTAGTCAACGTATATATTTTCGGTCTTTGGGG
65 GCTAGTCAACGTATATATTTTCGGTCTTTGGGG
61543 CCCAATATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 90 0.99
104 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (103 bp):
TCACTCTTATTAGTATAAATAATAAACTATGAACAAGGCCTGTAAGGGCAGGGCTTATGGATGGG
CTAGTCAACGTATATATTTTCGGTCTTTGGGGGTCGTA
Found at i:65833 original size:96 final size:97
Alignment explanation
Indices: 65652--65978 Score: 480
Period size: 96 Copynumber: 3.4 Consensus size: 97
65642 CGTGACTATA
* * * * *
65652 GCTTGTACCAATACATAAATACAAATCAAAAGTTTCCCGGTTCAACGCAACTATATCCGGAATAG
1 GCTTGTACCAATAAAGAAATACAAATCAAAAGTTTCCCGATTCAACGCAACTAGATCCGGATTAG
65717 TTAAAATTCAATGTGAGTATAAGATATTGGGG
66 TTAAAATTCAATGTGAGTATAAGATATTGGGG
*
65749 GCTTGTACCAATAAAGAAATACAAATCAAAAGTTTCCC-ATGCAACGCAACTAGATCCGGATTAG
1 GCTTGTACCAATAAAGAAATACAAATCAAAAGTTTCCCGATTCAACGCAACTAGATCCGGATTAG
* * *
65813 TTAACATTTAGTGTGAGTATAAGATATTGGGG
66 TTAAAATTCAATGTGAGTATAAGATATTGGGG
* * **
65845 GCTTGTACCAATAAAGAAATACAAATCAAAAGTTTCCCGGTTCATCGCAACTAGATCTAGATTAG
1 GCTTGTACCAATAAAGAAATACAAATCAAAAGTTTCCCGATTCAACGCAACTAGATCCGGATTAG
* *
65910 TTAAAATTCAATATGAGTATAAGATATTAGGG
66 TTAAAATTCAATGTGAGTATAAGATATTGGGG
*
65942 GATTGTACCAAT-AAGAAATACAAATCATAAA-TTTCCC
1 GCTTGTACCAATAAAGAAATACAAATCA-AAAGTTTCCC
65979 AAATAGTCCG
Statistics
Matches: 208, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
96 110 0.53
97 98 0.47
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (97 bp):
GCTTGTACCAATAAAGAAATACAAATCAAAAGTTTCCCGATTCAACGCAACTAGATCCGGATTAG
TTAAAATTCAATGTGAGTATAAGATATTGGGG
Found at i:70371 original size:22 final size:22
Alignment explanation
Indices: 70345--70386 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
70335 GACAAACCTG
*
70345 TAACCCGAATGACCCGAGAAGT
1 TAACCCGAATGACCCAAGAAGT
70367 TAACCCGAATGACCCAAGAA
1 TAACCCGAATGACCCAAGAA
70387 TATTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGT
Found at i:72997 original size:15 final size:15
Alignment explanation
Indices: 72977--73005 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
72967 GCATTATGGG
72977 TTATGGGTTTTTCTT
1 TTATGGGTTTTTCTT
72992 TTATGGGTTTTTCT
1 TTATGGGTTTTTCT
73006 CCTCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (15 bp):
TTATGGGTTTTTCTT
Found at i:76292 original size:54 final size:55
Alignment explanation
Indices: 76202--76309 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 55
76192 TTTGGTAACA
*
76202 AAGAAATATTAAAAAAAATTAAAACTACCCAACGTGATAATTTTTCTCATCAAAT
1 AAGAAATATTAAAAAAAATTAAAACTACCCAACGTGATAAATTTTCTCATCAAAT
*
76257 AAGAAATATTCAAAAAAATT-AAACTACCCAACGTGATAAATTTTCTCATCAAA
1 AAGAAATATTAAAAAAAATTAAAACTACCCAACGTGATAAATTTTCTCATCAAA
76310 AGGTTAAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 32 0.63
55 19 0.37
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.28
Consensus pattern (55 bp):
AAGAAATATTAAAAAAAATTAAAACTACCCAACGTGATAAATTTTCTCATCAAAT
Found at i:76532 original size:23 final size:25
Alignment explanation
Indices: 76482--76539 Score: 93
Period size: 23 Copynumber: 2.4 Consensus size: 25
76472 TGCTTCGATT
*
76482 AAGAAGGCAATTTTTGTTTTAAAGG
1 AAGAAGGCAATTTTTGTTTAAAAGG
76507 AAGAAGGCAA-TTTT-TTTAAAAGG
1 AAGAAGGCAATTTTTGTTTAAAAGG
76530 AAGAAGGCAA
1 AAGAAGGCAA
76540 GATGTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 18 0.56
24 4 0.12
25 10 0.31
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.28
Consensus pattern (25 bp):
AAGAAGGCAATTTTTGTTTAAAAGG
Found at i:76547 original size:23 final size:23
Alignment explanation
Indices: 76496--76549 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
76486 AGGCAATTTT
* **
76496 TGTTTTAAAGGAAGAAGGCAATT
1 TGTTTAAAAGGAAGAAGGCAAGA
*
76519 TTTTTAAAAGGAAGAAGGCAAGA
1 TGTTTAAAAGGAAGAAGGCAAGA
76542 TGTTTAAA
1 TGTTTAAA
76550 TAATTATTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.30
Consensus pattern (23 bp):
TGTTTAAAAGGAAGAAGGCAAGA
Found at i:79179 original size:46 final size:46
Alignment explanation
Indices: 79126--79217 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
79116 TTTTCCTTGA
79126 ATATTTCCTTCTTACCATAAATCCCATGATTGATGCCTTAAATCAG
1 ATATTTCCTTCTTACCATAAATCCCATGATTGATGCCTTAAATCAG
79172 ATATTTCCTTCTTACCATAAATCCCATGATTGATGCCTTAAATCAG
1 ATATTTCCTTCTTACCATAAATCCCATGATTGATGCCTTAAATCAG
79218 TTTCACCATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (46 bp):
ATATTTCCTTCTTACCATAAATCCCATGATTGATGCCTTAAATCAG
Found at i:80161 original size:68 final size:68
Alignment explanation
Indices: 80087--80214 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 68
80077 ATTCCATATT
* * * *
80087 CAGCAAGGATCACAGCCATAAGTG-CTTTCCTTTTTTATGCTTCTAGCTTATGTAGCCCATCAAG
1 CAGCAAGGATCACAGCCAAAAGTGCCTTTCCTTTTGT-TGATTCTAGCCTATGTAGCCCATCAAG
80151 ATTC
65 ATTC
*
80155 CAGCAAGGATCGCAGCCAAAAGTGCCTTTCCTTTTGTTGATTCTAGCCTATGTAGCCCAT
1 CAGCAAGGATCACAGCCAAAAGTGCCTTTCCTTTTGTTGATTCTAGCCTATGTAGCCCAT
80215 TAAAAAAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 43 0.80
69 11 0.20
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (68 bp):
CAGCAAGGATCACAGCCAAAAGTGCCTTTCCTTTTGTTGATTCTAGCCTATGTAGCCCATCAAGA
TTC
Found at i:80333 original size:110 final size:110
Alignment explanation
Indices: 80175--80411 Score: 352
Period size: 110 Copynumber: 2.2 Consensus size: 110
80165 CGCAGCCAAA
* * *
80175 AGTGCCTTTCCTT-TTGTTGATTCTAGCCTATGTAGCCCATTAAAAAAATCTATATTTTGACTTG
1 AGTGCCCTTCCTTGTTGATGATTCTAGCCTATGTAGACCATTAAAAAAATCTATATTTTGACTTG
* * *
80239 GAG-TGAGTGTACCCATAGGAGTGCTGCACTGGTTGCACCTCCAGG
66 GAGCAG-GTGCACCCATAGGAGTGCTGCACTGATTGCACCTCCAGG
* *
80284 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGACCATTAAAAAAATTTATATTTTGACTTG
1 AGTGCCCTTCCTTGTTGATGATTCTAGCCTATGTAGACCATTAAAAAAATCTATATTTTGACTTG
* *
80349 GAGCAGGTGCACCCTTAGGAGTGTTGCACTGATTGCACCTCCAGG
66 GAGCAGGTGCACCCATAGGAGTGCTGCACTGATTGCACCTCCAGG
*
80394 AGTGCCCCTCCTTGTTGA
1 AGTGCCCTTCCTTGTTGA
80412 CGCCTATGCA
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
109 12 0.10
110 102 0.89
111 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (110 bp):
AGTGCCCTTCCTTGTTGATGATTCTAGCCTATGTAGACCATTAAAAAAATCTATATTTTGACTTG
GAGCAGGTGCACCCATAGGAGTGCTGCACTGATTGCACCTCCAGG
Found at i:80511 original size:29 final size:29
Alignment explanation
Indices: 80415--80517 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
80405 TTGTTGACGC
*
80415 CTATGCAGCTTTACAACGTCTACTACAGT
1 CTATGCAGCTTTACAACGCCTACTACAGT
* * * * *
80444 CTATGCAGCTTAAAAAAAAAGGCTTACTATCAGC
1 CTATGCAGCTT----TACAACGCCTACTA-CAGT
80478 CTATGCAGCTTTACAACGCCTACTACAGT
1 CTATGCAGCTTTACAACGCCTACTACAGT
80507 CTATGCAGCTT
1 CTATGCAGCTT
80518 AAAAAAAAGG
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
29 25 0.43
30 10 0.17
33 9 0.16
34 14 0.24
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (29 bp):
CTATGCAGCTTTACAACGCCTACTACAGT
Found at i:80578 original size:67 final size:67
Alignment explanation
Indices: 80413--80608 Score: 269
Period size: 63 Copynumber: 3.0 Consensus size: 67
80403 CCTTGTTGAC
*
80413 GCCTATGCAGCTTTACAACGTCTACTACAGTCTATGCAGCTTAAAAAAAAAGGCTTACTA----T
1 GCCTATGCAGCTTTACAACGCCTACTACAGTCTATGCAGCTT-AAAAAAAAGGCTTACTACGCCT
*
80474 -CA
65 ATA
80476 GCCTATGCAGCTTTACAACGCCTACTACAGTCTATGCAGCTTAAAAAAAAGGCTTACTACGCCTA
1 GCCTATGCAGCTTTACAACGCCTACTACAGTCTATGCAGCTTAAAAAAAAGGCTTACTACGCCTA
80541 TA
66 TA
* * * * * *
80543 GTCTATGCAGCTTTGCAACGCCTACTATAGCCTATGCAGCTT-AAAAAAGGGCTTACAACGCCTA
1 GCCTATGCAGCTTTACAACGCCTACTACAGTCTATGCAGCTTAAAAAAAAGGCTTACTACGCCTA
80607 TA
66 TA
80609 TTCATTCTAT
Statistics
Matches: 120, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
62 17 0.14
63 41 0.34
66 23 0.19
67 39 0.32
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (67 bp):
GCCTATGCAGCTTTACAACGCCTACTACAGTCTATGCAGCTTAAAAAAAAGGCTTACTACGCCTA
TA
Found at i:81068 original size:46 final size:48
Alignment explanation
Indices: 80921--81076 Score: 208
Period size: 49 Copynumber: 3.2 Consensus size: 48
80911 ACTCTCTCTG
* *
80921 ATGGTATTGGAAGATTGTCGTTGTTGTTTCATATAGTTGGAAATTTCAT
1 ATGGTGTTGGAAGATTGTCGTTGTTGTTT-ATATAGTTGGAAATTCCAT
* * *
80970 TTCGTGTTGGAAGATTGTCGTTGCTGTTTCATATAGTTGGAAATTCCAT
1 ATGGTGTTGGAAGATTGTCGTTGTTGTTT-ATATAGTTGGAAATTCCAT
* * *
81019 ATGGTGTTGGAAGATTATCGTTGTTG-TT-TATAGCTGGAAGTTCCAT
1 ATGGTGTTGGAAGATTGTCGTTGTTGTTTATATAGTTGGAAATTCCAT
81065 ATGGTGTTGGAA
1 ATGGTGTTGGAA
81077 ACTTAACATA
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
46 28 0.29
48 2 0.02
49 66 0.69
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.42
Consensus pattern (48 bp):
ATGGTGTTGGAAGATTGTCGTTGTTGTTTATATAGTTGGAAATTCCAT
Found at i:81348 original size:47 final size:45
Alignment explanation
Indices: 81155--81604 Score: 253
Period size: 45 Copynumber: 9.8 Consensus size: 45
81145 ACAATGAGAA
* * ** * * *
81155 TTATACCCTCTTCCAACATGGTGGTGATGCTTCCAATGACAAAAAA
1 TTATACGCTCTTCCAACATGATGGTGGCGCTTCC-ATCACACAAAT
* *
81201 TTATAC-CGTCTTCCAAC---ATGGTGGTGCTTCCAATGACA-AAAT
1 TTATACGC-TCTTCCAACATGATGGTGGCGCTTCC-ATCACACAAAT
* * * * *
81243 TTATACCCTCTTCCAACATGGTGTTGGCGCTTCCA-AACA-AAAC
1 TTATACGCTCTTCCAACATGATGGTGGCGCTTCCATCACACAAAT
* * * * *
81286 CTATACTCACTTCCAACATGATGGTGACGCCTCCAGTCACACAAAT
1 TTATACGCTCTTCCAACATGATGGTGGCGCTTCCA-TCACACAAAT
* *
81332 TTATACGCTCTTTCCAACATGATGGTGGCGCTTCCAACGATA-AAATT
1 TTATACGCTC-TTCCAACATGATGGTGGCGCTTCCATC-ACACAAA-T
* * * * *
81379 TGACAAAACCTATACTCACTTCCAACATGATGGTGACGCCTCCAATCACAAAAAT
1 T---------TATACGCTCTTCCAACATGATGGTGGCGCTTCC-ATCACACAAAT
* * * *
81434 TTATACGCTCTTTCCAACATGATGATGGCACTTCCAACGATA-AAAT
1 TTATACGCTC-TTCCAACATGATGGTGGCGCTTCCATC-ACACAAAT
* * *
81480 TTATATGCGCTTCCAACATGATGGTGGCGCTTCCA--ACGACATTAT
1 TTATACGCTCTTCCAACATGATGGTGGCGCTTCCATCAC-ACA-AAT
* **
81525 TTATACTCTCTTCCAACATGATGGTGGCGCTTCCAATGGCA-AGAA-
1 TTATACGCTCTTCCAACATGATGGTGGCGCTTCC-ATCACACA-AAT
*
81570 TTATACCCTCTTCCAACAT-AGTGGTGGCGCTTCCA
1 TTATACGCTCTTCCAACATGA-TGGTGGCGCTTCCA
81605 ATGACAAGAA
Statistics
Matches: 322, Mismatches: 51, Indels: 64
0.74 0.12 0.15
Matches are distributed among these distances:
42 19 0.06
43 55 0.17
44 4 0.01
45 102 0.32
46 53 0.16
47 50 0.16
48 1 0.00
55 26 0.08
56 12 0.04
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (45 bp):
TTATACGCTCTTCCAACATGATGGTGGCGCTTCCATCACACAAAT
Found at i:81455 original size:102 final size:102
Alignment explanation
Indices: 81279--81481 Score: 370
Period size: 102 Copynumber: 2.0 Consensus size: 102
81269 GCGCTTCCAA
* *
81279 ACAAAACCTATACTCACTTCCAACATGATGGTGACGCCTCCAGTCACACAAATTTATACGCTCTT
1 ACAAAACCTATACTCACTTCCAACATGATGGTGACGCCTCCAATCACAAAAATTTATACGCTCTT
* *
81344 TCCAACATGATGGTGGCGCTTCCAACGATAAAATTTG
66 TCCAACATGATGATGGCACTTCCAACGATAAAATTTG
81381 ACAAAACCTATACTCACTTCCAACATGATGGTGACGCCTCCAATCACAAAAATTTATACGCTCTT
1 ACAAAACCTATACTCACTTCCAACATGATGGTGACGCCTCCAATCACAAAAATTTATACGCTCTT
81446 TCCAACATGATGATGGCACTTCCAACGATAAAATTT
66 TCCAACATGATGATGGCACTTCCAACGATAAAATTT
81482 ATATGCGCTT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (102 bp):
ACAAAACCTATACTCACTTCCAACATGATGGTGACGCCTCCAATCACAAAAATTTATACGCTCTT
TCCAACATGATGATGGCACTTCCAACGATAAAATTTG
Found at i:81513 original size:45 final size:45
Alignment explanation
Indices: 81397--81642 Score: 239
Period size: 45 Copynumber: 5.4 Consensus size: 45
81387 CCTATACTCA
* *
81397 CTTCCAACATGATGGTGACGCCTCCAATC-ACAAAAATTTATACGCT
1 CTTCCAACATGATGGTGGCGCTTCCAA-CGAC-AAAATTTATACGCT
* * * * *
81443 CTTTCCAACATGATGATGGCACTTCCAACGATAAAATTTATATGCG
1 C-TTCCAACATGATGGTGGCGCTTCCAACGACAAAATTTATACGCT
** *
81489 CTTCCAACATGATGGTGGCGCTTCCAACGACATTATTTATACTCT
1 CTTCCAACATGATGGTGGCGCTTCCAACGACAAAATTTATACGCT
* * *
81534 CTTCCAACATGATGGTGGCGCTTCCAATGGCAAGAA-TTATACCCT
1 CTTCCAACATGATGGTGGCGCTTCCAACGACAA-AATTTATACGCT
* **
81579 CTTCCAACAT-AGTGGTGGCGCTTCCAATGACAAGAA-TTATATTCT
1 CTTCCAACATGA-TGGTGGCGCTTCCAACGACAA-AATTTATACGCT
* *
81624 TTTCTCAACATGGTGGTGG
1 CTTC-CAACATGATGGTGG
81643 TGTCGATTAG
Statistics
Matches: 169, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
44 1 0.01
45 117 0.69
46 28 0.17
47 23 0.14
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
CTTCCAACATGATGGTGGCGCTTCCAACGACAAAATTTATACGCT
Found at i:81784 original size:51 final size:50
Alignment explanation
Indices: 81718--81814 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 50
81708 CTTTTAAACG
* *
81718 TGAAGCTATTGCATATTGTGTTCGCAAAATATCACCTCCTTCCAATGTTA
1 TGAAGCTATTGCATATGGCGTTCGCAAAATATCACCTCCTTCCAATGTTA
* * * *
81768 TGAAGTCTTTTGCATATGGCGTTGGCAAACTGTCACCTCCTTCCAAT
1 TGAAG-CTATTGCATATGGCGTTCGCAAAATATCACCTCCTTCCAAT
81815 ATCGAAGGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 5 0.12
51 35 0.88
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (50 bp):
TGAAGCTATTGCATATGGCGTTCGCAAAATATCACCTCCTTCCAATGTTA
Found at i:81969 original size:27 final size:27
Alignment explanation
Indices: 81910--81987 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
81900 ATTAGGGTCG
* * **
81910 CCCATGGGTATTTTGGTCATTTTTTGCA
1 CCCAGGGGCATTTTGGTCA-TTTTCACA
81938 CCCAGGGGCATTTTGGTCATTTTCACA
1 CCCAGGGGCATTTTGGTCATTTTCACA
* *
81965 TCCAGGGGCATTTAGGTCATTTT
1 CCCAGGGGCATTTTGGTCATTTT
81988 TGCATTTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 27 0.61
28 17 0.39
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.40
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTCACA
Found at i:86138 original size:12 final size:12
Alignment explanation
Indices: 86121--86145 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
86111 AAAAAATATG
86121 TTTAATATATAA
1 TTTAATATATAA
86133 TTTAATATATAA
1 TTTAATATATAA
86145 T
1 T
86146 AAAAGTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATATAA
Found at i:87433 original size:13 final size:13
Alignment explanation
Indices: 87415--87441 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
87405 TCTGCTCTCG
87415 TAAACTTGATGGC
1 TAAACTTGATGGC
87428 TAAACTTGATGGC
1 TAAACTTGATGGC
87441 T
1 T
87442 TAGTGCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TAAACTTGATGGC
Found at i:87572 original size:21 final size:21
Alignment explanation
Indices: 87543--87583 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
87533 TTCCGTCTCA
*
87543 TCAAAAGCACCATCCATCTTT
1 TCAAAAGCACCAGCCATCTTT
*
87564 TCAATAGCACCAGCCATCTT
1 TCAAAAGCACCAGCCATCTT
87584 AACTAAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (21 bp):
TCAAAAGCACCAGCCATCTTT
Found at i:87820 original size:31 final size:31
Alignment explanation
Indices: 87782--87843 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
87772 TATATTAAAC
*
87782 AAATAAGGATATAATAGGAATATT-AAAAGTT
1 AAATAAGGATACAATAGGAAT-TTCAAAAGTT
*
87813 AAATAAGGATACAATAGGCATTTCAAAAGTT
1 AAATAAGGATACAATAGGAATTTCAAAAGTT
87844 TCTCAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (31 bp):
AAATAAGGATACAATAGGAATTTCAAAAGTT
Found at i:88002 original size:3 final size:3
Alignment explanation
Indices: 87994--88028 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
87984 TACAATCCTA
87994 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
88029 AAATAGATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:88931 original size:26 final size:26
Alignment explanation
Indices: 88875--88932 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
88865 TTAACGTAAA
* **
88875 ATATTGCCAGAGGGTATTGGCAAAAG
1 ATATTGCCAGAGGGAATTCCCAAAAG
* * *
88901 GTATTGCCAGAGGGAATTCCCACATG
1 ATATTGCCAGAGGGAATTCCCAAAAG
88927 ATATTG
1 ATATTG
88933 TAAGAGGATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (26 bp):
ATATTGCCAGAGGGAATTCCCAAAAG
Found at i:89177 original size:20 final size:21
Alignment explanation
Indices: 89142--89187 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
89132 AAATATTATA
*
89142 TTTATCGTATAATGGGTAGTT
1 TTTATCGTAAAATGGGTAGTT
89163 TTTATC-TAAAATGGGTAGTT
1 TTTATCGTAAAATGGGTAGTT
89183 TTTAT
1 TTTAT
89188 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (21 bp):
TTTATCGTAAAATGGGTAGTT
Found at i:91113 original size:16 final size:16
Alignment explanation
Indices: 91092--91123 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
91082 CAACCTCGGG
*
91092 TTTTCGGGTTTGGGTC
1 TTTTCGGGTTCGGGTC
91108 TTTTCGGGTTCGGGTC
1 TTTTCGGGTTCGGGTC
91124 GTAACAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.38, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTC
Done.