Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003706.1 Hibiscus syriacus cultivar Beakdansim tig00007926_pilon, 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: 65935
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:2113 original size:42 final size:42
Alignment explanation
Indices: 2067--2157 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
2057 TTCTTGCTGC
2067 ATGAGGTTAAATTTGTTATGCAGTTCTAGATTCTCCTGATGA
1 ATGAGGTTAAATTTGTTATGCAGTTCTAGATTCTCCTGATGA
* * * *
2109 ATGAGGTTTACTTTGTTATGCTGTTCTAGATTCTCCTGCTGA
1 ATGAGGTTAAATTTGTTATGCAGTTCTAGATTCTCCTGATGA
2151 ATGAGGT
1 ATGAGGT
2158 GTCCCTGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (42 bp):
ATGAGGTTAAATTTGTTATGCAGTTCTAGATTCTCCTGATGA
Found at i:3886 original size:14 final size:14
Alignment explanation
Indices: 3867--3893 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3857 CCCTGTTGGA
3867 GGAAAGAATGCAAC
1 GGAAAGAATGCAAC
3881 GGAAAGAATGCAA
1 GGAAAGAATGCAA
3894 ACGACAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.30, T:0.07
Consensus pattern (14 bp):
GGAAAGAATGCAAC
Found at i:8294 original size:4 final size:4
Alignment explanation
Indices: 8285--8311 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
8275 CCAACTCTAA
8285 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
8312 AACAAACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:18534 original size:37 final size:37
Alignment explanation
Indices: 18479--18642 Score: 165
Period size: 37 Copynumber: 4.5 Consensus size: 37
18469 TATTTAAGTT
* *
18479 TTTATATTCAATTAAAATATGAACATGTTATTATAAA
1 TTTATATTCAATTAAAATATGAATATATTATTATAAA
* *
18516 TTTATATTTAATTGAAATATGAATATATTATTTATAAA
1 TTTATATTCAATTAAAATATGAATATATTA-TTATAAA
* ** * * *
18554 TATATATTTGACT-AAATA-CAA-ATA-TATTATGAA
1 TTTATATTCAATTAAAATATGAATATATTATTATAAA
* *
18587 TTTATGTTCAATTAAAATATGAATATATTATTACAAA
1 TTTATATTCAATTAAAATATGAATATATTATTATAAA
* *
18624 TTTATATTCGATTAGAATA
1 TTTATATTCAATTAAAATA
18643 CCACATTGTA
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
33 14 0.14
34 7 0.07
35 5 0.05
36 5 0.05
37 54 0.53
38 17 0.17
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTATATTCAATTAAAATATGAATATATTATTATAAA
Found at i:18643 original size:71 final size:71
Alignment explanation
Indices: 18507--18643 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
18497 ATGAACATGT
* * * *
18507 TATTATAAATTTATATTTAATTGAAATATGAATATATTATTTATAAATATATATTTGACTAAATA
1 TATTATAAATTTATATTCAATTAAAATATGAATATATTATTTACAAATATATATTCGACTAAATA
18572 CAAATA
66 CAAATA
* * * *
18578 TATTATGAATTTATGTTCAATTAAAATATGAATATATTA-TTACAAATTTATATTCGATTAGAAT
1 TATTATAAATTTATATTCAATTAAAATATGAATATATTATTTACAAATATATATTCGACTA-AAT
18642 AC
65 AC
18644 CACATTGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 17 0.30
71 40 0.70
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (71 bp):
TATTATAAATTTATATTCAATTAAAATATGAATATATTATTTACAAATATATATTCGACTAAATA
CAAATA
Found at i:19649 original size:41 final size:41
Alignment explanation
Indices: 19604--19681 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
19594 ATTCGCGTTG
19604 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
19645 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
19682 AGTTGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:19676 original size:62 final size:62
Alignment explanation
Indices: 19608--19725 Score: 227
Period size: 62 Copynumber: 1.9 Consensus size: 62
19598 GCGTTGCATT
19608 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
19670 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
19726 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (62 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:19722 original size:20 final size:21
Alignment explanation
Indices: 19608--19702 Score: 138
Period size: 21 Copynumber: 4.6 Consensus size: 21
19598 GCGTTGCATT
19608 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
19629 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
19649 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
19670 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
19691 TCGCGTTGCGAT
1 TCGCGTTGCGAT
19703 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.24
21 48 0.76
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:19765 original size:19 final size:19
Alignment explanation
Indices: 19738--19779 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
19728 ACAGTTGTCA
*
19738 TTGCGATTTTCCAAATTCG
1 TTGCAATTTTCCAAATTCG
19757 TTGCAATTTTCCAAATTCG
1 TTGCAATTTTCCAAATTCG
19776 TTGC
1 TTGC
19780 GATAGTCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (19 bp):
TTGCAATTTTCCAAATTCG
Found at i:28671 original size:93 final size:94
Alignment explanation
Indices: 28512--28702 Score: 366
Period size: 93 Copynumber: 2.0 Consensus size: 94
28502 AGAATGATCG
*
28512 AGATGTAGAATTCCAATTCCTAGGTGCATGCTTTAATTATTATAAAGCTCTCTAATTTGCTCACA
1 AGATGTAGAATTCCAATTCCTAGGTGCATGCTTTAACTATTATAAAGCTCTCTAATTTGCTCACA
28577 AATTGTTCACCGGTAGAAAACTTTTTCT-
66 AATTGTTCACCGGTAGAAAACTTTTTCTC
28605 AGATGTAGAATTCCAATTCCTAGGTGCATGCTTTAACTATTATAAAGCTCTCTAATTTGCTCACA
1 AGATGTAGAATTCCAATTCCTAGGTGCATGCTTTAACTATTATAAAGCTCTCTAATTTGCTCACA
28670 AATTGTTCACCGGTAGAAAACTTTTTCTC
66 AATTGTTCACCGGTAGAAAACTTTTTCTC
28699 AGAT
1 AGAT
28703 CTTGGTGTAC
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 92 0.96
94 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (94 bp):
AGATGTAGAATTCCAATTCCTAGGTGCATGCTTTAACTATTATAAAGCTCTCTAATTTGCTCACA
AATTGTTCACCGGTAGAAAACTTTTTCTC
Found at i:29807 original size:14 final size:14
Alignment explanation
Indices: 29768--29809 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
29758 TAATTTTTTT
* *
29768 GTTCATTTATGCTC
1 GTTCGTTTATGTTC
*
29782 GTTTGTTTATGTTC
1 GTTCGTTTATGTTC
29796 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
29810 TCCAGACTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.14, G:0.19, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:31329 original size:2 final size:2
Alignment explanation
Indices: 31317--31352 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
31307 TTAAATTCTT
31317 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31353 CTATTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31631 original size:106 final size:106
Alignment explanation
Indices: 31446--31652 Score: 396
Period size: 106 Copynumber: 2.0 Consensus size: 106
31436 TCTTACTTTC
31446 ATCTCTAAACGTATACAATGAAGATTCAGTACTACAATTGTCATATTTTCTTTATTTTCTCTACT
1 ATCTCTAAACGTATACAATGAAGATTCAGTACTACAATTGTCATATTTTCTTTATTTTCTCTACT
31511 CAAGAAAAGTTATTATATTCCTCTTATATACATTTTAAAGT
66 CAAGAAAAGTTATTATATTCCTCTTATATACATTTTAAAGT
*
31552 ATCTCTAAACGTATACAATGAAGATTCAGTACTGCAATTGTCATATTTTCTTTATTTTCTCTACT
1 ATCTCTAAACGTATACAATGAAGATTCAGTACTACAATTGTCATATTTTCTTTATTTTCTCTACT
*
31617 CAAGCAAAGTTATTATATTCCTCTTATATACATTTT
66 CAAGAAAAGTTATTATATTCCTCTTATATACATTTT
31653 GGATTCCTTA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (106 bp):
ATCTCTAAACGTATACAATGAAGATTCAGTACTACAATTGTCATATTTTCTTTATTTTCTCTACT
CAAGAAAAGTTATTATATTCCTCTTATATACATTTTAAAGT
Found at i:32655 original size:27 final size:26
Alignment explanation
Indices: 32600--32657 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
32590 CAAACCCGAG
* *
32600 CCGACTCGAAAATTTATATCTTCCAC
1 CCGACCCGAAAATATATATCTTCCAC
*
32626 CCGACCCGAAAA-ATATATACTCTCCTC
1 CCGACCCGAAAATATATAT-CT-TCCAC
32653 CCGAC
1 CCGAC
32658 TCTGACTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 13 0.48
27 9 0.33
ACGTcount: A:0.31, C:0.36, G:0.09, T:0.24
Consensus pattern (26 bp):
CCGACCCGAAAATATATATCTTCCAC
Found at i:33216 original size:20 final size:23
Alignment explanation
Indices: 33165--33217 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
33155 ATAAAACCTT
*
33165 ATAATTTTTATTAATATTAACAA
1 ATAATTTTAATTAATATTAACAA
*
33188 ATTACTTTTAATT-AT-TTAA-AA
1 A-TAATTTTAATTAATATTAACAA
33209 ATAATTTTA
1 ATAATTTTA
33218 TAATTTACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.27
21 3 0.12
22 4 0.15
23 3 0.12
24 9 0.35
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATTTTAATTAATATTAACAA
Found at i:33247 original size:14 final size:14
Alignment explanation
Indices: 33196--33257 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 14
33186 AAATTACTTT
33196 TAATTA-TTTA-AA
1 TAATTATTTTATAA
*
33208 -AATAATTTTATAA
1 TAATTATTTTATAA
* *
33221 T--TTACTCTATAA
1 TAATTATTTTATAA
33233 TAATTATTTTATAA
1 TAATTATTTTATAA
33247 TAATTTATTTT
1 TAA-TTATTTT
33258 GCTTATGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
11 4 0.11
12 13 0.34
13 2 0.05
14 12 0.32
15 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTATTTTATAA
Found at i:33254 original size:15 final size:15
Alignment explanation
Indices: 33217--33257 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
33207 AAATAATTTT
* *
33217 ATAATTTACTCTATA
1 ATAATTTATTTTATA
33232 ATAA-TTATTTTATA
1 ATAATTTATTTTATA
33246 ATAATTTATTTT
1 ATAATTTATTTT
33258 GCTTATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATTTATTTTATA
Found at i:34976 original size:19 final size:19
Alignment explanation
Indices: 34952--34995 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
34942 AAATTTCATC
34952 ACGGCAAGAAAGAAGAATG
1 ACGGCAAGAAAGAAGAATG
34971 ACGGCAAGAAAGAAGAATG
1 ACGGCAAGAAAGAAGAATG
*
34990 GCGGCA
1 ACGGCA
34996 GAGAGAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.34, T:0.05
Consensus pattern (19 bp):
ACGGCAAGAAAGAAGAATG
Found at i:38463 original size:8 final size:8
Alignment explanation
Indices: 38447--38485 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
38437 TAGCCACAGC
*
38447 TAGTGTTG
1 TAGTATTG
38455 TAGTATTG
1 TAGTATTG
*
38463 TAATATTG
1 TAGTATTG
38471 TAGTATTG
1 TAGTATTG
*
38479 TAATATT
1 TAGTATT
38486 ATAATATTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (8 bp):
TAGTATTG
Found at i:38473 original size:16 final size:16
Alignment explanation
Indices: 38452--38485 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38442 ACAGCTAGTG
38452 TTGTAGTATTGTAATA
1 TTGTAGTATTGTAATA
38468 TTGTAGTATTGTAATA
1 TTGTAGTATTGTAATA
38484 TT
1 TT
38486 ATAATATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (16 bp):
TTGTAGTATTGTAATA
Found at i:38474 original size:24 final size:24
Alignment explanation
Indices: 38447--38494 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38437 TAGCCACAGC
* * *
38447 TAGTGTTGTAGTATTGTAATATTG
1 TAGTATTGTAATATTATAATATTG
38471 TAGTATTGTAATATTATAATATTG
1 TAGTATTGTAATATTATAATATTG
38495 GGGTAACGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (24 bp):
TAGTATTGTAATATTATAATATTG
Found at i:38490 original size:8 final size:8
Alignment explanation
Indices: 38452--38494 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
38442 ACAGCTAGTG
*
38452 TTGTAGTA
1 TTGTAATA
38460 TTGTAATA
1 TTGTAATA
*
38468 TTGTAGTA
1 TTGTAATA
38476 TTGTAATA
1 TTGTAATA
*
38484 TTATAATA
1 TTGTAATA
38492 TTG
1 TTG
38495 GGGTAACGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (8 bp):
TTGTAATA
Found at i:38614 original size:21 final size:21
Alignment explanation
Indices: 38582--38621 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38572 CGCTTCCAAC
38582 AAAAATTACTATATATTTTTA
1 AAAAATTACTATATATTTTTA
38603 AAAACATT-CTATATATTTT
1 AAAA-ATTACTATATATTTT
38622 CTATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAAATTACTATATATTTTTA
Found at i:38639 original size:18 final size:19
Alignment explanation
Indices: 38616--38653 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38606 ACATTCTATA
38616 TATTTTC-TATTTAAAATT
1 TATTTTCATATTTAAAATT
*
38634 TATTTTCATCTTTAAAATT
1 TATTTTCATATTTAAAATT
38653 T
1 T
38654 TATAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTCATATTTAAAATT
Found at i:38665 original size:26 final size:26
Alignment explanation
Indices: 38636--38709 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 26
38626 TTAAAATTTA
38636 TTTTCATCTT-TAAAATTTTATA-AAT
1 TTTTCATCTTCTAAAATTTTA-AGAAT
38661 CTTTT-AT-TTCCTAAAATTTTAAGAAT
1 -TTTTCATCTT-CTAAAATTTTAAGAAT
*
38687 TTTTCATCTAATATAAAATTTTA
1 TTTTCATCT--TCTAAAATTTTA
38710 CGTCCGCCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
24 2 0.05
25 7 0.17
26 19 0.47
27 1 0.03
28 10 0.25
29 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.53
Consensus pattern (26 bp):
TTTTCATCTTCTAAAATTTTAAGAAT
Found at i:39132 original size:12 final size:12
Alignment explanation
Indices: 39117--39167 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
39107 ATCTTTTTTA
39117 TATTTTTTTAAT
1 TATTTTTTTAAT
*
39129 TATTTTTGTT-TT
1 TATTTTT-TTAAT
*
39141 TATTTTACTTAAAT
1 TATTTT--TTTAAT
39155 TATTTTTTTAAT
1 TATTTTTTTAAT
39167 T
1 T
39168 TTACAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
12 20 0.65
13 3 0.10
14 8 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (12 bp):
TATTTTTTTAAT
Found at i:39395 original size:45 final size:45
Alignment explanation
Indices: 39261--39397 Score: 229
Period size: 45 Copynumber: 3.0 Consensus size: 45
39251 CAAATGATAA
* *
39261 AATCTATAACATATCATCAATATGAAAAATCTCAATGGCGGATGA
1 AATCTATAACATATCATCAATATGCAAAATCTCAATGGCGGATGT
*
39306 AATCTATAACATATTATCAATATGCAAAATCTCAATGGCGGATGT
1 AATCTATAACATATCATCAATATGCAAAATCTCAATGGCGGATGT
* *
39351 AATCTATAACATATCATCAATATGCAAAATCTGAGTGGCGGATGT
1 AATCTATAACATATCATCAATATGCAAAATCTCAATGGCGGATGT
39396 AA
1 AA
39398 AATGGGCTCT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (45 bp):
AATCTATAACATATCATCAATATGCAAAATCTCAATGGCGGATGT
Found at i:41369 original size:29 final size:29
Alignment explanation
Indices: 41334--41415 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
41324 AAACTAAATT
*
41334 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
41363 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
41392 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
41416 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:42726 original size:15 final size:15
Alignment explanation
Indices: 42703--42732 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42693 ACGAGGCTGG
42703 AATTACAACAATAAC
1 AATTACAACAATAAC
*
42718 AATTCCAACAATAAC
1 AATTACAACAATAAC
42733 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:46135 original size:29 final size:29
Alignment explanation
Indices: 46100--46181 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
46090 AAACTAAATT
*
46100 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
46129 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
46158 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
46182 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:47017 original size:2 final size:2
Alignment explanation
Indices: 47010--47119 Score: 220
Period size: 2 Copynumber: 55.0 Consensus size: 2
47000 ATGTAAAATA
47010 AT AT AT AT 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 AT AT AT AT
47052 AT AT AT AT 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 AT AT AT AT
47094 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
47120 TATTTTATTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47888 original size:17 final size:18
Alignment explanation
Indices: 47857--47892 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
47847 GAACAAATTT
47857 TTTTATAATTTAAAAATA
1 TTTTATAATTTAAAAATA
47875 TTTTATAA-TTAAAAATA
1 TTTTATAATTTAAAAATA
47892 T
1 T
47893 ATAGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATAATTTAAAAATA
Found at i:51010 original size:13 final size:13
Alignment explanation
Indices: 50971--51012 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
50961 CATCGACTTT
50971 AAGAAATATAAAA
1 AAGAAATATAAAA
*
50984 AATAAA-AGTCAAAA
1 AAGAAATA-T-AAAA
50998 AAGAAATATAAAA
1 AAGAAATATAAAA
51011 AA
1 AA
51013 TATATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.50
14 10 0.42
15 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.14
Consensus pattern (13 bp):
AAGAAATATAAAA
Found at i:52326 original size:2 final size:2
Alignment explanation
Indices: 52314--52387 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
52304 TACATTATTG
*
52314 TA TA CA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52388 GATCACAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55538 original size:30 final size:31
Alignment explanation
Indices: 55498--55568 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
55488 TATAATGATG
* *
55498 ATTATTTTTTAAAAATA-TTATGAAATAATT
1 ATTATATTTTAAAAATATTTATAAAATAATT
**
55528 ATTATATTTT-ATTATATTTATAAAATAATT
1 ATTATATTTTAAAAATATTTATAAAATAATT
55558 ATTATATTTTA
1 ATTATATTTTA
55569 TCAAACTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
ATTATATTTTAAAAATATTTATAAAATAATT
Found at i:58270 original size:20 final size:20
Alignment explanation
Indices: 58245--58288 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
58235 TTTTGTGGTT
* *
58245 ATTTGGACCTGTTGGGGATG
1 ATTTGGACCCGTTGGGGATA
58265 ATTTGGACCCGTTGGGGATA
1 ATTTGGACCCGTTGGGGATA
58285 ATTT
1 ATTT
58289 TTCTACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.34, T:0.36
Consensus pattern (20 bp):
ATTTGGACCCGTTGGGGATA
Found at i:62595 original size:21 final size:23
Alignment explanation
Indices: 62551--62598 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
62541 TGCATAATTA
*
62551 TAAATTAGTTGAAAATTTAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
*
62574 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
62595 TAAA
1 TAAA
62599 CTATACCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTGAAAATTAAAAGG
Found at i:64002 original size:20 final size:21
Alignment explanation
Indices: 63952--64003 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
63942 ATTATGACTA
*
63952 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTCCCAATT
**
63973 TCGCGTTGCGATTTCCCAA-T
1 TCGCAATGCGATTTCCCAATT
63993 TCGCAATGCGA
1 TCGCAATGCGA
64004 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTCCCAATT
Found at i:64036 original size:21 final size:20
Alignment explanation
Indices: 63993--64039 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
63983 ATTTCCCAAT
*
63993 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
64013 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
64034 TCGCAA
1 TCGCAA
64040 CGCGGTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:64057 original size:41 final size:41
Alignment explanation
Indices: 64030--64167 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
64020 GCGAATTTGG
* *
64030 AAAATCGCAACGCGGTTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
64071 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
64111 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
64152 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
64168 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:64100 original size:20 final size:20
Alignment explanation
Indices: 64034--64147 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
64024 ATTTGGAAAA
* * *
64034 TCGCAACGCGGTTCTGACTA
1 TCGCAACGCGATACTGACTT
* **
64054 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
64075 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
64095 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
* *
64115 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
64135 TCGCAACGAGATA
1 TCGCAACGCGATA
64148 ATACATAATC
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
19 2 0.03
20 56 0.75
21 15 0.20
22 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:64666 original size:20 final size:20
Alignment explanation
Indices: 64617--64673 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
64607 TTTATTCTCT
* **
64617 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
64637 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
64657 TGTTGCGATTTTCATTT
1 CGTTGCGATTGTCATTT
64674 CAGAAACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Done.