Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004005.1 Hibiscus syriacus cultivar Beakdansim tig00008728_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: 58486
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4930 original size:16 final size:16
Alignment explanation
Indices: 4909--4951 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
4899 AGAGCCTCTG
4909 AATCATTCAACATTTA
1 AATCATTCAACATTTA
* * *
4925 AATCATTTAGCATTTG
1 AATCATTCAACATTTA
4941 AATCATTCAAC
1 AATCATTCAAC
4952 GCTTAATCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (16 bp):
AATCATTCAACATTTA
Found at i:7677 original size:18 final size:18
Alignment explanation
Indices: 7654--7698 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
7644 ACATTATTAC
7654 TAAAATTTA-AATTTATGT
1 TAAAATTTATAA-TTATGT
*
7672 TAAAATTTATAATTATTT
1 TAAAATTTATAATTATGT
7690 TAATAATTT
1 TAA-AATTT
7699 TATGAACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAAAATTTATAATTATGT
Found at i:8223 original size:22 final size:21
Alignment explanation
Indices: 8181--8224 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
8171 ATATTTTTAT
**
8181 TTTTTTAATATTCATTTTATA
1 TTTTTTAATATTCATAATATA
*
8202 TTTTTTAATTATTGATAATATA
1 TTTTTTAA-TATTCATAATATA
8224 T
1 T
8225 ATATATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTTAATATTCATAATATA
Found at i:8224 original size:2 final size:2
Alignment explanation
Indices: 8219--8248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8209 ATTATTGATA
8219 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
8249 CTTATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9219 original size:25 final size:26
Alignment explanation
Indices: 9171--9221 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
9161 ACATAACATA
*
9171 TTTATTTTAATCTTAGATCTTAAAAT
1 TTTATTTTAATCTTAGATCCTAAAAT
9197 TTTATTTT-ATCTTTA-ATCCTAAAAT
1 TTTATTTTAATC-TTAGATCCTAAAAT
9222 CTTACTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTATTTTAATCTTAGATCCTAAAAT
Found at i:16127 original size:3 final size:3
Alignment explanation
Indices: 16119--16182 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
16109 ACATGCCATT
16119 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16167 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
16183 CTAATACTCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18711 original size:28 final size:28
Alignment explanation
Indices: 18680--18762 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
18670 TAGGCTAGAG
*
18680 CACTCTGCGCCTTCTGTTGATGCTATAA
1 CACTCTGCTCCTTCTGTTGATGCTATAA
18708 CACTCTGCTCCTTCTGTTGATGCTATAA
1 CACTCTGCTCCTTCTGTTGATGCTATAA
*
18736 CACTCTGCTCCTTCTGTCGATGCTATA
1 CACTCTGCTCCTTCTGTTGATGCTATA
18763 GTTATTATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (28 bp):
CACTCTGCTCCTTCTGTTGATGCTATAA
Found at i:21354 original size:9 final size:9
Alignment explanation
Indices: 21340--21365 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21330 TTATGTGGCT
21340 AGTGTTCTA
1 AGTGTTCTA
21349 AGTGTTCTA
1 AGTGTTCTA
21358 AGTGTTCT
1 AGTGTTCT
21366 TGATCAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (9 bp):
AGTGTTCTA
Found at i:23624 original size:20 final size:19
Alignment explanation
Indices: 23599--23668 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
23589 CTAAATTTCA
23599 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTT-TG
*
23619 AATTCGCAACGCGAATTTTG
1 AATTCGCAACTCG-ATTTTG
**
23639 TTTTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTT-G
23659 AATTCGCAAC
1 AATTCGCAAC
23669 ACGAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.12
20 33 0.79
21 4 0.10
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (19 bp):
AATTCGCAACTCGATTTTG
Found at i:23646 original size:40 final size:40
Alignment explanation
Indices: 23601--23677 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
23591 AAATTTCAAA
*
23601 TTCGCAACTCGA-TTTCTGAATTCGCAACGCGAATTTTGTT
1 TTCGCAACTCGATTTTC-GAATTCGCAACACGAATTTTGTT
23641 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTT
1 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTT
23678 AATATTGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTGTT
Found at i:23688 original size:40 final size:40
Alignment explanation
Indices: 23600--23688 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
23590 TAAATTTCAA
* *
23600 ATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTTGT
1 ATTCGCAACTCGATTTCTGAATTCGCAACACGAATTTTAT
*
23640 TTTCGCAACTCGATTT-TCGAATTCGCAACACGAATTTTAAT
1 ATTCGCAACTCGATTTCT-GAATTCGCAACACGAATTTT-AT
23681 ATT-GCAAC
1 ATTCGCAAC
23689 AGGTTTTAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 39 0.91
41 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (40 bp):
ATTCGCAACTCGATTTCTGAATTCGCAACACGAATTTTAT
Found at i:26965 original size:12 final size:12
Alignment explanation
Indices: 26950--26990 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
26940 AGAAAAAGGA
26950 AATCAAAATCGC
1 AATCAAAATCGC
26962 AATCAAAATCGC
1 AATCAAAATCGC
* *
26974 AATCAAATTCCC
1 AATCAAAATCGC
26986 AATCA
1 AATCA
26991 CAACCGGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.20
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:28738 original size:21 final size:21
Alignment explanation
Indices: 28709--28779 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
28699 GTGAATCGGG
*
28709 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* ** *
28730 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGAC
28751 CTCTTGAACGGTGGGA-GGAGC
1 CTCTTGAACGGTGGGAGGGA-C
28772 CTCTTGAA
1 CTCTTGAA
28780 GGATGATAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 2 0.05
21 38 0.95
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Found at i:28775 original size:42 final size:42
Alignment explanation
Indices: 28709--28831 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
28699 GTGAATCGGG
*
28709 CTCTCGAACGGTGGGAGG-GACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGAG-CCTCTTGAACGATGACAGGGGC
* * *
28751 CTCTTGAACGGTGGGAGGAGCCTCTTGAAGGATGATAAGGGC
1 CTCTTGAACGGTGGGAGGAGCCTCTTGAACGATGACAGGGGC
* * * *
28793 CTCTTGAACGAT-AGAAGAGGCCTCTTGAATGATGACAGG
1 CTCTTGAACGGTGGGAGGA-GCCTCTTGAACGATGACAGG
28832 TGAATTGGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.06
42 64 0.93
43 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGAGCCTCTTGAACGATGACAGGGGC
Found at i:28794 original size:21 final size:21
Alignment explanation
Indices: 28724--28827 Score: 104
Period size: 21 Copynumber: 4.9 Consensus size: 21
28714 GAACGGTGGG
*
28724 AGGGACCTCTTGAACGATGACA
1 AGGG-CCTCTTGAACGATGAGA
* * *
28746 GGGGCCTCTTGAACGGTG-GG
1 AGGGCCTCTTGAACGATGAGA
* *
28766 AGGAGCCTCTTGAAGGATGATA
1 AGG-GCCTCTTGAACGATGAGA
28788 AGGGCCTCTTGAACGAT-AGA
1 AGGGCCTCTTGAACGATGAGA
*
28808 AGAGGCCTCTTGAATGATGA
1 AG-GGCCTCTTGAACGATGA
28828 CAGGTGAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.09
21 53 0.80
22 7 0.11
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (21 bp):
AGGGCCTCTTGAACGATGAGA
Found at i:29147 original size:21 final size:21
Alignment explanation
Indices: 29098--29155 Score: 100
Period size: 20 Copynumber: 2.8 Consensus size: 21
29088 GTAGAGCGGC
*
29098 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
29119 TA-CTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
29139 TACCTCACCACGTAAAG
1 TACCTCACCACGTAAAG
29156 CACCATTGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:31377 original size:22 final size:22
Alignment explanation
Indices: 31352--31394 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31342 TGGAGATAAA
31352 CGAATTTCGTCGAAGATGGGGT
1 CGAATTTCGTCGAAGATGGGGT
*
31374 CGAATTTCGTCGGAGATGGGG
1 CGAATTTCGTCGAAGATGGGG
31395 ACGGATGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.26
Consensus pattern (22 bp):
CGAATTTCGTCGAAGATGGGGT
Found at i:31533 original size:19 final size:20
Alignment explanation
Indices: 31511--31548 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31501 AATATTTTGT
*
31511 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCAAAAATAAAA
*
31530 TTCGCATTGCAAAAATAAA
1 TTCGAATTGCAAAAATAAA
31549 CGCATTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCAAAAATAAAA
Found at i:31597 original size:20 final size:20
Alignment explanation
Indices: 31574--31724 Score: 108
Period size: 20 Copynumber: 7.5 Consensus size: 20
31564 TGACTTCTGT
*
31574 GTTGCGAATTACAAATTTGC
1 GTTGCGAATTACAAATTCGC
* * *
31594 GTTGCGATTTATAGATTCGC
1 GTTGCGAATTACAAATTCGC
* * *
31614 GTTGCGATTTATAGATTCGC
1 GTTGCGAATTACAAATTCGC
* *
31634 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
*
31654 GTTGTGAATTTGA-AAATT-GC
1 GTTGCGAA-TT-ACAAATTCGC
** *
31674 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAA-TTACAAATTCGC
** * *
31695 AATGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
31715 GTTGCGAATT
1 GTTGCGAATT
31725 TGGAAACTGA
Statistics
Matches: 105, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
20 91 0.87
21 13 0.12
22 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:31618 original size:40 final size:40
Alignment explanation
Indices: 31574--31680 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
31564 TGACTTCTGT
*
31574 GTTGCGAATTACAAATTTGCGTTGCGATTTATAGATTCGC
1 GTTGCGAATTACAAATTTGCGTTGCGATTTACAGATTCGC
* * * * *
31614 GTTGCGATTTATAGATTCGCGTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTTGCGTTGCGATTTACAGATTCGC
* ** *
31654 GTTGTGAATTTGAAAATTGCGTTGCGA
1 GTTGCGAATTACAAATTTGCGTTGCGA
31681 ATTTGGAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.38
Consensus pattern (40 bp):
GTTGCGAATTACAAATTTGCGTTGCGATTTACAGATTCGC
Found at i:36715 original size:33 final size:33
Alignment explanation
Indices: 36678--36748 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
36668 AGGGAAGGAA
* *
36678 CAACAATC-AAAGTCCACTGAAACAACCCAAAGG
1 CAACAATCAAAAG-CCAATGAAACAACACAAAGG
*
36711 CAACAATCAAAAGCTAATGAAACAACACAAAGG
1 CAACAATCAAAAGCCAATGAAACAACACAAAGG
36744 CAACA
1 CAACA
36749 GTCGAAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.54, C:0.27, G:0.11, T:0.08
Consensus pattern (33 bp):
CAACAATCAAAAGCCAATGAAACAACACAAAGG
Found at i:39343 original size:26 final size:25
Alignment explanation
Indices: 39281--39343 Score: 58
Period size: 26 Copynumber: 2.4 Consensus size: 25
39271 AATTATTAAA
*
39281 AAAAATATAAAATAAGAAAAAAATG
1 AAAAATTTAAAATAAGAAAAAAATG
*
39306 AAAATTTATAAAATAA-AATAAAGAGAT-
1 AAAAATT-TAAAATAAGAA-AAA-A-ATG
39333 AAAAATTTAAA
1 AAAAATTTAAA
39344 GGTTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 7 0.23
26 15 0.48
27 7 0.23
28 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (25 bp):
AAAAATTTAAAATAAGAAAAAAATG
Found at i:41860 original size:15 final size:15
Alignment explanation
Indices: 41840--41871 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41830 TGGCAGATCC
41840 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
*
41855 AAATCAAGAATGGGA
1 AAATCAAGAACGGGA
41870 AA
1 AA
41872 GAAAGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.25, T:0.09
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:52123 original size:23 final size:22
Alignment explanation
Indices: 52090--52174 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
52080 TTTAGTGCAG
*
52090 AGGGAATCGATACCCCCCTTGA
1 AGGGAACCGATACCCCCCTTGA
* *
52112 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAACCGATACCCCCCTTGA
* *
52135 ATGGGAACCGATTCCCTCCTTG-
1 A-GGGAACCGATACCCCCCTTGA
* *
52157 AGGGAATCGATAACCCCC
1 AGGGAACCGATACCCCCC
52175 ACGGGTTCTG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 13 0.25
22 2 0.04
23 37 0.71
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATACCCCCCTTGA
Found at i:52167 original size:21 final size:22
Alignment explanation
Indices: 52103--52157 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 22
52093 GAATCGATAC
52103 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
*
52125 CCCCCTTTGAATGGGAACCGATT
1 CCCCC-TTGAAGGGGAACCGATT
52148 CCCTCCTTGA
1 CCC-CCTTGA
52158 GGGAATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.17
23 23 0.77
24 2 0.07
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.24
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:54410 original size:26 final size:26
Alignment explanation
Indices: 54352--54403 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54342 GAACATCGAA
* *
54352 TGCATTTTATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACTCAG
54378 TGCATTTGATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACTCAG
54404 GCTATTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (26 bp):
TGCATTTGATGCATCGATGCACTCAG
Found at i:56391 original size:23 final size:23
Alignment explanation
Indices: 56344--56393 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
56334 AATAACATAT
** **
56344 TAGGTAGTTCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
56367 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
56390 TAGG
1 TAGG
56394 CATTTAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:56453 original size:87 final size:87
Alignment explanation
Indices: 56307--56469 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
56297 TATGTTATAT
* **
56307 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGTTCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
56372 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
**
56394 CATTTAACCGAAAATATTATCAATTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
56459 AGCGCTTATAT
66 AGCGCTTATAT
56470 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:57193 original size:132 final size:130
Alignment explanation
Indices: 56956--57227 Score: 402
Period size: 132 Copynumber: 2.1 Consensus size: 130
56946 TTTAGAAAAA
*
56956 GTCGATACTTATATTAAATTATCGACACTTTCAACATATCTAGTAGCCTTTTACCAGTTTTGTCA
1 GTCGATACTTATATTAAAGTATCGACACTTTCAACATATCTAGTAGCCTTTTACCAGTTTTGTCA
* **
57021 TTTTAAGACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAA
66 TTTTAAGAACAGTTTTGTCATATTTTTACCTGTTATATTGTTA-GG-TCGATACATTTTCATAAA
57086 GT
129 GT
* * * *
57088 GTCGATACTTATATTTAAGTATCGACACTTTCAACATATCTGGTAG-TTATTTACCTGTTTTGTC
1 GTCGATACTTATATTAAAGTATCGACACTTTCAACATATCTAGTAGCCT-TTTACCAGTTTTGTC
* * *
57152 ATTTTGAGAACGGTTTTGTCATATTTTTAGCTGTTATATTGTTAGGTCGATACATTTTCATAAAG
65 ATTTTAAGAACAGTTTTGTCATATTTTTACCTGTTATATTGTTAGGTCGATACATTTTCATAAAG
57217 T
130 T
*
57218 GTCGACACTT
1 GTCGATACTT
57228 TTTAGGCGAT
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
130 27 0.21
131 3 0.02
132 97 0.76
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (130 bp):
GTCGATACTTATATTAAAGTATCGACACTTTCAACATATCTAGTAGCCTTTTACCAGTTTTGTCA
TTTTAAGAACAGTTTTGTCATATTTTTACCTGTTATATTGTTAGGTCGATACATTTTCATAAAGT
Done.