Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014297.1 Corchorus capsularis cultivar CVL-1 contig14318, 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: 8765
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1173 original size:57 final size:59
Alignment explanation
Indices: 1097--1499 Score: 374
Period size: 57 Copynumber: 6.7 Consensus size: 59
1087 AGATTGAAAC
* * **
1097 AGAAACTCTCGGCTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTGGGTTG-
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTAGAATTGA
* * * * * *
1155 A-AAACTCTCAATTAGAGACCTCGAGCAAGATTTGAAAATGAAACAGGACTTAGAATTG-
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAACAAGATTTAGAATTGA
* * * *
1213 A-TAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGATTGAAATA
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTAGAATTG----A
* ** * *
1275 AGAAACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G--ACAAGATTTAAAATTGAAACA
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTAGAATTG----A
* * * *
1335 AGAAACTCTGGACTAGAGACCTCAAGCAGGATTTTAAATGACACAAGACTTAGAATTG-
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTAGAATTGA
* * * *
1393 A-TAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACA
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGA-TTTAGAATTG----A
1456 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAAC
1 AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAAC
1500 TCTCCAACAG
Statistics
Matches: 281, Mismatches: 47, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
57 88 0.31
58 56 0.20
60 49 0.17
61 1 0.00
62 2 0.01
63 45 0.16
64 40 0.14
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (59 bp):
AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTAGAATTGA
Found at i:1487 original size:121 final size:119
Alignment explanation
Indices: 1078--1499 Score: 466
Period size: 121 Copynumber: 3.5 Consensus size: 119
1068 AACTCTCGAG
*
1078 CAAGATTTTAG-ATTGAAACAGAAACTCTCGGCTAGAGACCTCAAGCAGGATTTGAAATGAAACA
1 CAAGA-TTTAGAATTGAAACAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACA
* * * * *
1142 AGATTTTGGGTTGAAAACTCTCAATTAGAGACCTCGAGCAAGATTTGAAAATGAAA
65 AGATTTTGGATTGATAACTCTCGACTAGAGACCTCGAGCAGGATTT-AAAATGAAA
* * * *
1198 CAGGACTTAGAATTG----A-TAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAA
1 CAAGATTTAGAATTGAAACAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAA
** **
1258 GATTTTGGATTGAAATAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G--A
66 GATTTTGGATTG--AT----AACTCTCGACTAGAGACCTCGAGCAGGATTTAAAATGAAA
* * * *
1315 CAAGATTTAAAATTGAAACAAGAAACTCTGGACTAGAGACCTCAAGCAGGATTTTAAATGACACA
1 CAAGATTTAGAATTGAAAC-AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACA
* * * *
1380 AGACTTAGAATTGATAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAA
65 AGATTTTGGATTGATAACTCTCGACTAGAGACCTCGAGCAGGATTTAAAATGAAA
* *
1435 CAATATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAAC
1 CAAGA-TTTAGAATTGAAAC-AGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAAC
1500 TCTCCAACAG
Statistics
Matches: 250, Mismatches: 35, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
115 52 0.21
116 1 0.00
117 44 0.18
118 1 0.00
119 5 0.02
120 15 0.06
121 82 0.33
122 1 0.00
123 49 0.20
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (119 bp):
CAAGATTTAGAATTGAAACAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAA
GATTTTGGATTGATAACTCTCGACTAGAGACCTCGAGCAGGATTTAAAATGAAA
Found at i:1843 original size:63 final size:62
Alignment explanation
Indices: 1735--1853 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
1725 TCATAAAGTA
* *
1735 ATGAACCTAAATCAGGAGTGAAATCATGAAACAATAATCCTAAATTAGGATTGAAAAAAAGCC
1 ATGAACCTAAATCAGGAGAGAAATAATGAAACAATAATCCTAAATTAGGATT-AAAAAAAGCC
* * * *
1798 ATGATCCTAAATCAGG-GAGAAACTAATTAATCAATGATCCTAAATTAGGATTAAAA
1 ATGAACCTAAATCAGGAGAGAAA-TAATGAAACAATAATCCTAAATTAGGATTAAAA
1854 TGCATTAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
62 9 0.18
63 40 0.82
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (62 bp):
ATGAACCTAAATCAGGAGAGAAATAATGAAACAATAATCCTAAATTAGGATTAAAAAAAGCC
Found at i:1870 original size:38 final size:36
Alignment explanation
Indices: 1829--2067 Score: 219
Period size: 38 Copynumber: 6.7 Consensus size: 36
1819 ACTAATTAAT
* * *
1829 CAATGATCCTAAATTAGGATTAAAATGCATTAATAAAT
1 CAATGATCCTAGATCAGGATTAAAAT-CATT-ATAAAG
* * * *
1867 CAATGATCCTAAACCAGGATAAAAATGATCTTATAAAG
1 CAATGATCCTAGATCAGGATTAAAATCA--TTATAAAG
* *
1905 CAATGATCCTAGATCAGGATTAACATGAATTGATAAAG
1 CAATGATCCTAGATCAGGATTAAAAT-CATT-ATAAAG
1943 CAATGATCCTAGATCAGGATT--AA-C-TTATAAAG
1 CAATGATCCTAGATCAGGATTAAAATCATTATAAAG
1975 CAATGATCCTAGATCAGGATT--AA-C-TTATAAAG
1 CAATGATCCTAGATCAGGATTAAAATCATTATAAAG
* *
2007 CAATGATCCTAGATCAGGATCATAAAT--TGATAAAG
1 CAATGATCCTAGATCAGGATTA-AAATCATTATAAAG
* * *
2042 CAATGATCCTAAATTAGGATTGAAAT
1 CAATGATCCTAGATCAGGATTAAAAT
2068 AAACCCATAA
Statistics
Matches: 175, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
32 58 0.33
33 2 0.01
34 4 0.02
35 27 0.15
36 1 0.01
37 3 0.02
38 77 0.44
39 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (36 bp):
CAATGATCCTAGATCAGGATTAAAATCATTATAAAG
Found at i:1924 original size:76 final size:70
Alignment explanation
Indices: 1792--2067 Score: 213
Period size: 76 Copynumber: 3.9 Consensus size: 70
1782 GGATTGAAAA
* * ** * * * * * *
1792 AAAGCCATGATCCTAAATCAGGGAGAAACTAATTAATCAATGATCCTAAATTAGGATTAAAATGC
1 AAAGCAATGATCCTAAACCA-GGATTAACTTATAAAGCAATGATCCTAGATCAGGATTAAAATGA
1857 ATTAAT
65 ATTAAT
* *
1863 AAATCAATGATCCTAAACCAGGATAAAAATGATCTTATAAAGCAATGATCCTAGATCAGGATTAA
1 AAAGCAATGATCCTAAACCAGGAT-----T-AACTTATAAAGCAATGATCCTAGATCAGGATTAA
* *
1928 CATGAATTGAT
60 AATGAATTAAT
* * *
1939 AAAGCAATGATCCTAGATCAGGATTAACTTATAAAGCAATGATCCTAGATCAGGATT---A--AC
1 AAAGCAATGATCCTAAACCAGGATTAACTTATAAAGCAATGATCCTAGATCAGGATTAAAATGAA
1999 TT-AT
66 TTAAT
* * * * * *
2003 AAAGCAATGATCCTAGATCAGGATCATAAATTGATAAAGCAATGATCCTAAATTAGGATTGAAAT
1 AAAGCAATGATCCTAAACCAGGAT--TAACTT-ATAAAGCAATGATCCTAGATCAGGATTAAAAT
2068 AAACCCATAA
Statistics
Matches: 170, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
64 26 0.15
65 3 0.02
66 5 0.03
67 26 0.15
70 35 0.21
71 18 0.11
76 57 0.34
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (70 bp):
AAAGCAATGATCCTAAACCAGGATTAACTTATAAAGCAATGATCCTAGATCAGGATTAAAATGAA
TTAAT
Found at i:1978 original size:32 final size:32
Alignment explanation
Indices: 1896--2062 Score: 226
Period size: 32 Copynumber: 4.9 Consensus size: 32
1886 TAAAAATGAT
1896 CTTATAAAGCAATGATCCTAGATCAGGATTAA
1 CTTATAAAGCAATGATCCTAGATCAGGATTAA
1928 CATGAATTGATAAAGCAATGATCCTAGATCAGGATTAA
1 C-----TT-ATAAAGCAATGATCCTAGATCAGGATTAA
1966 CTTATAAAGCAATGATCCTAGATCAGGATTAA
1 CTTATAAAGCAATGATCCTAGATCAGGATTAA
1998 CTTATAAAGCAATGATCCTAGATCAGGATCATAA
1 CTTATAAAGCAATGATCCTAGATCAGGAT--TAA
* * *
2032 ATTGATAAAGCAATGATCCTAAATTAGGATT
1 CTT-ATAAAGCAATGATCCTAGATCAGGATT
2063 GAAATAAACC
Statistics
Matches: 123, Mismatches: 3, Indels: 17
0.86 0.02 0.12
Matches are distributed among these distances:
32 59 0.48
33 3 0.02
34 5 0.04
35 24 0.20
37 2 0.02
38 30 0.24
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (32 bp):
CTTATAAAGCAATGATCCTAGATCAGGATTAA
Found at i:2505 original size:49 final size:49
Alignment explanation
Indices: 2434--2534 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
2424 CGTTGAAACT
* * **
2434 ACTGAAGAAAGACCACCTTGGGTCGGCTGAATCGATCATTCTGACATAA
1 ACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAA
*
2483 ACTGGAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAA
1 ACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAA
2532 ACT
1 ACT
2535 TGAATAAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (49 bp):
ACTGAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAA
Found at i:2583 original size:119 final size:119
Alignment explanation
Indices: 2370--2594 Score: 328
Period size: 119 Copynumber: 1.9 Consensus size: 119
2360 AACACCTGAT
* * * *
2370 GAAAAGCCGCCCTGAGTCGACTGAATCGATCATTCTGACATAAACTTGGAAAAACGTTGAAACTA
1 GAAAAACCACCCTGAGTCAACTGAATCGATCATTCTGACATAAACTTGGAAAAACGTTGAAACAA
* * *
2435 CTGAAGAAAGACCACCTTGGGTCGGCTGAATCGATCATTCTGACATAAACTGGA
66 CTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTGGA
*
2489 GAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTT-GAATAAAC-TTGAAAAC
1 GAAAAACCACCCTGAGTCAACTGAATCGATCATTCTGACATAAACTTGGAA-AAACGTTG-AAAC
* *
2552 AATTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCT
64 AACTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCT
2595 AACAAAAAAC
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
118 6 0.06
119 88 0.94
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (119 bp):
GAAAAACCACCCTGAGTCAACTGAATCGATCATTCTGACATAAACTTGGAAAAACGTTGAAACAA
CTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTGGA
Found at i:2585 original size:70 final size:70
Alignment explanation
Indices: 2482--2675 Score: 235
Period size: 71 Copynumber: 2.8 Consensus size: 70
2472 TTCTGACATA
* * * *
2482 AACTGGAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGAATAAACTTG
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTGG
2547 AAAAC
66 AAAAC
* * * * * * *
2552 AATTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTAACAAAAAACTTGGATCAACTG
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGAC-ATAAACTTGAATAAACTG
* *
2617 GGAAGC
65 GAAAAC
* * *
2623 TACTGAAGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATGAACT
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
2676 AAAGAAAGAC
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
70 44 0.43
71 58 0.57
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (70 bp):
AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTGG
AAAAC
Found at i:2640 original size:190 final size:188
Alignment explanation
Indices: 2372--2722 Score: 526
Period size: 190 Copynumber: 1.9 Consensus size: 188
2362 CACCTGATGA
* * *
2372 AAAGCCGCCCTGAGTCGACTGAATCGATCATTCTGACATAAACTTGGAAAAACGTTGAAACTACT
1 AAAGCCGCCCTGAGTCGACTGAATCGATCATTCTAACAAAAACTTGGAAAAACGTGGAAACTACT
* **
2437 GAAGAAAGACCACCTTGGGTCGGCTGAATCGATCATTCTGACATAAACTGGAGAAAAACCACCCT
66 GAAGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATAAACTAAAGAAAAACCACCCT
* *
2502 GGGTCAACTGAATCGATCATTCTGACATAAACTTGAATAAACTTGAAAACAATTGAAG
131 AGGTCAACCGAATCGATCATTCTGACATAAACTTGAATAAACTTGAAAACAATTGAAG
** *
2560 AAAGACCGCCCT-AGGTCGACTGAATCGATCATTCTAACAAAAAACTTGGATCAAC-TGGGAAGC
1 AAAG-CCGCCCTGA-GTCGACTGAATCGATCATTCTAAC-AAAAACTTGGAAAAACGT-GGAAAC
* * *
2623 TACTGAAGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATGAACTAAAGAAAGACCG
62 TACTGAAGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATAAACTAAAGAAAAACCA
2688 CCCTAGGTCAACCGAATCGATCATTCTGACATAAA
127 CCCTAGGTCAACCGAATCGATCATTCTGACATAAA
2723 TTGTAGAAAA
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
188 5 0.03
189 31 0.21
190 109 0.75
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (188 bp):
AAAGCCGCCCTGAGTCGACTGAATCGATCATTCTAACAAAAACTTGGAAAAACGTGGAAACTACT
GAAGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATAAACTAAAGAAAAACCACCCT
AGGTCAACCGAATCGATCATTCTGACATAAACTTGAATAAACTTGAAAACAATTGAAG
Found at i:2681 original size:49 final size:49
Alignment explanation
Indices: 2628--2822 Score: 248
Period size: 49 Copynumber: 4.0 Consensus size: 49
2618 GAAGCTACTG
* * * * *
2628 AAGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATGAACTA
1 AAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTGACATAAACTA
* * *
2677 AAGAAAGACCGCCCTAGGTCAACCGAATCGATCATTCTGACATAAATTG
1 AAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTGACATAAACTA
* * * * * *
2726 TAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGAAATAAAACTT
1 AAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTGACAT-AAACTA
2776 AAGAAAGACC-CCCTAGGTCAACCGAATCGATCATTCTGACATAAACT
1 AAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTGACATAAACT
2823 TGGATAAACT
Statistics
Matches: 124, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
48 5 0.04
49 107 0.86
50 12 0.10
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (49 bp):
AAGAAAGACCACCCTAGGTCAACCGAATCGATCATTCTGACATAAACTA
Found at i:2790 original size:98 final size:98
Alignment explanation
Indices: 2629--2820 Score: 314
Period size: 98 Copynumber: 2.0 Consensus size: 98
2619 AAGCTACTGA
* * * * *
2629 AGAAAGACCACCTTGGGTCGACTGAATCGATCATTCTGACATGAACTAAAGAAAGACCGCCCTAG
1 AGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGAAATAAACTAAAGAAAGACCGCCCTAG
2694 GTCAACCGAATCGATCATTCTGACATAAATTGT
66 GTCAACCGAATCGATCATTCTGACATAAATTGT
*
2727 AGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGAAATAAAACTTAAGAAAGACC-CCCTA
1 AGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGAAAT-AAACTAAAGAAAGACCGCCCTA
2791 GGTCAACCGAATCGATCATTCTGACATAAA
65 GGTCAACCGAATCGATCATTCTGACATAAA
2821 CTTGGATAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 73 0.84
99 14 0.16
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (98 bp):
AGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGAAATAAACTAAAGAAAGACCGCCCTAG
GTCAACCGAATCGATCATTCTGACATAAATTGT
Found at i:4557 original size:6 final size:6
Alignment explanation
Indices: 4546--4592 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
4536 TTTAGGCTGA
*
4546 GTTTTT GTTTTT GTTTTT GTTTTCT GTTGTT GTTTTT -TTTTT -TTTTT
1 GTTTTT GTTTTT GTTTTT GTTTT-T GTTTTT GTTTTT GTTTTT GTTTTT
4593 AAAAGTCGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 10 0.26
6 23 0.61
7 5 0.13
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (6 bp):
GTTTTT
Found at i:4573 original size:19 final size:18
Alignment explanation
Indices: 4546--4587 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
4536 TTTAGGCTGA
*
4546 GTTTTTGTTTTTGTTTTT
1 GTTTTTGTTGTTGTTTTT
4564 GTTTTCTGTTGTTGTTTTT
1 GTTTT-TGTTGTTGTTTTT
4583 -TTTTT
1 GTTTTT
4588 TTTTTAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 9 0.41
19 12 0.55
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (18 bp):
GTTTTTGTTGTTGTTTTT
Found at i:5275 original size:14 final size:13
Alignment explanation
Indices: 5218--5274 Score: 71
Period size: 14 Copynumber: 4.3 Consensus size: 13
5208 AAAAAGACTC
5218 AAAACC-TTTTTG
1 AAAACCATTTTTG
5230 AAAACCCATTTTTG
1 AAAA-CCATTTTTG
*
5244 AAAACCTTTTATTG
1 AAAACCATTT-TTG
*
5258 AAAACAATTTTTG
1 AAAACCATTTTTG
5271 AAAA
1 AAAA
5275 ATATATCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.10
13 14 0.36
14 21 0.54
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:5376 original size:26 final size:26
Alignment explanation
Indices: 5338--5408 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
5328 ACTTGATTTT
*
5338 TCTTTTCTTTTTTCTTTT-TATTCTTCT
1 TCTTTTCTTTTTT-TTTTATA-TCTTCC
* *
5365 TTTTTCTCTTTTTTTTTTTTATCTTCC
1 TCTTT-TCTTTTTTTTTTATATCTTCC
5392 TCTTTTCTTTTTTTTTT
1 TCTTTTCTTTTTTTTTT
5409 GAAAGGAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 12 0.31
27 17 0.44
28 10 0.26
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (26 bp):
TCTTTTCTTTTTTTTTTATATCTTCC
Found at i:5389 original size:27 final size:27
Alignment explanation
Indices: 5338--5408 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
5328 ACTTGATTTT
* *
5338 TCTTTTCTTTTTTCTTTTTATTCTTCT
1 TCTTTTCTTTTTTTTTTTTATTCTTCC
*
5365 TTTTTCTCTTTTTTTTTTTTA-TCTTCC
1 TCTTT-TCTTTTTTTTTTTTATTCTTCC
5392 TCTTTTCTTTTTTTTTT
1 TCTTTTCTTTTTTTTTT
5409 GAAAGGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 12 0.31
27 13 0.33
28 14 0.36
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TCTTTTCTTTTTTTTTTTTATTCTTCC
Found at i:6540 original size:42 final size:42
Alignment explanation
Indices: 6450--6550 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
6440 CATACAAGTG
* * ** *
6450 AATGCATGATGGATGCATGAGCATATATACTAATTAATGGGT
1 AATGCATGATGGATGCATGAACATATATACAAAAGAATGGGC
* *
6492 AGTGCATGATCGATGCATGAACATATATACAAAAGAA-GGGAC
1 AATGCATGATGGATGCATGAACATATATACAAAAGAATGGG-C
6534 AATGCATGATGGATGCA
1 AATGCATGATGGATGCA
6551 GGCATATACA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.25
Consensus pattern (42 bp):
AATGCATGATGGATGCATGAACATATATACAAAAGAATGGGC
Done.