Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010618.1 Corchorus capsularis cultivar CVL-1 contig10639, 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: 26965
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:281 original size:112 final size:112
Alignment explanation
Indices: 81--303 Score: 392
Period size: 112 Copynumber: 2.0 Consensus size: 112
71 TCCATAATCT
* * * *
81 CACCCCGCCCATCCCAGGATTCGAACCCGGAACCTCTCGCAAGAAGTCCCAAGTTTTAACCGTTG
1 CACCCCGCCCATCCCAGGATTCGAACCCGAAACCTCTCGCAAGAAGTACCAAGTTTTAACCGCTA
*
146 GGGTGTCCCCTTGGGGACGGAACGTATAATTGATAGTCACGTGCAAC
66 GGGTGTCCCCTTGGGGACAGAACGTATAATTGATAGTCACGTGCAAC
*
193 CACCCCGCCCATCCCAGGATTCGAACCCGAAACCTCTCGCAAGAAGTACCAAGTTTTAACTGCTA
1 CACCCCGCCCATCCCAGGATTCGAACCCGAAACCTCTCGCAAGAAGTACCAAGTTTTAACCGCTA
258 GGGTGTCCCCTTGGGGACAGAACGTATAATTGATAGTCACGTGCAA
66 GGGTGTCCCCTTGGGGACAGAACGTATAATTGATAGTCACGTGCAA
304 TTCATATTGC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (112 bp):
CACCCCGCCCATCCCAGGATTCGAACCCGAAACCTCTCGCAAGAAGTACCAAGTTTTAACCGCTA
GGGTGTCCCCTTGGGGACAGAACGTATAATTGATAGTCACGTGCAAC
Found at i:3155 original size:18 final size:18
Alignment explanation
Indices: 3134--3202 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
3124 CTGTGTTCGA
3134 TGCTGGGACTGTATTTGG
1 TGCTGGGACTGTATTTGG
* *
3152 TGCTGGGACTGTGTTCGG
1 TGCTGGGACTGTATTTGG
* *
3170 TGCTGGGATTGTATTTGA
1 TGCTGGGACTGTATTTGG
3188 TGCTGGGACTGTATT
1 TGCTGGGACTGTATT
3203 AGCAGGTTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.39
Consensus pattern (18 bp):
TGCTGGGACTGTATTTGG
Found at i:3174 original size:36 final size:36
Alignment explanation
Indices: 3124--3199 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
3114 GGAACAAAAT
*
3124 CTGTGTTCGATGCTGGGACTGTATTTGGTGCTGGGA
1 CTGTGTTCGATGCTGGGACTGTATTTGATGCTGGGA
* *
3160 CTGTGTTCGGTGCTGGGATTGTATTTGATGCTGGGA
1 CTGTGTTCGATGCTGGGACTGTATTTGATGCTGGGA
3196 CTGT
1 CTGT
3200 ATTAGCAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.11, C:0.13, G:0.38, T:0.38
Consensus pattern (36 bp):
CTGTGTTCGATGCTGGGACTGTATTTGATGCTGGGA
Found at i:4711 original size:26 final size:26
Alignment explanation
Indices: 4682--4776 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 26
4672 TTTCTTACTC
4682 TTTTACTTAATACCATTTTGACCCTT
1 TTTTACTTAATACCATTTTGACCCTT
* * *
4708 TTTTACTTAATATCATTTTTACTAAATGCTAT
1 TTTTACTTAATACCATTTTGAC-----CCT-T
4740 TTTTACTTAATACCATTTTGA-CCTT
1 TTTTACTTAATACCATTTTGACCCTT
*
4765 TTTTACCTAATA
1 TTTTACTTAATA
4777 TGATTTTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
25 12 0.21
26 22 0.39
31 2 0.04
32 20 0.36
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (26 bp):
TTTTACTTAATACCATTTTGACCCTT
Found at i:4758 original size:15 final size:16
Alignment explanation
Indices: 4707--4758 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
4697 TTTTGACCCT
*
4707 TTTTTACTTAATATCA
1 TTTTTACTTAATACCA
* * *
4723 TTTTTACTAAATGCTA
1 TTTTTACTTAATACCA
4739 TTTTTACTTAATACCA
1 TTTTTACTTAATACCA
4755 TTTT
1 TTTT
4759 GACCTTTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTTTACTTAATACCA
Found at i:4785 original size:16 final size:16
Alignment explanation
Indices: 4764--4820 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
4754 ATTTTGACCT
4764 TTTTTACCTAATATGA
1 TTTTTACCTAATATGA
4780 TTTTTA-CTAA-ATGCCA
1 TTTTTACCTAATATG--A
* *
4796 CTTTTACCTAATATCA
1 TTTTTACCTAATATGA
*
4812 TTTTGACCT
1 TTTTTACCT
4821 TTTTTACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 20 0.61
17 4 0.12
18 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (16 bp):
TTTTTACCTAATATGA
Found at i:4790 original size:57 final size:57
Alignment explanation
Indices: 4681--4860 Score: 297
Period size: 57 Copynumber: 3.1 Consensus size: 57
4671 TTTTCTTACT
*
4681 CTTTTACTTAATACCATTTTGACCCTTTTTTACTTAATATCATTTTTACTAAATGCTA
1 CTTTTACTTAATACCATTTTGA-CCTTTTTTACTTAATATCATTTTTACTAAATGCCA
* * *
4739 TTTTTACTTAATACCATTTTGACCTTTTTTACCTAATATGATTTTTACTAAATGCCA
1 CTTTTACTTAATACCATTTTGACCTTTTTTACTTAATATCATTTTTACTAAATGCCA
* *
4796 CTTTTACCTAATATCATTTTGACCTTTTTTACTTAATATCATTTTTACTAAATGCCA
1 CTTTTACTTAATACCATTTTGACCTTTTTTACTTAATATCATTTTTACTAAATGCCA
4853 CTTTTACT
1 CTTTTACT
4861 GATCGCCATT
Statistics
Matches: 112, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
57 91 0.81
58 21 0.19
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.50
Consensus pattern (57 bp):
CTTTTACTTAATACCATTTTGACCTTTTTTACTTAATATCATTTTTACTAAATGCCA
Found at i:5326 original size:15 final size:15
Alignment explanation
Indices: 5308--5338 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5298 CTTAATTATC
*
5308 AATTTACTGATTACT
1 AATTTACTAATTACT
5323 AATTTACTAATTACT
1 AATTTACTAATTACT
5338 A
1 A
5339 TTACCTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (15 bp):
AATTTACTAATTACT
Found at i:5348 original size:52 final size:52
Alignment explanation
Indices: 5287--5424 Score: 231
Period size: 52 Copynumber: 2.7 Consensus size: 52
5277 GATTAATCTC
*
5287 TTACATTGACTCTTAATTATCAATTTACTGATTACTAATTTACTAATTACTA
1 TTACCTTGACTCTTAATTATCAATTTACTGATTACTAATTTACTAATTACTA
* *
5339 TTACCTTGACTCTTAATTATCAATTTACTGATTACTGATTTACTGATTACTA
1 TTACCTTGACTCTTAATTATCAATTTACTGATTACTAATTTACTAATTACTA
* *
5391 TTACCTTGACTCTAAATTATCAATTTATTGATTA
1 TTACCTTGACTCTTAATTATCAATTTACTGATTA
5425 ATCTCTTTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (52 bp):
TTACCTTGACTCTTAATTATCAATTTACTGATTACTAATTTACTAATTACTA
Found at i:5379 original size:15 final size:15
Alignment explanation
Indices: 5361--5389 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5351 TTAATTATCA
5361 ATTTACTGATTACTG
1 ATTTACTGATTACTG
5376 ATTTACTGATTACT
1 ATTTACTGATTACT
5390 ATTACCTTGA
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:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (15 bp):
ATTTACTGATTACTG
Found at i:5487 original size:37 final size:37
Alignment explanation
Indices: 5376--5511 Score: 176
Period size: 37 Copynumber: 3.8 Consensus size: 37
5366 CTGATTACTG
5376 ATTTACTGATTACTATTACCTTGACTCTAAATTATCA
1 ATTTACTGATTACTATTACCTTGACTCTAAATTATCA
* * *
5413 ATTTATTGATTA--ATCT-CTTTTTACT-T-AATTA-CTA
1 ATTTACTGATTACTAT-TAC-CTTGACTCTAAATTATC-A
5447 ATTTACTGATTACTATTACCTTGACTCTAAATTATCA
1 ATTTACTGATTACTATTACCTTGACTCTAAATTATCA
5484 ATTTACTGATTACTATTACCTTGACTCT
1 ATTTACTGATTACTATTACCTTGACTCT
5512 GATTAATCTG
Statistics
Matches: 84, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
33 1 0.01
34 17 0.20
35 10 0.12
36 10 0.12
37 45 0.54
38 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (37 bp):
ATTTACTGATTACTATTACCTTGACTCTAAATTATCA
Found at i:6363 original size:50 final size:50
Alignment explanation
Indices: 6318--6811 Score: 711
Period size: 50 Copynumber: 9.7 Consensus size: 50
6308 ACTAATGGCC
* *
6318 TAAAAGTTCAAACTTTTAATTCAAAGGTGACA-TTTTATTTACTAATTACTTT
1 TAAAAATTCAATCTTTT-ATTCAAAGGTGACATTTTTATTTACTAATTAC--T
* * * * *
6370 TAAAAAATTCAATCTTTTATTCGAAGGTTACATCTTTATTTACCAACTACT
1 T-AAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
**
6421 TAAAAATTCAATCTTTTGCTCAAAGGTGACATTTTTATTTACTAATTACT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
* * *
6471 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTATT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
** *
6521 CTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTACT
1 -TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
6572 TAAAAATTTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
1 TAAAAA-TTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
* *
6623 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTACT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
** *
6673 CTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTACT
1 -TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
6724 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
* *
6774 TAAAAATTCAATTTTTTATTCAAAGGTTACATCTTTTA
1 TAAAAATTCAATCTTTTATTCAAAGGTGACAT-TTTTA
6812 GCCAAATATC
Statistics
Matches: 396, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
50 212 0.54
51 143 0.36
52 13 0.03
53 28 0.07
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (50 bp):
TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT
Found at i:6603 original size:152 final size:151
Alignment explanation
Indices: 6318--6809 Score: 797
Period size: 152 Copynumber: 3.2 Consensus size: 151
6308 ACTAATGGCC
* * * *
6318 TAAAAGTTCAAACTTTTAATTCAAAGGTGACAT-TTTATTTACTAATTACTTTTAAAAAATTCAA
1 TAAAAATTCAATCTTTT-ATTCAAAGGTTACATCTTTATTTACTAATTA-TTCT-AAAAATTCAA
** * * * * * * **
6382 TCTTTTATTCGAAGGTTACATCTTTATTTACCAACTACTTAAAAATTCAATCTTTTGCTCAAAGG
63 TCTTTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGG
6447 TGACATTTTTATTTACTAATTACT
128 TGACATTTTTATTTACTAATTACT
6471 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTATTCTAAAAATTCAATCT
1 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTATTCTAAAAATTCAATCT
6536 TTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAATTTCAATCTTTTATTCAAAGGTG
66 TTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAA-TTCAATCTTTTATTCAAAGGTG
6601 ACATTTTTATTTACTAATTACT
130 ACATTTTTATTTACTAATTACT
*
6623 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTACTCTAAAAATTCAATCT
1 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTATTCTAAAAATTCAATCT
6688 TTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGA
66 TTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGA
6753 CATTTTTATTTACTAATTACT
131 CATTTTTATTTACTAATTACT
*
6774 TAAAAATTCAATTTTTTATTCAAAGGTTACATCTTT
1 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTT
6810 TAGCCAAATA
Statistics
Matches: 321, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
151 126 0.39
152 165 0.51
153 30 0.09
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (151 bp):
TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTATTCTAAAAATTCAATCT
TTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGA
CATTTTTATTTACTAATTACT
Found at i:6811 original size:101 final size:101
Alignment explanation
Indices: 6318--6811 Score: 719
Period size: 101 Copynumber: 4.9 Consensus size: 101
6308 ACTAATGGCC
* *
6318 TAAAAGTTCAAACTTTTAATTCAAAGGTGACA-TTTTATTTACTAATTACTTTTAAAAAATTCAA
1 TAAAAATTCAATCTTTT-ATTCAAAGGTGACATTTTTATTTACTAATTAC--TT-AAAAATTCAA
* * *
6382 TCTTTTATTCGAAGGTTACATC-TTTATTTACCAACTACT
62 TCTTTTATTCAAAGGTTACATCTTTTATTTACTAATTACT
**
6421 TAAAAATTCAATCTTTTGCTCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTT
*
6486 TTATTCAAAGGTTACATC-TTTATTTACTAATTATT
66 TTATTCAAAGGTTACATCTTTTATTTACTAATTACT
** *
6521 CTAAAAATTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTACTTAAAAATTTCAATC
1 -TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACTTAAAAA-TTCAATC
*
6586 TTTTATTCAAAGGTGACAT-TTTTATTTACTAATTACT
64 TTTTATTCAAAGGTTACATCTTTTATTTACTAATTACT
* *
6623 TAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTACTCTAAAAATTCAATCT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACT-TAAAAATTCAATCT
** * *
6688 TTTACCCAAAGATGACAT-TTTTATTTACTAATTACT
65 TTTATTCAAAGGTTACATCTTTTATTTACTAATTACT
*
6724 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATTTT
1 TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTT
6789 TTATTCAAAGGTTACATCTTTTA
66 TTATTCAAAGGTTACATCTTTTA
6812 GCCAAATATC
Statistics
Matches: 357, Mismatches: 28, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
100 72 0.20
101 194 0.54
102 59 0.17
103 32 0.09
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (101 bp):
TAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTT
TTATTCAAAGGTTACATCTTTTATTTACTAATTACT
Found at i:9255 original size:27 final size:27
Alignment explanation
Indices: 9214--9282 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
9204 ACCAATTTAC
*
9214 CAAAATGCCCTTGGGTGCAAAAATGA-
1 CAAAATGCCCCTGGGTGCAAAAATGAT
9240 CTAAAATGCCCCTGGGTGCAAAAATGAT
1 C-AAAATGCCCCTGGGTGCAAAAATGAT
*
9268 CAAAATGCTCCTGGG
1 CAAAATGCCCCTGGG
9283 CGACCCTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 1 0.03
27 37 0.95
28 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
CAAAATGCCCCTGGGTGCAAAAATGAT
Found at i:12729 original size:22 final size:21
Alignment explanation
Indices: 12681--12729 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
12671 TTTATGGAAG
**
12681 TTAA-ATATATTTTTATTGTA
1 TTAATATATATTTTTATTCCA
12701 TTAATATATATTTATTATTCCA
1 TTAATATATATTT-TTATTCCA
*
12723 TTTATAT
1 TTAATAT
12730 TACTACGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 8 0.33
22 12 0.50
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAATATATATTTTTATTCCA
Found at i:19159 original size:20 final size:21
Alignment explanation
Indices: 19120--19159 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19110 CAAATGCTCA
*
19120 ACTTAAGGAGACAAACGACTT
1 ACTTAAGAAGACAAACGACTT
*
19141 ACTTAAGAAG-CAAATGACT
1 ACTTAAGAAGACAAACGACT
19160 CAAGATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.20
Consensus pattern (21 bp):
ACTTAAGAAGACAAACGACTT
Found at i:23783 original size:23 final size:23
Alignment explanation
Indices: 23747--23798 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
23737 TTTATGTTGT
23747 TTTTAAATTGATTTAAGTTGTAA
1 TTTTAAATTGATTTAAGTTGTAA
* *
23770 TTTTAACTTTATTTAAGTTGTAA
1 TTTTAAATTGATTTAAGTTGTAA
23793 TTTTAA
1 TTTTAA
23799 GTTAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (23 bp):
TTTTAAATTGATTTAAGTTGTAA
Found at i:23799 original size:13 final size:13
Alignment explanation
Indices: 23758--23801 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
23748 TTTAAATTGA
23758 TTTAAGTTGTAAT
1 TTTAAGTTGTAAT
*
23771 TTTAACTT-T-A-
1 TTTAAGTTGTAAT
23781 TTTAAGTTGTAAT
1 TTTAAGTTGTAAT
23794 TTTAAGTT
1 TTTAAGTT
23802 AAGTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 15 0.58
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (13 bp):
TTTAAGTTGTAAT
Found at i:23873 original size:13 final size:13
Alignment explanation
Indices: 23857--23887 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
23847 ATTAAGTCTA
23857 AAAAATAATTATG
1 AAAAATAATTATG
23870 AAAAATAATTATG
1 AAAAATAATTATG
23883 AAAAA
1 AAAAA
23888 AACATATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (13 bp):
AAAAATAATTATG
Found at i:25071 original size:2 final size:2
Alignment explanation
Indices: 25066--25091 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25056 TATCTCTCCA
25066 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
25092 GTTTATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26286 original size:23 final size:24
Alignment explanation
Indices: 26259--26306 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
26249 GCAAATCAAA
26259 TCAAGCTCCAT-GCTTTCAAA-CTC
1 TCAAGC-CCATGGCTTTCAAATCTC
*
26282 TCAAGCCCTTGGCTTTCAAATCTC
1 TCAAGCCCATGGCTTTCAAATCTC
26306 T
1 T
26307 TTTGTAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 15 0.68
24 4 0.18
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (24 bp):
TCAAGCCCATGGCTTTCAAATCTC
Done.