Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014860.1 Corchorus capsularis cultivar CVL-1 contig14881, 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: 51983
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34 AAATAGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2760 original size:57 final size:57
Alignment explanation
Indices: 2672--2782 Score: 222
Period size: 57 Copynumber: 1.9 Consensus size: 57
2662 AATGCAGGGC
2672 CTAGGATTTGTGTAGGGAAGGAAATTGCTTTTACTGTGATGAAGGGCACTGTGTCTG
1 CTAGGATTTGTGTAGGGAAGGAAATTGCTTTTACTGTGATGAAGGGCACTGTGTCTG
2729 CTAGGATTTGTGTAGGGAAGGAAATTGCTTTTACTGTGATGAAGGGCACTGTGT
1 CTAGGATTTGTGTAGGGAAGGAAATTGCTTTTACTGTGATGAAGGGCACTGTGT
2783 GTAGGGAAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.33
Consensus pattern (57 bp):
CTAGGATTTGTGTAGGGAAGGAAATTGCTTTTACTGTGATGAAGGGCACTGTGTCTG
Found at i:3573 original size:21 final size:21
Alignment explanation
Indices: 3547--3587 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3537 GACTCTTTTT
*
3547 CACTATCTTCCACCACCTCTA
1 CACTATCCTCCACCACCTCTA
*
3568 CACTATCCTCTACCACCTCT
1 CACTATCCTCCACCACCTCT
3588 TCCTTGTCCT
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:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (21 bp):
CACTATCCTCCACCACCTCTA
Found at i:4415 original size:15 final size:15
Alignment explanation
Indices: 4391--4420 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4381 GGAAGGTCCA
*
4391 ACATGGGTAATGGTT
1 ACATGAGTAATGGTT
4406 ACATGAGTAATGGTT
1 ACATGAGTAATGGTT
4421 TGCTTCCAAC
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:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (15 bp):
ACATGAGTAATGGTT
Found at i:14406 original size:156 final size:155
Alignment explanation
Indices: 14097--14462 Score: 373
Period size: 156 Copynumber: 2.3 Consensus size: 155
14087 CCGAACCTCT
* * *
14097 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTTTAAGTCTGAATGAGCTGA
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGAGCTG-
* * * * * *
14162 AATTTTGCTAAGGGACTTATATTATCTCCATGAAACTATGGAAAAAATTATAAGTAAAACCGAGC
65 AATTTTGCCAAGAGAATTATACTATCCCCATGAAACTATGGAAAAAATTATAAGTAAAACCGAAC
* * * *
14227 TCCCCTTGATGGTGAACTAGGTTTCT
130 TCCCCTAGATAGAGAACTAGGTTTCA
* ***
14253 CTCCCCAGGTTGTCCTTAAATGGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATGAAGCT
1 CACCCCAAACTGTCCTTAAAT-GAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATG-AGCT
* * *
14317 G-ATTTT-CCACCAGTAGAATTA-ACTATCCCCATGAAGCTATGGGAAAAATTCTAAGTAAAACC
64 GAATTTTGCCA--AG-AGAATTATACTATCCCCATGAAACTATGGAAAAAATTATAAGTAAAACC
* * * *
14379 GAACT-CTCTAGCATAGAGAAGTTGGTTTGA
126 GAACTCCCCTAG-ATAGAGAACTAGGTTTCA
* * * * *
14409 CACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCATACGAAGTCT
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
14463 GTTTGAGATG
Statistics
Matches: 170, Mismatches: 33, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
154 2 0.01
155 38 0.22
156 89 0.52
157 41 0.24
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (155 bp):
CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGAGCTGA
ATTTTGCCAAGAGAATTATACTATCCCCATGAAACTATGGAAAAAATTATAAGTAAAACCGAACT
CCCCTAGATAGAGAACTAGGTTTCA
Found at i:16196 original size:19 final size:19
Alignment explanation
Indices: 16167--16212 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16157 ACTCAGTCTC
*
16167 AAACTAACTG-ATTCAAAA
1 AAACTAACTGAACTCAAAA
16185 AAACTGAACTGAACTC-AAA
1 AAACT-AACTGAACTCAAAA
16204 AAACTAACT
1 AAACTAACT
16213 AAACCCAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 13 0.52
20 3 0.12
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.20
Consensus pattern (19 bp):
AAACTAACTGAACTCAAAA
Found at i:22650 original size:13 final size:13
Alignment explanation
Indices: 22634--22658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22624 TGTTTTCTCA
22634 AAATATTTTTAAT
1 AAATATTTTTAAT
22647 AAATATTTTTAA
1 AAATATTTTTAA
22659 GTCTTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATATTTTTAAT
Found at i:23266 original size:19 final size:18
Alignment explanation
Indices: 23242--23278 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
23232 ATTTTGTTCA
23242 TTTCATCATTTTCTTTCTT
1 TTTCAT-ATTTTCTTTCTT
*
23261 TTTCATTTTTTCTTTCTT
1 TTTCATATTTTCTTTCTT
23279 CCTCCCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCATATTTTCTTTCTT
Found at i:24408 original size:138 final size:138
Alignment explanation
Indices: 24160--24677 Score: 894
Period size: 138 Copynumber: 3.8 Consensus size: 138
24150 AAGGTTAGAT
* *
24160 TTTTTGAATGTTGTATTTGATTTTCTGACATA-CCTTGGATAGTGTGCGGAAGAGATAAGGTTTT
1 TTTTTGAATGTTGTGTTTGATTTTCTGACA-AGCCTTGGATAGTGTGCGGAAGAGATAAGATTTT
* * *
24224 AATCAACGGTCACATTTGAATATGAACGTTTAAATGCAACTGTTGGATTGAAATAGGGTTAGATT
65 AACCAACGGTCACATTTGAATATGAACGTTTAAATCCAACCGTTGGATTGAAATAGGGTTAGATT
24289 TTCTGAAAG
130 TTCTGAAAG
* *
24298 TTTTTGAATGTTGTGTTTGATTTTCTGACAAGCCTTGAATTGTGTGCGGAAGAGATAAGATTTTA
1 TTTTTGAATGTTGTGTTTGATTTTCTGACAAGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTA
*
24363 ACCAACGGTCACATTTGAATATGAACGTTTAAATCCAACCGTTGGATTGAAATAGGGTTAAATTT
66 ACCAACGGTCACATTTGAATATGAACGTTTAAATCCAACCGTTGGATTGAAATAGGGTTAGATTT
24428 TCTGAAAG
131 TCTGAAAG
*
24436 TTTTTGAATATTGTGTTTGATTTTCTGACAAGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTA
1 TTTTTGAATGTTGTGTTTGATTTTCTGACAAGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTA
*
24501 ACCAACGGTCACATTTGAATATGAACGTTTAAATCCAATCGTTGGATTGAAATAGGGTTAGATTT
66 ACCAACGGTCACATTTGAATATGAACGTTTAAATCCAACCGTTGGATTGAAATAGGGTTAGATTT
24566 TCTGAAAG
131 TCTGAAAG
* *
24574 TTTTTGAATGTTGTGTTTGAATTTCTGACATGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTA
1 TTTTTGAATGTTGTGTTTGATTTTCTGACAAGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTA
* *
24639 ACCAATGTTCACATTTGAATATGAACGTTTAAATCCAAC
66 ACCAACGGTCACATTTGAATATGAACGTTTAAATCCAAC
24678 GACTACATTT
Statistics
Matches: 360, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
137 1 0.00
138 359 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (138 bp):
TTTTTGAATGTTGTGTTTGATTTTCTGACAAGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTA
ACCAACGGTCACATTTGAATATGAACGTTTAAATCCAACCGTTGGATTGAAATAGGGTTAGATTT
TCTGAAAG
Found at i:27070 original size:12 final size:12
Alignment explanation
Indices: 27053--27096 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
27043 ACAGCAACAC
*
27053 AAAAAATATATA
1 AAAAAATATACA
*
27065 AAAAAAAATACA
1 AAAAAATATACA
*
27077 GAAAAATATACA
1 AAAAAATATACA
27089 AAAAAATA
1 AAAAAATA
27097 CAGAAAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAATATACA
Found at i:27091 original size:22 final size:22
Alignment explanation
Indices: 27055--27104 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
27045 AGCAACACAA
27055 AAAATATATAAAAAAAAATACAG
1 AAAA-ATATAAAAAAAAATACAG
*
27078 AAAAATATACAAAAAAATACAG
1 AAAAATATAAAAAAAAATACAG
27100 AAAAA
1 AAAAA
27105 GAAAAGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (22 bp):
AAAAATATAAAAAAAAATACAG
Found at i:27103 original size:12 final size:12
Alignment explanation
Indices: 27066--27104 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
27056 AAATATATAA
27066 AAAAAAATACAG
1 AAAAAAATACAG
*
27078 AAAAATATAC--
1 AAAAAAATACAG
27088 AAAAAAATACAG
1 AAAAAAATACAG
27100 AAAAA
1 AAAAA
27105 GAAAAGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (12 bp):
AAAAAAATACAG
Found at i:27554 original size:21 final size:20
Alignment explanation
Indices: 27516--27554 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27506 TTATAGCTAT
* *
27516 TTTTCTATACTTTTTACCAC
1 TTTTATATACTTTATACCAC
27536 TTTTATATACATTTATACC
1 TTTTATATAC-TTTATACC
27555 TTATTTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATATACTTTATACCAC
Found at i:27723 original size:11 final size:11
Alignment explanation
Indices: 27707--27736 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
27697 AAGTTCGTGT
27707 TTGAAGATTTC
1 TTGAAGATTTC
27718 TTGAAGATTTC
1 TTGAAGATTTC
27729 TTGAAGAT
1 TTGAAGAT
27737 AATTTGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (11 bp):
TTGAAGATTTC
Found at i:35706 original size:22 final size:23
Alignment explanation
Indices: 35681--35725 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
35671 AGTTTAGTTA
35681 TTTAGTTTATG-CTTTATTTTTC
1 TTTAGTTTATGTCTTTATTTTTC
*
35703 TTTATTTTATGTCTTTATTTTTC
1 TTTAGTTTATGTCTTTATTTTTC
35726 AAGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.13, C:0.09, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTAGTTTATGTCTTTATTTTTC
Found at i:37074 original size:21 final size:20
Alignment explanation
Indices: 37036--37074 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37026 TTATAGCTAT
* *
37036 TTTTCTATACTTTTTACCAC
1 TTTTATATACTTTATACCAC
37056 TTTTATATACATTTATACC
1 TTTTATATAC-TTTATACC
37075 TTATTTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATATACTTTATACCAC
Found at i:39681 original size:29 final size:29
Alignment explanation
Indices: 39626--39688 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
39616 AATGGTAATC
39626 AGTAAACAGTAAAATAGTAAAAAGTAAAG
1 AGTAAACAGTAAAATAGTAAAAAGTAAAG
* * * *
39655 GGTAATCAGTGAAA-AGTAAAATGGTAAAG
1 AGTAAACAGTAAAATAGTAAAA-AGTAAAG
39684 AGTAA
1 AGTAA
39689 GAGTAATCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.19
Consensus pattern (29 bp):
AGTAAACAGTAAAATAGTAAAAAGTAAAG
Found at i:39708 original size:35 final size:35
Alignment explanation
Indices: 39620--40002 Score: 260
Period size: 35 Copynumber: 10.9 Consensus size: 35
39610 AGGTGAAATG
* * * *
39620 GTAATCAGTAAACAGTAAAATAGTAAAAAGTAAAGG
1 GTAATCAGTAAAGAGTAAAATGGTAAAGAGT-AAGA
39656 GTAATCAGTGAAA-AGTAAAATGGTAAAGAGTAAGA
1 GTAATCAGT-AAAGAGTAAAATGGTAAAGAGTAAGA
* *
39691 GTAATCAGTAAAGAGTAAAATGGTAAAAAGTTATG-
1 GTAATCAGTAAAGAGTAAAATGGTAAAGAG-TAAGA
* * * ** *
39726 GTAATTAGTAAACACTAAAACAGTAAAGAGTAAAA
1 GTAATCAGTAAAGAGTAAAATGGTAAAGAGTAAGA
* *
39761 TGGTAATCAGTAAAG-GAAAAATGGTAAAGAGTAAAA
1 --GTAATCAGTAAAGAGTAAAATGGTAAAGAGTAAGA
*
39797 TGGTAATCAGTAAAG-GAAAAATGGTATAA-AGTAAAGA
1 --GTAATCAGTAAAGAGTAAAATGGTA-AAGAGT-AAGA
* * *
39834 GTAATCAGTAAAG-GAAAAAAGGTAAAAAGTAAAGA
1 GTAATCAGTAAAGAGTAAAATGGTAAAGAGT-AAGA
* * * *
39869 GTAATCAGTAAAAGTGTAAGATGGTAAAAAATGGAAAAGA
1 GTAATCAGT-AAAGAGTAAAATGGT-AAAGA--G-TAAGA
*
39909 GTAAATCAGTAAAGA--AAAAAGGT----A--AAGA
1 GT-AATCAGTAAAGAGTAAAATGGTAAAGAGTAAGA
* *
39937 GTAATCAATAAAGA--AAAATGGTAAAGAGCAAAGA
1 GTAATCAGTAAAGAGTAAAATGGTAAAGAG-TAAGA
*
39971 GTAATCAGTAAAGA-AAAAATGGTAAAGAGTAA
1 GTAATCAGTAAAGAGTAAAATGGTAAAGAGTAA
40003 TCAGTAAAGA
Statistics
Matches: 291, Mismatches: 32, Indels: 50
0.78 0.09 0.13
Matches are distributed among these distances:
27 18 0.06
28 6 0.02
31 1 0.00
33 1 0.00
34 26 0.09
35 106 0.36
36 78 0.27
37 26 0.09
38 11 0.04
40 11 0.04
41 7 0.02
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.19
Consensus pattern (35 bp):
GTAATCAGTAAAGAGTAAAATGGTAAAGAGTAAGA
Found at i:39783 original size:21 final size:21
Alignment explanation
Indices: 39746--39822 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
39736 AACACTAAAA
*
39746 CAGTAAAGAGTAAAATGGTAAT
1 CAGTAAAG-GAAAAATGGTAAT
39768 CAGTAAAGGAAAAATGGTAA-
1 CAGTAAAGGAAAAATGGTAAT
*
39788 -AG---A-GTAAAATGGTAAT
1 CAGTAAAGGAAAAATGGTAAT
39804 CAGTAAAGGAAAAATGGTA
1 CAGTAAAGGAAAAATGGTA
39823 TAAAGTAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.24
16 1 0.02
17 2 0.04
19 2 0.04
20 1 0.02
21 21 0.46
22 8 0.17
ACGTcount: A:0.52, C:0.04, G:0.25, T:0.19
Consensus pattern (21 bp):
CAGTAAAGGAAAAATGGTAAT
Found at i:39935 original size:28 final size:29
Alignment explanation
Indices: 39894--40030 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
39884 GTAAGATGGT
*
39894 AAAAAATGGAAAAGAGTAAATCAGTAAAG
1 AAAAAATGGTAAAGAGTAAATCAGTAAAG
*
39923 AAAAAA-GGTAAAGAGT-AATCAATAAAG
1 AAAAAATGGTAAAGAGTAAATCAGTAAAG
*
39950 -AAAAATGGTAAAGAGCAAAGAGTAATCAGTAAAG
1 AAAAAATGGTAAAGAG----TA--AATCAGTAAAG
39984 AAAAAATGGTAAAGAGT-AATCAGTAAAG
1 AAAAAATGGTAAAGAGTAAATCAGTAAAG
40012 AAAAAAATGGTAAAGAGTA
1 -AAAAAATGGTAAAGAGTA
40031 GAATATTAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 21
0.78 0.04 0.18
Matches are distributed among these distances:
26 5 0.05
27 19 0.21
28 20 0.22
29 23 0.25
34 10 0.11
35 15 0.16
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.15
Consensus pattern (29 bp):
AAAAAATGGTAAAGAGTAAATCAGTAAAG
Found at i:39970 original size:62 final size:63
Alignment explanation
Indices: 39904--40046 Score: 209
Period size: 62 Copynumber: 2.3 Consensus size: 63
39894 AAAAAATGGA
39904 AAAGAGTAAATCAGTAAAGAAAAAA-GGTAAAGAGTAATCAATAAAG-AAAAATGGTAAAGAGC
1 AAAGAGT-AATCAGTAAAGAAAAAATGGTAAAGAGTAATCAATAAAGAAAAAATGGTAAAGAGC
* *
39966 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAATCAGTAAAGAAAAAAATGGTAAAGAGT
1 AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAATCAATAAAG-AAAAAATGGTAAAGAGC
* *
40030 AGAATATTAATCAGTAA
1 A-AAGAGTAATCAGTAA
40047 TGGTAATCAG
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
61 17 0.23
62 27 0.37
64 16 0.22
65 13 0.18
ACGTcount: A:0.58, C:0.04, G:0.20, T:0.17
Consensus pattern (63 bp):
AAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTAATCAATAAAGAAAAAATGGTAAAGAGC
Found at i:39983 original size:14 final size:14
Alignment explanation
Indices: 39966--40012 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
39956 GGTAAAGAGC
39966 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
** *
39980 AAAGAAAAAAT-GGT
1 AAAG-AGTAATCAGT
39994 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
40008 AAAGA
1 AAAGA
40013 AAAAAATGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.57, C:0.04, G:0.21, T:0.17
Consensus pattern (14 bp):
AAAGAGTAATCAGT
Found at i:40080 original size:29 final size:30
Alignment explanation
Indices: 40045--40103 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
40035 ATTAATCAGT
40045 AATGGTAATCAGTAAAAAA-AATAAAAAAA
1 AATGGTAATCAGTAAAAAAGAATAAAAAAA
* * *
40074 AATGGTATTTAGTAAAAAAGAGTAAAAAAA
1 AATGGTAATCAGTAAAAAAGAATAAAAAAA
40104 TGGTAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.64, C:0.02, G:0.14, T:0.20
Consensus pattern (30 bp):
AATGGTAATCAGTAAAAAAGAATAAAAAAA
Found at i:40167 original size:29 final size:27
Alignment explanation
Indices: 40129--40280 Score: 121
Period size: 29 Copynumber: 5.4 Consensus size: 27
40119 AAACAGTAAA
*
40129 AAAAAAGAGTAAAAGAAATGGTATTCAGT
1 AAAAAAGAGT--AAGAAATGGTAATCAGT
*
40158 AAAAAAGAGTAAGCAAAGGGTAATCAGT
1 AAAAAAGAGTAAG-AAATGGTAATCAGT
*
40186 AAAAAAAAAGTAA-AAATGGTAATCAGT
1 -AAAAAAGAGTAAGAAATGGTAATCAGT
* *
40213 -AAAAAGAGTAAGAAAAGAGTAATTAGT
1 AAAAAAGAGTAAGAAATG-GTAATCAGT
* * *
40240 AGAAGAAGAAGGT-AGAAAATTGTAATCATT
1 A-AAAAAG-A-GTAAG-AAATGGTAATCAGT
*
40270 AAAAAGGAGTA
1 AAAAAAGAGTA
40281 GAATAGAGTA
Statistics
Matches: 99, Mismatches: 14, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
25 10 0.10
26 4 0.04
27 26 0.26
28 13 0.13
29 30 0.30
30 11 0.11
31 5 0.05
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.18
Consensus pattern (27 bp):
AAAAAAGAGTAAGAAATGGTAATCAGT
Found at i:40170 original size:60 final size:55
Alignment explanation
Indices: 40098--40229 Score: 160
Period size: 60 Copynumber: 2.3 Consensus size: 55
40088 AAAAAGAGTA
*
40098 AAAAAATG-GTAAGAAAAGGGCAAACAGTAAAAAAAAAGAGTAAAAGAAATGGTATTCAGT
1 AAAAAA-GAGTAAGAAAAGGGCAAACAGT-AAAAAAAA-AGT--AA-AAATGGTAATCAGT
* * *
40158 AAAAAAGAGTAAGCAAAGGGTAATCAGTAAAAAAAAAGTAAAAATGGTAATCAGT
1 AAAAAAGAGTAAGAAAAGGGCAAACAGTAAAAAAAAAGTAAAAATGGTAATCAGT
40213 -AAAAAGAGTAAGAAAAG
1 AAAAAAGAGTAAGAAAAG
40230 AGTAATTAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
54 16 0.24
55 13 0.20
56 2 0.03
58 3 0.05
59 9 0.14
60 23 0.35
ACGTcount: A:0.60, C:0.05, G:0.21, T:0.14
Consensus pattern (55 bp):
AAAAAAGAGTAAGAAAAGGGCAAACAGTAAAAAAAAAGTAAAAATGGTAATCAGT
Found at i:40228 original size:27 final size:27
Alignment explanation
Indices: 40130--40280 Score: 112
Period size: 27 Copynumber: 5.4 Consensus size: 27
40120 AACAGTAAAA
* *
40130 AAAAAGAGTAAAAGAAATGGTATTCAGT
1 AAAAAGAGTAAGA-AAATGGTAATCAGT
* *
40158 AAAAAAGAGTAAGCAAAGGGTAATCAGT
1 -AAAAAGAGTAAGAAAATGGTAATCAGT
*
40186 AAAAA-A-AAAGTAAAAATGGTAATCAGT
1 AAAAAGAGTAAG--AAAATGGTAATCAGT
*
40213 AAAAAGAGTAAGAAAA-GAGTAATTAGT
1 AAAAAGAGTAAGAAAATG-GTAATCAGT
* *
40240 AGAAGAAGAAGGT-AGAAAATTGTAATCATT
1 A-AA-AAG-A-GTAAGAAAATGGTAATCAGT
40270 AAAAAGGAGTA
1 AAAAA-GAGTA
40281 GAATAGAGTA
Statistics
Matches: 98, Mismatches: 12, Indels: 25
0.73 0.09 0.19
Matches are distributed among these distances:
25 3 0.03
26 2 0.02
27 38 0.39
28 18 0.18
29 20 0.20
30 15 0.15
31 2 0.02
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.19
Consensus pattern (27 bp):
AAAAAGAGTAAGAAAATGGTAATCAGT
Found at i:40273 original size:57 final size:54
Alignment explanation
Indices: 40106--40294 Score: 173
Period size: 57 Copynumber: 3.3 Consensus size: 54
40096 TAAAAAAATG
* * * *
40106 GTAAGAAAAGGGCAAACAGTAAAAAAAAAGAGTAAAAGAAATGGTATTCAGTAAAAAAGA
1 GTAAGAAAAGAGTAATCAGT-AAAAAAAA-AGT--AA-AAATGGTAATCAGT-AAAAAGA
* *
40166 GTAAGCAAAGGGTAATCAGTAAAAAAAAAGTAAAAATGGTAATCAGTAAAAAGA
1 GTAAGAAAAGAGTAATCAGTAAAAAAAAAGTAAAAATGGTAATCAGTAAAAAGA
* * * * *
40220 GTAAGAAAAGAGTAATTAGTAGAAGAAGAAGGTAGAAAATTGTAATCATTAAAAAGGA
1 GTAAGAAAAGAGTAATCAGTA-AA-AAAAAAGTA-AAAATGGTAATCAGTAAAAA-GA
*
40278 GT-AGAATAGAGTAATCA
1 GTAAGAAAAGAGTAATCA
40295 ATAATTTAGT
Statistics
Matches: 112, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
54 25 0.22
55 15 0.13
56 9 0.08
57 31 0.28
58 7 0.06
59 8 0.07
60 17 0.15
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.17
Consensus pattern (54 bp):
GTAAGAAAAGAGTAATCAGTAAAAAAAAAGTAAAAATGGTAATCAGTAAAAAGA
Found at i:42349 original size:36 final size:38
Alignment explanation
Indices: 42309--42379 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
42299 TGAATATATA
*
42309 AATTAATATTACATGTA-TATACTAA-TA-ATTATTATT
1 AATTAATATTACAGGTATTAT-CTAACTATATTATTATT
42345 AATTAATATTACAGGTATTATCTAACTATATTATT
1 AATTAATATTACAGGTATTATCTAACTATATTATT
42380 TTTATTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 20 0.65
37 5 0.16
38 6 0.19
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
AATTAATATTACAGGTATTATCTAACTATATTATTATT
Found at i:45831 original size:21 final size:22
Alignment explanation
Indices: 45783--45834 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
45773 GCGCCAAAGA
45783 TATGGGGCCCAAGTTCCACCAT
1 TATGGGGCCCAAGTTCCACCAT
*
45805 T-CGGGGCCCAAGTTCCACC-T
1 TATGGGGCCCAAGTTCCACCAT
45825 TATGGGGCCC
1 TATGGGGCCC
45835 CCCAACCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (22 bp):
TATGGGGCCCAAGTTCCACCAT
Done.