Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007735.1 Corchorus capsularis cultivar CVL-1 contig07756, 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: 75474
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1172 original size:70 final size:71
Alignment explanation
Indices: 1090--1321 Score: 299
Period size: 70 Copynumber: 3.2 Consensus size: 71
1080 AAATAAAATT
* *
1090 GTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 GTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1154 AGTTGA
66 AGTTGA
* *
1160 GTAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAG
1 GT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
1225 AGTTTTTAGTTGA
59 AGTTTTTAGTTGA
* * * * *
1238 GTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 GTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1302 AGTTGA
66 AGTTGA
1308 GTAAAACTA-TAAAA
1 GTAAAACTAGTAAAA
1322 CCCCAAACAA
Statistics
Matches: 144, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
70 69 0.48
71 5 0.03
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 62 0.43
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (71 bp):
GTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTGA
Found at i:1172 original size:78 final size:77
Alignment explanation
Indices: 1083--1321 Score: 341
Period size: 78 Copynumber: 3.2 Consensus size: 77
1073 TTTTTTTAAA
* *
1083 TAAAATTGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1148 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
1161 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1226 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
1239 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
1297 TTTTTAGTTGAG
66 TTTTTAGTTGAG
1309 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
1322 CCCCAAACAA
Statistics
Matches: 152, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 55 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 86 0.57
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:4077 original size:19 final size:21
Alignment explanation
Indices: 4034--4077 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4024 AATCTAACCA
*
4034 TTTCTATATCAAAATCGATAT
1 TTTCAATATCAAAATCGATAT
*
4055 TTTCAATATCATAAT-GA-AT
1 TTTCAATATCAAAATCGATAT
4074 TTTC
1 TTTC
4078 CATTTTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTCAATATCAAAATCGATAT
Found at i:12829 original size:29 final size:29
Alignment explanation
Indices: 12774--12829 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
12764 AAGAAGCTGA
* *
12774 GTTTTTTCTTTGCTTATTACTCGAAATGG
1 GTTTTTTCTTTCCTTATCACTCGAAATGG
*
12803 GTTTTTTACTTTCCTTGTCACTC-AAAT
1 GTTTTTT-CTTTCCTTATCACTCGAAAT
12830 TGGGAACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (29 bp):
GTTTTTTCTTTCCTTATCACTCGAAATGG
Found at i:20782 original size:21 final size:21
Alignment explanation
Indices: 20757--20800 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20747 AACACCATAT
20757 TTGTCTCAAATCGAATTTTTG
1 TTGTCTCAAATCGAATTTTTG
20778 TTGTCTCAAATCGAATTTTTG
1 TTGTCTCAAATCGAATTTTTG
20799 TT
1 TT
20801 TTTTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (21 bp):
TTGTCTCAAATCGAATTTTTG
Found at i:24473 original size:15 final size:16
Alignment explanation
Indices: 24439--24473 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
24429 TCCTTTACAG
*
24439 AAAACTTTAAAAAATA
1 AAAACTTTAAAAAAAA
24455 AAAAC-TTAAAAAAAA
1 AAAACTTTAAAAAAAA
24470 AAAA
1 AAAA
24474 AACTCTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAACTTTAAAAAAAA
Found at i:24473 original size:16 final size:16
Alignment explanation
Indices: 24439--24474 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
24429 TCCTTTACAG
* *
24439 AAAACTTTAAAAAATA
1 AAAACTTAAAAAAAAA
24455 AAAACTTAAAAAAAAA
1 AAAACTTAAAAAAAAA
24471 AAAA
1 AAAA
24475 ACTCTGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAACTTAAAAAAAAA
Found at i:25507 original size:107 final size:107
Alignment explanation
Indices: 25299--25580 Score: 403
Period size: 107 Copynumber: 2.7 Consensus size: 107
25289 ATAAAATTTT
* * *
25299 AATTTTAATTTG-GGCTAAACTTAGTG-AATTAATTATATATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
* *
25362 AT--ATTATTAATTATGGAATTTACCTTTAAAATAAAAATAA
66 ATAAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* * * *
25402 AATTTTAATTTGAGACTAAACTTGGTGAAATTAGTTTTGTATTTTATTTCTAAAACGCTATAATA
1 AATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
* * *
25467 ATAAATTATTAATTTTGAAATTTACCCTTAAAATAGAAATAC
66 ATAAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* *
25509 AATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTATGATA
1 AATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
25574 A-AAATTA
66 ATAAATTA
25581 CTATACTAAA
Statistics
Matches: 158, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
103 12 0.08
104 12 0.08
105 34 0.22
106 6 0.04
107 94 0.59
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.43
Consensus pattern (107 bp):
AATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAATA
ATAAATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
Found at i:28870 original size:21 final size:19
Alignment explanation
Indices: 28844--28898 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
28834 CGCTGCTCTA
28844 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
28863 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
*
28884 ATAATTTCATCTGTA
1 ATAATCTCATCTGTA
28899 TAGTTGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:29329 original size:26 final size:26
Alignment explanation
Indices: 29296--29346 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
29286 ACTCCAAGGA
29296 AGAAACAAGGGAACTATTGAAGGAAG
1 AGAAACAAGGGAACTATTGAAGGAAG
29322 AGAAACAAGGGAACTATTGAAGGAA
1 AGAAACAAGGGAACTATTGAAGGAA
29347 AAACAGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.29, T:0.12
Consensus pattern (26 bp):
AGAAACAAGGGAACTATTGAAGGAAG
Found at i:36366 original size:7 final size:7
Alignment explanation
Indices: 36354--36387 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
36344 CTATTATAGT
36354 TTGGAAG
1 TTGGAAG
36361 TTGGAAG
1 TTGGAAG
36368 TTGGAAG
1 TTGGAAG
36375 TTGGAAG
1 TTGGAAG
36382 TTGGAA
1 TTGGAA
36388 CCATGAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (7 bp):
TTGGAAG
Found at i:36892 original size:7 final size:7
Alignment explanation
Indices: 36857--36888 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
36847 ATCCAACCAT
36857 CCCATTC
1 CCCATTC
36864 CCCATTC
1 CCCATTC
36871 CCCATTC
1 CCCATTC
36878 CCCATTTC
1 CCCA-TTC
36886 CCC
1 CCC
36889 TTTCTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.12, C:0.59, G:0.00, T:0.28
Consensus pattern (7 bp):
CCCATTC
Found at i:37711 original size:21 final size:21
Alignment explanation
Indices: 37682--37733 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
37672 TATGGTCGGG
* * *
37682 TTTGAGTCAGGTTAATTTGAA
1 TTTGGGTCAAGTTAATTCGAA
* *
37703 TTTGGGTCAAGTTGATTCGGA
1 TTTGGGTCAAGTTAATTCGAA
37724 TTTGGGTCAA
1 TTTGGGTCAA
37734 TTTTGGGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.08, G:0.29, T:0.40
Consensus pattern (21 bp):
TTTGGGTCAAGTTAATTCGAA
Found at i:37988 original size:4 final size:4
Alignment explanation
Indices: 37979--38003 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
37969 GCGGATTTTA
37979 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
38004 TTTTTTTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:45170 original size:13 final size:13
Alignment explanation
Indices: 45152--45176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45142 TACGTCAAGC
45152 CCAGCCCAATATA
1 CCAGCCCAATATA
45165 CCAGCCCAATAT
1 CCAGCCCAATAT
45177 TCCAAATTGC
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:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (13 bp):
CCAGCCCAATATA
Found at i:55790 original size:22 final size:22
Alignment explanation
Indices: 55765--55833 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
55755 GAATTGTTAG
55765 TAATCACACTCTGAAATTTTGA
1 TAATCACACTCTGAAATTTTGA
*
55787 TAATCACACTATGAAATTTTGA
1 TAATCACACTCTGAAATTTTGA
* * *
55809 TAACCTCGCTAC-GAAATTTTGA
1 TAATCACACT-CTGAAATTTTGA
55831 TAA
1 TAA
55834 ATTTTCCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
TAATCACACTCTGAAATTTTGA
Found at i:55825 original size:44 final size:42
Alignment explanation
Indices: 55776--56542 Score: 207
Period size: 44 Copynumber: 17.8 Consensus size: 42
55766 AATCACACTC
*
55776 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCGCTA
1 TGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTC-CTA
* * *
55820 CGAAATTTTGATAAATTTTCCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AA-TCTCCTATGAAATTTTGAT-AACCT-CCTA
* * * * *
55866 TAAAAGTTTGATAACTTTCTTATGAAATCTTGATAA----CTA
1 TGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCTCCTA
* * * * *
55905 -AAAATTTTGATAAGCTCCCCAT-AATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCT-CCTATGAA-ATTTTGATAACCTC-CTA
* *
55948 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAATCT-CCTATGAAATTTTGATAA-CCTCCTA
* * *
55992 TGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTTCGTA
1 TGAAATTTTGATAATCT--CCTATGAAATTTTGATAACC-TCCTA
* *
56036 TGAAATTTTGAT-ATCCTCC-CTGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAAT-CTCCTATGAAATTTTGATAACCTCC-T-A
* * * * *
56078 TAAAAGTTTCATAA-CATTCC--T--AA-TTTGGTAACCATACTA
1 TGAAATTTTGATAATC--TCCTATGAAATTTTGATAACC-TCCTA
* * *
56117 TGAAATTTTGATAACCTCCCCA-G-AA-----AT-ACC-ACTA
1 TGAAATTTTGATAATCT-CCTATGAAATTTTGATAACCTCCTA
* * * * *
56151 TGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTA
1 TGAAA-TTTTGATAATCTC-CTATGAAATTTTGATAACCTC-CTA
* * ** * * *
56195 TGAAATTTTGATAACCTCTTTACAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTC-CTA
* * * * *
56239 TGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTC-CTA
* * * *
56283 TGAAATTTTGATAA-CAACACTATAAAATTTTGATAATCTTCATA
1 TGAAATTTTGATAATC-TC-CTATGAAATTTTGATAA-CCTCCTA
*
56327 T-AAATTTTGATAATCTGATCTCTATGAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAATC---TC-CTATGAAATTTTGATAA-C-CTCCTA
** * * * *
56373 TGGGA-TTTGATAACCTTCTATCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAATCTCCTATGAAATTTTGATAACCTCC-TA
* * * * *
56413 TTAAATTGAGACTTTTATAACCTTCATATGAAATTTTGATAACCTCCCCA
1 TGAAA-T-----TTTGATAATC-TCCTATGAAATTTTGATAACCT-CCTA
* * * *
56463 TGAAATATT-AGTAACCTCCTAATGAAATTTTGTTAACCGCACTA
1 TGAAATTTTGA-TAATCTCCT-ATGAAATTTTGATAACCTC-CTA
* * *
56507 TGAGATTCTT-ATAACCTCGCTATGACATTTTGATAA
1 TGAAATT-TTGATAATCTC-CTATGAAATTTTGATAA
56543 TCTCTTTGAT
Statistics
Matches: 542, Mismatches: 113, Indels: 136
0.69 0.14 0.17
Matches are distributed among these distances:
33 1 0.00
34 13 0.02
35 6 0.01
36 5 0.01
37 4 0.01
38 26 0.05
39 24 0.04
40 11 0.02
41 10 0.02
42 39 0.07
43 37 0.07
44 230 0.42
45 50 0.09
46 50 0.09
47 12 0.02
48 13 0.02
49 2 0.00
50 7 0.01
51 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (42 bp):
TGAAATTTTGATAATCTCCTATGAAATTTTGATAACCTCCTA
Found at i:55852 original size:23 final size:23
Alignment explanation
Indices: 55822--55901 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
55812 CCTCGCTACG
*
55822 AAATTTTGATAAATTTTCCTATA
1 AAATTTTGATAAACTTTCCTATA
* *
55845 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACTTTCCTATA
* * *
55868 AAAGTTTGAT-AACTTTCTTATG
1 AAATTTTGATAAACTTTCCTATA
*
55890 AAATCTTGATAA
1 AAATTTTGATAA
55902 CTAAAAATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 16 0.35
23 30 0.65
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAACTTTCCTATA
Found at i:55899 original size:45 final size:46
Alignment explanation
Indices: 55795--55901 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 46
55785 GATAATCACA
* * * *
55795 CTATGAAATTTTGAT-AACCTCGCTACGAAATTTTGATAAATTTTC
1 CTATGAAATTTTGATAAACCTCCCTACAAAAGTTTGATAAACTTTC
* *
55840 CTATAAAATTTTGATAAACCTCCCTATAAAAGTTTGAT-AACTTTC
1 CTATGAAATTTTGATAAACCTCCCTACAAAAGTTTGATAAACTTTC
* *
55885 TTATGAAATCTTGATAA
1 CTATGAAATTTTGATAA
55902 CTAAAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 34 0.65
46 18 0.35
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (46 bp):
CTATGAAATTTTGATAAACCTCCCTACAAAAGTTTGATAAACTTTC
Found at i:55956 original size:22 final size:21
Alignment explanation
Indices: 55931--56067 Score: 125
Period size: 22 Copynumber: 6.3 Consensus size: 21
55921 CCCCATAATT
*
55931 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
55953 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
55975 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAA-CCTCCTATGAAA
* *
55997 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT--CCTATGAAA
*
56019 TTTTGATAACCTTCGTATGAAA
1 TTTTGATAACC-TCCTATGAAA
* *
56041 TTTTGATATCCTCC-CTGAAA
1 TTTTGATAACCTCCTATGAAA
56061 TTTTGAT
1 TTTTGAT
56068 TACTCCATAA
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
20 14 0.15
21 4 0.04
22 69 0.73
23 6 0.06
24 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:56356 original size:25 final size:21
Alignment explanation
Indices: 56285--56366 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
56275 CCTCGCTTTG
**
56285 AAATTTTGATAA-CAACACTAT
1 AAATTTTGATAATCTTC-CTAT
*
56306 AAAATTTTGATAATCTTCATAT
1 -AAATTTTGATAATCTTCCTAT
56328 AAATTTTGATAATCTGATCTCTAT
1 AAATTTTGATAATCT--TC-CTAT
*
56352 GAAATTTCGATAATC
1 -AAATTTTGATAATC
56367 ACTCTATGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
21 15 0.30
22 15 0.30
23 4 0.08
24 3 0.06
25 13 0.26
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTTTGATAATCTTCCTAT
Found at i:56374 original size:22 final size:22
Alignment explanation
Indices: 56148--56374 Score: 124
Period size: 22 Copynumber: 10.2 Consensus size: 22
56138 AGAAATACCA
56148 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
56171 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
56192 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* ** * * * *
56214 TTACAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
*
56236 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
56259 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
56280 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
* *
56302 CTATAAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
56323 CATAT-AAATTTTGATAATCTGATCT
1 C-TATGAAATTTTGATAATC--A-CT
*
56348 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
56370 CTATG
1 CTATG
56375 GGATTTGATA
Statistics
Matches: 158, Mismatches: 34, Indels: 25
0.73 0.16 0.12
Matches are distributed among these distances:
21 21 0.13
22 116 0.73
23 3 0.02
24 3 0.02
25 15 0.09
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:56454 original size:22 final size:21
Alignment explanation
Indices: 56425--56542 Score: 71
Period size: 22 Copynumber: 5.4 Consensus size: 21
56415 AAATTGAGAC
56425 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
**
56446 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
56468 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* * *
56490 TTTTGTTAACCGCACTATGAGA
1 TTTTGATAACCTCA-TATGAAA
* *
56512 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
56534 TTTTGATAA
1 TTTTGATAA
56543 TCTCTTTGAT
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
21 10 0.13
22 62 0.83
23 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:57336 original size:37 final size:36
Alignment explanation
Indices: 57295--57390 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 36
57285 ATCAAAGCGC
*
57295 AAATAGGACGTTGAAGATAAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGAA-ACAAAGACAAAAAGCAAAATT
** *
57332 AAATACAACGATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACG-TT-GAAACAAAGACAAAAAGCAAAATT
57370 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTT-GAAACAAA
57391 AAGCCAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
37 19 0.37
38 29 0.57
39 3 0.06
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (36 bp):
AAATAGGACGTTGAAACAAAGACAAAAAGCAAAATT
Found at i:57353 original size:32 final size:31
Alignment explanation
Indices: 57317--57400 Score: 78
Period size: 38 Copynumber: 2.5 Consensus size: 31
57307 GAAGATAAAG
57317 ACAAAAAGCAAAATTAAATACAACGATTGGAA
1 ACAAAAAGCAAAATTAAATACAACG-TTGGAA
**
57349 ACAAAGACAAAAGGCAAAATTAAATAGGACGTTGGAA
1 AC----A-AAAA-GCAAAATTAAATACAACGTTGGAA
*
57386 ACAAAAAGCCAAATT
1 ACAAAAAGCAAAATT
57401 GACTTTCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
31 7 0.16
32 6 0.14
33 1 0.02
36 1 0.02
37 12 0.28
38 16 0.37
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.14
Consensus pattern (31 bp):
ACAAAAAGCAAAATTAAATACAACGTTGGAA
Found at i:57551 original size:30 final size:31
Alignment explanation
Indices: 57517--57581 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
57507 TGCCAATTTA
*
57517 GAAATATGTTTTTAAAAA-AA-GGTACAATTG
1 GAAATATG-TTTTAAAAATAATGGTACAATCG
57547 GAAATATGTTTTAAAAATAATGGTACAATCG
1 GAAATATGTTTTAAAAATAATGGTACAATCG
57578 GAAA
1 GAAA
57582 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 9 0.28
30 10 0.31
31 13 0.41
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAATGGTACAATCG
Found at i:62861 original size:29 final size:29
Alignment explanation
Indices: 62824--62886 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
62814 AACTCTTTAA
*
62824 AATAAAGAAAATAAACGATA-TAAAAAAAT
1 AATAAAGAAAATAAA-GATACCAAAAAAAT
* *
62853 AATAAAGAAAGTAAATATACCAAAAAAAT
1 AATAAAGAAAATAAAGATACCAAAAAAAT
62882 AATAA
1 AATAA
62887 TAAAGTGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.17
Consensus pattern (29 bp):
AATAAAGAAAATAAAGATACCAAAAAAAT
Found at i:64775 original size:11 final size:11
Alignment explanation
Indices: 64759--64793 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
64749 TTTTTCTGTT
64759 TTTTGTTTTTG
1 TTTTGTTTTTG
*
64770 TTTTGTTTTCG
1 TTTTGTTTTTG
64781 TTTTGTTTTTG
1 TTTTGTTTTTG
64792 TT
1 TT
64794 GCGTTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:73786 original size:32 final size:32
Alignment explanation
Indices: 73750--73848 Score: 189
Period size: 32 Copynumber: 3.1 Consensus size: 32
73740 AGCCACGCGG
73750 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
*
73782 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
73814 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
73846 AGC
1 AGC
73849 TACCCCCTAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.16, C:0.41, G:0.28, T:0.14
Consensus pattern (32 bp):
AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
Found at i:73964 original size:33 final size:33
Alignment explanation
Indices: 73922--74032 Score: 102
Period size: 33 Copynumber: 3.4 Consensus size: 33
73912 TAGTATCGGT
* * * *
73922 GCCGCCCCAGGGGGGTGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGAGGCGGCCTAGCCATGGTAGG
* *
73955 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGAGGCGGCCTAGCCATGGTAGG
* *
73988 GCCGCCCCA-GGAGGGCGGCTTGGCCATGGCTCA--
1 GCCGCCCCAGGGA-GGCGGCCTAGCCATGG-T-AGG
74021 GCCGCCCCAGGG
1 GCCGCCCCAGGG
74033 GGACGGCACC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.04
33 60 0.90
34 3 0.04
35 1 0.01
ACGTcount: A:0.12, C:0.34, G:0.41, T:0.13
Consensus pattern (33 bp):
GCCGCCCCAGGGAGGCGGCCTAGCCATGGTAGG
Found at i:74243 original size:65 final size:64
Alignment explanation
Indices: 74113--74249 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 64
74103 CCGCCCCACC
* * *
74113 GGGGCGGCCTGCCGTGGCGAAGCCGCCCCACAGGGACGGCCTGCCCTGGCTAAGCCGCCCCAGT
1 GGGGCGGCCTGCCATGGCGAAGCCGCCCCACAGGGACGGCCTGCCCTGGCGAAGCCGCCCAAGT
* * * * *
74177 GGGGCGGCCTGCCCATGGTGAAGCCGCCCCATGAGGG-CGGCTTGCCGTGGCGAAGCCTCCCAAG
1 GGGGCGGCCTG-CCATGGCGAAGCCGCCCCA-CAGGGACGGCCTGCCCTGGCGAAGCCGCCCAAG
74241 T
64 T
74242 GGGGCGGC
1 GGGGCGGC
74250 TTCGCCACGG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 11 0.17
65 48 0.76
66 4 0.06
ACGTcount: A:0.12, C:0.36, G:0.40, T:0.11
Consensus pattern (64 bp):
GGGGCGGCCTGCCATGGCGAAGCCGCCCCACAGGGACGGCCTGCCCTGGCGAAGCCGCCCAAGT
Found at i:74251 original size:32 final size:32
Alignment explanation
Indices: 74101--74249 Score: 165
Period size: 32 Copynumber: 4.6 Consensus size: 32
74091 AAAAAAGCTG
**
74101 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCGTGGCGA
** * * *
74133 AGCCGCCCCACAGGGACGGCCTGCCCTGGCTA
1 AGCCGCCCCAGTGGGGCGGCCTGCCGTGGCGA
* *
74165 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTG-CCGTGGCGA
*
74198 AGCCGCCCCA-TGAGGGCGGCTTGCCGTGGCGA
1 AGCCGCCCCAGTG-GGGCGGCCTGCCGTGGCGA
* *
74230 AGCCTCCCAAGTGGGGCGGC
1 AGCCGCCCCAGTGGGGCGGC
74250 TTCGCCACGG
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
32 72 0.73
33 27 0.27
ACGTcount: A:0.13, C:0.39, G:0.38, T:0.10
Consensus pattern (32 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCGTGGCGA
Done.