Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011921.1 Corchorus capsularis cultivar CVL-1 contig11942, 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: 48280
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1153 original size:23 final size:21
Alignment explanation
Indices: 1123--1185 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
1113 CATTCTATTG
1123 AAAAAAGTCAGAGAATACAACAT
1 AAAAAAGTCAGAGAA-ACAA-AT
*
1146 AAAAAAGTTAGAGAAACAAAT
1 AAAAAAGTCAGAGAAACAAAT
* *
1167 AATAAA-TCA-AGAAAAAAAT
1 AAAAAAGTCAGAGAAACAAAT
1186 TGTAATTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.25
20 2 0.06
21 7 0.19
22 4 0.11
23 14 0.39
ACGTcount: A:0.67, C:0.08, G:0.11, T:0.14
Consensus pattern (21 bp):
AAAAAAGTCAGAGAAACAAAT
Found at i:1168 original size:21 final size:23
Alignment explanation
Indices: 1123--1168 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1113 CATTCTATTG
1123 AAAAAAGTCAGAGAATACAACAT
1 AAAAAAGTCAGAGAATACAACAT
*
1146 AAAAAAGTTAGAGAA-ACAA-AT
1 AAAAAAGTCAGAGAATACAACAT
1167 AA
1 AA
1169 TAAATCAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 4 0.18
23 14 0.64
ACGTcount: A:0.65, C:0.09, G:0.13, T:0.13
Consensus pattern (23 bp):
AAAAAAGTCAGAGAATACAACAT
Found at i:2499 original size:82 final size:80
Alignment explanation
Indices: 2410--2566 Score: 237
Period size: 82 Copynumber: 1.9 Consensus size: 80
2400 GTAGTTACAG
*
2410 AATACTAAATTTAATT-GA-AAATGGATAATCAACAAAAGCCTATCTAATTCATATAAATAAGCT
1 AATACTAAATTTAATTGGATAAA--GATAATCAACAAAAGCCTATATAATTCATATAAATAAGC-
2473 GGAGAATCATAAAAAATTT
63 -GAGAATCATAAAAAATTT
* *
2492 AATACTAAATTTAATTGGATAAAGATAATCAATAAAAGGCTATATAATTCATATAAATAAGCGAG
1 AATACTAAATTTAATTGGATAAAGATAATCAACAAAAGCCTATATAATTCATATAAATAAGCGAG
2557 AATCATAAAA
66 AATCATAAAA
2567 TTTTTCACAA
Statistics
Matches: 70, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
80 13 0.19
82 52 0.74
83 2 0.03
84 3 0.04
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (80 bp):
AATACTAAATTTAATTGGATAAAGATAATCAACAAAAGCCTATATAATTCATATAAATAAGCGAG
AATCATAAAAAATTT
Found at i:4427 original size:38 final size:39
Alignment explanation
Indices: 4267--4454 Score: 283
Period size: 39 Copynumber: 4.9 Consensus size: 39
4257 GGCTGTGCAT
* * *
4267 AGTGGACCCGCGCCTCAGGGGGCTAAACTGATGGTAAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG
* *
4306 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG
4345 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGT-AAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTG-TTGGTAAAG
*
4384 AGTGGACCCGTGCCTCAGGAGGTTAAACTGTTGGT-AAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG
*
4422 AGTGGACCCGTGCCTCAGGTGGTT-AACTGTTGG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGG
4455 CTAGATTGTG
Statistics
Matches: 143, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
37 9 0.06
38 31 0.22
39 99 0.69
40 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (39 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAAG
Found at i:4469 original size:6 final size:6
Alignment explanation
Indices: 4458--4482 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4448 CTGTTGGCTA
4458 GATTGT GATTGT GATTGT GATTGT G
1 GATTGT GATTGT GATTGT GATTGT G
4483 GTGCAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GATTGT
Found at i:6494 original size:23 final size:23
Alignment explanation
Indices: 6439--6532 Score: 143
Period size: 23 Copynumber: 4.0 Consensus size: 23
6429 CAAACAATCT
* *
6439 TGAGCATTCTAGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
6462 TTTGAGCACTCTCGCTCGGTCTCTA
1 --TGAGCACTCTCGCTCGGTCTCTA
*
6487 TGAGCACTCTTGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
6510 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
6533 CAAACCAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
23 44 0.68
25 21 0.32
ACGTcount: A:0.14, C:0.31, G:0.21, T:0.34
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:7389 original size:23 final size:23
Alignment explanation
Indices: 7334--7427 Score: 134
Period size: 23 Copynumber: 4.0 Consensus size: 23
7324 CAAACAATCT
* *
7334 TGAGCATTCTAGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
7357 TTTGAGCACTCTCGCTCGGTCTCTA
1 --TGAGCACTCTCGCTCGGTCTCTA
*
7382 TGAGCACTCTTGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
7405 CGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
7428 CAGACCAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 43 0.67
25 21 0.33
ACGTcount: A:0.14, C:0.32, G:0.21, T:0.33
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:22167 original size:16 final size:16
Alignment explanation
Indices: 22146--22288 Score: 157
Period size: 16 Copynumber: 9.1 Consensus size: 16
22136 CATGTAGTTT
*
22146 TTTCGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
22162 TTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTC-GGG
*
22178 -TTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* **
22193 TCTCGGGTTGTTCGGG
1 TTTCGGGTCATTCGGG
* *
22209 TATC-GGTCATACGGG
1 TTTCGGGTCATTCGGG
*
22224 TTTCGGGTCATACGGG
1 TTTCGGGTCATTCGGG
22240 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
22256 TCTCGGGTCATTCGAG
1 TTTCGGGTCATTCGGG
*
22272 TTTCAGGTCATTCGGG
1 TTTCGGGTCATTCGGG
22288 T
1 T
22289 CTACCGGGTC
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
15 23 0.21
16 85 0.79
ACGTcount: A:0.09, C:0.18, G:0.36, T:0.36
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:22256 original size:32 final size:32
Alignment explanation
Indices: 22146--22290 Score: 161
Period size: 31 Copynumber: 4.6 Consensus size: 32
22136 CATGTAGTTT
* *
22146 TTTCGGGTCATTTGGGTTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTCGGGTCTCGGGTCATTC-GGG
* **
22178 -TTCGGGTTATTCGGGTCTCGGGTTGTTCGGG
1 TTTCGGGTCATTCGGGTCTCGGGTCATTCGGG
* * * *
22209 TATC-GGTCATACGGGTTTCGGGTCATACGGG
1 TTTCGGGTCATTCGGGTCTCGGGTCATTCGGG
*
22240 TTTCGGGTCATTCGGGTCTCGGGTCATTCGAG
1 TTTCGGGTCATTCGGGTCTCGGGTCATTCGGG
*
22272 TTTCAGGTCATTCGGGTCT
1 TTTCGGGTCATTCGGGTCT
22291 ACCGGGTCTC
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
31 47 0.51
32 45 0.49
ACGTcount: A:0.09, C:0.19, G:0.36, T:0.37
Consensus pattern (32 bp):
TTTCGGGTCATTCGGGTCTCGGGTCATTCGGG
Found at i:22303 original size:48 final size:46
Alignment explanation
Indices: 22204--22304 Score: 105
Period size: 48 Copynumber: 2.1 Consensus size: 46
22194 CTCGGGTTGT
* * *
22204 TCGGGTATCGGTCATACGGGTTTCGGGTCATACGGGTTTCGGGTCA
1 TCGGGTATCGGTCATACGAGTTTCAGGTCATACGGGTTCCGGGTCA
* * *
22250 TTCGGGTCTCGGGTCATTCGAGTTTCAGGTCATTCGGGTCTACCGGGTC-
1 -TCGGGTATC-GGTCATACGAGTTTCAGGTCATACGGGT-T-CCGGGTCA
22299 TCGGGT
1 TCGGGT
22305 TGGGCGAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
47 8 0.18
48 30 0.67
49 1 0.02
50 6 0.13
ACGTcount: A:0.11, C:0.22, G:0.36, T:0.32
Consensus pattern (46 bp):
TCGGGTATCGGTCATACGAGTTTCAGGTCATACGGGTTCCGGGTCA
Found at i:22776 original size:21 final size:21
Alignment explanation
Indices: 22751--22798 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
22741 TAGCCAATTT
22751 ATAATAGGTAAAATCT-TAACA
1 ATAATAGGTAAAAT-TATAACA
*
22772 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATTATAACA
22793 ATAATA
1 ATAATA
22799 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.31
Consensus pattern (21 bp):
ATAATAGGTAAAATTATAACA
Found at i:23000 original size:16 final size:16
Alignment explanation
Indices: 22903--22994 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
22893 TCGGGTTAAT
*
22903 GTCTCGGGTTATTCGG
1 GTCTCGGGTCATTCGG
* * *
22919 G-CTTCGGATCATACAG
1 GTC-TCGGGTCATTCGG
*
22935 GTCTCGAGTCATTCGG
1 GTCTCGGGTCATTCGG
*
22951 GTTTCGGGTCA-TCTGG
1 GTCTCGGGTCATTC-GG
*
22967 GT-TACGGGTCGTTCGG
1 GTCT-CGGGTCATTCGG
22983 GTCTCGGGTCAT
1 GTCTCGGGTCAT
22995 CTGGGTTACA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
15 4 0.07
16 50 0.86
17 4 0.07
ACGTcount: A:0.11, C:0.22, G:0.35, T:0.33
Consensus pattern (16 bp):
GTCTCGGGTCATTCGG
Found at i:23014 original size:32 final size:32
Alignment explanation
Indices: 22943--23023 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
22933 AGGTCTCGAG
* * *
22943 TCATTCGGGTTTCGGGTCATCTGGGTTACGGG
1 TCATTCGGGTCTCGGGTCATCTGGGTTACAGA
*
22975 TCGTTCGGGTCTCGGGTCATCTGGGTTACAGA
1 TCATTCGGGTCTCGGGTCATCTGGGTTACAGA
* *
23007 TCATTCGGATCACGGGT
1 TCATTCGGGTCTCGGGT
23024 TTGTCGGGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.12, C:0.21, G:0.35, T:0.32
Consensus pattern (32 bp):
TCATTCGGGTCTCGGGTCATCTGGGTTACAGA
Found at i:35429 original size:53 final size:53
Alignment explanation
Indices: 35346--35452 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
35336 TTGTTAGCAT
*
35346 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAAAATTTATAAAA
* *
35399 TTCACAATAAAATTTGATTTCTTAATTGAATTTTCTTAAAAAAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAAAATTTATAAAA
35452 T
1 T
35453 AAAACAGCCG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAAAATTTATAAAA
Found at i:36610 original size:45 final size:45
Alignment explanation
Indices: 36560--36649 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
36550 TAATAGAGTA
* *
36560 GTGGAATTATTAAAAGATCCCTACCCCGAATTGATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
* *
36605 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
36650 AGAAGTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
Found at i:41692 original size:13 final size:13
Alignment explanation
Indices: 41674--41700 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41664 CGTATTCTAT
41674 TTTTGTTTTTTTG
1 TTTTGTTTTTTTG
41687 TTTTGTTTTTTTG
1 TTTTGTTTTTTTG
41700 T
1 T
41701 GTTTTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTTGTTTTTTTG
Found at i:47472 original size:107 final size:105
Alignment explanation
Indices: 47266--47528 Score: 374
Period size: 107 Copynumber: 2.5 Consensus size: 105
47256 TTATTATCGA
* * * * *
47266 GTTTTAGACATAAAATATAAAACTAATTTCACTAAGTTTAACTTCAAAT--TA-TTTTTTTTATT
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCTCAAATAAAATTTTTTTTTATC
47328 TTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGG
66 TTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGG
* *
47368 GTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAACTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCTCAAA-TAAAATTTT-TTTTTA
**
47433 TCTTAAGGGTAAATTTCATGATTAATAATTTATTGTTATAGG
64 TCTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGG
*
47475 GTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAG-CTCAAATTAAAATT
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCTCAAA-TAAAATT
47529 AAATTTTTTA
Statistics
Matches: 143, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
102 43 0.30
103 1 0.01
105 13 0.09
106 17 0.12
107 69 0.48
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (105 bp):
GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCTCAAATAAAATTTTTTTTTATC
TTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGG
Found at i:48248 original size:2 final size:2
Alignment explanation
Indices: 48241--48274 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48231 ACAATTAGAC
48241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48275 AGTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.