Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009461.1 Corchorus capsularis cultivar CVL-1 contig09482, 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: 38226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1501 original size:2 final size:2
Alignment explanation
Indices: 1496--1520 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1486 AGTAAAAAAA
1496 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1521 AACATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2794 original size:16 final size:16
Alignment explanation
Indices: 2774--2819 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2764 AATAAGTACT
*
2774 ATAACCCGAAACCGAT
1 ATAACCCGAAACCGAG
* *
2790 TTAACCCG-AATCGAG
1 ATAACCCGAAACCGAG
2805 ATAACCCGAAACCGA
1 ATAACCCGAAACCGA
2820 CAAAATCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (16 bp):
ATAACCCGAAACCGAG
Found at i:2948 original size:15 final size:15
Alignment explanation
Indices: 2913--2941 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2903 TGACCGACCC
2913 CGAATTAACCCGAAT
1 CGAATTAACCCGAAT
2928 CGAATTAACCCGAA
1 CGAATTAACCCGAA
2942 CTCAATTTAT
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:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (15 bp):
CGAATTAACCCGAAT
Found at i:4513 original size:58 final size:58
Alignment explanation
Indices: 4444--4559 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
4434 TTGATAAGAA
*
4444 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGT
1 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCACTTGGTGTGAAAGT
*
4502 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGT
1 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCACTTGGTGTGAAAGT
4560 AATAAAATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42
Consensus pattern (58 bp):
TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCACTTGGTGTGAAAGT
Found at i:4808 original size:58 final size:58
Alignment explanation
Indices: 4739--4854 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
4729 TTGATAAGAA
*
4739 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGT
1 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCACTTGGTGTGAAAGT
* *
4797 TATCAAGGATTTTAGTTGATTTGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGT
1 TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCACTTGGTGTGAAAGT
4855 AATAAAATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (58 bp):
TATCAAGGATTTTAGTTGATTGGATTGTAATACCTTGTATCTCACTTGGTGTGAAAGT
Found at i:4854 original size:295 final size:296
Alignment explanation
Indices: 4323--4911 Score: 1144
Period size: 295 Copynumber: 2.0 Consensus size: 296
4313 GAAGTAGTTA
**
4323 TATTGGCTATTTTAATATCCTCTCGTTTTTATTAGAAAGGAAAAACTTTATTATATAAAAGGAAT
1 TATTGGCTATTTTAATATCCTCTCGTTTTTATTAGAAAGGAAAAAAATTATTATATAAAAGGAAT
4388 ATTGTTATTATAGAGTGGATTTGAATTGCAATTGTGATGGTTAGCCTTGATAAGAATATCAAGGA
66 ATTGTTATTATAGAGTGGATTTGAATTGCAATTGTGATGGTTAGCCTTGATAAGAATATCAAGGA
4453 TTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGTTATCAAGGATTTTAGT
131 TTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGTTATCAAGGATTTTAGT
4518 TGATTGGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGTAATAAAATATATATGTGCACATA
196 TGATTGGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGTAATAAAATATATATGTGCACATA
4583 CATACATTTACATATATACATACATCGCCTCCCCCC
261 CATACATTTACATATATACATACATCGCCTCCCCCC
4619 TATTGGCTATTTTAATATCCTCTCGTTTTTATTAGAAA-GAAAAAAATTATTATATAAAAGGAAT
1 TATTGGCTATTTTAATATCCTCTCGTTTTTATTAGAAAGGAAAAAAATTATTATATAAAAGGAAT
4683 ATTGTTATTATAGAGTGGATTTGAATTGCAATTGTGATGGTTAGCCTTGATAAGAATATCAAGGA
66 ATTGTTATTATAGAGTGGATTTGAATTGCAATTGTGATGGTTAGCCTTGATAAGAATATCAAGGA
4748 TTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGTTATCAAGGATTTTAGT
131 TTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGTTATCAAGGATTTTAGT
*
4813 TGATTTGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGTAATAAAATATATATGTGCACATA
196 TGATTGGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGTAATAAAATATATATGTGCACATA
4878 CATACATTTACATATATACATACATCGCCTCCCC
261 CATACATTTACATATATACATACATCGCCTCCCC
4912 ACCCCCACCC
Statistics
Matches: 290, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
295 252 0.87
296 38 0.13
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (296 bp):
TATTGGCTATTTTAATATCCTCTCGTTTTTATTAGAAAGGAAAAAAATTATTATATAAAAGGAAT
ATTGTTATTATAGAGTGGATTTGAATTGCAATTGTGATGGTTAGCCTTGATAAGAATATCAAGGA
TTTTAGTTGATTGGATTGTAATACCTTGTATCTCATTTGGTGTGAAAGTTATCAAGGATTTTAGT
TGATTGGATTGTAATACCTTGTCTCTCACTTGGTGTGAAAGTAATAAAATATATATGTGCACATA
CATACATTTACATATATACATACATCGCCTCCCCCC
Found at i:7489 original size:114 final size:117
Alignment explanation
Indices: 7339--7564 Score: 370
Period size: 114 Copynumber: 1.9 Consensus size: 117
7329 CGTTTTCTGC
*
7339 TTTGATAATTTTTTTTTCGTTTAAGATATTTTTTTTTCAAAATTTGAAATATCCTCCTCATTTTT
1 TTTGATAATTTTTTTTTCGTTTAAGATATTTTTTTTTCAAAATATGAAATATCCTCCTCA-TTTT
* *
7404 TTAATACGTGTGTT-AGAGAAAAA-AATAAATCAAGTAAAAAAATGTGTGTTT
65 TTAATACGTGTCTTGAGAAAAAAATAATAAATCAAGTAAAAAAATGTGTGTTT
7455 TTTGATAA-TTTTTTTT-GTTTAAGATATTTTTTTTTCAAAATATGAAATATCCTCCTCATTTTT
1 TTTGATAATTTTTTTTTCGTTTAAGATATTTTTTTTTCAAAATATGAAATATCCTCCTCATTTTT
*
7518 TAATATGTGTCTTGGAGAAAAAAATAATAAATCAAGTAAAAAAATGT
66 TAATACGTGTCTT-GAGAAAAAAATAATAAATCAAGTAAAAAAATGT
7565 AGTTGATATC
Statistics
Matches: 103, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
113 16 0.16
114 41 0.40
115 16 0.16
116 30 0.29
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (117 bp):
TTTGATAATTTTTTTTTCGTTTAAGATATTTTTTTTTCAAAATATGAAATATCCTCCTCATTTTT
TAATACGTGTCTTGAGAAAAAAATAATAAATCAAGTAAAAAAATGTGTGTTT
Found at i:12191 original size:59 final size:60
Alignment explanation
Indices: 12031--12192 Score: 263
Period size: 60 Copynumber: 2.7 Consensus size: 60
12021 GCTAATTGCT
* * ** *
12031 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
*
12091 CATATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
12151 CAAATAAGGG-CTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
12193 TGTCTCATGC
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 32 0.34
60 63 0.66
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
Found at i:12263 original size:31 final size:31
Alignment explanation
Indices: 12221--12419 Score: 137
Period size: 31 Copynumber: 6.5 Consensus size: 31
12211 AACTGACAAC
** **
12221 AGGCCCTTATTTGAGCATTTTTTATAATTTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
*
12252 AGGTCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
** * *
12283 AGGCCCTTATTTG-GCCAAATT--A-AAAGAT
1 AGGCCCTTATTTGAG-CATTTTCGATAACGTT
* *
12311 CGGACCCTTATTTGAGCATTTTCGATAAGGTT
1 AGG-CCCTTATTTGAGCATTTTCGATAACGTT
* ** *
12343 AGACCCTTATTTG-GCCAAATT--A-AAAGATT
1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
* *
12372 GGGCCCTTATTTGAGCATTTTGGCA-AACGTT
1 AGGCCCTTATTTGAGCATTTTCG-ATAACGTT
12403 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
12420 ATTAGCCATC
Statistics
Matches: 130, Mismatches: 26, Indels: 24
0.72 0.14 0.13
Matches are distributed among these distances:
28 9 0.07
29 33 0.25
30 4 0.03
31 75 0.58
32 9 0.07
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:12323 original size:29 final size:29
Alignment explanation
Indices: 12286--12384 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
12276 TAACGTTAGG
*
12286 CCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGGCCAAATTAAAAGATTGGA
** * * *
12315 CCCTTATTTGAG-CATTTTCGATAAGGTTAGA
1 CCCTTATTTG-GCCAAATT--AAAAGATTGGA
*
12346 CCCTTATTTGGCCAAATTAAAAGATTGGG
1 CCCTTATTTGGCCAAATTAAAAGATTGGA
12375 CCCTTATTTG
1 CCCTTATTTG
12385 AGCATTTTGG
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 31 0.57
30 2 0.04
31 21 0.39
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATTGGA
Found at i:12328 original size:60 final size:60
Alignment explanation
Indices: 12256--12415 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
12246 AATTTTAGGT
12256 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGAC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGAC
* * * *
12316 CCTTATTTGAGCATTTTCGATAAGGTTAGACCCTTATTTGGCCAAATTAAAAGATTGGGC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGAC
*
12376 CCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
12416 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGAC
Found at i:16011 original size:16 final size:17
Alignment explanation
Indices: 15981--16015 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
15971 TTTTTAAATT
*
15981 TTTTCCAAAATTTTTGC
1 TTTTCCAAAACTTTTGC
15998 TTTT-CAAAACTTTTGC
1 TTTTCCAAAACTTTTGC
16014 TT
1 TT
16016 CTCTGGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTTCCAAAACTTTTGC
Found at i:16275 original size:18 final size:17
Alignment explanation
Indices: 16234--16276 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
16224 ATTTGTTTGC
*
16234 TTGTCTTTAGTTTTGTT
1 TTGTTTTTAGTTTTGTT
*
16251 TAAGTTTTTAGTTTTTGTT
1 T-TGTTTTTAG-TTTTGTT
16270 TTGTTTT
1 TTGTTTT
16277 CTAGCTTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72
Consensus pattern (17 bp):
TTGTTTTTAGTTTTGTT
Found at i:21758 original size:31 final size:29
Alignment explanation
Indices: 21700--21762 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
21690 GATTCTCTCG
*
21700 AAATAATATACTTCCTTGTGGCCAAAAAA
1 AAATAATATACTTCCTTATGGCCAAAAAA
*
21729 AAATAATATACTTCCTTTCATTGCCAAAAAA
1 AAATAATATACTTCC-TT-ATGGCCAAAAAA
21760 AAA
1 AAA
21763 AATCTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.50
30 2 0.07
31 13 0.43
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (29 bp):
AAATAATATACTTCCTTATGGCCAAAAAA
Found at i:21904 original size:2 final size:2
Alignment explanation
Indices: 21872--21896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21862 ACACACATAC
21872 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 A
21897 ACATATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23029 original size:2 final size:2
Alignment explanation
Indices: 23022--23050 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23012 GGAACTAGTG
23022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23051 TAATTAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32194 original size:83 final size:83
Alignment explanation
Indices: 32055--32293 Score: 325
Period size: 83 Copynumber: 2.8 Consensus size: 83
32045 CTGCGCTGAC
* * * *
32055 ACACACATATAGAAATTCCACACATAAATACTTCAGATATGAGTATTTCATACATAAAAGGGTCA
1 ACACACATATAGATATTCCACACATAAATACTTCACATATAAGTATTTCACACATAAAAGGGTCA
32120 CACATACATACCCTATAA
66 CACATACATACCCTATAA
* *
32138 ACACACATATAGATATTCCACACATAAATACTTCATATATAAGTATTTCACACATAAAAAGGTCA
1 ACACACATATAGATATTCCACACATAAATACTTCACATATAAGTATTTCACACATAAAAGGGTCA
*
32203 CACATACATACCCTATAC
66 CACATACATACCCTATAA
* * * * * *
32221 ACACACATATAGGTATCCCATATATGAATACTTCACATGTAAGTATTTCTTTCACACATAAAAGG
1 ACACACATATAGATATTCCACACATAAATACTTCACATATAAGTA----TTTCACACATAAAAGG
32286 GTCACACA
62 GTCACACA
32294 CATATATGCC
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 115 0.83
87 23 0.17
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.27
Consensus pattern (83 bp):
ACACACATATAGATATTCCACACATAAATACTTCACATATAAGTATTTCACACATAAAAGGGTCA
CACATACATACCCTATAA
Done.