Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015291.1 Corchorus capsularis cultivar CVL-1 contig15312, 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: 34529
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3320 original size:200 final size:200
Alignment explanation
Indices: 2974--3376 Score: 736
Period size: 200 Copynumber: 2.0 Consensus size: 200
2964 GATGAAAGAC
*
2974 TATCGGCCCATAGCTTTGTGTAATGTAATTTTAAAAATTGTTTCCAAAGCAATTGCGAATTGTCT
1 TATCGGCCCATAGCTTTGTGTAATGTAATTTTAAAAATTGTTTCCAAAGCAATTGCGAATCGTCT
3039 GAAGTTGGTATTACCTAGCGTGATAGGCGAGAGTCAGAGCGCTTTTGTACCAGATAGGATGATAT
66 GAAGTTGGTATTACCTAGCGTGATAGGCGAGAGTCAGAGCGCTTTTGTACCAGATAGGATGATAT
*
3104 ATGACAATGTAATCATTGCTTTTGAAAA-AATTCATTTTATGCGCAATAAGTGGGCTGGGAAGAG
131 ATGACAATGCAATCATTGCTTTT-AAAACAATTCATTTTATGCGCAATAAGTGGGCTGGGAAGAG
3168 GTCACA
195 GTCACA
* * *
3174 TATCGGCCCATAGTTTTGTGTAATTTAATTTTAAAAATTGTTTCCAAAGCAATTGCTAATCGTCT
1 TATCGGCCCATAGCTTTGTGTAATGTAATTTTAAAAATTGTTTCCAAAGCAATTGCGAATCGTCT
*
3239 GAAGTTGGTATTGCCTAGCGTGATAGGCGAGAGTCAGAGCGCTTTTGTACCAGATAGGATGATAT
66 GAAGTTGGTATTACCTAGCGTGATAGGCGAGAGTCAGAGCGCTTTTGTACCAGATAGGATGATAT
3304 ATGACAATGCAATCATTGCTTTTAAAACAATTCATTTTATGCGCAATAAGTGGGCTGGGAAGAGG
131 ATGACAATGCAATCATTGCTTTTAAAACAATTCATTTTATGCGCAATAAGTGGGCTGGGAAGAGG
3369 TCACA
196 TCACA
3374 TAT
1 TAT
3377 GGTGCTTAAA
Statistics
Matches: 196, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
199 4 0.02
200 192 0.98
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (200 bp):
TATCGGCCCATAGCTTTGTGTAATGTAATTTTAAAAATTGTTTCCAAAGCAATTGCGAATCGTCT
GAAGTTGGTATTACCTAGCGTGATAGGCGAGAGTCAGAGCGCTTTTGTACCAGATAGGATGATAT
ATGACAATGCAATCATTGCTTTTAAAACAATTCATTTTATGCGCAATAAGTGGGCTGGGAAGAGG
TCACA
Found at i:9014 original size:12 final size:12
Alignment explanation
Indices: 8997--9021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8987 AGACACATTG
8997 TTCTTTTTTTTT
1 TTCTTTTTTTTT
9009 TTCTTTTTTTTT
1 TTCTTTTTTTTT
9021 T
1 T
9022 ATTTGGCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:12694 original size:11 final size:11
Alignment explanation
Indices: 12675--12710 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12665 ATTGACAGCG
12675 AAACAAAAACA
1 AAACAAAAACA
* *
12686 AAACGAAAACG
1 AAACAAAAACA
12697 AAACAAAAACA
1 AAACAAAAACA
12708 AAA
1 AAA
12711 AACAGAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.78, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:13003 original size:33 final size:32
Alignment explanation
Indices: 12961--13042 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 32
12951 CACGCGAAGT
12961 CTCCCCACTAGGACGGCTCTGCCACGGCGGAGC
1 CTCCCCACTAGGACGGCTCTGCCACGGC-GAGC
* *
12994 CTCCCCACTAGGACGGTTCTGCCACGGCTAGC
1 CTCCCCACTAGGACGGCTCTGCCACGGCGAGC
* *
13026 CGCCCCACTAGGGCGGC
1 CTCCCCACTAGGACGGC
13043 AAGGCTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 17 0.39
33 27 0.61
ACGTcount: A:0.15, C:0.43, G:0.29, T:0.13
Consensus pattern (32 bp):
CTCCCCACTAGGACGGCTCTGCCACGGCGAGC
Found at i:13202 original size:33 final size:33
Alignment explanation
Indices: 13106--13191 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
13096 TTTAGTACCG
13106 GTGCCGCCCCAGGGGGGCGGTCTATCCATGGTA
1 GTGCCGCCCCAGGGGGGCGGTCTATCCATGGTA
* *
13139 GGGCCGCCCCAGGGGGGTGGTCTATCCATGGTA
1 GTGCCGCCCCAGGGGGGCGGTCTATCCATGGTA
*
13172 GTGCCGCCCCAGGAGGGCGG
1 GTGCCGCCCCAGGGGGGCGG
13192 CTTGGCCATG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.12, C:0.30, G:0.43, T:0.15
Consensus pattern (33 bp):
GTGCCGCCCCAGGGGGGCGGTCTATCCATGGTA
Found at i:13969 original size:21 final size:18
Alignment explanation
Indices: 13945--13990 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
13935 CTAAAAAGTG
13945 ATAATTTAATTTCTATTTTAA
1 ATAATTT-ATTTC--TTTTAA
*
13966 ATAATTTCTTTCTTTTAA
1 ATAATTTATTTCTTTTAA
13984 ATAATTT
1 ATAATTT
13991 CACTCTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
20 4 0.17
21 7 0.29
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATTTATTTCTTTTAA
Found at i:13972 original size:16 final size:17
Alignment explanation
Indices: 13951--13991 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
13941 AGTGATAATT
13951 TAATTTC-TATTTTAAA
1 TAATTTCTTATTTTAAA
*
13967 TAATTTCTTTCTTTTAAA
1 TAATTTC-TTATTTTAAA
13985 TAATTTC
1 TAATTTC
13992 ACTCTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTTCTTATTTTAAA
Found at i:13997 original size:18 final size:18
Alignment explanation
Indices: 13960--13997 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13950 TTAATTTCTA
**
13960 TTTTAAATAATTTCTTTC
1 TTTTAAATAATTTCACTC
13978 TTTTAAATAATTTCACTC
1 TTTTAAATAATTTCACTC
13996 TT
1 TT
13998 ATGTTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAATAATTTCACTC
Found at i:15367 original size:27 final size:24
Alignment explanation
Indices: 15308--15359 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
15298 ATTAAAATCC
* **
15308 AAAATTGAAGCATAAATTCTAAAA
1 AAAAATGAAGCATAAATAATAAAA
*
15332 AAAAATGAAGCATAAATAATAAAT
1 AAAAATGAAGCATAAATAATAAAA
15356 AAAA
1 AAAA
15360 TAAATGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (24 bp):
AAAAATGAAGCATAAATAATAAAA
Found at i:21493 original size:19 final size:19
Alignment explanation
Indices: 21469--21510 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
21459 TCTCCTAACA
*
21469 CCTGTTTTCGTCTTTGGCC
1 CCTGTTTTCGTCTCTGGCC
21488 CCTGTTTTCGTCTCTGGCC
1 CCTGTTTTCGTCTCTGGCC
21507 CCTG
1 CCTG
21511 ACTAGTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.21, T:0.43
Consensus pattern (19 bp):
CCTGTTTTCGTCTCTGGCC
Found at i:21604 original size:42 final size:42
Alignment explanation
Indices: 21545--21630 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
21535 AGGTCCATAC
21545 GGGGAGAAACTCTCCTAATAACAGTTTGTTAAAAATAAAAAA
1 GGGGAGAAACTCTCCTAATAACAGTTTGTTAAAAATAAAAAA
21587 GGGGAGAAACTCTCCTAATAACAGTTTGTTAAAAATAAAAAA
1 GGGGAGAAACTCTCCTAATAACAGTTTGTTAAAAATAAAAAA
21629 GG
1 GG
21631 CAAATTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (42 bp):
GGGGAGAAACTCTCCTAATAACAGTTTGTTAAAAATAAAAAA
Found at i:22054 original size:21 final size:21
Alignment explanation
Indices: 22030--22073 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22020 AATTTGGGGG
*
22030 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
22051 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
22072 TT
1 TT
22074 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:22209 original size:32 final size:32
Alignment explanation
Indices: 22130--22342 Score: 354
Period size: 32 Copynumber: 6.6 Consensus size: 32
22120 AGCCACGCGG
* *
22130 AGCCTCCCCACTAGGACGGCTCTGCCACGGCGG
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGC-T
* *
22163 ATCCTCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
22195 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
22227 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
22259 AGCCGCCCCACTAGGACGGCTCTGCTACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
22291 AGCCGTCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
22323 AGCCGCCCCACTAGGGCGGC
1 AGCCGCCCCACTAGGACGGC
22343 AAGGCTTTTT
Statistics
Matches: 171, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 141 0.82
33 30 0.18
ACGTcount: A:0.15, C:0.43, G:0.28, T:0.14
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:22422 original size:33 final size:33
Alignment explanation
Indices: 22380--22537 Score: 230
Period size: 33 Copynumber: 4.8 Consensus size: 33
22370 TTTAGTACCG
22380 GTGCCGCCCCAGGGGGGCGGCCTGGCCATGGTA
1 GTGCCGCCCCAGGGGGGCGGCCTGGCCATGGTA
*
22413 GTGCCGCCCCAGGGAGGCGGCCTGGCCATGGTA
1 GTGCCGCCCCAGGGGGGCGGCCTGGCCATGGTA
*
22446 GTGCCGCCCCAGGGAGGCGGCCTGGCCATGGTA
1 GTGCCGCCCCAGGGGGGCGGCCTGGCCATGGTA
* *
22479 GTGCCGCCCCAGGAGGGCGGCTTGGCCATGGCTCA
1 GTGCCGCCCCAGGGGGGCGGCCTGGCCATGG-T-A
*
22514 --GCCGCCCCAGGGGGACGGCACTGG
1 GTGCCGCCCCAGGGGGGCGGC-CTGG
22538 TGGGGCGGCT
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
33 110 0.96
34 4 0.03
35 1 0.01
ACGTcount: A:0.11, C:0.34, G:0.43, T:0.11
Consensus pattern (33 bp):
GTGCCGCCCCAGGGGGGCGGCCTGGCCATGGTA
Found at i:22642 original size:32 final size:32
Alignment explanation
Indices: 22601--22686 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
22591 AAAATAGCCG
*
22601 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCG-A
1 AGCCGCCCCACCGGGGCGGCCTGCCCTGG-GTA
*
22633 AGCCGCCCCACCGGGACGGCCTGCCCTGGGTA
1 AGCCGCCCCACCGGGGCGGCCTGCCCTGGGTA
**
22665 AGCCGCCCCAGTGGGGCGGCCT
1 AGCCGCCCCACCGGGGCGGCCT
22687 TTTCATGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.02
32 47 0.98
ACGTcount: A:0.10, C:0.43, G:0.38, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGGGGCGGCCTGCCCTGGGTA
Found at i:30651 original size:27 final size:26
Alignment explanation
Indices: 30595--30652 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
30585 TTTCTTGCAT
30595 AGAATTTACAGTAATTACTCCTAAAAA
1 AGAATTTACAGTAATTACT-CTAAAAA
*
30622 AGAATTTACTGTAATTAACT-TAAAACA
1 AGAATTTACAGTAATT-ACTCTAAAA-A
30649 AGAA
1 AGAA
30653 CGAAATCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 20 0.71
28 3 0.11
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (26 bp):
AGAATTTACAGTAATTACTCTAAAAA
Found at i:31880 original size:28 final size:31
Alignment explanation
Indices: 31839--31906 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 31
31829 GAGAGTTTAG
*
31839 GGGGTAAAACGTCCAAAAT-TA-AAGTTC-A
1 GGGGCAAAACGTCCAAAATGTACAAGTTCGA
* * *
31867 GGGGCAAAATGTCCAAATTGTACAAGTTCGG
1 GGGGCAAAACGTCCAAAATGTACAAGTTCGA
31898 GGGGCAAAA
1 GGGGCAAAA
31907 ACGGTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 16 0.48
29 2 0.06
30 6 0.18
31 9 0.27
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (31 bp):
GGGGCAAAACGTCCAAAATGTACAAGTTCGA
Done.