Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013095.1 Corchorus capsularis cultivar CVL-1 contig13116, 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: 20203
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2159 original size:33 final size:32
Alignment explanation
Indices: 2089--2195 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
2079 AAATGATCAT
**
2089 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAA
1 GTGGCCGGTTGTGGCCGGGCATGGCC-AGTCGC
2122 GTGGCCGGTTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGGCCA-GTCGC
** **
2155 GTGGCCGG-TGATGATCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTG-TGGCCGGGCATGGCC-AGTCGC
2188 GTGGCCGG
1 GTGGCCGG
2196 CTCTCCAAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
32 3 0.05
33 61 0.94
34 1 0.02
ACGTcount: A:0.10, C:0.26, G:0.44, T:0.20
Consensus pattern (32 bp):
GTGGCCGGTTGTGGCCGGGCATGGCCAGTCGC
Found at i:2202 original size:21 final size:21
Alignment explanation
Indices: 2176--2216 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2166 TGATCGGGCA
*
2176 TCTCCAAGTCGCGTGGCCGGC
1 TCTCCAAGTCGCATGGCCGGC
2197 TCTCCAAGTCGCATGGCCGG
1 TCTCCAAGTCGCATGGCCGG
2217 TCACTTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.37, G:0.32, T:0.20
Consensus pattern (21 bp):
TCTCCAAGTCGCATGGCCGGC
Found at i:6136 original size:33 final size:33
Alignment explanation
Indices: 6042--6137 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
6032 CAAAGAACGT
* * * *
6042 TTTAGATGTTGTTTGCGATGATACTAAACCTAA
1 TTTAGGTGTTGTTTGTGATGAAACTAAATCTAA
* *
6075 TTT-GAGTGTTGTTTGTGATGACACTAAATCTGA
1 TTTAG-GTGTTGTTTGTGATGAAACTAAATCTAA
*
6108 TTTAGGTGTTGTTTGTGATGAAAATAAATC
1 TTTAGGTGTTGTTTGTGATGAAACTAAATC
6138 CGTTTTGGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 52 0.96
34 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (33 bp):
TTTAGGTGTTGTTTGTGATGAAACTAAATCTAA
Found at i:6166 original size:33 final size:32
Alignment explanation
Indices: 6129--6274 Score: 181
Period size: 33 Copynumber: 4.5 Consensus size: 32
6119 TTTGTGATGA
* *
6129 AAATAAATCCGTTTTGGTTGATCATAGCATAGC
1 AAATAATTCTGTTTTGGTTGATCATAGCAT-GC
*
6162 AAATAATTCTGTTTTGGTTGATCATAGCATTGA
1 AAATAATTCTGTTTTGGTTGATCATAGCA-TGC
*
6195 AAATAATTCTGTTTTGGTTGATCATAGCATTC
1 AAATAATTCTGTTTTGGTTGATCATAGCATGC
* *
6227 GAAATAATTCTGTTTTGGTTG---ATGGCATTGA
1 -AAATAATTCTGTTTTGGTTGATCATAGCA-TGC
6258 AAATAATTCTGTTTTGG
1 AAATAATTCTGTTTTGG
6275 GTGAAAAGAA
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
30 22 0.22
31 1 0.01
32 1 0.01
33 77 0.75
34 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (32 bp):
AAATAATTCTGTTTTGGTTGATCATAGCATGC
Found at i:6232 original size:66 final size:63
Alignment explanation
Indices: 6126--6274 Score: 219
Period size: 66 Copynumber: 2.3 Consensus size: 63
6116 TTGTTTGTGA
* *
6126 TGAAAATAAATCCGTTTTGGTTGATCATAGCATAGCAAATAATTCTGTTTTGGTTGATCATAGCA
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCATAGCAAATAATTCTGTTTTGGTTG---ATAGCA
6191 T
63 T
* *
6192 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT-TCGAAATAATTCTGTTTTGGTTGATGGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCATAGC-AAATAATTCTGTTTTGGTTGATAGCAT
6255 TGAAAATAATTCTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
6275 GTGAAAAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
63 26 0.33
65 1 0.01
66 51 0.65
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (63 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCATAGCAAATAATTCTGTTTTGGTTGATAGCAT
Found at i:6705 original size:30 final size:30
Alignment explanation
Indices: 6653--6711 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
6643 CAATGGGGAG
*
6653 GGAATGATGCGCCCAAGGCTTATCATGGAA
1 GGAATGATGCGCCCAAGACTTATCATGGAA
* *
6683 GGAATGATGC-CCGAAGTACTTATTATGGA
1 GGAATGATGCGCCCAAG-ACTTATCATGGA
6712 CTTGAAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCCAAGACTTATCATGGAA
Found at i:7670 original size:33 final size:33
Alignment explanation
Indices: 7633--7709 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
7623 TTGCAAAGAG
*
7633 TGTTTTAGATGTTGTTTAAAATGGCACAAAATC
1 TGTTTTAGATGTTGTTTAAAATGACACAAAATC
** * *
7666 TGTTTTA-AGTGTTGTTTGCAATGATACTAAATC
1 TGTTTTAGA-TGTTGTTTAAAATGACACAAAATC
*
7699 TGTTTTGGATG
1 TGTTTTAGATG
7710 CTAATTGTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 1 0.03
33 34 0.94
34 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (33 bp):
TGTTTTAGATGTTGTTTAAAATGACACAAAATC
Found at i:9923 original size:22 final size:22
Alignment explanation
Indices: 9886--9929 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9876 GAATTTCAGG
*
9886 ACAACTTCGGCCCAGAACTTGT
1 ACAACTTCGGCACAGAACTTGT
* *
9908 ACAACTTCGGGACAGAAGTTGT
1 ACAACTTCGGCACAGAACTTGT
9930 TACGGGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTTCGGCACAGAACTTGT
Found at i:13993 original size:19 final size:18
Alignment explanation
Indices: 13960--13996 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
13950 TTGAAATAAT
13960 TCTTCAATGGTCTTCAAG
1 TCTTCAATGGTCTTCAAG
*
13978 TCTTCAAATTGTCTTCAAG
1 TCTTC-AATGGTCTTCAAG
13997 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAG
Found at i:16637 original size:33 final size:33
Alignment explanation
Indices: 16559--16638 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
16549 ACATGCCCAT
* *
16559 GTCGCGTGGCCAGTGTTGGCCGGGCATCTCCGA
1 GTCGCGTGGCCGGTGTTGGCCGGGCATCTCCAA
* * *
16592 GTCGCTTTGCCGGTGTTGGCCGGGCTTCTCCAA
1 GTCGCGTGGCCGGTGTTGGCCGGGCATCTCCAA
16625 GTCGCGTGGCCGGT
1 GTCGCGTGGCCGGT
16639 CACTAGTGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.25
Consensus pattern (33 bp):
GTCGCGTGGCCGGTGTTGGCCGGGCATCTCCAA
Found at i:17595 original size:27 final size:28
Alignment explanation
Indices: 17563--17618 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
17553 CCAAAACAGG
17563 ATTATTTGCAATGCTATGATCAA-CAAA
1 ATTATTTGCAATGCTATGATCAACCAAA
*
17590 ATTATTTGTAATGCTATGATCAACCAAA
1 ATTATTTGCAATGCTATGATCAACCAAA
17618 A
1 A
17619 CAGAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (28 bp):
ATTATTTGCAATGCTATGATCAACCAAA
Found at i:20194 original size:33 final size:34
Alignment explanation
Indices: 20134--20199 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
20124 GCCCATGTCG
*
20134 CGTGGCCGGTGTTGGCCCGGGCATCTCCGAGTCA
1 CGTGGCCGGTGTTGGCCCGGGCATCTCCAAGTCA
* *
20168 CGTGGCCGGTGTT-TCCCGGGCTTCTCCAAGTC
1 CGTGGCCGGTGTTGGCCCGGGCATCTCCAAGTC
20200 GCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.55
34 13 0.45
ACGTcount: A:0.08, C:0.33, G:0.35, T:0.24
Consensus pattern (34 bp):
CGTGGCCGGTGTTGGCCCGGGCATCTCCAAGTCA
Done.