Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013100.1 Corchorus capsularis cultivar CVL-1 contig13121, 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: 27277
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1348 original size:33 final size:33
Alignment explanation
Indices: 1306--1393 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 33
1296 GTGTTTTAGA
*
1306 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTAAG
* * * **
1339 TGTTGTTTGCAATGACACTAAATCTCTTTTAAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTAAG
* * *
1372 TGTTATTTGTGACGATACTAAA
1 TGTTGTTTGCGATGATACTAAA
1394 TCTGTTTTGG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (33 bp):
TGTTGTTTGCGATGATACTAAACCTAATTTAAG
Found at i:1464 original size:33 final size:33
Alignment explanation
Indices: 1427--1502 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
1417 TGAAAACAAA
1427 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1460 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1493 TCTGTTTTGG
1 TCTGTTTTGG
1503 GTGAAAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:1917 original size:30 final size:30
Alignment explanation
Indices: 1881--1939 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1871 CAAGGGGGAG
*
1881 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATACG-CCAAGGACTTATCATGGAA
1911 GGAATGATACGCCAAGGACTTATCATGGA
1 GGAATGATACGCCAAGGACTTATCATGGA
1940 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (30 bp):
GGAATGATACGCCAAGGACTTATCATGGAA
Found at i:3501 original size:19 final size:18
Alignment explanation
Indices: 3477--3512 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3467 TGAAGATTTC
3477 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
3496 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
3513 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:5549 original size:30 final size:30
Alignment explanation
Indices: 5509--5567 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5499 TGTCTTCAAG
5509 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
5539 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
5568 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:5994 original size:33 final size:33
Alignment explanation
Indices: 5957--6031 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
5947 CAAAATAGTC
5957 TTATTTTCAATGCTATGATCAACCAAAACAGAA
1 TTATTTTCAATGCTATGATCAACCAAAACAGAA
*
5990 TTATTTTCAATGCTATGATCAACCAAAACAGAT
1 TTATTTTCAATGCTATGATCAACCAAAACAGAA
*
6023 TTGTTTTCA
1 TTATTTTCA
6032 TCACAATTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (33 bp):
TTATTTTCAATGCTATGATCAACCAAAACAGAA
Found at i:8691 original size:30 final size:30
Alignment explanation
Indices: 8651--8707 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
8641 TGTCTTCAGG
8651 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
* *
8681 TCCATGATAAGCCTTGGGTGCATCATT
1 TCCATAATAAGCCTTGGGCGCATCATT
8708 ATGTTCTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:9388 original size:33 final size:33
Alignment explanation
Indices: 9321--9426 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
9311 TTCTTTTCCC
*
9321 CCAAAACAGAATTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTTCAATGCTATAATCAA
* * *
9351 CCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATAATCAA
9384 CCAAAACAGAATTATTTTCAATGCTATAATCAA
1 CCAAAACAGAATTATTTTCAATGCTATAATCAA
9417 CCAAAACAGA
1 CCAAAACAGA
9427 TTTGTTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
30 22 0.33
33 45 0.67
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATAATCAA
Found at i:12860 original size:21 final size:21
Alignment explanation
Indices: 12835--12874 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12825 TGGTGATGTC
**
12835 GACTTCAATGTTCTCTAAATG
1 GACTTCAATGGACTCTAAATG
12856 GACTTCAATGGACTCTAAA
1 GACTTCAATGGACTCTAAA
12875 CCTCCAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (21 bp):
GACTTCAATGGACTCTAAATG
Found at i:13042 original size:12 final size:12
Alignment explanation
Indices: 13025--13058 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13015 GCCGGCTGCC
*
13025 CCATGCGTTGCT
1 CCATGCGATGCT
*
13037 CCATGCCATGCT
1 CCATGCGATGCT
13049 CCATGCGATG
1 CCATGCGATG
13059 GCCGGTCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (12 bp):
CCATGCGATGCT
Found at i:14089 original size:33 final size:33
Alignment explanation
Indices: 14018--14125 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
14008 GCGCCTAGCG
* * *
14018 ATGGCCGGT-TGTGGCTGGACATGC-CCATGTTGC
1 ATGGCCGGTGT-TGGCCGGACAT-CTCCAAGTCGC
* *
14051 GTGGCCGGTGTTGGCCGGACATCTCCGAGTCGC
1 ATGGCCGGTGTTGGCCGGACATCTCCAAGTCGC
* *
14084 ATGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGC
1 ATGGCCGGTGTTGGCCGGACATCTCCAAGTCGC
*
14117 GTGGCCGGT
1 ATGGCCGGT
14126 CACTAGTGCT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 1 0.02
33 61 0.97
34 1 0.02
ACGTcount: A:0.09, C:0.28, G:0.39, T:0.24
Consensus pattern (33 bp):
ATGGCCGGTGTTGGCCGGACATCTCCAAGTCGC
Found at i:15948 original size:27 final size:28
Alignment explanation
Indices: 15916--15971 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
15906 CCAAAACAGG
15916 ATTATTTGCAATGCTATGATCAA-CAAA
1 ATTATTTGCAATGCTATGATCAACCAAA
*
15943 ATTATTTGTAATGCTATGATCAACCAAA
1 ATTATTTGCAATGCTATGATCAACCAAA
15971 A
1 A
15972 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:18678 original size:17 final size:17
Alignment explanation
Indices: 18656--18689 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18646 GAATCGGCTA
18656 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
18673 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
18690 AAGAAGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:19519 original size:33 final size:33
Alignment explanation
Indices: 19477--19567 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
19467 TCCGGATGGC
* *
19477 CCTATCGATGTCCGGTTGTGGCCGGTTGGTGCG
1 CCTAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
19510 CCTAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
1 CCTAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
*
19543 CCTAGCGATGGCCGGTTTTGGCCGG
1 CCTAGCGATGGCCGGTTGTGGCCGG
19568 ACATGCCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.07, C:0.25, G:0.42, T:0.26
Consensus pattern (33 bp):
CCTAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
Found at i:19588 original size:33 final size:33
Alignment explanation
Indices: 19551--19657 Score: 128
Period size: 33 Copynumber: 3.2 Consensus size: 33
19541 CGCCTAGCGA
*
19551 TGGCCGGTTTTGGCCGGACATGC-CC-ATGTCGCG
1 TGGCCGGTGTTGGCCGGACAT-CTCCGA-GTCGCG
19584 TGGCCGGTGTTGGCCGGACATCTCCGAGTCGCG
1 TGGCCGGTGTTGGCCGGACATCTCCGAGTCGCG
* * * **
19617 TGGCCGGTGTTGGCCGGGCTTTTCAAAGTCGCG
1 TGGCCGGTGTTGGCCGGACATCTCCGAGTCGCG
19650 TGGCCGGT
1 TGGCCGGT
19658 CACTAGTGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.02
33 64 0.97
34 1 0.02
ACGTcount: A:0.08, C:0.28, G:0.39, T:0.24
Consensus pattern (33 bp):
TGGCCGGTGTTGGCCGGACATCTCCGAGTCGCG
Found at i:19802 original size:59 final size:59
Alignment explanation
Indices: 19710--19826 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
19700 TGACATCTCT
* *
19710 ATGATCTTCATTGGCTCCAATGTGTCCTTCTAAGCCATGATAAGCCCTTGGCGCATCAC
1 ATGATCTCCAATGGCTCCAATGTGTCCTTCTAAGCCATGATAAGCCCTTGGCGCATCAC
* *
19769 ATGATCTCCAATGGCTCCATTGTG-CTCTTCTAAGCCGTGATAAGCCCTTGGCGCATCA
1 ATGATCTCCAATGGCTCCAATGTGTC-CTTCTAAGCCATGATAAGCCCTTGGCGCATCA
19827 TCCCCTCTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 1 0.02
59 52 0.98
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (59 bp):
ATGATCTCCAATGGCTCCAATGTGTCCTTCTAAGCCATGATAAGCCCTTGGCGCATCAC
Found at i:23090 original size:33 final size:33
Alignment explanation
Indices: 23053--23132 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
23043 AGCACTAGTG
* *
23053 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
*
23086 ACCGGCCACGCGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
*
23119 ACCGGCCACACGAC
1 ACCGGCCACGCGAC
23133 ATGGGCATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.41, G:0.29, T:0.06
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
Found at i:24929 original size:33 final size:33
Alignment explanation
Indices: 24892--24971 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
24882 AGCACTAGTG
*
24892 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
*
24925 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
24958 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
24972 ATGGGCATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
Found at i:24995 original size:33 final size:33
Alignment explanation
Indices: 24892--24998 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
24882 AGCACTAGTG
* * * *
24892 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACATGGAGATGCCCAGCCAAC
* *
24925 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACATGGAGATGCCCAGCCAAC
*
24958 ACCGGCCACGCGACATGG-GCATGTCCAGCC-AC
1 ACCGGCCACGCGACATGGAG-ATGCCCAGCCAAC
24990 AACCGGCCA
1 -ACCGGCCA
24999 TCGCTAGGCG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.04
33 64 0.96
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCAGCCAAC
Found at i:25983 original size:17 final size:17
Alignment explanation
Indices: 25958--25991 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25948 CACCCTTCTT
25958 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
25975 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
25992 TAGCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Done.