Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012074.1 Corchorus capsularis cultivar CVL-1 contig12095, 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: 47407
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1422 original size:20 final size:20
Alignment explanation
Indices: 1397--1437 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1387 TTAATTATTG
1397 ATATGTTAAGTGGATTTTTA
1 ATATGTTAAGTGGATTTTTA
*
1417 ATATGTTAAGTGGGTTTTTA
1 ATATGTTAAGTGGATTTTTA
1437 A
1 A
1438 GACATCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
ATATGTTAAGTGGATTTTTA
Found at i:1495 original size:20 final size:20
Alignment explanation
Indices: 1470--1510 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1460 TTAATTATTG
1470 ATATGTTAAGTGAGTTTTTA
1 ATATGTTAAGTGAGTTTTTA
*
1490 ATATGTTAAGTGGGTTTTTA
1 ATATGTTAAGTGAGTTTTTA
1510 A
1 A
1511 GACATCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
ATATGTTAAGTGAGTTTTTA
Found at i:1497 original size:73 final size:72
Alignment explanation
Indices: 1378--1521 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 72
1368 CAGTAATTTG
1378 AGGTTCCCTTTAATTATTGATATGTTAAGTGGATTTTTAATATGTTAAGTGGGTTTTTAAGACAT
1 AGGTTCCCTTTAATTATTGATATGTTAAGTGGATTTTTAATATGTTAAGTGGGTTTTTAAGACAT
1443 CTTCATTA
66 C-TCATTA
1451 AGGTTCCCTTTAATTATTGATATGTTAAGT-GAGTTTTTAATATGTTAAGTGGGTTTTTAAGACA
1 AGGTTCCCTTTAATTATTGATATGTTAAGTGGA-TTTTTAATATGTTAAGTGGGTTTTTAAGACA
1515 TCTCATT
65 TCTCATT
1522 TTTAGACCCA
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
72 7 0.10
73 63 0.90
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (72 bp):
AGGTTCCCTTTAATTATTGATATGTTAAGTGGATTTTTAATATGTTAAGTGGGTTTTTAAGACAT
CTCATTA
Found at i:2565 original size:17 final size:17
Alignment explanation
Indices: 2543--2577 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2533 ATATGGTAGT
2543 ATAAATAGAAAAAGAAA
1 ATAAATAGAAAAAGAAA
2560 ATAAATAGAAAAAGAAA
1 ATAAATAGAAAAAGAAA
2577 A
1 A
2578 ATAACTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (17 bp):
ATAAATAGAAAAAGAAA
Found at i:4877 original size:36 final size:36
Alignment explanation
Indices: 4836--4908 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
4826 TTAGCCATGG
4836 CTATATTCTCAAAGATACTTAGCCAAACAGATGTTA
1 CTATATTCTCAAAGATACTTAGCCAAACAGATGTTA
4872 CTATATTCTCAAAGATACTTAGCCAAACAGATGTTA
1 CTATATTCTCAAAGATACTTAGCCAAACAGATGTTA
4908 C
1 C
4909 CAGGAGATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (36 bp):
CTATATTCTCAAAGATACTTAGCCAAACAGATGTTA
Found at i:8675 original size:59 final size:59
Alignment explanation
Indices: 8576--8687 Score: 134
Period size: 59 Copynumber: 1.9 Consensus size: 59
8566 AAAAAGTCAC
* * * * * *
8576 TGTGGTTATGAGATTAGTAATTATAGTCGTGAGGCTGTTGATATCAGTAATGTAGTAAT
1 TGTGGTTATAAGATTAGCAATTATAGTCATGAGACCGTTGATATCAATAATGTAGTAAT
* * * *
8635 TGTGGTTGTAAGATTAGCAATTGTAGTTATGAGACCGTTGATGTCAATAATGT
1 TGTGGTTATAAGATTAGCAATTATAGTCATGAGACCGTTGATATCAATAATGT
8688 TGTGGTCCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 43 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (59 bp):
TGTGGTTATAAGATTAGCAATTATAGTCATGAGACCGTTGATATCAATAATGTAGTAAT
Found at i:10317 original size:10 final size:10
Alignment explanation
Indices: 10304--10328 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10294 AATTTAAATG
10304 AATTTGTTTA
1 AATTTGTTTA
10314 AATTTGTTTA
1 AATTTGTTTA
10324 AATTT
1 AATTT
10329 TTTTTAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
AATTTGTTTA
Found at i:11779 original size:12 final size:12
Alignment explanation
Indices: 11762--11793 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11752 ACCTGAAAAT
*
11762 TCGTGTTTCGTG
1 TCGTGTTTCATG
11774 TCGTGTTTCATG
1 TCGTGTTTCATG
11786 TCGTGTTT
1 TCGTGTTT
11794 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.16, G:0.28, T:0.53
Consensus pattern (12 bp):
TCGTGTTTCATG
Found at i:12207 original size:20 final size:21
Alignment explanation
Indices: 12170--12212 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12160 AACCCGTTAA
*
12170 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
12191 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
12211 TT
1 TT
12213 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:12270 original size:42 final size:43
Alignment explanation
Indices: 12200--12282 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
12190 CTTAAACGTG
* *
12200 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACAATAATC
*
12243 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACAATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACAATAA
12283 GCCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACAATAATC
Found at i:12745 original size:14 final size:14
Alignment explanation
Indices: 12726--12752 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12716 TATTTTATTG
12726 TAATAATAATAATA
1 TAATAATAATAATA
12740 TAATAATAATAAT
1 TAATAATAATAAT
12753 GATCTACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:12814 original size:18 final size:18
Alignment explanation
Indices: 12775--12815 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12765 AAAAGCCCTC
*
12775 AATACATTTTATTTTCGT
1 AATATATTTTATTTTCGT
12793 -ATATATTTATATTTT-GT
1 AATATATTT-TATTTTCGT
12810 AATATA
1 AATATA
12816 ATACAGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
AATATATTTTATTTTCGT
Found at i:13962 original size:10 final size:10
Alignment explanation
Indices: 13949--13984 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
13939 AAATCTCGAT
13949 ATATCCGTAA
1 ATATCCGTAA
13959 ATATCCGTAA
1 ATATCCGTAA
13969 ATATCCGTAA
1 ATATCCGTAA
13979 ATATCC
1 ATATCC
13985 ATATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:16007 original size:12 final size:12
Alignment explanation
Indices: 15990--16043 Score: 99
Period size: 12 Copynumber: 4.4 Consensus size: 12
15980 CATTGATACC
15990 TCGATATATCCG
1 TCGATATATCCG
16002 TCGATATATCCG
1 TCGATATATCCG
16014 TCGATATATCCG
1 TCGATATATCCG
16026 TTCGATATATCCG
1 -TCGATATATCCG
16039 TCGAT
1 TCGAT
16044 GCCTGTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:16036 original size:25 final size:24
Alignment explanation
Indices: 15990--16043 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 24
15980 CATTGATACC
15990 TCGATATATCCGTCGATATATCCG
1 TCGATATATCCGTCGATATATCCG
16014 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCG-TCGATATATCCG
16039 TCGAT
1 TCGAT
16044 GCCTGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (24 bp):
TCGATATATCCGTCGATATATCCG
Found at i:16153 original size:28 final size:28
Alignment explanation
Indices: 16099--16154 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
16089 CTCCATTCAT
* *
16099 AAAATTCCTGACTAATTAATGCCAAAAA
1 AAAATTCCTGACTAATTAAAGACAAAAA
*
16127 AAAATTCCTGACTAATTAAAGAGAAAAA
1 AAAATTCCTGACTAATTAAAGACAAAAA
16155 CATAAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.23
Consensus pattern (28 bp):
AAAATTCCTGACTAATTAAAGACAAAAA
Found at i:20006 original size:22 final size:22
Alignment explanation
Indices: 19978--20019 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19968 ACATGTGGCA
*
19978 TGCCACATGTACTAAAAAGTCG
1 TGCCACATGTACCAAAAAGTCG
20000 TGCCACATGTACCAAAAAGT
1 TGCCACATGTACCAAAAAGT
20020 GACACATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (22 bp):
TGCCACATGTACCAAAAAGTCG
Found at i:20036 original size:31 final size:31
Alignment explanation
Indices: 20001--20097 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 31
19991 AAAAAGTCGT
*
20001 GCCACATGTACCAAAAAGTGACACATGTCAC
1 GCCACATGTACCAAAAAGTGACACATGGCAC
* * * *
20032 GCCACGTG-CCCAAAAAGTGACACGTGGCAT
1 GCCACATGTACCAAAAAGTGACACATGGCAC
** * * *
20062 GCCACATGTTTCAAAAAGTGGCACGTGGCAT
1 GCCACATGTACCAAAAAGTGACACATGGCAC
20093 GCCAC
1 GCCAC
20098 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 25 0.45
31 31 0.55
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (31 bp):
GCCACATGTACCAAAAAGTGACACATGGCAC
Found at i:20066 original size:30 final size:30
Alignment explanation
Indices: 20011--20107 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
20001 GCCACATGTA
* * *
20011 CCAAAAAGTGACACATGTCACGCCACGTGC
1 CCAAAAAGTGACACGTGGCATGCCACGTGC
* *
20041 CCAAAAAGTGACACGTGGCATGCCACATGTT
1 CCAAAAAGTGACACGTGGCATGCCACGTG-C
* *
20072 TCAAAAAGTGGCACGTGGCATGCCACGTGC
1 CCAAAAAGTGACACGTGGCATGCCACGTGC
*
20102 ACAAAA
1 CCAAAA
20108 GGATACGTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 30 0.54
31 26 0.46
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (30 bp):
CCAAAAAGTGACACGTGGCATGCCACGTGC
Found at i:35085 original size:145 final size:145
Alignment explanation
Indices: 34822--35113 Score: 548
Period size: 145 Copynumber: 2.0 Consensus size: 145
34812 TAAGGCGGTT
*
34822 ATCCACACCGCTGTCATCCCTATTTCTGACACATGGTACCCCACAAGCTGTTTCACATGTGGCAA
1 ATCCACACCGCTGTCATCCCTATTTCTGACACATGGTACCCCACAAGCTGTTTCACATGAGGCAA
34887 TTTCATCCCATTTTGGATGCTAATTGTTTAAAAATGATAATTTGGGTATCATATTGGTCAAAATT
66 TTTCATCCCATTTTGGATGCTAATTGTTTAAAAATGATAATTTGGGTATCATATTGGTCAAAATT
34952 AAAGTTTGTGGTATA
131 AAAGTTTGTGGTATA
*
34967 ATCCACACCGTTGTCATCCCTATTTCTGACACATGGTACCCCACAAGCTGTTTCACATGAGGCAA
1 ATCCACACCGCTGTCATCCCTATTTCTGACACATGGTACCCCACAAGCTGTTTCACATGAGGCAA
* *
35032 TTTCATCCCATTTTGGATGCTAATTGTTTAAAAATGATACTTTGGGTATCATATTGGTCAAGATT
66 TTTCATCCCATTTTGGATGCTAATTGTTTAAAAATGATAATTTGGGTATCATATTGGTCAAAATT
35097 AAAGTTTGTGGTATA
131 AAAGTTTGTGGTATA
35112 AT
1 AT
35114 GTCCATCTGT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (145 bp):
ATCCACACCGCTGTCATCCCTATTTCTGACACATGGTACCCCACAAGCTGTTTCACATGAGGCAA
TTTCATCCCATTTTGGATGCTAATTGTTTAAAAATGATAATTTGGGTATCATATTGGTCAAAATT
AAAGTTTGTGGTATA
Found at i:35244 original size:2 final size:2
Alignment explanation
Indices: 35237--35267 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35227 CTCTTAGGTG
35237 TA 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 TA T
35268 TTAAGATGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43681 original size:18 final size:15
Alignment explanation
Indices: 43645--43679 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
43635 AAAAAATCTA
43645 ATATTGAGAATCCAT
1 ATATTGAGAATCCAT
43660 ATATTAGAGAATCCAT
1 ATATT-GAGAATCCAT
43676 ATAT
1 ATAT
43680 ATACTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (15 bp):
ATATTGAGAATCCAT
Found at i:46924 original size:40 final size:40
Alignment explanation
Indices: 46857--46934 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
46847 GCACGCCTCA
* * *
46857 CTATTGCCCACATATGTATCCGGGATTTAAAAAGAAGCAG
1 CTATTGCCCACAAATGTACCCGAGATTTAAAAAGAAGCAG
*
46897 CTATTGCCCACAAATGTGCCCGAGATTTAAAAAGAAGC
1 CTATTGCCCACAAATGTACCCGAGATTTAAAAAGAAGC
46935 GGGAGACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (40 bp):
CTATTGCCCACAAATGTACCCGAGATTTAAAAAGAAGCAG
Done.