Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010430.1 Corchorus capsularis cultivar CVL-1 contig10451, 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: 34087
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3830 original size:154 final size:154
Alignment explanation
Indices: 3553--3930 Score: 674
Period size: 154 Copynumber: 2.5 Consensus size: 154
3543 TAGAGTTATG
3553 AGAATAAATACGTACGTGGTTTAATTTTCTACCAAGTGTTTTATTAC-TTT-TA-TAGTCTTTCT
1 AGAATAAATACGTACGTGGTTTAATTTTCTACCAAGTGTTTTATTACTTTTATATTAGTCTTTCT
3615 TTAATTATAAAAGTCTAAGGATCACCTAATTATCTGCCTGAAATAAATCTAGTTGATACTCCATA
66 TTAATTATAAAAGTCTAAGGATCACCTAATTATCTGCCTGAAATAAATCTAGTTGATACTCCATA
*
3680 ATCATTAATAAATAACCAACATTA
131 ATCATTAATAAATAACCAACAGTA
* *
3704 AGAATAAATACTTTCGTGGTTTAATTTTCTACCAAGTGTTTTATTACTTTTATATTAGTCTTTCT
1 AGAATAAATACGTACGTGGTTTAATTTTCTACCAAGTGTTTTATTACTTTTATATTAGTCTTTCT
* *
3769 TTAATTACT-GAAGTCTAAGGATCACTTAATTATCTGCCTGAAATAAATCTAGTTGATACTCCAT
66 TTAATTA-TAAAAGTCTAAGGATCACCTAATTATCTGCCTGAAATAAATCTAGTTGATACTCCAT
3833 AATCATTAATAAATAACCAACAGTA
130 AATCATTAATAAATAACCAACAGTA
3858 AGAATAAATACGTACGTGGTTTAATTTTCTACCAAGTGTTTTATTACTTTTATATTAGTCTTTCT
1 AGAATAAATACGTACGTGGTTTAATTTTCTACCAAGTGTTTTATTACTTTTATATTAGTCTTTCT
3923 TTAATTAT
66 TTAATTAT
3931 CTAATTATCT
Statistics
Matches: 216, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
151 45 0.21
152 3 0.01
153 3 0.01
154 164 0.76
155 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (154 bp):
AGAATAAATACGTACGTGGTTTAATTTTCTACCAAGTGTTTTATTACTTTTATATTAGTCTTTCT
TTAATTATAAAAGTCTAAGGATCACCTAATTATCTGCCTGAAATAAATCTAGTTGATACTCCATA
ATCATTAATAAATAACCAACAGTA
Found at i:5458 original size:87 final size:87
Alignment explanation
Indices: 5312--5482 Score: 315
Period size: 87 Copynumber: 2.0 Consensus size: 87
5302 ACCTAGGTCT
5312 GGGAGTCGGTTACGTGTGGGGAAGGATTAGCACTAGGGATGCAACCGGGTTGTCTTTAATCGGGT
1 GGGAGTCGGTTACGTGTGGGGAAGGATTAGCACTAGGGATGCAACCGGGTTGTCTTTAATCGGGT
5377 ACCAGGGACTACCCGACCCTCC
66 ACCAGGGACTACCCGACCCTCC
*
5399 GGGAGTGGGTTACGTGTGGGGAAGGATTAGCACTAGGGATGCAACCGGGTTGTCTTTAATCGGGT
1 GGGAGTCGGTTACGTGTGGGGAAGGATTAGCACTAGGGATGCAACCGGGTTGTCTTTAATCGGGT
* *
5464 ACTAGGGACTACCTGACCC
66 ACCAGGGACTACCCGACCC
5483 GATTTTGTAG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (87 bp):
GGGAGTCGGTTACGTGTGGGGAAGGATTAGCACTAGGGATGCAACCGGGTTGTCTTTAATCGGGT
ACCAGGGACTACCCGACCCTCC
Found at i:6957 original size:67 final size:67
Alignment explanation
Indices: 6798--7267 Score: 509
Period size: 67 Copynumber: 7.0 Consensus size: 67
6788 AAATTGCCAG
* * * * * * * *
6798 TAAACTCAAATGCGAAAATGAAGAAACTGACCCTTTCACCGAAGGGGCATTTTTGGAAGATAAAA
1 TAAACTTAAATGCGAAAA-GACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAACAAAA
6863 --C
65 TGC
* * * * * * * **
6864 TAAATTTTAGATGCAAAAAGACGAAAATAACCCTTCGACCGGAAGGGCATTTTTGGAAATGAAAA
1 TAAA-CTTAAATGCGAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAACAAAA
6929 TGC
65 TGC
** * ** *
6932 TAATTTTAAATGCGAAAAGAAGAAAATGACCCTTTGACCGAAAGGGGTATTTTT-GAAAAGAAAA
1 TAAACTTAAATGCGAAAAGACGAAAATGACCCTTCCACCGAAA-GGGTATTTTTGGAAAACAAAA
*
6996 TAC
65 TGC
* * *
6999 TAAACTTAAATGCAAAAAGACGAAAATGACCCTTCCACCAAAAGGGTATTCTTGGAAAAACAAAA
1 TAAACTTAAATGCGAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGG-AAAACAAAA
7064 TGC
65 TGC
* *
7067 TAAACTTAAATGCGGAAAGAC-AGAAATGACCCTTCCACCGAAAGGGTATTTTGGGAAAACAAAA
1 TAAACTTAAATGCGAAAAGACGA-AAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAACAAAA
*
7131 TAC
65 TGC
* *
7134 TAAACTAAAATGC-AGAAAGACGGAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACAAA
1 TAAACTTAAATGCGA-AAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGG-AAAACAAA
7198 ATGC
64 ATGC
* * * *
7202 TAAACATAAATGCGGAAAGACGGAAATGACCCTTCCACCAAAAGGGTATTTTTGGGAAAACAAAA
1 TAAACTTAAATGCGAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTT-GGAAAACAAAA
7267 T
65 T
7268 ACTTTTCCTT
Statistics
Matches: 343, Mismatches: 49, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
66 49 0.14
67 152 0.44
68 140 0.41
69 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (67 bp):
TAAACTTAAATGCGAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAACAAAAT
GC
Found at i:7111 original size:135 final size:134
Alignment explanation
Indices: 6798--7270 Score: 553
Period size: 135 Copynumber: 3.5 Consensus size: 134
6788 AAATTGCCAG
* * * * *
6798 TAAACTCAAATGCGAAAATGAAGAAACTGACCCTTTCACCG-AAGGGGCATTTTTGGAAGA-TAA
1 TAAACTTAAATGCGAAAA-GAAGAAA-TGACCCTTCCACCGAAAGGGGTATTTTT-GAAAACAAA
* * * * * * *
6861 A-ACTAAATTTTAGATGCAAAAAGACGAAAATAACCCTTCGACCGGAAGGGCATTTTTGG-AAAT
63 ATACTAAA-CTTAAATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAA
*
6924 GAAAATGC
127 CAAAATGC
** ** *
6932 TAATTTTAAATGCGAAAAGAAGAAAATGACCCTTTGACCGAAAGGGGTATTTTTGAAAAGAAAAT
1 TAAACTTAAATGCGAAAAGAAG-AAATGACCCTTCCACCGAAAGGGGTATTTTTGAAAACAAAAT
* *
6997 ACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCCACCAAAAGGGTATTCTTGGAAAAACAA
65 ACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACAA
7062 AATGC
130 AATGC
* *
7067 TAAACTTAAATGCGGAAAGACAGAAATGACCCTTCCACCGAAA-GGGTATTTTGGGAAAACAAAA
1 TAAACTTAAATGCGAAAAGA-AGAAATGACCCTTCCACCGAAAGGGGTATTTT-TGAAAACAAAA
* * *
7131 TACTAAACTAAAATGCAGAAAGACGGAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACA
64 TACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACA
7196 AAATGC
129 AAATGC
* * * *
7202 TAAACATAAATGCGGAAAGACGGAAATGACCCTTCCACC-AAAAGGGTATTTTTGGGAAAACAAA
1 TAAACTTAAATGCGAAAAGA-AGAAATGACCCTTCCACCGAAAGGGGTATTTTT--GAAAACAAA
7266 ATACT
63 ATACT
7271 TTTCCTTTTT
Statistics
Matches: 297, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
133 21 0.07
134 88 0.30
135 172 0.58
136 16 0.05
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (134 bp):
TAAACTTAAATGCGAAAAGAAGAAATGACCCTTCCACCGAAAGGGGTATTTTTGAAAACAAAATA
CTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACAAA
ATGC
Found at i:10575 original size:22 final size:23
Alignment explanation
Indices: 10534--10576 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10524 CAATGCTATG
10534 CTAAAGGCCAAAGAGTGAATTTA
1 CTAAAGGCCAAAGAGTGAATTTA
*
10557 CTAAATGCCAAA-AGTGAATT
1 CTAAAGGCCAAAGAGTGAATT
10577 AGAAAATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (23 bp):
CTAAAGGCCAAAGAGTGAATTTA
Found at i:13385 original size:16 final size:16
Alignment explanation
Indices: 13364--13417 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
13354 CTTTACTACT
13364 AACAAATTTTGATACA
1 AACAAATTTTGATACA
*
13380 AACAAATTTT-A-GC-
1 AACAAATTTTGATACA
* *
13393 CAC-ACTTTTGATACA
1 AACAAATTTTGATACA
13408 AACAAATTTT
1 AACAAATTTT
13418 ATAGGGTAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
12 5 0.18
13 3 0.11
14 2 0.07
15 3 0.11
16 15 0.54
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (16 bp):
AACAAATTTTGATACA
Found at i:16083 original size:27 final size:27
Alignment explanation
Indices: 16031--16086 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
16021 TAATACTCCA
**
16031 TTTATCCCTTTTTATCTGTCGGTTTTC
1 TTTATCCCTTTTTATCTGTAAGTTTTC
16058 TTTATCCCTTTTTATCTGTAA-TTTT-
1 TTTATCCCTTTTTATCTGTAAGTTTTC
16083 TTTA
1 TTTA
16087 CATAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 19 0.70
ACGTcount: A:0.12, C:0.18, G:0.07, T:0.62
Consensus pattern (27 bp):
TTTATCCCTTTTTATCTGTAAGTTTTC
Found at i:17852 original size:31 final size:31
Alignment explanation
Indices: 17809--17870 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
17799 AGTTTTGAGA
* *
17809 AACTTTTGAAATGCTTATTATA-CTCTTATTT
1 AACTTTTAAAATGCCTATTATATC-CTTATTT
17840 AACTTTTAAAATGCCTATTATATCCTTATTT
1 AACTTTTAAAATGCCTATTATATCCTTATTT
17871 GTCTAACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.50
Consensus pattern (31 bp):
AACTTTTAAAATGCCTATTATATCCTTATTT
Found at i:28783 original size:31 final size:31
Alignment explanation
Indices: 28736--28796 Score: 59
Period size: 31 Copynumber: 2.0 Consensus size: 31
28726 TTTGAAATAT
* *
28736 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCGTGCCACATGTCACTTTTTGGTACAC
* * ** *
28767 GTGACGTGACATGTGTCACTTTTTAGTACA
1 GTGGCGTGCCACATGTCACTTTTTGGTACA
28797 TGTAGCACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (31 bp):
GTGGCGTGCCACATGTCACTTTTTGGTACAC
Found at i:28812 original size:84 final size:84
Alignment explanation
Indices: 28724--28880 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 84
28714 CACGTGCCAT
* * * **
28724 TTTTTGAAATATGTGGCATGCCACGTGTCACTTTTTGGTACACGTGACGTGACATGTGTCACTTT
1 TTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGAACACGTGACGTGACACATGTCACTTT
28789 TTAGTACATGTAGCACGAC
66 TTAGTACATGTAGCACGAC
** * * * *
28808 TTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGAACATGTGGCGTGCCACATGTCACTTT
1 TTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGAACACGTGACGTGACACATGTCACTTT
*
28873 TTGGTACA
66 TTAGTACA
28881 CGTGGCGTGC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 61 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (84 bp):
TTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGAACACGTGACGTGACACATGTCACTTT
TTAGTACATGTAGCACGAC
Found at i:28830 original size:115 final size:115
Alignment explanation
Indices: 28705--28911 Score: 297
Period size: 115 Copynumber: 1.8 Consensus size: 115
28695 TTTTGTGCAC
* * * *
28705 GTGGCATGCCACGTGCCATTTTTTGAAATATGTGGCATGCCACGTGTCACTTTTTGGTACACGTG
1 GTGGCATGCCACATGCCACTTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACACGTG
**
28770 ACGTGACATGTGTCACTTTTTAGTACATGTAGCACGACTTTTTGGTACAT
66 ACGTGACACATGTCACTTTTTAGTACATGTAGCACGACTTTTTGGTACAT
* * * *
28820 GTGGCGTGCCACATGTCACTTTTTGGAACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTG
1 GTGGCATGCCACATGCCACTTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACACGTG
* * *
28885 GCGTGCCACATGTCACTTTTTGGTACA
66 ACGTGACACATGTCACTTTTTAGTACA
28912 CGTGGCGTGC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
115 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (115 bp):
GTGGCATGCCACATGCCACTTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACACGTG
ACGTGACACATGTCACTTTTTAGTACATGTAGCACGACTTTTTGGTACAT
Found at i:28844 original size:31 final size:31
Alignment explanation
Indices: 28806--28924 Score: 211
Period size: 31 Copynumber: 3.8 Consensus size: 31
28796 ATGTAGCACG
*
28806 ACTTTTTGGTACATGTGGCGTGCCACATGTC
1 ACTTTTTGGTACACGTGGCGTGCCACATGTC
* *
28837 ACTTTTTGGAACATGTGGCGTGCCACATGTC
1 ACTTTTTGGTACACGTGGCGTGCCACATGTC
28868 ACTTTTTGGTACACGTGGCGTGCCACATGTC
1 ACTTTTTGGTACACGTGGCGTGCCACATGTC
28899 ACTTTTTGGTACACGTGGCGTGCCAC
1 ACTTTTTGGTACACGTGGCGTGCCAC
28925 GTCGGACACC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (31 bp):
ACTTTTTGGTACACGTGGCGTGCCACATGTC
Found at i:29706 original size:30 final size:30
Alignment explanation
Indices: 29665--29734 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
29655 TTTTATACTT
* *
29665 TTTTG-CCCCTAACCTGT-AATGTTTGAATG
1 TTTTGCCCCCTAAACTCTCAAT-TTTGAATG
*
29694 TTTTGCCCCCTAAACTCTCAATTTTGGATG
1 TTTTGCCCCCTAAACTCTCAATTTTGAATG
*
29724 TTTTGCTCCCT
1 TTTTGCCCCCT
29735 TTTAAACGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.14
30 27 0.77
31 3 0.09
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (30 bp):
TTTTGCCCCCTAAACTCTCAATTTTGAATG
Done.