Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007666.1 Corchorus capsularis cultivar CVL-1 contig07687, 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: 24255
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1052 original size:27 final size:27
Alignment explanation
Indices: 991--1056 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
981 AAAAGAATAA
**
991 AATAAAGAAAAATCTAATTTTTTTGGT
1 AATAAAGAAAAATCTAATTTTTTTGCC
*
1018 AATAAAGAAAAATGTAATTTTTTTTGCC
1 AATAAAGAAAAATCTAA-TTTTTTTGCC
*
1046 AA-CAAGAAAAA
1 AATAAAGAAAAA
1057 AAAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (27 bp):
AATAAAGAAAAATCTAATTTTTTTGCC
Found at i:2829 original size:14 final size:14
Alignment explanation
Indices: 2790--2835 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2780 TTTCCTTTAG
2790 TTTTGTTTTGTTTCGT
1 TTTTGTTTT-TTT-GT
2806 ATTTTGTTTTTTTGT
1 -TTTTGTTTTTTTGT
*
2821 TTTTTTTTTTTTGT
1 TTTTGTTTTTTTGT
2835 T
1 T
2836 AATTTTGCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 14 0.50
15 2 0.07
16 3 0.11
17 9 0.32
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTTTTGT
Found at i:4005 original size:5 final size:5
Alignment explanation
Indices: 3995--4039 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
3985 GCAACCCATG
*
3995 ATTTT ATTTT ATTTT GTTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
4040 TTTATGCCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:6676 original size:104 final size:108
Alignment explanation
Indices: 6414--6680 Score: 364
Period size: 111 Copynumber: 2.5 Consensus size: 108
6404 AGTTTAGCCT
*
6414 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
6479 AATAATTTATTATTATAGGATTTTAGAAATAAAATACAAAACTAAT
66 AATAA-TTATTATTATAGGATTTTAGAAATAAAAT--AAAACTAAC
* *
6525 TAATTTCACTTAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
6590 AATAA-TATTGTTATAGGGTTTTAGAAATAAAAT-ATA-TAAC
66 AATAATTATTATTATAGGATTTTAGAAATAAAATAAAACTAAC
* ** *
6630 TAA-TTCACTAAGTTTAG-TCCAAATTAAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATT-AAAATTTTATTTTTATTTTAAGGGT
6681 TAGAAAAAAT
Statistics
Matches: 143, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
103 7 0.05
104 35 0.24
105 6 0.04
106 2 0.01
109 26 0.18
111 67 0.47
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (108 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATTATTATTATAGGATTTTAGAAATAAAATAAAACTAAC
Found at i:7173 original size:7 final size:7
Alignment explanation
Indices: 7163--7212 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
7153 TTATAATGAT
7163 ATGTTGC
1 ATGTTGC
7170 ATGTTGC
1 ATGTTGC
7177 ATGTTGC
1 ATGTTGC
7184 ATGTTGC
1 ATGTTGC
7191 ATGTTGC
1 ATGTTGC
7198 ATGTTGC
1 ATGTTGC
7205 ATGTTGC
1 ATGTTGC
7212 A
1 A
7213 AGTTCAAAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.42
Consensus pattern (7 bp):
ATGTTGC
Found at i:8364 original size:45 final size:45
Alignment explanation
Indices: 8300--8424 Score: 189
Period size: 45 Copynumber: 2.8 Consensus size: 45
8290 TCATGGCTAT
*
8300 CTCTTTCTTTGTCTTTTCAGATGAGCCATTCACTGCCACAGCCAA
1 CTCTTTCTTCGTCTTTTCAGATGAGCCATTCACTGCCACAGCCAA
* *
8345 CTCTTTCTTCGTCTTTTCAGCTGAGCCACTCACTGCCACAGCCAA
1 CTCTTTCTTCGTCTTTTCAGATGAGCCATTCACTGCCACAGCCAA
* *
8390 CTCTTTCTTCGTCTTCTCA-ACTGAGCCATTTACTG
1 CTCTTTCTTCGTCTTTTCAGA-TGAGCCATTCACTG
8425 TCAATGTCGT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.36
Consensus pattern (45 bp):
CTCTTTCTTCGTCTTTTCAGATGAGCCATTCACTGCCACAGCCAA
Found at i:8612 original size:45 final size:45
Alignment explanation
Indices: 8390--8617 Score: 180
Period size: 45 Copynumber: 5.1 Consensus size: 45
8380 CCACAGCCAA
* * * *
8390 CTCTTTCTTCGTCTTCTCAACTGAGCCATTTACTGTCAATG-TCGT
1 CTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGGCT-GT
* * * * * *
8435 TTCTCTCTTCATCTTCTCGGCTGACCCATTTGCTG-C-A-GCTGT
1 CTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGGCTGT
* * * * * *
8477 TTCTCTT-TTCACCTTCTCAGTTGAACTATTTACTGTCATGGAC-AT
1 CTCT-TTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGG-CTGT
* * * * ***
8522 CTCTTTCTTGACCTTCTCAGCTAAGCTATTTACTGCCATCACTGT
1 CTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGGCTGT
8567 CTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGGCTGT
1 CTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGGCTGT
8612 CTCTTT
1 CTCTTT
8618 GAATGTCTTC
Statistics
Matches: 143, Mismatches: 32, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
42 29 0.20
43 4 0.03
44 4 0.03
45 105 0.73
46 1 0.01
ACGTcount: A:0.15, C:0.29, G:0.13, T:0.43
Consensus pattern (45 bp):
CTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCAAGGCTGT
Found at i:8627 original size:45 final size:45
Alignment explanation
Indices: 8534--8632 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
8524 CTTTCTTGAC
* **
8534 CTTCTCAGCTAAGCTATTTACTGCCATCACTGTCTCTTTCTTCAT
1 CTTCTCAGCTAAGCTATTTACTGCCAACACTGTCTCTTTAATCAT
* * ** *
8579 CTTCTCAGCTGAGCTATTTACTGTCAAGGCTGTCTCTTTGAAT-GT
1 CTTCTCAGCTAAGCTATTTACTGCCAACACTGTCTCTTT-AATCAT
8624 CTTCTCAGC
1 CTTCTCAGC
8633 AGAATTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.40
Consensus pattern (45 bp):
CTTCTCAGCTAAGCTATTTACTGCCAACACTGTCTCTTTAATCAT
Found at i:12567 original size:2 final size:2
Alignment explanation
Indices: 12560--12584 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12550 AAGAAGTTTT
12560 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
12585 TGAGTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19380 original size:2 final size:2
Alignment explanation
Indices: 19373--19408 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19363 CTCTTATTTC
*
19373 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19409 GCAAAGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19493 original size:20 final size:20
Alignment explanation
Indices: 19456--19494 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19446 AAGGAAATCT
* * *
19456 TTCAGTAATGGAAGACAAGC
1 TTCAATAATGCAAAACAAGC
19476 TTCAATAATGCAAAACAAG
1 TTCAATAATGCAAAACAAG
19495 TCAAAAGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (20 bp):
TTCAATAATGCAAAACAAGC
Found at i:19871 original size:2 final size:2
Alignment explanation
Indices: 19864--19901 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19854 GATTGTCTGG
19864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19902 AAGCAAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20883 original size:30 final size:31
Alignment explanation
Indices: 20847--20919 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
20837 GGGCAAAATG
* * *
20847 CAATTCAGGATATAATGTTA-CCTATTGTTT
1 CAATTCAGGATATAACGTTATCCTATTATGT
* *
20877 CAATTCAGGATATAACGTTATCGTTTTATGT
1 CAATTCAGGATATAACGTTATCCTATTATGT
20908 CAATTCAGGATA
1 CAATTCAGGATA
20920 AAAATTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (31 bp):
CAATTCAGGATATAACGTTATCCTATTATGT
Found at i:21287 original size:122 final size:119
Alignment explanation
Indices: 21122--21362 Score: 331
Period size: 122 Copynumber: 2.0 Consensus size: 119
21112 AAAATTAAAA
* * *
21122 TAACATAAAATGCTTTCATACCAAATCTAATCTTCTCTTCTTCCCTACGTTACTCCATCTTCTTT
1 TAACATAAAATACTTTCATACCAAATCTAATCTTCCCTTCTTCCCTACGTTACTCCATCTTCTTC
*
21187 CGCCAATTTTTTTTTTAATTTATCATTCTTCCATCACTCTCCC-TTCAACCCATCTCT
66 CGCCAA-TTTTTTTTT-A--TATCATTATTCCATCACTCTCCCGTTCAACCCATCTCT
* * * * *
21244 TAACATAAAATATTTTCCTACCAGATCTATTCTTCCCTTCTTCCCTGCGTTACTCCATCTTCTTC
1 TAACATAAAATACTTTCATACCAAATCTAATCTTCCCTTCTTCCCTACGTTACTCCATCTTCTTC
** *
21309 CTTCAATTTTTTTTTATATCATTATTCCATCTCTCTCCCGTTCAACCCATCTCT
66 CGCCAATTTTTTTTTATATCATTATTCCATCACTCTCCCGTTCAACCCATCTCT
21363 ATTTTGTCTT
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
118 21 0.20
119 14 0.13
120 1 0.01
121 9 0.08
122 61 0.58
ACGTcount: A:0.22, C:0.32, G:0.03, T:0.44
Consensus pattern (119 bp):
TAACATAAAATACTTTCATACCAAATCTAATCTTCCCTTCTTCCCTACGTTACTCCATCTTCTTC
CGCCAATTTTTTTTTATATCATTATTCCATCACTCTCCCGTTCAACCCATCTCT
Found at i:23890 original size:20 final size:20
Alignment explanation
Indices: 23865--23904 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23855 TATATGTGAA
23865 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
23885 TTACTAGCTACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
23905 GGACTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.42, G:0.07, T:0.30
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:23910 original size:20 final size:20
Alignment explanation
Indices: 23873--23910 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23863 AATTACTAAA
**
23873 TACCGCCCCCTTTTACTAGC
1 TACCGCCCCCTTGGACTAGC
23893 TACCGCCCCCTTGGACTA
1 TACCGCCCCCTTGGACTA
23911 TTTTGCCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.45, G:0.13, T:0.26
Consensus pattern (20 bp):
TACCGCCCCCTTGGACTAGC
Done.