Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015597.1 Corchorus capsularis cultivar CVL-1 contig15618, 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: 14039
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:861 original size:14 final size:14
Alignment explanation
Indices: 851--880 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
841 CTCTTAAATT
851 CAAATTATTAAGAA
1 CAAATTATTAAGAA
865 CAAATTATTAAGAA
1 CAAATTATTAAGAA
879 CA
1 CA
881 GAGATAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (14 bp):
CAAATTATTAAGAA
Found at i:3031 original size:13 final size:13
Alignment explanation
Indices: 3001--3030 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2991 ATGTTTGAGG
3001 GTTTTCTTTAATT
1 GTTTTCTTTAATT
3014 GTTTTCTTTAATT
1 GTTTTCTTTAATT
3027 -TTTT
1 GTTTT
3031 TGATTGCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (13 bp):
GTTTTCTTTAATT
Found at i:3678 original size:21 final size:19
Alignment explanation
Indices: 3646--3693 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
3636 TAGAATTAGG
3646 GTTTTTAATTTAAGTTTAT
1 GTTTTTAATTTAAGTTTAT
* *
3665 GTTTTCTAGATTTAGGTTTTT
1 GTTTT-TA-ATTTAAGTTTAT
*
3686 ATTTTTAA
1 GTTTTTAA
3694 GCATCCTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 14 0.58
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.62
Consensus pattern (19 bp):
GTTTTTAATTTAAGTTTAT
Found at i:3986 original size:16 final size:16
Alignment explanation
Indices: 3965--3997 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3955 CGTGGGGGGT
3965 TGAATACTTGATAGGG
1 TGAATACTTGATAGGG
3981 TGAATACTTGATAGGG
1 TGAATACTTGATAGGG
3997 T
1 T
3998 TATTGTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (16 bp):
TGAATACTTGATAGGG
Found at i:5310 original size:19 final size:18
Alignment explanation
Indices: 5286--5321 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5276 AGTTCGTGAT
5286 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
5305 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
5322 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:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:5860 original size:15 final size:15
Alignment explanation
Indices: 5842--5872 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5832 TTACTTTTGC
*
5842 TACTTTTATCATTTT
1 TACTTTTACCATTTT
5857 TACTTTTACCATTTT
1 TACTTTTACCATTTT
5872 T
1 T
5873 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:5872 original size:24 final size:24
Alignment explanation
Indices: 5827--5872 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5817 TACTGATTAC
* *
5827 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCACTTTTAT
*
5851 CATTTTTACTTTTACCATTTTT
1 CATTTTTACTTTTACCACTTTT
5873 CTTACTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (24 bp):
CATTTTTACTTTTACCACTTTTAT
Found at i:6086 original size:14 final size:14
Alignment explanation
Indices: 6069--6114 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
6059 CTCTTTGCCA
**
6069 TTTTTACTTTTTAC
1 TTTTTACTGATTAC
6083 TTTTTACTGATTAC
1 TTTTTACTGATTAC
*
6097 TCTTTACTGATTAC
1 TTTTTACTGATTAC
6111 TTTT
1 TTTT
6115 ACCTTTTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.63
Consensus pattern (14 bp):
TTTTTACTGATTAC
Found at i:6087 original size:8 final size:7
Alignment explanation
Indices: 6069--6125 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
6059 CTCTTTGCCA
6069 TTTTTAC
1 TTTTTAC
6076 TTTTTAC
1 TTTTTAC
6083 TTTTTAC
1 TTTTTAC
**
6090 TGATTAC
1 TTTTTAC
*
6097 TCTTTAC
1 TTTTTAC
**
6104 TGATTAC
1 TTTTTAC
6111 -TTTTACC
1 TTTTTA-C
6118 TTTTTAC
1 TTTTTAC
6125 T
1 T
6126 GATTAATCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 3 0.08
7 32 0.80
8 5 0.12
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.61
Consensus pattern (7 bp):
TTTTTAC
Found at i:6110 original size:21 final size:20
Alignment explanation
Indices: 6072--6130 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
6062 TTTGCCATTT
**
6072 TTACTTTTTACTTTTTACTGA
1 TTACTTTTTACTGATTACT-A
* *
6093 TTACTCTTTACTGATTACTT
1 TTACTTTTTACTGATTACTA
6113 TTACCTTTTTACTGATTA
1 TTA-CTTTTTACTGATTA
6131 ATCTTAGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.58
Consensus pattern (20 bp):
TTACTTTTTACTGATTACTA
Found at i:6424 original size:32 final size:32
Alignment explanation
Indices: 6361--6445 Score: 125
Period size: 32 Copynumber: 2.6 Consensus size: 32
6351 TTCTTAATTA
* *
6361 TTAATTTACTGATTAGTCCTTTTTACTTCCTTTC
1 TTAA-TTACTGATTAAT-CTTCTTACTTCCTTTC
6395 TTAATTACTGATTAATCTTCTTACTTCCTTTC
1 TTAATTACTGATTAATCTTCTTACTTCCTTTC
*
6427 TTAATTACTGATTACTCTT
1 TTAATTACTGATTAATCTT
6446 TACTCTCTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
32 33 0.69
33 11 0.23
34 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (32 bp):
TTAATTACTGATTAATCTTCTTACTTCCTTTC
Found at i:6579 original size:38 final size:38
Alignment explanation
Indices: 6534--6800 Score: 414
Period size: 38 Copynumber: 7.1 Consensus size: 38
6524 TTGACCCTTG
*
6534 ATTATCAATTTTACTGAGTATTCTTACTTTGGCTCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
6572 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
*
6610 ATTATCAATTTTACTGATTATTCTTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
*
6648 ATTATCAATTTTACTGATTATTCTTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
*
6686 A-T-TCAATTTTACTGATTATTCTTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
* * *
6722 ATTATCAATTTTACTGATTACTATTACTTTGGTTCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
* * *
6760 ATTATCAATTTTATTGATTACTATTACTTTGG-TCCTTA
1 ATTATCAATTTTACTGATTATTCTTACTTTGGCT-CTTA
6798 ATT
1 ATT
6801 TTACTGGGGT
Statistics
Matches: 219, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
36 35 0.16
37 3 0.01
38 181 0.83
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.52
Consensus pattern (38 bp):
ATTATCAATTTTACTGATTATTCTTACTTTGGCTCTTA
Found at i:7668 original size:52 final size:50
Alignment explanation
Indices: 7605--7775 Score: 234
Period size: 51 Copynumber: 3.3 Consensus size: 50
7595 CAAAACTATC
* * * * *
7605 AAGATTCAATTTTTTATTGTTAAAATTACTAAAACCCAACTCTTACTACATA
1 AAGATTCAA-TTTTTATGGCTAAAATCACTAGAACTCAAC-CTTACTACATA
*
7657 AAGATTTAATTTTTTATGGCTAAAATCACTAGAACTCAACCTTTACTACATA
1 AAGATTCAA-TTTTTATGGCTAAAATCACTAGAACTCAACC-TTACTACATA
7709 AAGATTCAATTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
1 AAGATTCAATTTTTATGGCTAAAATCACTAGAACTCAA-CCTTACTACATA
*
7760 AAAATTCAATTTTTAT
1 AAGATTCAATTTTTAT
7776 TGTCAAGGTC
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
51 55 0.50
52 54 0.50
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.37
Consensus pattern (50 bp):
AAGATTCAATTTTTATGGCTAAAATCACTAGAACTCAACCTTACTACATA
Found at i:7775 original size:51 final size:52
Alignment explanation
Indices: 7605--7773 Score: 250
Period size: 52 Copynumber: 3.3 Consensus size: 52
7595 CAAAACTATC
* * * * * *
7605 AAGATTCAATTTTTTATTGTTAAAATTACTAAAACCCAACTCTTACTACATA
1 AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
* *
7657 AAGATTTAATTTTTTATGGCTAAAATCACTAGAACTCAACCTTTACTACATA
1 AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
7709 AAGATTCAA-TTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
1 AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
*
7760 AAAATTCAATTTTT
1 AAGATTCAATTTTT
7774 ATTGTCAAGG
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 49 0.47
52 56 0.53
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.37
Consensus pattern (52 bp):
AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
Found at i:9210 original size:27 final size:27
Alignment explanation
Indices: 9180--9254 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
9170 TCGGGTCGTC
**
9180 CAGGGGCATTTTGGTCATTTTCATGTT
1 CAGGGGCATTTTGGTCATTTTCACATT
* *
9207 CAGGGACATTTTGGTCATTTGCACATT
1 CAGGGGCATTTTGGTCATTTTCACATT
*
9234 CAGGGGCATTTTGGTCGTTTT
1 CAGGGGCATTTTGGTCATTTT
9255 TAGTTCACTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTTCACATT
Done.