Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008551.1 Corchorus capsularis cultivar CVL-1 contig08572, 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: 12072
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Found at i:1026 original size:45 final size:45
Alignment explanation
Indices: 962--1053 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
952 ACTTTTATTT
962 TGTACTTTGGGGATATATCTAACTAGTGCAAAATGAATAAATGAA
1 TGTACTTTGGGGATATATCTAACTAGTGCAAAATGAATAAATGAA
1007 TGTACTTTGGGGATATATCTAACTAGTGCAAAATGAATAAATGAA
1 TGTACTTTGGGGATATATCTAACTAGTGCAAAATGAATAAATGAA
1052 TG
1 TG
1054 CTCTTTTTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (45 bp):
TGTACTTTGGGGATATATCTAACTAGTGCAAAATGAATAAATGAA
Found at i:1462 original size:27 final size:27
Alignment explanation
Indices: 1422--1491 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
1412 CTGAATGTGC
* *
1422 AAAATGACCAAAATGCCCCTTAGTCTA
1 AAAATGACCAAAATGCCCCTAAATCTA
* * *
1449 AGAATGACCAAAATACCCCTAAATGTA
1 AAAATGACCAAAATGCCCCTAAATCTA
*
1476 AAAAAGACCAAAATGC
1 AAAATGACCAAAATGC
1492 TAATTCGACC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.49, C:0.23, G:0.11, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATCTA
Found at i:1977 original size:59 final size:59
Alignment explanation
Indices: 1767--1970 Score: 311
Period size: 59 Copynumber: 3.5 Consensus size: 59
1757 ACGCTTTCAG
* ** * * * * *
1767 GAACTGTCTTCAG-ATCTGTCTACAAGCAGCCGTCATACTCATACTTGGTTTCCTTTAG
1 GAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCATACTTGATTTCCTTTAT
1825 GAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCATACTTGATTTCCTTTAT
1 GAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCATACTTGATTTCCTTTAT
1884 GAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCATACTTGATTTCCTTTAT
1 GAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCATACTTGATTTCCTTTAT
* *
1943 GAACTGTCTTCAGAACCCACCTATGAGC
1 GAACTGTCTTCAGAACCCATCTACGAGC
1971 TATCTTCGAA
Statistics
Matches: 135, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 13 0.10
59 122 0.90
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (59 bp):
GAACTGTCTTCAGAACCCATCTACGAGCAGTCTTCATACTCATACTTGATTTCCTTTAT
Found at i:3316 original size:6 final size:6
Alignment explanation
Indices: 3298--3330 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3288 ACCTTTTGTC
*
3298 TTCTTT CTCTTT TT-TTT TTCTTT TTCTTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
3331 CTCTGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:3333 original size:27 final size:28
Alignment explanation
Indices: 3290--3345 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
3280 AGAGCTATAC
3290 CTTTTGTCTTCTTTCTCT-TTTTTTTTT
1 CTTTTGTCTTCTTTCTCTGTTTTTTTTT
*
3317 CTTTT-TCTTTTTCTCTCTGTTTTTTTTT
1 CTTTTGTCTTCTT-TCTCTGTTTTTTTTT
3345 C
1 C
3346 ATGCACTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 10 0.38
28 10 0.38
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.77
Consensus pattern (28 bp):
CTTTTGTCTTCTTTCTCTGTTTTTTTTT
Found at i:3931 original size:7 final size:7
Alignment explanation
Indices: 3919--3962 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
3909 AAGGTTTTTC
3919 TTTTCTT
1 TTTTCTT
3926 TTTTCTT
1 TTTTCTT
3933 TTTTCTT
1 TTTTCTT
3940 TCTCTTC-T
1 T-T-TTCTT
3948 TTTTCTT
1 TTTTCTT
*
3955 TCTTCTT
1 TTTTCTT
3962 T
1 T
3963 GAGTTGATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 3 0.09
7 24 0.73
8 3 0.09
9 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:3947 original size:23 final size:22
Alignment explanation
Indices: 3915--3962 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
3905 GGTCAAGGTT
* *
3915 TTTCTTTTCTTTTTTCTTTTTTC
1 TTTCTCTTC-TTTTTCTTTCTTC
3938 TTTCTCTTCTTTTTCTTTCTTC
1 TTTCTCTTCTTTTTCTTTCTTC
3960 TTT
1 TTT
3963 GAGTTGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTCTTCTTTTTCTTTCTTC
Found at i:3952 original size:15 final size:15
Alignment explanation
Indices: 3919--3962 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3909 AAGGTTTTTC
3919 TTTTCTTT-TTTCTT
1 TTTTCTTTCTTTCTT
3933 TTTTCTTTCTCTTC-T
1 TTTTCTTTCT-TTCTT
3948 TTTTCTTTC-TTCTT
1 TTTTCTTTCTTTCTT
3962 T
1 T
3963 GAGTTGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.11
14 10 0.37
15 11 0.41
16 3 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTCTTTCTT
Found at i:3958 original size:13 final size:13
Alignment explanation
Indices: 3919--3962 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
3909 AAGGTTTTTC
*
3919 TTTTCTTTTTTCTT
1 TTTTCTTTCTTC-T
3933 TTTTCTTTCTCTTCT
1 TTTTC-TT-TCTTCT
3948 TTTTCTTTCTTCT
1 TTTTCTTTCTTCT
3961 TT
1 TT
3963 GAGTTGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.30
14 7 0.26
15 8 0.30
16 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTCTTCT
Found at i:4612 original size:14 final size:14
Alignment explanation
Indices: 4589--4633 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
4579 TAAAAACACG
4589 AAAC-CTTTTTTGA
1 AAACTCTTTTTTGA
4602 AAACTCTTTTTTGA
1 AAACTCTTTTTTGA
4616 AAA-TCTTTTCTTGA
1 AAACTCTTTT-TTGA
4630 AAAC
1 AAAC
4634 AATTTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (14 bp):
AAACTCTTTTTTGA
Found at i:4642 original size:13 final size:12
Alignment explanation
Indices: 4588--4645 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 12
4578 CTAAAAACAC
*
4588 GAAACCTTTTTT
1 GAAAACTTTTTT
4600 GAAAACTCTTTTTT
1 GAAAA--CTTTTTT
4614 GAAAATCTTTTCTT
1 GAAAA-CTTTT-TT
*
4628 GAAAACAATTTTT
1 GAAAAC-TTTTTT
4641 GAAAA
1 GAAAA
4646 ACGTTCCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 4 0.10
13 14 0.35
14 22 0.55
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (12 bp):
GAAAACTTTTTT
Found at i:7349 original size:22 final size:22
Alignment explanation
Indices: 7323--7677 Score: 259
Period size: 22 Copynumber: 16.2 Consensus size: 22
7313 TTACTCTTGT
*
7323 TGATTACCTTCTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
*
7345 TGATTACCATTTTACTCTTTTAC
1 TGATTACCTTTTTACT-TTTTAC
* *
7368 TGATTACTATTTTCTGCTCCTTTTTTAC
1 TGATTAC--CTTT-T--TAC-TTTTTAC
*
7396 TGATTA-CTCTTTTAGTTTTTAC
1 TGATTACCT-TTTTACTTTTTAC
* *
7418 TGATTACC-TTTTGCGTTTTAC
1 TGATTACCTTTTTACTTTTTAC
* *
7439 TGATTACCTTTTTACTTCTTGC
1 TGATTACCTTTTTACTTTTTAC
* *
7461 TGATTAGCTTTTTACTCTTTAC
1 TGATTACCTTTTTACTTTTTAC
** *
7483 TGACCACCTTTTTAC-TCTTAC
1 TGATTACCTTTTTACTTTTTAC
* *
7504 TGATTTCC-TTTTACTTCTTAC
1 TGATTACCTTTTTACTTTTTAC
* *
7525 TTATTA-CTTTTTAC-TCTTAC
1 TGATTACCTTTTTACTTTTTAC
*
7545 TGATTA-CTATTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
* *
7566 TGACTA-CTATTTTACTCTTGT--
1 TGATTACCT-TTTTACT-TTTTAC
*
7587 TGATTACCTTCTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
*
7609 TGATTA-CTATTTTACTCTTTAC
1 TGATTACCT-TTTTACTTTTTAC
* * **
7631 TAATTACCATTTTACCCTTT-C
1 TGATTACCTTTTTACTTTTTAC
* *
7652 AG-GTACCTTTTTACTTTTTAC
1 TGATTACCTTTTTACTTTTTAC
7673 TGATT
1 TGATT
7678 GCATGCTATT
Statistics
Matches: 260, Mismatches: 51, Indels: 44
0.73 0.14 0.12
Matches are distributed among these distances:
20 41 0.16
21 71 0.27
22 107 0.41
23 19 0.07
25 4 0.02
26 3 0.01
28 14 0.05
29 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (22 bp):
TGATTACCTTTTTACTTTTTAC
Found at i:7374 original size:15 final size:15
Alignment explanation
Indices: 7356--7409 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
7346 GATTACCATT
7356 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
7371 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
7384 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
7399 TTACTCTTTTA
1 TTACTCTTTTA
7410 GTTTTTACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 17 0.57
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:7923 original size:55 final size:55
Alignment explanation
Indices: 7862--8112 Score: 421
Period size: 55 Copynumber: 4.6 Consensus size: 55
7852 CATTTTAACT
* *
7862 CTTAATTATCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
** *
7917 CTTAATTATTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
7972 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
8027 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCCCTTTTTC
1 CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
8082 CTTAATTACTGATTTACTGATTTCTATTACT
1 CTTAATTACCGATTTACTGATTACTATTACT
8113 CTTTACGATT
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 186 1.00
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (55 bp):
CTTAATTACCGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:8153 original size:22 final size:22
Alignment explanation
Indices: 8108--8168 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
8098 CTGATTTCTA
**
8108 TTACTCTTTAC-GATTATCACT
1 TTACTCTTTACTGATTGCCACT
*
8129 TTACTCTTTACTGATTGCCATT
1 TTACTCTTTACTGATTGCCACT
8151 TTAC-CTTTTACTGATTGC
1 TTACTC-TTTACTGATTGC
8169 ATCTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.34
22 23 0.66
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (22 bp):
TTACTCTTTACTGATTGCCACT
Done.