Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011438.1 Corchorus capsularis cultivar CVL-1 contig11459, 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: 50423
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 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
37 AAGATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1589 original size:64 final size:64
Alignment explanation
Indices: 1510--1636 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
1500 CTATGGTTCA
*
1510 GGTCTAACTCAAAATATTGTATGTAAGTGATGTACATTGGGAGGGAACGGGAGAGTACTAATAC
1 GGTCTAACTCAAAATATTGCATGTAAGTGATGTACATTGGGAGGGAACGGGAGAGTACTAATAC
1574 GGTCTAACTCAAAATATTGCATGTAAGTGATGTACATTGGGAGGGAACGGGAGAGTACTAATA
1 GGTCTAACTCAAAATATTGCATGTAAGTGATGTACATTGGGAGGGAACGGGAGAGTACTAATA
1637 GTAAAGTAGG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (64 bp):
GGTCTAACTCAAAATATTGCATGTAAGTGATGTACATTGGGAGGGAACGGGAGAGTACTAATAC
Found at i:3786 original size:15 final size:15
Alignment explanation
Indices: 3766--3820 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
3756 GTCGGGTTAA
3766 ATTTGGGTCAGATTG
1 ATTTGGGTCAGATTG
* * *
3781 ATTTGGGTTCGGGTTAA
1 ATTTGGG-TCAGATT-G
3798 ATTTGGGTCAGATTG
1 ATTTGGGTCAGATTG
*
3813 ATTCGGGT
1 ATTTGGGT
3821 TCGGGTCAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 14 0.45
16 10 0.32
17 7 0.23
ACGTcount: A:0.18, C:0.07, G:0.35, T:0.40
Consensus pattern (15 bp):
ATTTGGGTCAGATTG
Found at i:3793 original size:32 final size:32
Alignment explanation
Indices: 3757--3835 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
3747 TCGAGTCAGG
*
3757 TCGGGTTAAATTTGGGTCAGATTGATTTGGGT
1 TCGGGTTAAATTTGGGTCAGATTGATTCGGGT
3789 TCGGGTTAAATTTGGGTCAGATTGATTCGGGT
1 TCGGGTTAAATTTGGGTCAGATTGATTCGGGT
* *
3821 TCGGGTCAATTTTGG
1 TCGGGTTAAATTTGG
3836 ATTAGGTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.39
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTCAGATTGATTCGGGT
Found at i:3849 original size:32 final size:32
Alignment explanation
Indices: 3757--3849 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 32
3747 TCGAGTCAGG
* * * *
3757 TCGGGTTAAATTTGGGTCAGATTGATTTGGGT
1 TCGGGTCAAATTTGGATCAGATTAATTCGGGT
* * *
3789 TCGGGTTAAATTTGGGTCAGATTGATTCGGGT
1 TCGGGTCAAATTTGGATCAGATTAATTCGGGT
* * *
3821 TCGGGTCAATTTTGGATTAGGTTAATTCG
1 TCGGGTCAAATTTGGATCAGATTAATTCG
3850 ATTTCGGACT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.19, C:0.09, G:0.32, T:0.40
Consensus pattern (32 bp):
TCGGGTCAAATTTGGATCAGATTAATTCGGGT
Found at i:4670 original size:16 final size:17
Alignment explanation
Indices: 4639--4671 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4629 TTAATTCGTT
*
4639 TTATTTATATTTATAAA
1 TTATTTATAATTATAAA
4656 TTATTTA-AATTATAAA
1 TTATTTATAATTATAAA
4672 AATTTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTATAATTATAAA
Found at i:4755 original size:16 final size:16
Alignment explanation
Indices: 4736--4841 Score: 65
Period size: 16 Copynumber: 6.6 Consensus size: 16
4726 TTTTTTCAAA
4736 TTCGGGTTCGGATTTT
1 TTCGGGTTCGGATTTT
* *
4752 TTCGGATTCAGATTTT
1 TTCGGGTTCGGATTTT
* **
4768 ATCGGGTTTTAGA-TTT
1 TTCGGG-TTCGGATTTT
*
4784 TTCGGGTTCTGAATTTT
1 TTCGGGTTC-GGATTTT
* *
4801 TT-GGGTT-TGAGCTTT
1 TTCGGGTTCGGA-TTTT
* *
4816 TTCGGGTTTGGGTTTT
1 TTCGGGTTCGGATTTT
*
4832 TTTGGGTTCG
1 TTCGGGTTCG
4842 AGTTCGGACG
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 1 0.01
15 7 0.10
16 48 0.72
17 11 0.16
ACGTcount: A:0.09, C:0.09, G:0.29, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCGGATTTT
Found at i:4785 original size:32 final size:32
Alignment explanation
Indices: 4736--4820 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
4726 TTTTTTCAAA
*
4736 TTCGGGTTCG-GATTTTTTCGGATTCAG-ATTT
1 TTCGGGTTTGAGA-TTTTTCGGATTCAGAATTT
* * *
4767 TATCGGGTTTTAGATTTTTCGGGTTCTGAATTT
1 T-TCGGGTTTGAGATTTTTCGGATTCAGAATTT
* *
4800 TTTGGGTTTGAGCTTTTTCGG
1 TTCGGGTTTGAGATTTTTCGG
4821 GTTTGGGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.82
33 7 0.16
ACGTcount: A:0.12, C:0.11, G:0.27, T:0.51
Consensus pattern (32 bp):
TTCGGGTTTGAGATTTTTCGGATTCAGAATTT
Found at i:4833 original size:48 final size:48
Alignment explanation
Indices: 4736--4842 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
4726 TTTTTTCAAA
* *
4736 TTCGGGTTCGGATTTTTTCGGATTCAGATTTTATCGGGTTTTAGATTT
1 TTCGGGTTCGAATTTTTTCGGATTCAGATTTTATCGGGTTTGAGATTT
* * * * * *
4784 TTCGGGTTCTGAATTTTTTGGGTTTGAGCTTTT-TCGGGTTTGGGTTTT
1 TTCGGGTTC-GAATTTTTTCGGATTCAGATTTTATCGGGTTTGAGATTT
*
4832 TTTGGGTTCGA
1 TTCGGGTTCGA
4843 GTTCGGACGG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
47 2 0.04
48 29 0.59
49 18 0.37
ACGTcount: A:0.10, C:0.09, G:0.29, T:0.51
Consensus pattern (48 bp):
TTCGGGTTCGAATTTTTTCGGATTCAGATTTTATCGGGTTTGAGATTT
Found at i:4839 original size:32 final size:32
Alignment explanation
Indices: 4749--4823 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
4739 GGGTTCGGAT
* * * *
4749 TTTTTCGGATTCAG-ATTTTATCGGGTTTTAGA
1 TTTTTCGGGTTCTGAATTTT-TTGGGTTTGAGA
*
4781 TTTTTCGGGTTCTGAATTTTTTGGGTTTGAGC
1 TTTTTCGGGTTCTGAATTTTTTGGGTTTGAGA
4813 TTTTTCGGGTT
1 TTTTTCGGGTT
4824 TGGGTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.12, C:0.09, G:0.25, T:0.53
Consensus pattern (32 bp):
TTTTTCGGGTTCTGAATTTTTTGGGTTTGAGA
Found at i:6018 original size:32 final size:32
Alignment explanation
Indices: 5951--6030 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
5941 TCTGTCTCGG
* **
5951 TGCCGCCCTCCTGGGATGGCATGTCCATAGAA
1 TGCCGCCCTCCTGGGGTGGCACCTCCATAGAA
* * *
5983 TGCCGCCCTCCTGGGGTGGCACCTTCATGGCA
1 TGCCGCCCTCCTGGGGTGGCACCTCCATAGAA
*
6015 TGCCGCCCTCTTGGGG
1 TGCCGCCCTCCTGGGG
6031 CGGTTTGGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.11, C:0.35, G:0.31, T:0.23
Consensus pattern (32 bp):
TGCCGCCCTCCTGGGGTGGCACCTCCATAGAA
Found at i:6058 original size:33 final size:33
Alignment explanation
Indices: 6008--6100 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
5998 GTGGCACCTT
6008 CATGGCATGCCGCCCTCTTGGGGCGG-TTTGGTC
1 CATGGCATGCCGCCCTCTTGGGGCGGCTTT-GTC
* *
6041 CATGGCATGTCGTCCTCTTGGGGCGGCTTTGTC
1 CATGGCATGCCGCCCTCTTGGGGCGGCTTTGTC
* * *
6074 CTTGGCATGCCGCCCTCCTGAGGCGGC
1 CATGGCATGCCGCCCTCTTGGGGCGGC
6101 ACCGAGACAG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 49 0.94
34 3 0.06
ACGTcount: A:0.06, C:0.32, G:0.34, T:0.27
Consensus pattern (33 bp):
CATGGCATGCCGCCCTCTTGGGGCGGCTTTGTC
Found at i:9974 original size:19 final size:18
Alignment explanation
Indices: 9941--9976 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9931 TTGAAATAAT
9941 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
9959 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
9977 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:12250 original size:6 final size:6
Alignment explanation
Indices: 12241--12282 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
12231 CTAAAACCTA
* * *
12241 AAAATA AAAACT AAAATT AAAATT AAAATT AAAATT AGAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
12283 GGGTTGCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:18809 original size:19 final size:18
Alignment explanation
Indices: 18776--18811 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18766 TTGAAATAAT
18776 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
18794 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
18812 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:22986 original size:7 final size:7
Alignment explanation
Indices: 22969--22999 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
22959 TTGTTGTGGC
22969 AAAAAAT
1 AAAAAAT
22976 -AAAAAT
1 AAAAAAT
22982 AAAAAAT
1 AAAAAAT
22989 AAAAAAT
1 AAAAAAT
22996 AAAA
1 AAAA
23000 GAGAAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:28238 original size:13 final size:13
Alignment explanation
Indices: 28220--28244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28210 AACCTTATTT
28220 ATGCTTACAATTG
1 ATGCTTACAATTG
28233 ATGCTTACAATT
1 ATGCTTACAATT
28245 AACCCGGTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
ATGCTTACAATTG
Found at i:31609 original size:2 final size:2
Alignment explanation
Indices: 31602--31635 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31592 ATGAACAATG
31602 AT AT AT AT AT AT AT 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
31636 TGCTAGCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33351 original size:12 final size:13
Alignment explanation
Indices: 33310--33354 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
33300 AATTATTGTT
33310 TGCTTTATTAATC
1 TGCTTTATTAATC
*
33323 TGCTTTATTAATT
1 TGCTTTATTAATC
33336 TGCTTTA-TAATC
1 TGCTTTATTAATC
33348 TGCTTTA
1 TGCTTTA
33355 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:33362 original size:6 final size:6
Alignment explanation
Indices: 33351--33385 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
33341 TATAATCTGC
33351 TTTAGA TTTAGA TTTTAAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA -TTT-AGA TTTAGA TTTAGA TTT
33386 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.67
7 6 0.22
8 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:33703 original size:22 final size:22
Alignment explanation
Indices: 33672--33713 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
33662 AGTTTTGATT
*
33672 TTCCGTTTTTCTAAAAAAAACA
1 TTCCGATTTTCTAAAAAAAACA
33694 TTCCGATTTTCTAAAAAAAA
1 TTCCGATTTTCTAAAAAAAA
33714 GTTAATTTTT
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:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TTCCGATTTTCTAAAAAAAACA
Found at i:34825 original size:6 final size:6
Alignment explanation
Indices: 34814--34847 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
34804 TATAATCTGC
34814 TTTAGA TTTAGA TTTAAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTT-AGA TTTAGA TTTAGA TTT
34848 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:34835 original size:13 final size:12
Alignment explanation
Indices: 34814--34847 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
34804 TATAATCTGC
34814 TTTAGATTTAGA
1 TTTAGATTTAGA
34826 TTTAAGATTTAGA
1 TTT-AGATTTAGA
34839 TTTAGATTT
1 TTTAGATTT
34848 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (12 bp):
TTTAGATTTAGA
Found at i:35473 original size:42 final size:43
Alignment explanation
Indices: 35355--35482 Score: 177
Period size: 43 Copynumber: 3.0 Consensus size: 43
35345 TGACAGGTCG
* * * * *
35355 CCCTCAATGTAATGGATATGGCATTCATTGCTGAGAGCTCCAG
1 CCCTCAATGTAAGGGACATGGCCTTCATTGTTGAGAGCTCCAT
* *
35398 CCCTCAATGTAAGGGACATGGCCTTCATAGTTGAGAGTTCCAT
1 CCCTCAATGTAAGGGACATGGCCTTCATTGTTGAGAGCTCCAT
*
35441 CCCTCAATGTAA-GGACATGGCCTTCATTGTTGAAAGCTCCAT
1 CCCTCAATGTAAGGGACATGGCCTTCATTGTTGAGAGCTCCAT
35483 TGCGAAAATG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 27 0.36
43 48 0.64
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (43 bp):
CCCTCAATGTAAGGGACATGGCCTTCATTGTTGAGAGCTCCAT
Found at i:38724 original size:57 final size:57
Alignment explanation
Indices: 38663--38821 Score: 300
Period size: 57 Copynumber: 2.8 Consensus size: 57
38653 CCGTTGAAGT
38663 TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAACCCCTGCGAAGAGCTTGAAAG
1 TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAACCCCTGCGAAGAGCTTGAAAG
*
38720 TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAACCCCTGCGAAGAGCTTGAAGG
1 TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAACCCCTGCGAAGAGCTTGAAAG
*
38777 TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAAACCCTGCGA
1 TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAACCCCTGCGA
38822 CCCCATTCCG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 100 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (57 bp):
TTGTGAAGCTCCCCCTTTGAGTAGTCAATTCTTCAACCCCTGCGAAGAGCTTGAAAG
Found at i:39688 original size:18 final size:18
Alignment explanation
Indices: 39665--39705 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39655 TTCATCAACC
* *
39665 TCTTCATCAGATTCTTCT
1 TCTTCAGCAGATCCTTCT
*
39683 TCTTCAGCAGCTCCTTCT
1 TCTTCAGCAGATCCTTCT
39701 TCTTC
1 TCTTC
39706 CTCGTTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.34, G:0.07, T:0.46
Consensus pattern (18 bp):
TCTTCAGCAGATCCTTCT
Done.