Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008736.1 Corchorus capsularis cultivar CVL-1 contig08757, 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: 7863
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:777 original size:70 final size:70
Alignment explanation
Indices: 648--1221 Score: 832
Period size: 70 Copynumber: 8.2 Consensus size: 70
638 CTCATTGAAC
* * * * * * *
648 TTGGCTTATGGAAATGCCCATG-TTGCTTGGGTGGAACCAAAACTTAAACTGA-CTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACT-ATCTCGTATGGAA
711 ACGAGT
65 ACGAGT
* * * * *
717 TTGGCTTGTGGAAAAGCCCTTGAACGCTTAGATGGAACCAAAGCTTGAACTATCTTGTATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
782 CGAGT
66 CGAGT
* * * *
787 TTGGTTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAGAGCTTGAAGTATCTCATATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
*
852 TGAGT
66 CGAGT
*
857 TTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
922 C-AGT
66 CGAGT
* * *
926 TTGGCTTGTGGAAAAGCCCTTGCATGATTGGATGGAACCAAAACTTGAACTATCTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
991 CGAGT
66 CGAGT
* * *
996 TTGGCTTGTGGAAGAGCCCCCAG-ATGCTTGGATGGAACCAAAGTTTGAACTATCTCGTATGGAA
1 TTGGCTTGTGGAAAAG-CCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAA
*
1060 ACAAGT
65 ACGAGT
*
1066 TTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
1131 CGAGT
66 CGAGT
* *
1136 TTGGCTTGTGGAAAAGCCCCTGGATGCTTGGATGGAACCAAAGTTTGAACTATCTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
1201 CGAGT
66 CGAGT
* *
1206 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
1222 TGAAAATTGA
Statistics
Matches: 453, Mismatches: 47, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
69 90 0.20
70 359 0.79
71 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (70 bp):
TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAA
CGAGT
Found at i:1186 original size:279 final size:279
Alignment explanation
Indices: 648--1221 Score: 875
Period size: 279 Copynumber: 2.1 Consensus size: 279
638 CTCATTGAAC
* * * *
648 TTGGCTTATGGAAATGCCCATGTTGCTTGGGTGGAACCAAAACTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGATGATTGGATGGAACCAAAACTTAAACTGACTCGTATGGAAAC
** *
713 GAGTTTGGCTTGTGGAAAAGCCCTTGAACGCTTAGATGGAACCAAAGCTTGAACTATCTTGTATG
66 GAGTTTGGCTTGTGGAAAAGCCCCAGAACGCTTAGATGGAACCAAAGCTTGAACTATCTCGTATG
* * * * *
778 GAAACGAGTTTGGTTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAGAGCTTGAAGTATCTC
131 GAAACAAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTC
*
843 ATATGGAAATGAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACT
196 ATATGGAAACGAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACT
908 ATCTCGTATGGAAAC-AGT
261 ATCTCGTATGGAAACGAGT
* * *
926 TTGGCTTGTGGAAAAGCCCTTGCATGATTGGATGGAACCAAAACTTGAACT-ATCTCGTATGGAA
1 TTGGCTTATGGAAAAGCCCATG-ATGATTGGATGGAACCAAAACTTAAACTGA-CTCGTATGGAA
* * * *
990 ACGAGTTTGGCTTGTGGAAGAGCCCCCAG-ATGCTTGGATGGAACCAAAGTTTGAACTATCTCGT
64 ACGAGTTTGGCTTGTGGAAAAG-CCCCAGAACGCTTAGATGGAACCAAAGCTTGAACTATCTCGT
1054 ATGGAAACAAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTAT
128 ATGGAAACAAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTAT
* * * *
1119 CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGGATGCTTGGATGGAACCAAAGTTTGA
193 CTCATATGGAAACGAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGA
1184 ACTATCTCGTATGGAAACGAGT
258 ACTATCTCGTATGGAAACGAGT
*
1206 TTGACTTATGGAAAAG
1 TTGGCTTATGGAAAAG
1222 TGAAAATTGA
Statistics
Matches: 266, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
278 20 0.08
279 225 0.85
280 21 0.08
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (279 bp):
TTGGCTTATGGAAAAGCCCATGATGATTGGATGGAACCAAAACTTAAACTGACTCGTATGGAAAC
GAGTTTGGCTTGTGGAAAAGCCCCAGAACGCTTAGATGGAACCAAAGCTTGAACTATCTCGTATG
GAAACAAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTATCTC
ATATGGAAACGAGTTTGGCTTATGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACT
ATCTCGTATGGAAACGAGT
Found at i:1723 original size:50 final size:50
Alignment explanation
Indices: 1659--1757 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
1649 AAAATGCCCT
*
1659 TTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATC
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
* * *
1709 TTGAAAATCGAATTTTGATATTGGACTTACAAATGGAATGCAATCTTAT
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
1758 TATAAAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (50 bp):
TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
Found at i:2058 original size:16 final size:16
Alignment explanation
Indices: 2030--2067 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
2020 CTAGAGCTTC
2030 TTTTCTTCATTCTCTTT
1 TTTTCTTCATTCT-TTT
2047 TTTTCTTC-TTCTTTT
1 TTTTCTTCATTCTTTT
2062 TCTTTC
1 T-TTTC
2068 ATTTTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCTTCATTCTTTT
Found at i:2062 original size:14 final size:15
Alignment explanation
Indices: 2026--2062 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2016 CACCCTAGAG
*
2026 CTTCTTTTCTTCATT
1 CTTCTTTTTTTCATT
2041 C-TCTTTTTTTC-TT
1 CTTCTTTTTTTCATT
2054 CTTCTTTTT
1 CTTCTTTTT
2063 CTTTCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTCTTTTTTTCATT
Found at i:2674 original size:25 final size:26
Alignment explanation
Indices: 2626--2684 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
2616 TTCCGACCTC
2626 TTTCTTTTTTAGGCCAAGGTTTTTTT
1 TTTCTTTTTTAGGCCAAGGTTTTTTT
*
2652 TTTCTTTTTTAGGCGAAGG-TTTTTT
1 TTTCTTTTTTAGGCCAAGGTTTTTTT
2677 TTTCTTTT
1 TTTCTTTT
2685 CTCTTTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.64
Consensus pattern (26 bp):
TTTCTTTTTTAGGCCAAGGTTTTTTT
Found at i:3367 original size:8 final size:8
Alignment explanation
Indices: 3356--3419 Score: 65
Period size: 8 Copynumber: 7.6 Consensus size: 8
3346 TTTTTCTTTC
*
3356 TTTTTCCT
1 TTTTTCAT
3364 TTTTTCATT
1 TTTTTCA-T
3373 TTTTTCAT
1 TTTTTCAT
**
3381 CATTTCAT
1 TTTTTCAT
3389 TTTTTCATT
1 TTTTTCA-T
3398 TTTTTCAT
1 TTTTTCAT
*
3406 TTCATTCAT
1 TT-TTTCAT
3415 TTTTT
1 TTTTT
3420 TTGGGAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 23 0.50
9 23 0.50
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTCAT
Found at i:3376 original size:17 final size:17
Alignment explanation
Indices: 3344--3407 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
3334 CTTTTTTACT
*
3344 CTTTTTTCTTTCTTTTTC
1 CTTTTTTCATT-TTTTTC
3362 CTTTTTTCATTTTTTTC
1 CTTTTTTCATTTTTTTC
* **
3379 ATCATTTCA-TTTTTTC
1 CTTTTTTCATTTTTTTC
*
3395 ATTTTTTTCATTT
1 -CTTTTTTCATTT
3408 CATTCATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.19
17 18 0.49
18 12 0.32
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTTTTTCATTTTTTTC
Found at i:3379 original size:9 final size:9
Alignment explanation
Indices: 3345--3420 Score: 68
Period size: 9 Copynumber: 8.7 Consensus size: 9
3335 TTTTTTACTC
*
3345 TTTTTTCTT
1 TTTTTTCAT
*
3354 TCTTTTTC-C
1 T-TTTTTCAT
3363 TTTTTTCAT
1 TTTTTTCAT
3372 TTTTTTCA-
1 TTTTTTCAT
**
3380 TCATTTCA-
1 TTTTTTCAT
3388 TTTTTTCAT
1 TTTTTTCAT
3397 TTTTTTCAT
1 TTTTTTCAT
**
3406 TTCATTCAT
1 TTTTTTCAT
3415 TTTTTT
1 TTTTTT
3421 TGGGAAATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
8 18 0.33
9 30 0.56
10 6 0.11
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:3386 original size:25 final size:25
Alignment explanation
Indices: 3358--3419 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 25
3348 TTTCTTTCTT
*
3358 TTTCCTTTTTTCATTTTTTTCATCA
1 TTTCATTTTTTCATTTTTTTCATCA
3383 TTTCATTTTTTCATTTTTTTCATTTCA
1 TTTCATTTTTTCATTTTTTTCA--TCA
3410 -TTCATTTTTT
1 TTTCATTTTTT
3420 TTGGGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 21 0.62
26 10 0.29
27 3 0.09
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTCATTTTTTCATTTTTTTCATCA
Found at i:3417 original size:17 final size:16
Alignment explanation
Indices: 3356--3419 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
3346 TTTTTCTTTC
*
3356 TTTTTCCTTTTTTCATT
1 TTTTTCATTTTTTCA-T
**
3373 TTTTTCATCATTTCAT
1 TTTTTCATTTTTTCAT
3389 TTTTTCATTTTTTTCAT
1 TTTTTCA-TTTTTTCAT
*
3406 TTCATTCATTTTTT
1 TT-TTTCATTTTTT
3420 TTGGGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.21
17 27 0.69
18 4 0.10
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTCATTTTTTCAT
Done.