Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016224.1 Corchorus capsularis cultivar CVL-1 contig16245, 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: 42987
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:794 original size:14 final size:13
Alignment explanation
Indices: 762--799 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
752 TAAGAACTAT
*
762 TAAAT-TAATATA
1 TAAATATAATAAA
774 TAAATATAATAAA
1 TAAATATAATAAA
787 TAAAATATAATAA
1 T-AAATATAATAA
800 TTTGTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 5 0.22
13 7 0.30
14 11 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATATAATAAA
Found at i:5209 original size:21 final size:20
Alignment explanation
Indices: 5170--5209 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5160 CAATTTTCTC
* *
5170 ATTATAAGGTTATCGAGAAA
1 ATTATAAGGTTACCAAGAAA
5190 ATTATAAAGGTTACCAAGAA
1 ATTAT-AAGGTTACCAAGAA
5210 CGTTATACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (20 bp):
ATTATAAGGTTACCAAGAAA
Found at i:5349 original size:20 final size:20
Alignment explanation
Indices: 5320--5368 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5310 CTTCAGAAGG
*
5320 TATAAAATTATTAA-AAATGT
1 TATAATATTATTAATAAAT-T
5340 TATAATATTATTAATAAATT
1 TATAATATTATTAATAAATT
5360 TAGTAATAT
1 TA-TAATAT
5369 CTTACATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAATATTATTAATAAATT
Found at i:14146 original size:14 final size:14
Alignment explanation
Indices: 14103--14140 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
14093 TACTCCCTCT
14103 GTCCCTTTTTATAA
1 GTCCCTTTTTATAA
14117 GTCCCTTTTTATAA
1 GTCCCTTTTTATAA
14131 GTCCTCTTTT
1 GTCC-CTTTT
14141 AGAAGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.53
Consensus pattern (14 bp):
GTCCCTTTTTATAA
Found at i:14956 original size:20 final size:21
Alignment explanation
Indices: 14926--14964 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14916 CCAAAGTAAA
14926 AAAAAAGGAAAAACAAAATGG
1 AAAAAAGGAAAAACAAAATGG
*
14947 AAAAAA-GAAAAAGAAAAT
1 AAAAAAGGAAAAACAAAAT
14965 AAAAGGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAAAAGGAAAAACAAAATGG
Found at i:16185 original size:13 final size:14
Alignment explanation
Indices: 16166--16217 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
16156 AGAAGATCTT
*
16166 TTTTTTTCTTTTTC
1 TTTTTTACTTTTTC
* *
16180 TTTTTTCCATTTT-
1 TTTTTTACTTTTTC
* *
16193 GTTTTTCCTTTTTC
1 TTTTTTACTTTTTC
16207 TTTTTTACTTT
1 TTTTTTACTTT
16218 GGGCGGGATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTACTTTTTC
Found at i:16197 original size:20 final size:20
Alignment explanation
Indices: 16169--16206 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16159 AGATCTTTTT
*
16169 TTTTCTTTTTCTTTTTTCCA
1 TTTTCTTTTTCCTTTTTCCA
*
16189 TTTTGTTTTTCCTTTTTC
1 TTTTCTTTTTCCTTTTTC
16207 TTTTTTACTT
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:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTTCCTTTTTCCA
Found at i:20411 original size:30 final size:30
Alignment explanation
Indices: 20377--20439 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
20367 TCATCTTTTT
*
20377 TAGTTTCTTACTTTCCTTTAACATTGAAAC
1 TAGTTTCTTACTTTCCTTTAAAATTGAAAC
*
20407 TAGTTTCTTTCTTTCCTTTAAAATTGAAAC
1 TAGTTTCTTACTTTCCTTTAAAATTGAAAC
20437 TAG
1 TAG
20440 GCAGACACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (30 bp):
TAGTTTCTTACTTTCCTTTAAAATTGAAAC
Found at i:21734 original size:24 final size:20
Alignment explanation
Indices: 21688--21738 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 20
21678 TTGCCCTTTT
*
21688 TCTCTCTCTCCCCCAGTTAA
1 TCTCTCTCTCCCCCAGTCAA
21708 TCTCTCTCCTCCTCCCAGTCACTA
1 TCTCTCT-CTCC-CCCAGTCA--A
21732 TCTCTCT
1 TCTCTCT
21739 TCATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 4 0.15
22 7 0.27
24 8 0.31
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (20 bp):
TCTCTCTCTCCCCCAGTCAA
Found at i:21735 original size:22 final size:22
Alignment explanation
Indices: 21688--21738 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
21678 TTGCCCTTTT
* *
21688 TCTCTCTCTCCCCCAGTTAATC
1 TCTCTCTCTCCCCCAGTCAATA
*
21710 TCTCTC-CTCCTCCCAGTCACTA
1 TCTCTCTCTCC-CCCAGTCAATA
21732 TCTCTCT
1 TCTCTCT
21739 TCATAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (22 bp):
TCTCTCTCTCCCCCAGTCAATA
Found at i:24328 original size:22 final size:22
Alignment explanation
Indices: 24303--24518 Score: 102
Period size: 22 Copynumber: 9.8 Consensus size: 22
24293 ATGATCCCGT
24303 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
24325 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
24347 TAT-AGAATTTCGAGAACATTTT
1 TATGA-AATTTTGATAACCTTCC
** * *
24369 TAT-AAATTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
24390 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
24412 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
24434 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
24456 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
24479 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
24500 ATATGATATATTGATAACC
1 -TATGAAATTTTGATAACC
24519 ACGTTATGAA
Statistics
Matches: 144, Mismatches: 40, Indels: 20
0.71 0.20 0.10
Matches are distributed among these distances:
21 19 0.13
22 106 0.74
23 19 0.13
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:24492 original size:45 final size:45
Alignment explanation
Indices: 24434--24519 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
24424 AAGACCTCAA
* * *
24434 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
24479 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
24520 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:24768 original size:37 final size:37
Alignment explanation
Indices: 24676--24771 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 37
24666 ATCTAAGCCC
*
24676 AAATAGGACGTTGGAGACAAAGACTAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACTAAAAGCAAAATT
** * *
24713 AAATACAACGATTCGAAACAAAGAC-AAAAGGTAAAATT
1 AAATAGGACG-TTGGAAACAAAGACTAAAA-GCAAAATT
*
24751 AAATAGGATGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
24772 AAATCAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
37 22 0.46
38 26 0.54
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACTAAAAGCAAAATT
Found at i:25683 original size:55 final size:55
Alignment explanation
Indices: 25616--25736 Score: 224
Period size: 55 Copynumber: 2.2 Consensus size: 55
25606 TATTTGTAAT
*
25616 TATTATTTATAATTATCTATTTATTGCTATTATTTATTTAATACTATTATTTTTC
1 TATTATTTATAATTATCTATTTATTGCTATTATCTATTTAATACTATTATTTTTC
25671 TATTATTTATAATTATCTATTTATTGCTATTATCTATTTAATACTATTATTTTTC
1 TATTATTTATAATTATCTATTTATTGCTATTATCTATTTAATACTATTATTTTTC
25726 TATCTATTTAT
1 TAT-TATTTAT
25737 TTCAGTATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 57 0.89
56 7 0.11
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (55 bp):
TATTATTTATAATTATCTATTTATTGCTATTATCTATTTAATACTATTATTTTTC
Found at i:25702 original size:17 final size:17
Alignment explanation
Indices: 25627--25720 Score: 75
Period size: 17 Copynumber: 5.3 Consensus size: 17
25617 ATTATTTATA
*
25627 ATTATCTATTTATTGCT
1 ATTATCTATTTATTACT
* *
25644 ATTATTTATTTAATACT
1 ATTATCTATTTATTACT
25661 ATTATTTTTCTA-TTATTTA-T
1 ATTA----TCTATTTA-TTACT
*
25681 AATTATCTATTTATTGCT
1 -ATTATCTATTTATTACT
*
25699 ATTATCTATTTAATACT
1 ATTATCTATTTATTACT
25716 ATTAT
1 ATTAT
25721 TTTTCTATCT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
17 44 0.72
18 4 0.07
20 4 0.07
21 9 0.15
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTATCTATTTATTACT
Found at i:25836 original size:12 final size:12
Alignment explanation
Indices: 25821--25873 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
25811 GTTTACATAC
25821 CTATTTATCTAT
1 CTATTTATCTAT
25833 CTATTTATCTAT
1 CTATTTATCTAT
* *
25845 ATATCTAAT-TAT
1 CTAT-TTATCTAT
* *
25857 CTTTTTATGTAT
1 CTATTTATCTAT
25869 CTATT
1 CTATT
25874 ATTTTTACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 3 0.09
12 27 0.82
13 3 0.09
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.58
Consensus pattern (12 bp):
CTATTTATCTAT
Found at i:26364 original size:6 final size:6
Alignment explanation
Indices: 26353--26436 Score: 109
Period size: 6 Copynumber: 13.8 Consensus size: 6
26343 TTTTTCCTGA
26353 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTG TTTTTG -TTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
* *
26399 TTTTTG TTTTTTT TGTTTTG TTTTTT TTTCTTG TTTTT
1 TTTTTG -TTTTTG T-TTTTG TTTTTG TTT-TTG TTTTT
26437 TGATTTTTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
5 10 0.14
6 44 0.64
7 15 0.22
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:26368 original size:11 final size:11
Alignment explanation
Indices: 26354--26427 Score: 102
Period size: 11 Copynumber: 6.9 Consensus size: 11
26344 TTTTCCTGAT
26354 TTTTGTTTTTG
1 TTTTGTTTTTG
26365 TTTTTGTTTTTG
1 -TTTTGTTTTTG
26377 TTTTGTTTTTG
1 TTTTGTTTTTG
26388 TTTTGTTTTTG
1 TTTTGTTTTTG
26399 TTTT-TGTTTT-
1 TTTTGT-TTTTG
26409 TTTTG-TTTTG
1 TTTTGTTTTTG
26419 TTTT-TTTTT
1 TTTTGTTTTT
26428 CTTGTTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.07
10 13 0.22
11 30 0.52
12 11 0.19
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:26374 original size:17 final size:16
Alignment explanation
Indices: 26354--26453 Score: 112
Period size: 17 Copynumber: 5.9 Consensus size: 16
26344 TTTTCCTGAT
26354 TTTTGTTTTTGTTTTTG
1 TTTT-TTTTTGTTTTTG
26371 TTTTTGTTTTGTTTTTG
1 TTTTT-TTTTGTTTTTG
26388 TTTTGTTTTTGTTTTTG
1 TTTT-TTTTTGTTTTTG
*
26405 -TTTTTTTTGTTTTGTT
1 TTTTTTTTTGTTTT-TG
26421 TTTTTTTCTTGTTTTTTG
1 TTTTTTT-TTG-TTTTTG
* *
26439 ATTTTTTATGTTTTT
1 TTTTTTTTTGTTTTT
26454 TATTTGATTG
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
15 10 0.14
16 10 0.14
17 38 0.52
18 11 0.15
19 4 0.05
ACGTcount: A:0.02, C:0.01, G:0.14, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTGTTTTTG
Found at i:26435 original size:11 final size:10
Alignment explanation
Indices: 26354--26459 Score: 97
Period size: 10 Copynumber: 10.0 Consensus size: 10
26344 TTTTCCTGAT
26354 TTTTGTTTTTG
1 TTTT-TTTTTG
26365 TTTTTGTTTTTG
1 -TTTT-TTTTTG
26377 TTTTGTTTTTG
1 TTTT-TTTTTG
26388 TTTTGTTTTTG
1 TTTT-TTTTTG
26399 TTTTTGTTTT-
1 TTTTT-TTTTG
*
26409 TTTTGTTTTG
1 TTTTTTTTTG
*
26419 TTTTTTTTTC
1 TTTTTTTTTG
*
26429 TTGTTTTTTG
1 TTTTTTTTTG
* *
26439 ATTTTTTATG
1 TTTTTTTTTG
26449 TTTTTTATTTG
1 TTTTTT-TTTG
26460 ATTGTATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
9 4 0.05
10 33 0.41
11 33 0.41
12 11 0.14
ACGTcount: A:0.03, C:0.01, G:0.14, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:26454 original size:1 final size:1
Alignment explanation
Indices: 26353--26437 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
26343 TTTTTCCTGA
* * * * * * * * * *
26353 TTTTTGTTTTTGTTTTTGTTTTTGTTTTGTTTTTGTTTTGTTTTTGTTTTTGTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
26418 GTTTTTTTTTCTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTT
26438 GATTTTTTAT
Statistics
Matches: 58, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (1 bp):
T
Found at i:26456 original size:9 final size:8
Alignment explanation
Indices: 26359--26454 Score: 74
Period size: 9 Copynumber: 11.5 Consensus size: 8
26349 CTGATTTTTG
26359 TTTTTGTT
1 TTTTTGTT
26367 TTTGTT-TT
1 TTT-TTGTT
26375 TGTTTTGTT
1 T-TTTTGTT
26384 TTTGTT-TT
1 TTT-TTGTT
26392 GTTTTTGTT
1 -TTTTTGTT
*
26401 TTTGT-TT
1 TTTTTGTT
26408 TTTTTGTT
1 TTTTTGTT
*
26416 TTGTTTTTT
1 TT-TTTGTT
26425 TTTCTTG-T
1 TTT-TTGTT
26433 TTTTTGATT
1 TTTTTG-TT
26442 TTTTATGTT
1 TTTT-TGTT
26451 TTTT
1 TTTT
26455 ATTTGATTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
7 9 0.12
8 27 0.38
9 34 0.47
10 2 0.03
ACGTcount: A:0.02, C:0.01, G:0.14, T:0.83
Consensus pattern (8 bp):
TTTTTGTT
Found at i:30147 original size:21 final size:21
Alignment explanation
Indices: 30123--30164 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30113 CCAATAGTTA
* *
30123 AGGCAGTCGCAGGGAGAAATG
1 AGGCAGTCGCAAGAAGAAATG
30144 AGGCAGTCGCAAGAAGAAATG
1 AGGCAGTCGCAAGAAGAAATG
30165 GGACAGGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.38, T:0.10
Consensus pattern (21 bp):
AGGCAGTCGCAAGAAGAAATG
Found at i:39303 original size:21 final size:21
Alignment explanation
Indices: 39274--39316 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39264 CCCGACTCCC
* *
39274 CTTGGGCGCCCATGTCGTTGG
1 CTTGGGCGCCCAGGGCGTTGG
*
39295 CTTGTGCGCCCAGGGCGTTGG
1 CTTGGGCGCCCAGGGCGTTGG
39316 C
1 C
39317 CTCAGGCCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.30, G:0.40, T:0.26
Consensus pattern (21 bp):
CTTGGGCGCCCAGGGCGTTGG
Done.