Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016465.1 Corchorus capsularis cultivar CVL-1 contig16486, 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: 57373
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:3387 original size:19 final size:18
Alignment explanation
Indices: 3354--3389 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3344 TTGAAATAAT
3354 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
3372 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
3390 AAAATCTTCA
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:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:14638 original size:18 final size:19
Alignment explanation
Indices: 14615--14655 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
14605 TTAATTATAT
14615 CAATTATA-AAAAAAAAAG
1 CAATTATACAAAAAAAAAG
*
14633 CAATTATACTAAAAACAAAG
1 CAATTATAC-AAAAAAAAAG
14653 CAA
1 CAA
14656 AGTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.66, C:0.12, G:0.05, T:0.17
Consensus pattern (19 bp):
CAATTATACAAAAAAAAAG
Found at i:16068 original size:53 final size:54
Alignment explanation
Indices: 16007--16185 Score: 231
Period size: 53 Copynumber: 3.4 Consensus size: 54
15997 AATATGGATG
* ** **
16007 CCCTTGTGCTTGAGGAC-TTTGATGTAGAAGTCATGAGTGTTCGGGGATGAATA
1 CCCTTGTGCTTGAGGACTTTTGATGTAGAAGTCCTCTGTGTTTAGGGATGAATA
*
16060 CCCTTGTGCTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGCTTGAGGACTTTTGATGTAGAAGT-CCTCTGTGTTTAGGGATGAATA
* * *
16113 CCCTTGTGTTTGAGGACTTTTGATATAGATG-CCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGCTTGAGGACTTTTGATGTAGAAGTCCTCTGTGTTTAGGGATGAATA
*
16166 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGCTTGAGGACTTT
16186 AATTATTGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
52 5 0.04
53 99 0.88
54 5 0.04
55 4 0.04
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.36
Consensus pattern (54 bp):
CCCTTGTGCTTGAGGACTTTTGATGTAGAAGTCCTCTGTGTTTAGGGATGAATA
Found at i:18227 original size:6 final size:6
Alignment explanation
Indices: 18211--18246 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
18201 AAAGCAAAGC
*
18211 AAATCT TAATCT AAATCT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
18247 GAAGCAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATCT
Found at i:19207 original size:10 final size:10
Alignment explanation
Indices: 19192--19217 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19182 GAGGACTCTA
19192 GAATTTTCTG
1 GAATTTTCTG
19202 GAATTTTCTG
1 GAATTTTCTG
19212 GAATTT
1 GAATTT
19218 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:22921 original size:15 final size:16
Alignment explanation
Indices: 22894--22938 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
22884 ATATGATGGG
22894 TATTTGAATATTTGGA
1 TATTTGAATATTTGGA
*
22910 TATTTG-ATATTTGGG
1 TATTTGAATATTTGGA
22925 TATGTATGAATATT
1 TAT-T-TGAATATT
22939 CTAGGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
16 7 0.28
17 2 0.08
18 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (16 bp):
TATTTGAATATTTGGA
Found at i:30524 original size:30 final size:29
Alignment explanation
Indices: 30488--30589 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
30478 CTGTGTTATA
30488 TGTGTTTGGGGACTTTATTATAGATGCCTC
1 TGTGTTTGGGGACTTTA-TATAGATGCCTC
* *
30518 TGTGTTTAGGGACTTTAATATGGATGCC-C
1 TGTGTTTGGGGACTTT-ATATAGATGCCTC
* * *
30547 TTGTGCTTGAGGACTTTGATGTAGATGCCTC
1 -TGTGTTTGGGGACTTT-ATATAGATGCCTC
*
30578 TGTGTTCGGGGA
1 TGTGTTTGGGGA
30590 TGAATACCCT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.02
30 55 0.95
31 2 0.03
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (29 bp):
TGTGTTTGGGGACTTTATATAGATGCCTC
Found at i:30643 original size:53 final size:52
Alignment explanation
Indices: 30544--30721 Score: 252
Period size: 53 Copynumber: 3.4 Consensus size: 52
30534 AATATGGATG
**
30544 CCCTTGTGCTTGAGGAC-TTTGATGTAGA-TGCCTCTGTGTTCGGGGATGAATA
1 CCCTTGTGCTTGAGGACTTTTGA-G-AGAGTGCCTCTGTGTTTAGGGATGAATA
30596 CCCTTGTGCTTGAGGACTTTTGAGAGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGCTTGAGGACTTTTGAGAGA-GTGCCTCTGTGTTTAGGGATGAATA
* * *
30649 CCCTTGTGTTTGAGGACTTTTGATATAGATGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGCTTGAGGACTTTTGAGAGAG-TGCCTCTGTGTTTAGGGATGAATA
*
30702 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGCTTGAGGACTTT
30722 AATTATTGAG
Statistics
Matches: 117, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
51 3 0.03
52 19 0.16
53 95 0.81
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (52 bp):
CCCTTGTGCTTGAGGACTTTTGAGAGAGTGCCTCTGTGTTTAGGGATGAATA
Found at i:34371 original size:13 final size:14
Alignment explanation
Indices: 34353--34381 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34343 ATAACCGGAT
34353 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
34366 TTTGCATTCATGCA
1 TTTGCATTCATGCA
34380 TT
1 TT
34382 AAGTAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:34666 original size:38 final size:40
Alignment explanation
Indices: 34587--34685 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
34577 TTAAGTAATT
*
34587 CAAAGAGAAGACTTTTGGAAAATAAATGTGTTTAGCAAATC
1 CAAA-AGAAGACTTTTGGAAAATAAATGTGTTTAGAAAATC
34628 CAAAAGAAGACTTTTGGAAAATAAATGT-TTTA-AAAATC
1 CAAAAGAAGACTTTTGGAAAATAAATGTGTTTAGAAAATC
* *
34666 CAAGACAAGACTTTTGGAAA
1 CAAAAGAAGACTTTTGGAAA
34686 TTAATAAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 23 0.42
39 4 0.07
40 24 0.44
41 4 0.07
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.26
Consensus pattern (40 bp):
CAAAAGAAGACTTTTGGAAAATAAATGTGTTTAGAAAATC
Found at i:39497 original size:28 final size:28
Alignment explanation
Indices: 39456--39527 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
39446 AGAATTTCAT
*
39456 TCAAGGTTTTCAAAGTGGGAAAGCTCCTA
1 TCAA-GTTTTCAAAGTGGGAAAGCTCCCA
* *
39485 TCAAGTTCTCAAAGTGGGAAAGTTCCCA
1 TCAAGTTTTCAAAGTGGGAAAGCTCCCA
39513 TCAAGTTTTCAAAGT
1 TCAAGTTTTCAAAGT
39528 ATTCAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (28 bp):
TCAAGTTTTCAAAGTGGGAAAGCTCCCA
Found at i:39558 original size:52 final size:52
Alignment explanation
Indices: 39493--39638 Score: 204
Period size: 53 Copynumber: 2.8 Consensus size: 52
39483 TATCAAGTTC
*
39493 TCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGATCTTT
1 TCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGATCTCT
* * * *
39545 TCAAAGTGAGAAAGTTCACATCAAGTTTTTGTAAA-TATTCAATTTAGGTCTCT
1 TCAAAGTGGGAAAGTTCCCATCAAG-TTTT-CAAAGTATTCAATTTAGATCTCT
* *
39598 TCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGCATTCAA
1 TCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAA
39639 ACAACATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 3 0.04
52 33 0.41
53 42 0.52
54 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (52 bp):
TCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGATCTCT
Found at i:40532 original size:34 final size:32
Alignment explanation
Indices: 40472--40535 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 32
40462 ATGGGTTTTC
40472 ATAATAACTAAACTAAACTAGAAAACAATTAA
1 ATAATAACTAAACTAAACTAGAAAACAATTAA
40504 ATAA-AACTAAACTAAAGATCTAGAAAACAATT
1 ATAATAACTAAACT-AA-A-CTAGAAAACAATT
40536 TAAGAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 9 0.31
32 6 0.21
33 1 0.03
34 13 0.45
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (32 bp):
ATAATAACTAAACTAAACTAGAAAACAATTAA
Found at i:41934 original size:76 final size:76
Alignment explanation
Indices: 41795--41935 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 76
41785 GGACAAAGGC
* * *
41795 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCAATGTGGTTTGCCTGAAGACCCAG
1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCAATGTGATTGGCCTGAACACCCAG
41860 CTGGGTAGTGT
66 CTGGGTAGTGT
* * * * * * *
41871 CCCGACTCTACCTGGGTGCCCACATGCTTTGTC-TGAGGACCTATGTGATTGGCCTGATCACCCA
1 CCCGACTCCACCTGGGCGCCCACATG-GTTGCCTTGAGCACCAATGTGATTGGCCTGAACACCCA
41935 G
65 G
41936 GTAGGCAGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
76 50 0.93
77 4 0.07
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.24
Consensus pattern (76 bp):
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCAATGTGATTGGCCTGAACACCCAG
CTGGGTAGTGT
Found at i:43996 original size:28 final size:28
Alignment explanation
Indices: 43961--44045 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
43951 ATAACATTAT
*
43961 GCTCTTATTTGGCCAAATTAAAAGATCG
1 GCTCTTATTTGGCCAAATTAAAAGATAG
* ** * *
43989 GCTCTTATTTGGGCATTTTCGATAACATTAG
1 GCTCTTATTTGGCCAAATT--AAAAGA-TAG
*
44020 ACTCTTATTTGGCCAAATTAAAAGAT
1 GCTCTTATTTGGCCAAATTAAAAGAT
44046 TTGACCCTTA
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
28 17 0.40
29 4 0.10
30 4 0.10
31 17 0.40
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (28 bp):
GCTCTTATTTGGCCAAATTAAAAGATAG
Found at i:44025 original size:59 final size:59
Alignment explanation
Indices: 43933--44067 Score: 200
Period size: 59 Copynumber: 2.3 Consensus size: 59
43923 ATACTAGGCC
*
43933 CTTATTTGAGTATTTTCGATAACATTATGCTCTTATTTGGCCAAATTAAAAGATCGGCT
1 CTTATTTGAGCATTTTCGATAACATTATGCTCTTATTTGGCCAAATTAAAAGATCGGCT
* * * *
43992 CTTATTTGGGCATTTTCGATAACATTA-GACTCTTATTTGGCCAAATTAAAAGATTTGACC
1 CTTATTTGAGCATTTTCGATAACATTATG-CTCTTATTTGGCCAAATTAAAAGA-TCGGCT
44052 CTTATTTGAGCATTTT
1 CTTATTTGAGCATTTT
44068 GACAAACGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
58 1 0.01
59 49 0.72
60 18 0.26
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (59 bp):
CTTATTTGAGCATTTTCGATAACATTATGCTCTTATTTGGCCAAATTAAAAGATCGGCT
Found at i:44087 original size:60 final size:59
Alignment explanation
Indices: 43931--44090 Score: 180
Period size: 59 Copynumber: 2.7 Consensus size: 59
43921 CGATACTAGG
* * * *
43931 CCCTTATTTGAGTATTTTCGATAACATTATG-CTCTTATTTGGCCAAATTAAAAGATCGG
1 CCCTTATTTGAGCATTTTCGAAAACATTA-GACCCTTATTTGGCCAAATTAAAAGATCGA
* * * * *
43990 CTCTTATTTGGGCATTTTCGATAACATTAGACTCTTATTTGGCCAAATTAAAAGATTTGA
1 CCCTTATTTGAGCATTTTCGAAAACATTAGACCCTTATTTGGCCAAATTAAAAGA-TCGA
* *
44050 CCCTTATTTGAGCATTTT-GACAAACGTTAGTCCCTTATTTG
1 CCCTTATTTGAGCATTTTCGA-AAACATTAGACCCTTATTTG
44091 AGCAATTAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.01
59 52 0.60
60 34 0.39
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTCGAAAACATTAGACCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:45631 original size:10 final size:10
Alignment explanation
Indices: 45616--45640 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45606 TATTTCTCCC
45616 TTTTTTTTCT
1 TTTTTTTTCT
45626 TTTTTTTTCT
1 TTTTTTTTCT
45636 TTTTT
1 TTTTT
45641 CACATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:46264 original size:30 final size:30
Alignment explanation
Indices: 46224--46281 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
46214 TTTGACATTC
*
46224 TTGAACTTCATGGTTGGGGTGGCATGTTCA
1 TTGAAATTCATGGTTGGGGTGGCATGTTCA
46254 TTGAAATTCATGGTTGGGGTGGCATGTT
1 TTGAAATTCATGGTTGGGGTGGCATGTT
46282 TGGGCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.38
Consensus pattern (30 bp):
TTGAAATTCATGGTTGGGGTGGCATGTTCA
Found at i:57351 original size:3 final size:3
Alignment explanation
Indices: 57343--57373 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
57333 TTGCACTTAT
57343 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.