Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013408.1 Corchorus capsularis cultivar CVL-1 contig13429, 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: 59194
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2145 original size:2 final size:2
Alignment explanation
Indices: 2138--2169 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2128 TCAAAATTTC
2138 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
2170 TTCTTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4224 original size:57 final size:55
Alignment explanation
Indices: 4145--4265 Score: 172
Period size: 57 Copynumber: 2.2 Consensus size: 55
4135 GTGACTAAAT
* *
4145 AAAAATTAAATAAATAAATATAATAAATCACATATTAATTTGTAATCATAAATCAT-A
1 AAAAAATAAATAAATAAATATAATAAATCACATAATAATTTGTAAT-AT-AA-CATGA
* *
4202 AAAAAATAAATTAATAAATATAATAAATCGCATAATAATTTGTAATATAACATGA
1 AAAAAATAAATAAATAAATATAATAAATCACATAATAATTTGTAATATAACATGA
4257 AAAAAATAA
1 AAAAAATAA
4266 TCTTCATCTA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
54 3 0.05
55 12 0.20
56 2 0.03
57 42 0.71
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (55 bp):
AAAAAATAAATAAATAAATATAATAAATCACATAATAATTTGTAATATAACATGA
Found at i:5253 original size:38 final size:38
Alignment explanation
Indices: 5202--5279 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
5192 TTTCAACAAA
*
5202 TTCAACAATCTTACATTCTTACTTAGTACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
5240 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
5278 TT
1 TT
5280 GGTAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:29585 original size:15 final size:15
Alignment explanation
Indices: 29565--29602 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
29555 GGAAAATGGC
* *
29565 GGAGGAGGTGGTGGT
1 GGAGGAGGTGGAGAT
29580 GGAGGAGGTGGAGAT
1 GGAGGAGGTGGAGAT
29595 GGAGGAGG
1 GGAGGAGG
29603 AGGAAGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.66, T:0.13
Consensus pattern (15 bp):
GGAGGAGGTGGAGAT
Found at i:29813 original size:30 final size:30
Alignment explanation
Indices: 29779--29837 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29769 CCTTTGGATT
*
29779 TTTTTTTTTCTTTG-AAAATTTACATTAAGA
1 TTTTTTTTT-TTGGTAAAATTTACATTAAGA
*
29809 TTTTTTTTTTTGGTACAATTTACATTAAG
1 TTTTTTTTTTTGGTAAAATTTACATTAAG
29838 TTATGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTTTTTTTTGGTAAAATTTACATTAAGA
Found at i:33015 original size:17 final size:15
Alignment explanation
Indices: 32994--33024 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32984 TCTCGTATCA
32994 TATATATTATACGAG
1 TATATATTATACGAG
33009 TATATATTATACGAG
1 TATATATTATACGAG
33024 T
1 T
33025 GCATGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
TATATATTATACGAG
Found at i:42251 original size:122 final size:122
Alignment explanation
Indices: 42083--42326 Score: 434
Period size: 122 Copynumber: 2.0 Consensus size: 122
42073 AGATATTAAG
* *
42083 CATCAAATCAACATTCTGAAAGACTATTTAGGAAAATAAACATTGATTAAAATCTACTAATTTGG
1 CATCAAATCAACAGTCTGAAAGACTATTTAGGAAAATAAACATTGATCAAAATCTACTAATTTGG
*
42148 CTTAACTAATATGGATAAGTACATACATAGAAGGAACATATGCAATTTTCCTAATAA
66 CTTAACTAATATGGATAAGTACATACATAGAAGGAACATATGCAACTTTCCTAATAA
*
42205 CATCAAATCAACAGTCTGAAAGACTATTTAGGAAAATAAACATTGATCAAAGTCTACTAATTTGG
1 CATCAAATCAACAGTCTGAAAGACTATTTAGGAAAATAAACATTGATCAAAATCTACTAATTTGG
* *
42270 CTTAACTAGTATGGATAAGTACATACATATAAGGAACATATGCAACTTTCCTAATAA
66 CTTAACTAATATGGATAAGTACATACATAGAAGGAACATATGCAACTTTCCTAATAA
42327 AATGTTTATA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (122 bp):
CATCAAATCAACAGTCTGAAAGACTATTTAGGAAAATAAACATTGATCAAAATCTACTAATTTGG
CTTAACTAATATGGATAAGTACATACATAGAAGGAACATATGCAACTTTCCTAATAA
Found at i:45374 original size:15 final size:15
Alignment explanation
Indices: 45354--45389 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
45344 TTACAAATTT
*
45354 ACTCTCCTGGGAATC
1 ACTCTCCTAGGAATC
45369 ACTCTCCTAGGAATC
1 ACTCTCCTAGGAATC
45384 ACTCTC
1 ACTCTC
45390 TCATGGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.28
Consensus pattern (15 bp):
ACTCTCCTAGGAATC
Found at i:46119 original size:34 final size:31
Alignment explanation
Indices: 46065--46132 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 31
46055 TATATGTTAT
* *
46065 TATAAATTAAAAATCCGAAAATATATAAATATA
1 TATAAATTAAAAATCAGAAAAT-CA-AAATATA
*
46098 TATAACATTAATAATCAGAAAATCAAAATATA
1 TATAA-ATTAAAAATCAGAAAATCAAAATATA
46130 TAT
1 TAT
46133 TTTTAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 10 0.32
33 6 0.19
34 15 0.48
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (31 bp):
TATAAATTAAAAATCAGAAAATCAAAATATA
Found at i:46925 original size:78 final size:78
Alignment explanation
Indices: 46796--46950 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 78
46786 CCTTTTTTTT
* * *
46796 GGGATTTTTATAATTTAATTATTCTCAACTGCTTTGCTGTATTTGATACTGTCTATTTGTTGCGT
1 GGGATTTTTATAATTTAATTATTCTCAACTGATTTGCCGTATTTGATACTGTCTATTTGCTGCGT
46861 CTGTATGTGATTG
66 CTGTATGTGATTG
* *
46874 GGGATTTTTATAATTTAATTATTCTCAATTGATTTGCCGTATTTGATACTGTCTATTTGCTGTGT
1 GGGATTTTTATAATTTAATTATTCTCAACTGATTTGCCGTATTTGATACTGTCTATTTGCTGCGT
46939 CTGTATGTGATT
66 CTGTATGTGATT
46951 ACCCCCCTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (78 bp):
GGGATTTTTATAATTTAATTATTCTCAACTGATTTGCCGTATTTGATACTGTCTATTTGCTGCGT
CTGTATGTGATTG
Found at i:51788 original size:331 final size:328
Alignment explanation
Indices: 51089--51894 Score: 828
Period size: 331 Copynumber: 2.4 Consensus size: 328
51079 AAAACAATGA
51089 CTGAGATTTCG-TTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCAT-TCAAAA
1 CTGAGATTT-GATTAGATGAATAT-GATATTTCAAGGAGTCTCGGTGCCAAAAATCATGT---AA
* * * * * *
51152 TTGAAC-CGAGCCCCGGAACGCGTTTTGGCCAAAAAACCGTGA-CGATATTACACGATTTCGGCT
61 CTGAGCTCG-GCCCCGAAACGCGTTTTAGCCAAAAAACCGTGATGGTTATTACACGATTTCGGCT
* * * ** * * *
51215 ATAATTTTGC-AAAAATTTGACCCGAAAGGTATTTCCTCAATTTTTAGCCATAATACTCATAAAA
125 AAAATTTTGCAAAAAAATAGACCCGAAAAATATTTCCCCAATTTTTAGACAAAATACTCATAAAA
** * * * *
51279 ATGTATAATTCAATAGCAAAAATATTGAAGAGTTTTTCACGCTTTTAATAGCGTTTTTCATATTT
190 ATAAATAATTCAACAGCAAAAAGATTGAAGAGCTTTTCACACTTTTAATAGCGTTTTTCATA---
* ** *
51344 TTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAGATTCTTA
252 TTTTTCAGAATTAATTTCCAATTAAATAAAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTA
* *
51409 AATGCAATGTGG
317 AATCCAATGAGG
* * *
51421 CTAAGATTTTATTAGATGAATATAAGTATTTCAAGGAGT-TCCGGTGCCAAAAATCATGTAACTG
1 CTGAGATTTGATTAGATGAATATGA-TATTTCAAGGAGTCT-CGGTGCCAAAAATCATGTAACTG
* * * *
51485 AGCCTCGGCCCCGAAACGCGGCTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTTGACTAA
64 AG-CTCGGCCCCGAAACGC-GTTTTAGCCAAAAAACCGTGATGGTTATTACACGATTTCGGCTAA
*
51550 AATTTTGCAAAAAAATAG-CCCGAAAAAT-TTTCCCCCAATTTTTGGAACAAAATACTCATAAAA
127 AATTTTGCAAAAAAATAGACCCGAAAAATATTT-CCCCAATTTTTAG-ACAAAATACTCATAAAA
* *
51613 TATAAATAATTTAACA-CTAAAAAGATTAGAAGA-CTTTTCACACTTTTAATATCGTTTTTCATA
190 -ATAAATAATTCAACAGC-AAAAAGATT-GAAGAGCTTTTCACACTTTTAATAGCGTTTTTCATA
* ** *
51676 -TTTTCTGAATTAATTTCCAATTAAATAAAAACAAGATTCAGATGCTTTTAAAATCAAATTCTTA
252 TTTTTCAGAATTAATTTCCAATTAAATAAAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTA
51740 AATCCAATGAGG
317 AATCCAATGAGG
* * * * * * *
51752 CTGAGATTTGATCAGATAAATATGGATATCTCAAGGAGTCTTGGCGCAAAAAATCATGCAAACAT
1 CTGAGATTTGATTAGATGAATAT-GATATTTCAAGGAGTCTCGGTGCCAAAAATCATG-TAAC-T
* * * * *
51817 GAGCTGGGGCCCC-AGAACGCTTTTTTAG-CTAAAAACTGTGATGGTTATTACATGATTTCGGCT
63 GAGCT-CGGCCCCGA-AACGC-GTTTTAGCCAAAAAACCGTGATGGTTATTACACGATTTCGGCT
*
51880 AAAATTTTGTAAAAA
125 AAAATTTTGCAAAAA
51895 TTTACCCGAA
Statistics
Matches: 393, Mismatches: 61, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
330 5 0.01
331 125 0.32
332 124 0.32
333 65 0.17
334 23 0.06
335 46 0.12
336 5 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (328 bp):
CTGAGATTTGATTAGATGAATATGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGTAACTGAG
CTCGGCCCCGAAACGCGTTTTAGCCAAAAAACCGTGATGGTTATTACACGATTTCGGCTAAAATT
TTGCAAAAAAATAGACCCGAAAAATATTTCCCCAATTTTTAGACAAAATACTCATAAAAATAAAT
AATTCAACAGCAAAAAGATTGAAGAGCTTTTCACACTTTTAATAGCGTTTTTCATATTTTTCAGA
ATTAATTTCCAATTAAATAAAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATG
AGG
Found at i:52092 original size:15 final size:15
Alignment explanation
Indices: 52072--52111 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 15
52062 ATAAGTTCTT
52072 TTAAGAAAAATTAAG
1 TTAAGAAAAATTAAG
52087 TTAAGAGAAAAATTAAG
1 TT-A-AGAAAAATTAAG
52104 TTAAGAAA
1 TTAAGAAA
52112 TGGAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 2 0.09
17 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (15 bp):
TTAAGAAAAATTAAG
Found at i:52097 original size:17 final size:17
Alignment explanation
Indices: 52075--52109 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52065 AGTTCTTTTA
52075 AGAAAAATTAAGTTAAG
1 AGAAAAATTAAGTTAAG
52092 AGAAAAATTAAGTTAAG
1 AGAAAAATTAAGTTAAG
52109 A
1 A
52110 AATGGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (17 bp):
AGAAAAATTAAGTTAAG
Found at i:58617 original size:22 final size:22
Alignment explanation
Indices: 58573--58650 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
58563 CCACACTATA
* * *
58573 AAATTTCGATAACTTGCATATG
1 AAATTTCGATAACCTCCACATG
* * *
58595 AATTTTTGATAACCTCCCCATG
1 AAATTTCGATAACCTCCACATG
* *
58617 AAATTTCGACAACTTCCACATG
1 AAATTTCGATAACCTCCACATG
58639 AAATTTCGATAA
1 AAATTTCGATAA
58651 TATCACCACA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTTCGATAACCTCCACATG
Found at i:58761 original size:42 final size:44
Alignment explanation
Indices: 58655--58779 Score: 128
Period size: 42 Copynumber: 2.9 Consensus size: 44
58645 CGATAATATC
* * * *
58655 ACCACAATATGAAATTTTGATAACATCTGTATGATATTTTGGTA
1 ACCACAATATGAAATTTTGATAACATCTATATGAAATTTCGGAA
* **
58699 ACCATAATACAAAATTTTGATAAC-T-TATATGAAATTTCGGAA
1 ACCACAATATGAAATTTTGATAACATCTATATGAAATTTCGGAA
* * * **
58741 ACCACACTATGAAATCTTGATAACCTCCCTATGAAATTT
1 ACCACAATATGAAATTTTGATAACATCTATATGAAATTT
58780 TGATATCCTC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 32 0.49
43 2 0.03
44 31 0.48
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (44 bp):
ACCACAATATGAAATTTTGATAACATCTATATGAAATTTCGGAA
Found at i:58765 original size:22 final size:22
Alignment explanation
Indices: 58740--58799 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
58730 AAATTTCGGA
*
58740 AACCACACTATGAAATCTTGAT
1 AACCTCACTATGAAATCTTGAT
* *
58762 AACCTCCCTATGAAATTTTGAT
1 AACCTCACTATGAAATCTTGAT
* *
58784 ATCCTCTCTATGAAAT
1 AACCTCACTATGAAAT
58800 TTCGATTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (22 bp):
AACCTCACTATGAAATCTTGAT
Found at i:58795 original size:44 final size:44
Alignment explanation
Indices: 58747--58844 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
58737 GGAAACCACA
*
58747 CTATGAAATCTT-GATAACCTCCCTATGAAATTTTGATAT-CCTCT
1 CTATGAAATCTTCGATAACCTCCCTATGAAA-TTGGAT-TGCCTCT
** *
58791 CTATGAAAT-TTCGATTGCCTCCTTATGAAATTGGATTGCCTCT
1 CTATGAAATCTTCGATAACCTCCCTATGAAATTGGATTGCCTCT
58834 CTATGAAATCT
1 CTATGAAATCT
58845 ATACTACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 1 0.02
43 21 0.45
44 25 0.53
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (44 bp):
CTATGAAATCTTCGATAACCTCCCTATGAAATTGGATTGCCTCT
Found at i:58800 original size:22 final size:22
Alignment explanation
Indices: 58747--58842 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
58737 GGAAACCACA
* ** *
58747 CTATGAAATCTTGATAACCTCC
1 CTATGAAATTTTGATTGCCTCT
58769 CTATGAAATTTTGATAT-CCTCT
1 CTATGAAATTTTGAT-TGCCTCT
*
58791 CTATGAAATTTCGATTGCCTC-
1 CTATGAAATTTTGATTGCCTCT
*
58812 CTTATGAAA-TTGGATTGCCTCT
1 C-TATGAAATTTTGATTGCCTCT
58834 CTATGAAAT
1 CTATGAAAT
58843 CTATACTACA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
21 20 0.31
22 44 0.69
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATTGCCTCT
Done.