Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016437.1 Corchorus capsularis cultivar CVL-1 contig16458, 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: 63004
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:365 original size:2 final size:2
Alignment explanation
Indices: 358--388 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
348 TAAATACTAG
358 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
389 TAAGTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3172 original size:24 final size:24
Alignment explanation
Indices: 3123--3180 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
3113 CCACAATTTA
* * *
3123 TTATATTCATTATTATTTAATTAT
1 TTATTTTCATTAATATTTAATAAT
3147 TTATTTTCATTGAATATTT-ATAAT
1 TTATTTTCATT-AATATTTAATAAT
3171 TT-TTTT-ATTA
1 TTATTTTCATTA
3181 TTTAAAGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 3 0.10
23 4 0.13
24 16 0.53
25 6 0.20
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (24 bp):
TTATTTTCATTAATATTTAATAAT
Found at i:27865 original size:23 final size:24
Alignment explanation
Indices: 27835--27903 Score: 110
Period size: 23 Copynumber: 3.0 Consensus size: 24
27825 TATAAAAACT
27835 TTACAAATTAAATTTGAAT-GAGA
1 TTACAAATTAAATTTGAATGGAGA
27858 TTACAAATTAAATTTGAATGGAGA
1 TTACAAATTAAATTTGAATGGAGA
27882 -TAC--ATTAAATTTGAATGGAGA
1 TTACAAATTAAATTTGAATGGAGA
27903 T
1 T
27904 ACATTATCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.41
23 22 0.50
24 4 0.09
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (24 bp):
TTACAAATTAAATTTGAATGGAGA
Found at i:27890 original size:21 final size:21
Alignment explanation
Indices: 27841--27909 Score: 104
Period size: 21 Copynumber: 3.2 Consensus size: 21
27831 AACTTTACAA
27841 ATTAAATTTGAAT-GAGATTAC
1 ATTAAATTTGAATGGAGA-TAC
27862 AAATTAAATTTGAATGGAGATAC
1 --ATTAAATTTGAATGGAGATAC
27885 ATTAAATTTGAATGGAGATAC
1 ATTAAATTTGAATGGAGATAC
27906 ATTA
1 ATTA
27910 TCCCTTACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
21 25 0.56
23 16 0.36
24 4 0.09
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTAAATTTGAATGGAGATAC
Found at i:31430 original size:47 final size:47
Alignment explanation
Indices: 31361--31457 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
31351 ATCAAAAGAC
31361 ATTCATCCTCTTTTCCTATATAAAATAAATTAATCAAATAATTATAA
1 ATTCATCCTCTTTTCCTATATAAAATAAATTAATCAAATAATTATAA
31408 ATTCATCCTCTTTTCCTATATAAAATAAATTAATCAAATAATTATAA
1 ATTCATCCTCTTTTCCTATATAAAATAAATTAATCAAATAATTATAA
31455 ATT
1 ATT
31458 TGTTATGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.41
Consensus pattern (47 bp):
ATTCATCCTCTTTTCCTATATAAAATAAATTAATCAAATAATTATAA
Found at i:35026 original size:2 final size:2
Alignment explanation
Indices: 35019--35043 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35009 TTATATGTGC
35019 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35044 ATGGAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36273 original size:26 final size:26
Alignment explanation
Indices: 36208--36341 Score: 96
Period size: 26 Copynumber: 4.7 Consensus size: 26
36198 GGGATGAATA
*
36208 CCCTTGTGTTTGAGGACTTTTGAGAGAGGTG
1 CCCTTGTGTTTGAGGACTTAT-A-A-A--TG
36239 -CCTCTGTGTTT-AGGGACTTATAAATG
1 CCCT-TGTGTTTGA-GGACTTATAAATG
36265 CCCTTGTGTTTGAGGACTTTGATATATAATTG
1 CCCTTGTGTTTGAGGAC--T--TATA-AA-TG
36297 -CCTCTGTGTTT-AGGGACTTATAAATG
1 CCCT-TGTGTTTGA-GGACTTATAAATG
36323 CCCTTGTGTTTGAGGACTT
1 CCCTTGTGTTTGAGGACTT
36342 TTAATTGTTG
Statistics
Matches: 88, Mismatches: 1, Indels: 33
0.72 0.01 0.27
Matches are distributed among these distances:
26 28 0.32
27 10 0.11
28 6 0.07
29 1 0.01
30 10 0.11
31 20 0.23
32 13 0.15
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (26 bp):
CCCTTGTGTTTGAGGACTTATAAATG
Found at i:36314 original size:58 final size:56
Alignment explanation
Indices: 36123--36342 Score: 243
Period size: 58 Copynumber: 3.9 Consensus size: 56
36113 ATTGGTAATC
* * *
36123 ATGCCTCTGTGTTTAGGGACTT-TAATATAGGTACCCTTGTGCTTGAGGACTTTGATGTAG
1 ATGCCTCTGTGTTTAGGGACTTATAA-AT--G--CCCTTGTGTTTGAGGACTTTGATATAA
* * * * * *
36183 ATGCCTCTGTGCTTAGGG----ATGAATACCCTTGTGTTTGAGGACTTTTGAGAGAG
1 ATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGAC-TTTGATATAA
*
36236 GTGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTGATATATA
1 ATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTGATATA-A
36293 ATTGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTT
1 A-TGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTT
36343 TAATTGTTGG
Statistics
Matches: 137, Mismatches: 15, Indels: 18
0.81 0.09 0.11
Matches are distributed among these distances:
52 16 0.12
53 23 0.17
56 9 0.07
57 24 0.18
58 48 0.35
60 17 0.12
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (56 bp):
ATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTGATATAA
Found at i:40001 original size:7 final size:7
Alignment explanation
Indices: 39981--40024 Score: 70
Period size: 7 Copynumber: 6.0 Consensus size: 7
39971 AGTATTTGAA
39981 TATTTGG
1 TATTTGG
39988 ATATTTGG
1 -TATTTGG
39996 TATTTGG
1 TATTTGG
40003 TATTTGG
1 TATTTGG
40010 ATATTTGG
1 -TATTTGG
40018 TATTTGG
1 TATTTGG
40025 GTATGTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 21 0.60
8 14 0.40
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (7 bp):
TATTTGG
Found at i:40001 original size:15 final size:15
Alignment explanation
Indices: 39972--40024 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
39962 AATCTGATGA
*
39972 GTATTTGAATATTTG
1 GTATTTGGATATTTG
39987 GATATTTGG-TATTTG
1 G-TATTTGGATATTTG
40002 GTATTTGGATATTTG
1 GTATTTGGATATTTG
40017 GTATTTGG
1 GTATTTGG
40025 GTATGTATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
14 7 0.20
15 22 0.63
16 6 0.17
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (15 bp):
GTATTTGGATATTTG
Found at i:40009 original size:22 final size:22
Alignment explanation
Indices: 39982--40024 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
39972 GTATTTGAAT
39982 ATTTGGATATTTGGTATTTGGT
1 ATTTGGATATTTGGTATTTGGT
40004 ATTTGGATATTTGGTATTTGG
1 ATTTGGATATTTGGTATTTGG
40025 GTATGTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (22 bp):
ATTTGGATATTTGGTATTTGGT
Found at i:46620 original size:11 final size:11
Alignment explanation
Indices: 46604--46634 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
46594 ATTTAGCATG
46604 TCTTTTGTTCA
1 TCTTTTGTTCA
46615 TCTTTTGTTCA
1 TCTTTTGTTCA
*
46626 ACTTTTGTT
1 TCTTTTGTT
46635 GGCCTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.65
Consensus pattern (11 bp):
TCTTTTGTTCA
Found at i:55379 original size:6 final size:6
Alignment explanation
Indices: 55368--55392 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55358 CAGGTTGCAC
55368 CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT C
55393 TAGCCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:55453 original size:38 final size:38
Alignment explanation
Indices: 55396--55581 Score: 286
Period size: 38 Copynumber: 4.9 Consensus size: 38
55386 CACAATCTAG
55396 CCAACAG-TTAA-CCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
55432 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
55470 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTTA
1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
55510 CCATCAGTTTAACCCCCTGAGGCGCGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * * *
55548 CCATCAGTTTAAACCCCTGAGCCGCGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
55582 ATGCACAGCC
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
36 7 0.05
37 4 0.03
38 64 0.45
39 61 0.43
40 6 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:55554 original size:77 final size:76
Alignment explanation
Indices: 55396--55581 Score: 288
Period size: 77 Copynumber: 2.4 Consensus size: 76
55386 CACAATCTAG
55396 CCAA-CAG-TTAACCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGG
1 CCAATCAGTTTAACCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGG
55459 GTCCACTCTTA
66 GTCCACTCTTA
* *
55470 CCAATCAGTTTAACCCCCTGAGGCACGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGCGC
1 CCAATCAGTTTAA-CCCCTGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCAC
55535 GGGTCCACTCTTA
64 GGGTCCACTCTTA
* *
55548 CC-ATCAGTTTAAACCCCTGAGCCGCGGGTCCACT
1 CCAATCAGTTT-AACCCCTGAGGCACGGGTCCACT
55582 ATGCACAGCC
Statistics
Matches: 103, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
74 4 0.04
75 3 0.03
76 4 0.04
77 49 0.48
78 43 0.42
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (76 bp):
CCAATCAGTTTAACCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGG
GTCCACTCTTA
Found at i:58689 original size:11 final size:11
Alignment explanation
Indices: 58673--58704 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
58663 GAAGTTCGTG
58673 TTTGAAGATTA
1 TTTGAAGATTA
*
58684 TTTGAAGATAA
1 TTTGAAGATTA
58695 TTTGAAGATT
1 TTTGAAGATT
58705 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:60073 original size:6 final size:6
Alignment explanation
Indices: 60062--60099 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
60052 ATAATTGCCA
60062 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
60100 TTTTGTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TAGATT
Found at i:62686 original size:6 final size:6
Alignment explanation
Indices: 62675--62712 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
62665 ATAATTGCCA
62675 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
62713 TTTTGTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TAGATT
Done.