Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016008.1 Corchorus capsularis cultivar CVL-1 contig16029, 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: 95117
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:9115 original size:18 final size:18
Alignment explanation
Indices: 9073--9109 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9063 TCCTCGGGAG
* *
9073 CTACTTTCGTGTCAGGAC
1 CTACTTCCGTGTCAAGAC
9091 CTACTTCCGTGTCAAGAC
1 CTACTTCCGTGTCAAGAC
9109 C
1 C
9110 AGCTTCTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (18 bp):
CTACTTCCGTGTCAAGAC
Found at i:31828 original size:121 final size:121
Alignment explanation
Indices: 31658--31887 Score: 433
Period size: 121 Copynumber: 1.9 Consensus size: 121
31648 GTAATCGATT
31658 ACTTTTTGCACCGGAAAAACTGGATCTTCCTTGAAAATCCAAAACACCTGTCGTGAATCATGTTG
1 ACTTTTTGCACCGGAAAAACTGGATCTTCCTTGAAAATCCAAAACACCTGTCGTGAATCATGTTG
*
31723 ATGTCTCGATATCACGCTCATCACTCCCTCGTTGTCGCTTGTTCATCGAATCAATC
66 ATGTCTCGATATCACGCCCATCACTCCCTCGTTGTCGCTTGTTCATCGAATCAATC
*
31779 ACTTTTTGCACCGGAAAAACTGGATCTTCCTTGAAAATCCAAAATACCTGTCGTGAATCATGTTG
1 ACTTTTTGCACCGGAAAAACTGGATCTTCCTTGAAAATCCAAAACACCTGTCGTGAATCATGTTG
*
31844 ATGTCTCGCTATCACGCCCATCACTCCCTCGTTGTCGCTTGTTC
66 ATGTCTCGATATCACGCCCATCACTCCCTCGTTGTCGCTTGTTC
31888 TTCCAAACAA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 106 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (121 bp):
ACTTTTTGCACCGGAAAAACTGGATCTTCCTTGAAAATCCAAAACACCTGTCGTGAATCATGTTG
ATGTCTCGATATCACGCCCATCACTCCCTCGTTGTCGCTTGTTCATCGAATCAATC
Found at i:32799 original size:32 final size:33
Alignment explanation
Indices: 32759--32830 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
32749 CAAAGTTTAT
*
32759 TTTA-CATGCATAATCT-CTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
32790 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
32823 TTTATCAT
1 TTTATCAT
32831 TAAAAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 4 0.11
32 12 0.32
33 22 0.58
ACGTcount: A:0.19, C:0.29, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Found at i:32905 original size:33 final size:33
Alignment explanation
Indices: 32863--32967 Score: 210
Period size: 33 Copynumber: 3.2 Consensus size: 33
32853 ACTACCTTGT
32863 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
32896 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
32929 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
32962 ATATTA
1 ATATTA
32968 CTTTGACACC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (33 bp):
ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
Found at i:33933 original size:42 final size:42
Alignment explanation
Indices: 33886--33969 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
33876 CGCGGTCGTG
* * *
33886 ATCGTGATCGTAGCTCTGGCTATAATGGTGATCATTTGAAAA
1 ATCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAA
* *
33928 ATCGTGGTCGTAGCTATGGATATAATGTTGATCATTCGAAAA
1 ATCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAA
33970 CATATCTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (42 bp):
ATCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAA
Found at i:38695 original size:31 final size:31
Alignment explanation
Indices: 38647--38705 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
38637 AGTTTGGAGA
* * *
38647 AACTTTTGAAATGCCTATTGTACCCTTATTT
1 AACTTTTAAAATACCTATTATACCCTTATTT
*
38678 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATACCCTTA
38706 CTTATCTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATACCCTTATTT
Found at i:40195 original size:22 final size:20
Alignment explanation
Indices: 40169--40220 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
40159 ATAAAATAAA
40169 AATAATATATTATTATATTATT
1 AATAATATATTATTATA--ATT
* **
40191 AATAAGATAAAATTATAATT
1 AATAATATATTATTATAATT
40211 -ATAATATATT
1 AATAATATATT
40221 GAATAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
22 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AATAATATATTATTATAATT
Found at i:40201 original size:33 final size:30
Alignment explanation
Indices: 40157--40231 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 30
40147 AGTATTTTCA
*
40157 TAATAAAATAAAAATAATATATTATTATATTAT
1 TAATAAAAT-AAAATAATA-ATTATAATA-TAT
* *
40190 TAATAAGATAAAATTATAATTATAATATAT
1 TAATAAAATAAAATAATAATTATAATATAT
40220 TGAATAATAATA
1 T-AATAA-AATA
40232 CTCCTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 4 0.11
31 13 0.36
32 11 0.31
33 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (30 bp):
TAATAAAATAAAATAATAATTATAATATAT
Found at i:50235 original size:19 final size:19
Alignment explanation
Indices: 50208--50244 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50198 AAACTTATCT
*
50208 ATATGCTATAGTACTAATA
1 ATATACTATAGTACTAATA
*
50227 ATATACTATAGTATTAAT
1 ATATACTATAGTACTAAT
50245 TAAAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATACTATAGTACTAATA
Found at i:50315 original size:4 final size:4
Alignment explanation
Indices: 50306--50330 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
50296 TAAAATTTGT
50306 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
50331 AACAATCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:55284 original size:109 final size:109
Alignment explanation
Indices: 55017--55290 Score: 446
Period size: 108 Copynumber: 2.5 Consensus size: 109
55007 ACTATTATAG
* * *
55017 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
55082 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
62 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
55130 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
55194 TTTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTTACCAAAAAATTTGGATATACTAAAA-TTTTTCTAATATACAA
55239 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-AATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATA
55291 TATATATTTT
Statistics
Matches: 155, Mismatches: 4, Indels: 9
0.92 0.02 0.05
Matches are distributed among these distances:
108 59 0.38
109 59 0.38
110 2 0.01
113 35 0.23
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
Found at i:63240 original size:13 final size:13
Alignment explanation
Indices: 63219--63249 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
63209 CCGCTAGCAG
*
63219 TTTTATCTTTTTT
1 TTTTTTCTTTTTT
63232 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
63245 TTTTT
1 TTTTT
63250 CATTGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:64248 original size:32 final size:33
Alignment explanation
Indices: 64211--64279 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 33
64201 CAGTTATTGG
*
64211 GAAATTATTG-AAGAAGATCCACGTATGTGAAA
1 GAAATTATTGAAAAAAGATCCACGTATGTGAAA
64243 GAAATTATTGAAAAAAAGATCCACGTATGTGAAA
1 GAAATTATTG-AAAAAAGATCCACGTATGTGAAA
64277 GAA
1 GAA
64280 GATCCAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 10 0.29
34 24 0.71
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (33 bp):
GAAATTATTGAAAAAAGATCCACGTATGTGAAA
Found at i:64283 original size:20 final size:20
Alignment explanation
Indices: 64221--64285 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
64211 GAAATTATTG
64221 AAGAAGATCCACGTATGTGA
1 AAGAAGATCCACGTATGTGA
64241 AAGAA-AT-----TAT-TGAA
1 AAGAAGATCCACGTATGTG-A
*
64255 AAAAAGATCCACGTATGTGA
1 AAGAAGATCCACGTATGTGA
64275 AAGAAGATCCA
1 AAGAAGATCCA
64286 AGGAAGATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
13 2 0.06
14 8 0.23
15 2 0.06
19 2 0.06
20 19 0.54
21 2 0.06
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGAAGATCCACGTATGTGA
Found at i:66549 original size:20 final size:20
Alignment explanation
Indices: 66524--66564 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
66514 GGAGGGAGAT
66524 ATAAGAGGGATAAAATTGGA
1 ATAAGAGGGATAAAATTGGA
66544 ATAAGAGGGATAAAATTGGA
1 ATAAGAGGGATAAAATTGGA
66564 A
1 A
66565 AGAGAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (20 bp):
ATAAGAGGGATAAAATTGGA
Found at i:66576 original size:19 final size:20
Alignment explanation
Indices: 66524--66577 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
66514 GGAGGGAGAT
*
66524 ATAAGAGGGATAAAATTGGA
1 ATAAGAGAGATAAAATTGGA
*
66544 ATAAGAGGGATAAAATTGG-
1 ATAAGAGAGATAAAATTGGA
66563 A-AAGAGAAGATAAAA
1 ATAAGAG-AGATAAAA
66578 ATTTATAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 19 0.59
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.17
Consensus pattern (20 bp):
ATAAGAGAGATAAAATTGGA
Found at i:67072 original size:113 final size:112
Alignment explanation
Indices: 66840--67068 Score: 289
Period size: 112 Copynumber: 2.0 Consensus size: 112
66830 TTCTCAATTG
* * ** * *
66840 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGTTGGAGAAGT
1 ACTTTGATAGAGTAGTAGAATTACTAAAAGATCCCTACCAAGGATTAATGATGAGTTAGAGAACT
66905 AATTTTTTTCGTCTTTACCTACCTAACAGATTACTTAAATGTCCTAA
66 AATTTTTTTCGTCTTTACCTACCTAACAGATTACTTAAATGTCCTAA
* ** **
66952 ACTTTGATAGAGTAGTAGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAAC
1 ACTTTGATAGAGTAGTAGAATTACTAAAAGATCCCTACCAAGGATTAATGAT-GAGTTAGAGAAC
* * * ** *
67017 TTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGT-CTTA
65 TAATTTTTTTCGTCTTTACCTACCTAACAGATTACTTAAATGTCCTAA
67064 ACTTT
1 ACTTT
67069 TGATTCTTGA
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
112 51 0.52
113 48 0.48
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (112 bp):
ACTTTGATAGAGTAGTAGAATTACTAAAAGATCCCTACCAAGGATTAATGATGAGTTAGAGAACT
AATTTTTTTCGTCTTTACCTACCTAACAGATTACTTAAATGTCCTAA
Found at i:68986 original size:2 final size:2
Alignment explanation
Indices: 68979--69011 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
68969 TATCTATTCC
68979 AT AT AT AT GAT 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
69012 CTGCACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76243 original size:48 final size:48
Alignment explanation
Indices: 76172--76274 Score: 197
Period size: 48 Copynumber: 2.1 Consensus size: 48
76162 ATGATCCTTG
*
76172 TACGAATCTTAGACCAAGGGCAAATGTGGTGAATCCTGGTTTGAAGGT
1 TACGAACCTTAGACCAAGGGCAAATGTGGTGAATCCTGGTTTGAAGGT
76220 TACGAACCTTAGACCAAGGGCAAATGTGGTGAATCCTGGTTTGAAGGT
1 TACGAACCTTAGACCAAGGGCAAATGTGGTGAATCCTGGTTTGAAGGT
76268 TACGAAC
1 TACGAAC
76275 ATGATGGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (48 bp):
TACGAACCTTAGACCAAGGGCAAATGTGGTGAATCCTGGTTTGAAGGT
Found at i:85033 original size:25 final size:25
Alignment explanation
Indices: 85004--85054 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
84994 CTTAAGGGAA
85004 CTACTGATTACATGCTATGTTATCG
1 CTACTGATTACATGCTATGTTATCG
85029 CTACTGATTACATGCTATGTTATCG
1 CTACTGATTACATGCTATGTTATCG
85054 C
1 C
85055 GGTTCAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (25 bp):
CTACTGATTACATGCTATGTTATCG
Found at i:87839 original size:22 final size:20
Alignment explanation
Indices: 87812--87851 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
87802 CAAAGTAAAA
87812 ACTACTTATTTGAAAGATTACT
1 ACTACTTATTT-AAA-ATTACT
87834 ACTACTTATTTAAAATTA
1 ACTACTTATTTAAAATTA
87852 TATATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (20 bp):
ACTACTTATTTAAAATTACT
Done.