Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009179.1 Corchorus capsularis cultivar CVL-1 contig09200, 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: 52859
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2214 original size:18 final size:19
Alignment explanation
Indices: 2188--2227 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2178 ATAATTATTC
2188 ATTAAAAAGAATTA-TAAT
1 ATTAAAAAGAATTAGTAAT
* *
2206 ATTATAAAGATTTAGTAAT
1 ATTAAAAAGAATTAGTAAT
2225 ATT
1 ATT
2228 TTTCAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
ATTAAAAAGAATTAGTAAT
Found at i:20980 original size:16 final size:16
Alignment explanation
Indices: 20959--20995 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20949 TATATATAGG
20959 ATAGCACACATAAAGA
1 ATAGCACACATAAAGA
* *
20975 ATAGCACATATAAAGG
1 ATAGCACACATAAAGA
20991 ATAGC
1 ATAGC
20996 GCAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (16 bp):
ATAGCACACATAAAGA
Found at i:21541 original size:21 final size:21
Alignment explanation
Indices: 21517--21789 Score: 96
Period size: 21 Copynumber: 12.6 Consensus size: 21
21507 GTGAGGAAAC
21517 TGGTGGTGGTGGGGAGTGGAT
1 TGGTGGTGGTGGGGAGTGGAT
* *
21538 TGGTGGTGGCGGGGAATGGACT
1 TGGTGGTGGTGGGGAGTGGA-T
* * * *
21560 GGTGGCGGTGGTGGAGAGTGCAC
1 --TGGTGGTGGTGGGGAGTGGAT
* * * ** *
21583 TGGTGGAGGAGGAGAGTATAC
1 TGGTGGTGGTGGGGAGTGGAT
* * *
21604 TGGTGGAGGCGGTGAGTGGACT
1 TGGTGGTGGTGGGGAGTGGA-T
* * * *
21626 GGAGGTGGTGGAGGGGAATGTAT
1 --TGGTGGTGGTGGGGAGTGGAT
* * **
21649 TGGAGGTGGTGGAGAGTTTAGT
1 TGGTGGTGGTGGGGAGTGGA-T
* *
21671 GGTGGTGGTGGAGGGGAGTGGAC
1 --TGGTGGTGGTGGGGAGTGGAT
* * * * * *
21694 AGGAGGGGGTGGGGAATAGAC
1 TGGTGGTGGTGGGGAGTGGAT
* *
21715 AGGTGGTGGAGGGGAGTGGAT
1 TGGTGGTGGTGGGGAGTGGAT
* * * *
21736 TGGAGGTGGTGGGGAATAGAC
1 TGGTGGTGGTGGGGAGTGGAT
* *
21757 TGGTGGTGGAGGGGAGTAGAT
1 TGGTGGTGGTGGGGAGTGGAT
* *
21778 AGGAGGTGGTGG
1 TGGTGGTGGTGG
21790 AGATTGTACA
Statistics
Matches: 182, Mismatches: 61, Indels: 18
0.70 0.23 0.07
Matches are distributed among these distances:
21 135 0.74
22 2 0.01
23 1 0.01
24 44 0.24
ACGTcount: A:0.18, C:0.04, G:0.57, T:0.21
Consensus pattern (21 bp):
TGGTGGTGGTGGGGAGTGGAT
Found at i:21544 original size:24 final size:24
Alignment explanation
Indices: 21517--21588 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
21507 GTGAGGAAAC
21517 TGGTGGTGGTGGGGAGTGGA-T--
1 TGGTGGTGGTGGGGAGTGGACTGG
* *
21538 TGGTGGTGGCGGGGAATGGACTGG
1 TGGTGGTGGTGGGGAGTGGACTGG
* * *
21562 TGGCGGTGGTGGAGAGTGCACTGG
1 TGGTGGTGGTGGGGAGTGGACTGG
21586 TGG
1 TGG
21589 AGGAGGAGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.44
22 1 0.02
24 22 0.54
ACGTcount: A:0.11, C:0.07, G:0.58, T:0.24
Consensus pattern (24 bp):
TGGTGGTGGTGGGGAGTGGACTGG
Found at i:21675 original size:42 final size:42
Alignment explanation
Indices: 21629--21792 Score: 184
Period size: 42 Copynumber: 3.8 Consensus size: 42
21619 GTGGACTGGA
* * * * **
21629 GGTGGTGGAGGGGAATGTATTGGAGGTGGTGGAGAGTTTAGTGGT
1 GGTGGTGGAGGGGAGTGGATAGGAGGTGGTGGAGA--ATAG-ACT
* * * *
21674 GGTGGTGGAGGGGAGTGGACAGGAGGGGGTGGGGAATAGACA
1 GGTGGTGGAGGGGAGTGGATAGGAGGTGGTGGAGAATAGACT
* *
21716 GGTGGTGGAGGGGAGTGGATTGGAGGTGGTGGGGAATAGACT
1 GGTGGTGGAGGGGAGTGGATAGGAGGTGGTGGAGAATAGACT
*
21758 GGTGGTGGAGGGGAGTAGATAGGAGGTGGTGGAGA
1 GGTGGTGGAGGGGAGTGGATAGGAGGTGGTGGAGA
21793 TTGTACAGGA
Statistics
Matches: 102, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
42 70 0.69
43 3 0.03
45 29 0.28
ACGTcount: A:0.21, C:0.02, G:0.57, T:0.20
Consensus pattern (42 bp):
GGTGGTGGAGGGGAGTGGATAGGAGGTGGTGGAGAATAGACT
Found at i:21761 original size:87 final size:84
Alignment explanation
Indices: 21628--21789 Score: 216
Period size: 87 Copynumber: 1.9 Consensus size: 84
21618 AGTGGACTGG
* * ** *
21628 AGGTGGTGGAGGGGAATGTATTGGAGGTGGTGGAGAGTTTAGTGGTGGTGGTGGAGGGGAGTGGA
1 AGGTGGTGGAGGGGAATGGATTGGAGGTGGTGGAGA--ATAG-ACTGGTGGTGGAGGGGAGTAGA
21693 CAGGAGGGGGTGGGGAATAGAC
63 CAGGAGGGGGTGGGGAATAGAC
* * *
21715 AGGTGGTGGAGGGGAGTGGATTGGAGGTGGTGGGGAATAGACTGGTGGTGGAGGGGAGTAGATAG
1 AGGTGGTGGAGGGGAATGGATTGGAGGTGGTGGAGAATAGACTGGTGGTGGAGGGGAGTAGACAG
*
21780 GAGGTGGTGG
66 GAGGGGGTGG
21790 AGATTGTACA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
84 30 0.45
85 3 0.05
87 33 0.50
ACGTcount: A:0.20, C:0.02, G:0.57, T:0.20
Consensus pattern (84 bp):
AGGTGGTGGAGGGGAATGGATTGGAGGTGGTGGAGAATAGACTGGTGGTGGAGGGGAGTAGACAG
GAGGGGGTGGGGAATAGAC
Found at i:22059 original size:153 final size:153
Alignment explanation
Indices: 21757--22071 Score: 540
Period size: 153 Copynumber: 2.1 Consensus size: 153
21747 GGGAATAGAC
*
21757 TGGTGGTGGAGGGGAGTAGATAGGAGGTGGTGGAGATTGTACAGGAGGAGGCGACCGTTGCCTTG
1 TGGTGGTGGAGGGGAGTAGATAGGAGGTGATGGAGATTGTACAGGAGGAGGCGACCGTTGCCTTG
*
21822 TCATGGGTGATTCCTTATGGGGATCATCTATTGGTGCTGGGGCCGAAGGTTTTAATGGAGGGTGC
66 TCATGGGTGATTCCTTATGGGGATCATCTAATGGTGCTGGGGCCGAAGGTTTTAATGGAGGGTGC
*
21887 ATTGGTGGAGGAGAATTTACTGG
131 ATTGGTGGAGGAGAATTTACAGG
* *
21910 TGTTGGTGGAGGGGAGTAGATAGGAGGTGATGGAGATTGTACAGGAGGAGGTGACCGTTGCCTTG
1 TGGTGGTGGAGGGGAGTAGATAGGAGGTGATGGAGATTGTACAGGAGGAGGCGACCGTTGCCTTG
* * * *
21975 TCATGGGTGATTCCTTATGTGGATCGTCTAATGGTGCTGGGGCTGAAGGTTTTAATGGAGGTTGC
66 TCATGGGTGATTCCTTATGGGGATCATCTAATGGTGCTGGGGCCGAAGGTTTTAATGGAGGGTGC
*
22040 ATTGGTGGAGGAGAGTTTACAGG
131 ATTGGTGGAGGAGAATTTACAGG
22063 TGGTGGTGG
1 TGGTGGTGG
22072 TGAGTAAACT
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.19, C:0.10, G:0.43, T:0.29
Consensus pattern (153 bp):
TGGTGGTGGAGGGGAGTAGATAGGAGGTGATGGAGATTGTACAGGAGGAGGCGACCGTTGCCTTG
TCATGGGTGATTCCTTATGGGGATCATCTAATGGTGCTGGGGCCGAAGGTTTTAATGGAGGGTGC
ATTGGTGGAGGAGAATTTACAGG
Found at i:22233 original size:198 final size:194
Alignment explanation
Indices: 21890--22427 Score: 563
Period size: 198 Copynumber: 2.7 Consensus size: 194
21880 AGGGTGCATT
* *
21890 GGTGGAGGAGAATTTACTGGTGTTGGTGGAGGGGAGTAGATAGGAGGTGATGGAGATTGTACAGG
1 GGTGGAGGAGAATTTACCGGTGTTGGTGGAGGGGAATAGATAGGAGGTGA-GGAGATTGTACAGG
* ** * * *
21955 AGGAGGTGACCGTTGCCTTGTCATGGGTGATTCCTTATGTGGATCGTCTAATGGTGCTGGGGCTG
65 AGGAGGCGACCGTTGCCTCATCATGGGTGATTCCTTATGTGAATCGTCCAATGGTGCTGGGGCTC
* *
22020 AAGGTTTTAATGGAGGTTGCATTGGTGGAGGAGAGTTTACAGGTGGTGGTGGTGAGTAAACTGCA
130 AAGGTTTTAATGGAGGGTGCATTGGTGGAGGAGAGTATACAGGTGGTGGTGGTGAGTAAACTGCA
* *
22085 GGTGGAGGAGAATTTACCGGTGTTGGTGGTGGAGGGGAATGGATTGGAGGTG-GCGAGGATTGTA
1 GGTGGAGGAGAATTTACCGGTG-T--TGGTGGAGGGGAATAGATAGGAGGTGAG-GA-GATTGTA
* *
22149 CAGGAGGAGGCGA-TGTTTGCCTCAT-ATTGGGTGATTCCTTATGTGAATCGTCCAATGGTTCTG
61 CAGGAGGAGGCGACCG-TTGCCTCATCA-TGGGTGATTCCTTATGTGAATCGTCCAATGGTGCTG
*
22212 GGG-TCAATGGTTTTGATGGAGGGTGCATTGGTGGAGGAGAGTATACAGGTGGTGGTGGTG-GTG
124 GGGCTCAA-GGTTTTAATGGAGGGTGCATTGGTGGAGGAGAGTATACAGGTGGTGGTGGTGAGT-
*
22275 ACTGAACTGGA
187 A---AACTGCA
** * ** * * * * *
22286 GGTGCCGGTGAACGTACTGGTACTT-GTGGTGGTGAAGAATAGACAGGTGGT--GGAGATTGTAC
1 GGTGGAGGAGAATTTACCGGT-GTTGGTGGAGG-G--GAATAGATAGGAGGTGAGGAGATTGTAC
* ** * * *
22348 AGGAGGAGGCGACCGTAGCCTTGTCATGGGTGATTCTTTATGTGGATCGTCTAATGGTGCTGGGG
62 AGGAGGAGGCGACCGTTGCCTCATCATGGGTGATTCCTTATGTGAATCGTCCAATGGTGCTGGGG
22413 C-CGAAGGTTTTAATG
127 CTC-AAGGTTTTAATG
22428 TAGGTGGTGG
Statistics
Matches: 286, Mismatches: 37, Indels: 37
0.79 0.10 0.10
Matches are distributed among these distances:
195 21 0.07
196 2 0.01
197 9 0.03
198 212 0.74
199 8 0.03
200 1 0.00
201 33 0.12
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.28
Consensus pattern (194 bp):
GGTGGAGGAGAATTTACCGGTGTTGGTGGAGGGGAATAGATAGGAGGTGAGGAGATTGTACAGGA
GGAGGCGACCGTTGCCTCATCATGGGTGATTCCTTATGTGAATCGTCCAATGGTGCTGGGGCTCA
AGGTTTTAATGGAGGGTGCATTGGTGGAGGAGAGTATACAGGTGGTGGTGGTGAGTAAACTGCA
Found at i:22524 original size:45 final size:45
Alignment explanation
Indices: 22430--22524 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
22420 TTTTAATGTA
* * * *
22430 GGTGGTGGAGAACTTACTGGTAATGGTGGGGGAGAGTATGCAGGT
1 GGTGGCGGAGAACTTACTGGTAATGGTGGGGGAGAATATACAGGC
** **
22475 GGTGGCGGAGAACTTACTGGTGGTGG-GGGTGGAGAATATATGGGC
1 GGTGGCGGAGAACTTACTGGTAATGGTGGG-GGAGAATATACAGGC
22520 GGTGG
1 GGTGG
22525 TGGGGATTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 3 0.07
45 38 0.93
ACGTcount: A:0.20, C:0.07, G:0.49, T:0.23
Consensus pattern (45 bp):
GGTGGCGGAGAACTTACTGGTAATGGTGGGGGAGAATATACAGGC
Found at i:34418 original size:12 final size:12
Alignment explanation
Indices: 34401--34432 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34391 GATCACCCGT
34401 ATAAAAGTTGCA
1 ATAAAAGTTGCA
*
34413 ATAAAACTTGCA
1 ATAAAAGTTGCA
34425 ATAAAAGT
1 ATAAAAGT
34433 ATAAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (12 bp):
ATAAAAGTTGCA
Found at i:37370 original size:45 final size:45
Alignment explanation
Indices: 37306--37395 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
37296 AAAAGTGAAA
37306 GGAGTTAATAGAAAATTACTCCTACAACAGACACTTATCTCAATC
1 GGAGTTAATAGAAAATTACTCCTACAACAGACACTTATCTCAATC
37351 GGAGTTAATAGAAAATTACTCCTACAACAGACACTTATCTCAATC
1 GGAGTTAATAGAAAATTACTCCTACAACAGACACTTATCTCAATC
37396 TAATTTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (45 bp):
GGAGTTAATAGAAAATTACTCCTACAACAGACACTTATCTCAATC
Found at i:40514 original size:11 final size:11
Alignment explanation
Indices: 40498--40522 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40488 TTAAAATCAA
40498 TATTTTATTTT
1 TATTTTATTTT
40509 TATTTTATTTT
1 TATTTTATTTT
40520 TAT
1 TAT
40523 CATTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:43502 original size:22 final size:22
Alignment explanation
Indices: 43471--43516 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
43461 TTTTAAGCAA
*
43471 TTTTAGTAATCTTATAAAATTT
1 TTTTAATAATCTTATAAAATTT
43493 TTTTAATAATCTTATAAAATTT
1 TTTTAATAATCTTATAAAATTT
43515 TT
1 TT
43517 AACCCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTAATAATCTTATAAAATTT
Found at i:44003 original size:12 final size:12
Alignment explanation
Indices: 43986--44022 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
43976 ATAAGGTTTT
43986 AGAAACCATATA
1 AGAAACCATATA
*
43998 AGAAA-CA-AGA
1 AGAAACCATATA
44008 AGAAACCATATA
1 AGAAACCATATA
44020 AGA
1 AGA
44023 TTTTTTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.11
Consensus pattern (12 bp):
AGAAACCATATA
Found at i:45971 original size:96 final size:96
Alignment explanation
Indices: 45807--46131 Score: 479
Period size: 96 Copynumber: 3.4 Consensus size: 96
45797 CATTGTTTCA
* * * * *
45807 TCCCCATTTTTGTGGAAGTAAACCATGTTGTACTTGTCGCTGAGCACTTTCGCAAGTTTGGAAGG
1 TCCCCATTATTGTGGAAGTAAACCATGGTGTACTTGTCGCCGAGCACTTTCACAAGTTCGGAAGG
*
45872 CAATTCAGGCGAAGAGTTTCCTTCTTGGGTG
66 CAATTCAGGCGAAGAGTTTCCTTCTTGGCTG
* * *
45903 TCCCCATTATTGTGGAAGTAAACCATGGTATACTTGTTGCCGAGCACTTTCACAAGTTCGGAGGG
1 TCCCCATTATTGTGGAAGTAAACCATGGTGTACTTGTCGCCGAGCACTTTCACAAGTTCGGAAGG
* *
45968 CAATTCAGGGGAAGAGTTTCTTTCTTGGCTG
66 CAATTCAGGCGAAGAGTTTCCTTCTTGGCTG
* * **
45999 TCCCCATTTTTGTGGAAGTAAACCATGGTGTACTTGTCGCCGAGCACTTCCACAAGTTCAAAAGG
1 TCCCCATTATTGTGGAAGTAAACCATGGTGTACTTGTCGCCGAGCACTTTCACAAGTTCGGAAGG
* * * *
46064 TAATTCAGGCAAAGAGTTTCCTTCCTGGTTG
66 CAATTCAGGCGAAGAGTTTCCTTCTTGGCTG
46095 TCCCCATTATTGTGGAAGTAAACCATGGTGTACTTGT
1 TCCCCATTATTGTGGAAGTAAACCATGGTGTACTTGT
46132 TTTTTAGTTC
Statistics
Matches: 204, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 204 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (96 bp):
TCCCCATTATTGTGGAAGTAAACCATGGTGTACTTGTCGCCGAGCACTTTCACAAGTTCGGAAGG
CAATTCAGGCGAAGAGTTTCCTTCTTGGCTG
Done.