Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012738.1 Corchorus capsularis cultivar CVL-1 contig12759, 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: 21745
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--37 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 TAT
4 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38 ATAAGGCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1532 original size:16 final size:16
Alignment explanation
Indices: 1511--1541 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1501 TTGAAAAATA
1511 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
1527 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
1542 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:2662 original size:199 final size:201
Alignment explanation
Indices: 1879--2863 Score: 1311
Period size: 199 Copynumber: 5.0 Consensus size: 201
1869 TTATAATAAG
* *
1879 GATTATTATACAATACAATGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
*
1944 ATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* * *
2009 AACCCTTAAA--CTATGCATGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTTT
131 AACCCTTAAACCCCA-GCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTC
2072 TTATA-A
195 TTATAGA
* * * * *
2078 GATTATTATACAATACACTGTTAG-GATAAATTCTGAACTCCATAAGCGGGATAAGAAGTAGACA
1 GATTATTATACAATACACTGTCAGTG-TAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
* ** *
2142 CATATCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGAGGACACATGT
65 CATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT
** * * *
2207 CAACCCCAAAAACCCCCGGTGCATGT--AGTCTGCTAAATTCCACTGACGGTGTATTATATAATT
130 CAA-CCCTTAAA-CCCC--AGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATT
2270 TTT-TTATA-A
191 TTTCTTATAGA
* * * *
2279 GATTATTATACAATAGACTGTCAGTGTAAATTTTGAATTCCATAAGCGGGTTAAAAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * *
2344 ATACCCTATTTCATAATTAATT-AA-A--TAATATTAATACATATTCCCTAAAGGAATACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
*
2405 AACCCTTAAACCCC-GCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
131 AACCCTTAAACCCCAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
2469 TATAGA
196 TATAGA
* * *
2475 -ATTATTATAAAATACACTGTCAGTATAAATTTTGGATTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* *
2539 ATACTCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* * * * * *
2604 AACCCTTAAACCCCAG-ATTTGCAATTTCCTAAACTCCACTGAAGGTGTATTGTATAATTTTTTT
131 AACCCTTAAACCCCAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAA-TTTTTC
2668 TTATAG-
195 TTATAGA
*
2674 GATTATTATACAATACACTGTCAGTGCAAATTTTGGACTCCATAAGC----T--G--G-TGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* *
2730 ATACCATATTTCAAAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* * * *
2795 AACTCTTAAA-CCCTGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTTCT
131 AACCCTTAAACCCCAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
2859 TATAG
196 TATAG
2864 TGAACTTATA
Statistics
Matches: 695, Mismatches: 71, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
190 15 0.02
191 110 0.16
192 6 0.01
194 39 0.06
195 89 0.13
196 10 0.01
197 34 0.05
198 1 0.00
199 201 0.29
200 62 0.09
201 83 0.12
202 38 0.05
203 1 0.00
204 6 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (201 bp):
GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
AACCCTTAAACCCCAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
TATAGA
Found at i:5578 original size:19 final size:20
Alignment explanation
Indices: 5554--5593 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5544 ATATAAATTT
5554 TAATTTATTTT-AGGGAAAA
1 TAATTTATTTTGAGGGAAAA
* *
5573 TAATTTTTTTTGAGGTAAAA
1 TAATTTATTTTGAGGGAAAA
5593 T
1 T
5594 TTTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (20 bp):
TAATTTATTTTGAGGGAAAA
Found at i:8379 original size:72 final size:71
Alignment explanation
Indices: 8262--8485 Score: 322
Period size: 72 Copynumber: 3.1 Consensus size: 71
8252 GGAATTTGAC
* * * * *
8262 GGCGGCGGGGTCTGTTGATTCAAGGCCAGGGGCGTTACTTGGTCATGTTGACAGCCAACTTCTAC
1 GGCGGTGGGGTCTGTGGATTCAAGGCCAGCGGCGTT-CTTGGTCATGTTGATAGCCAACTGCTAC
8327 GGGGAGG
65 GGGGAGG
*
8334 GGCGGTGGGGTCTGTGGATTCAAGGCCAGCCGCGCTTCTTGGTCATGTTGATAGCCAACTGCTAC
1 GGCGGTGGGGTCTGTGGATTCAAGGCCAGCGGCG-TTCTTGGTCATGTTGATAGCCAACTGCTAC
8399 GGGGAGG
65 GGGGAGG
* * * *
8406 GGCGGTAGGTTCGGTGGATTCAAGGCCAGCGGCGTTTCTTGGTCATGTTGATAGCCAACTGCTAT
1 GGCGGTGGGGTCTGTGGATTCAAGGCCAGCGGCG-TTCTTGGTCATGTTGATAGCCAACTGCTAC
*
8471 AGGGAGG
65 GGGGAGG
8478 GGCGGTGG
1 GGCGGTGG
8486 CTAACGCCGT
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 135 0.99
73 2 0.01
ACGTcount: A:0.16, C:0.20, G:0.40, T:0.24
Consensus pattern (71 bp):
GGCGGTGGGGTCTGTGGATTCAAGGCCAGCGGCGTTCTTGGTCATGTTGATAGCCAACTGCTACG
GGGAGG
Found at i:15584 original size:2 final size:2
Alignment explanation
Indices: 15577--15639 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
15567 GTTTAATAAT
*
15577 TA TA TA TA TA -A T- TA TA TA TA T- TA GA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
15614 TA TA -A TA TA TA TT TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15640 TGCTAAACGG
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
1 8 0.16
2 41 0.84
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15604 original size:21 final size:20
Alignment explanation
Indices: 15575--15640 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 20
15565 CCGTTTAATA
15575 ATTATATATATAATTATATAT
1 ATTATATAT-TAATTATATAT
*
15596 ATTAGATATT-ATTATATAT
1 ATTATATATTAATTATATAT
15615 ATAATATATATTTAATTATATAT
1 AT--TATATA-TTAATTATATAT
15638 ATT
1 ATT
15641 GCTAAACGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 11 0.28
20 1 0.03
21 14 0.36
22 2 0.05
23 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTATATATTAATTATATAT
Found at i:15615 original size:23 final size:23
Alignment explanation
Indices: 15580--15639 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 23
15570 TAATAATTAT
*
15580 ATATATAATTATATATAT--TAG
1 ATATTTAATTATATATATAATAG
*
15601 ATA-TT-ATTATATATATAATAT
1 ATATTTAATTATATATATAATAG
15622 ATATTTAATTATATATAT
1 ATATTTAATTATATATAT
15640 TGCTAAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 11 0.33
20 1 0.03
21 8 0.24
22 2 0.06
23 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTTAATTATATATATAATAG
Found at i:18066 original size:21 final size:21
Alignment explanation
Indices: 18020--18066 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
18010 TTTCATTAAC
* *
18020 TCATTAATTCTTTTATTAGAG
1 TCATTAATTATTATATTAGAG
*
18041 CCATTATATTATTATATTAG-G
1 TCATTA-ATTATTATATTAGAG
18062 TCATT
1 TCATT
18067 TTCTTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (21 bp):
TCATTAATTATTATATTAGAG
Found at i:20943 original size:21 final size:24
Alignment explanation
Indices: 20894--20945 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
20884 TATTTTAGAT
20894 ATAATATATATTCATAAATAAATA
1 ATAATATATATTCATAAATAAATA
*
20918 ATAAT-TATATT-TTAAATACAAATA
1 ATAATATATATTCATAAAT--AAATA
20942 ATAA
1 ATAA
20946 GTTAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 6 0.24
24 14 0.56
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATATATATTCATAAATAAATA
Done.