Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018277.1 Corchorus olitorius cultivar O-4 contig18310, 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: 4886
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:1445 original size:618 final size:618
Alignment explanation
Indices: 269--1474 Score: 2358
Period size: 618 Copynumber: 2.0 Consensus size: 618
259 GTCCATATGA
269 AGAAGAGAGTAAACTTAATTTTCTGTTTAAGTGTTACACACTTTAGAAGAGAAAACAAAATTGAA
1 AGAAGAGAGTAAACTTAATTTTCTGTTTAAGTGTTACACACTTTAGAAGAGAAAACAAAATTGAA
334 GCTATTGCACCTGTCCATGTACAAACTAATATTTACTATTTATTGCCAACTTTAGGGCATATGCT
66 GCTATTGCACCTGTCCATGTACAAACTAATATTTACTATTTATTGCCAACTTTAGGGCATATGCT
399 CAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTTCGAAATTTT
131 CAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTTCGAAATTTT
464 CCACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAGTAGATTTCTGAACGCCCGA
196 CCACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAGTAGATTTCTGAACGCCCGA
529 CGTGCCAGCCCTTTTATGTAATTCCAAGGGTTTTTAACCAGCTGAATGTGAAAGCATTTATTAAC
261 CGTGCCAGCCCTTTTATGTAATTCCAAGGGTTTTTAACCAGCTGAATGTGAAAGCATTTATTAAC
594 CATAAAATCATGTATTATTTATTTACTAAGAAGACCCTTAATTAGTTTCTCACCATTCATTTTGG
326 CATAAAATCATGTATTATTTATTTACTAAGAAGACCCTTAATTAGTTTCTCACCATTCATTTTGG
659 TCTTTTACCACTTTTTTGGAAGACCCAATTACCCACTTTGTGCCCTCTTTTTGTTCTTCCTAATT
391 TCTTTTACCACTTTTTTGGAAGACCCAATTACCCACTTTGTGCCCTCTTTTTGTTCTTCCTAATT
724 TGATTATTTCTGTAATTTTATGTGTAAAACCCATCAAAGTCTTCAGACTAATTGGTTTTGTTTTA
456 TGATTATTTCTGTAATTTTATGTGTAAAACCCATCAAAGTCTTCAGACTAATTGGTTTTGTTTTA
789 ATTTAATGATTTTCTTTTAAAAGATAAAAACGTCTCTCATCTTTCTCAAACTATAATGATAGAAA
521 ATTTAATGATTTTCTTTTAAAAGATAAAAACGTCTCTCATCTTTCTCAAACTATAATGATAGAAA
854 GAATTTAATTACAGAAATATGCTCAATGTTAAT
586 GAATTTAATTACAGAAATATGCTCAATGTTAAT
* * *
887 AGAAGAGAGTAAATTTAGTTTTCTGTTTAAGTGTTACACACTTTAGAAGAGGAAACAAAATTGAA
1 AGAAGAGAGTAAACTTAATTTTCTGTTTAAGTGTTACACACTTTAGAAGAGAAAACAAAATTGAA
952 GCTATTGCACCTGTCCATGTACAAACTAATATTTACTATTTATTGCCAACTTTAGGGCATATGCT
66 GCTATTGCACCTGTCCATGTACAAACTAATATTTACTATTTATTGCCAACTTTAGGGCATATGCT
1017 CAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTTCGAAATTTT
131 CAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTTCGAAATTTT
1082 CCACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAGTAGATTTCTGAACGCCCGA
196 CCACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAGTAGATTTCTGAACGCCCGA
1147 CGTGCCAGCCCTTTTATGTAATTCCAAGGGTTTTTAACCAGCTGAATGTGAAAGCATTTATTAAC
261 CGTGCCAGCCCTTTTATGTAATTCCAAGGGTTTTTAACCAGCTGAATGTGAAAGCATTTATTAAC
1212 CATAAAATCATGTATTATTTATTTACTAAGAAGACCCTTAATTAGTTTCTCACCATTCATTTTGG
326 CATAAAATCATGTATTATTTATTTACTAAGAAGACCCTTAATTAGTTTCTCACCATTCATTTTGG
*
1277 TCTTTTACCACTTTTTTGGAAGACCCATTTACCCACTTTGTGCCCTCTTTTTGTTCTTCCTAATT
391 TCTTTTACCACTTTTTTGGAAGACCCAATTACCCACTTTGTGCCCTCTTTTTGTTCTTCCTAATT
*
1342 TGATTATTTCTGTAATTTTCTGTGTAAAACCCATCAAAGTCTTCAGACTAATTGGTTTTGTTTTA
456 TGATTATTTCTGTAATTTTATGTGTAAAACCCATCAAAGTCTTCAGACTAATTGGTTTTGTTTTA
*
1407 ATTTAATGATTTTCTTTTAAAAGATAAAAACGTCTCTCATCTTTTTCAAACTATAATGATAGAAA
521 ATTTAATGATTTTCTTTTAAAAGATAAAAACGTCTCTCATCTTTCTCAAACTATAATGATAGAAA
1472 GAA
586 GAA
1475 CTATAATGAT
Statistics
Matches: 582, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
618 582 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (618 bp):
AGAAGAGAGTAAACTTAATTTTCTGTTTAAGTGTTACACACTTTAGAAGAGAAAACAAAATTGAA
GCTATTGCACCTGTCCATGTACAAACTAATATTTACTATTTATTGCCAACTTTAGGGCATATGCT
CAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTTCGAAATTTT
CCACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAGTAGATTTCTGAACGCCCGA
CGTGCCAGCCCTTTTATGTAATTCCAAGGGTTTTTAACCAGCTGAATGTGAAAGCATTTATTAAC
CATAAAATCATGTATTATTTATTTACTAAGAAGACCCTTAATTAGTTTCTCACCATTCATTTTGG
TCTTTTACCACTTTTTTGGAAGACCCAATTACCCACTTTGTGCCCTCTTTTTGTTCTTCCTAATT
TGATTATTTCTGTAATTTTATGTGTAAAACCCATCAAAGTCTTCAGACTAATTGGTTTTGTTTTA
ATTTAATGATTTTCTTTTAAAAGATAAAAACGTCTCTCATCTTTCTCAAACTATAATGATAGAAA
GAATTTAATTACAGAAATATGCTCAATGTTAAT
Found at i:1478 original size:18 final size:18
Alignment explanation
Indices: 1455--1492 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1445 ATCTTTTTCA
1455 AACTATAATGATAGAAAG
1 AACTATAATGATAGAAAG
1473 AACTATAATGATAGAAAG
1 AACTATAATGATAGAAAG
1491 AA
1 AA
1493 TTTAATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (18 bp):
AACTATAATGATAGAAAG
Found at i:2174 original size:17 final size:19
Alignment explanation
Indices: 2144--2179 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2134 AGTAGTTTTT
2144 GGCAGTTCTTTTTA-AATG
1 GGCAGTTCTTTTTAGAATG
2162 GGCAGTT-TTTTTAGAATG
1 GGCAGTTCTTTTTAGAATG
2180 ATATAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (19 bp):
GGCAGTTCTTTTTAGAATG
Found at i:2240 original size:19 final size:20
Alignment explanation
Indices: 2216--2253 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2206 ATTTATCTTG
*
2216 AAATGGGTAG-TTTTATTTA
1 AAATGGATAGTTTTTATTTA
2235 AAATGGATAGTTTTTATTT
1 AAATGGATAGTTTTTATTT
2254 TGTTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
AAATGGATAGTTTTTATTTA
Found at i:2469 original size:31 final size:29
Alignment explanation
Indices: 2398--2472 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
2388 GCCGCAAAAT
*
2398 GCAATTTGGGATATAACGTTACAAAACAA
1 GCAATTTAGGATATAACGTTACAAAACAA
* *
2427 ACAATTAAGGATATAACGTTACGAAAA-ATGA
1 GCAATTTAGGATATAACGTTAC-AAAACA--A
2458 GCAATTTAGGATATA
1 GCAATTTAGGATATA
2473 GTCCGTTAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 20 0.53
30 4 0.11
31 14 0.37
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (29 bp):
GCAATTTAGGATATAACGTTACAAAACAA
Found at i:2668 original size:29 final size:29
Alignment explanation
Indices: 2602--2708 Score: 133
Period size: 29 Copynumber: 3.6 Consensus size: 29
2592 CCCTTACTGA
2602 TTATATCCTTAATTGCTTGAAATCAAAAACG
1 TTATATCCTTAATTGCTT-AAAT-AAAAACG
*
2633 TCATATCCTTAATTGCTTAAATAAAAACG
1 TTATATCCTTAATTGCTTAAATAAAAACG
*** ***
2662 TTATATCCTTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTAAATAAAAACG
2691 TTATATCCTTAATTGCTT
1 TTATATCCTTAATTGCTT
2709 GCGGCTGAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 47 0.69
30 4 0.06
31 17 0.25
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTAAATAAAAACG
Found at i:2706 original size:58 final size:59
Alignment explanation
Indices: 2629--2740 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
2619 TGAAATCAAA
*
2629 AACGTCATATCCTTAATTGCTT-AAATAAAAACGTTATATCCTTAATTGCTTGTTTTGT
1 AACGTCATATCCTTAATTGCTTCAAATAAAAACGTTATATCCTAAATTGCTTGTTTTGT
* *** *
2687 AACGTTATATCCTTAATTGCTTGCGGCTGAAAACGTTATATCCTAAATTGCTTG
1 AACGTCATATCCTTAATTGCTT-CAAATAAAAACGTTATATCCTAAATTGCTTG
2741 CTTATCATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 21 0.46
60 25 0.54
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (59 bp):
AACGTCATATCCTTAATTGCTTCAAATAAAAACGTTATATCCTAAATTGCTTGTTTTGT
Found at i:2725 original size:31 final size:31
Alignment explanation
Indices: 2656--2741 Score: 113
Period size: 29 Copynumber: 2.8 Consensus size: 31
2646 TGCTTAAATA
***
2656 AAAACGTTATATCCTTAATTGCTTG-TTTTG
1 AAAACGTTATATCCTTAATTGCTTGCGGCTG
*
2686 -TAACGTTATATCCTTAATTGCTTGCGGCTG
1 AAAACGTTATATCCTTAATTGCTTGCGGCTG
*
2716 AAAACGTTATATCCTAAATTGCTTGC
1 AAAACGTTATATCCTTAATTGCTTGC
2742 TTATCATCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 23 0.48
30 2 0.04
31 23 0.48
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (31 bp):
AAAACGTTATATCCTTAATTGCTTGCGGCTG
Found at i:3793 original size:31 final size:31
Alignment explanation
Indices: 3699--3835 Score: 127
Period size: 31 Copynumber: 4.5 Consensus size: 31
3689 GTCAAATAAT
* * **
3699 CAATTTAGGATATAACGTTTGCTG-TCACAAG
1 CAATTAAGGATATAACGTTTTC-GATTTCAAG
* * ***
3730 CAATTAAGGATATAAC-ATTAC-AAAACAAG
1 CAATTAAGGATATAACGTTTTCGATTTCAAG
* *
3759 CAATTAATGATATAACGTTTTCTATTTCAAG
1 CAATTAAGGATATAACGTTTTCGATTTCAAG
*
3790 CAATTAAGGATATGACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTTCGATTTCAAG
*
3821 CAATCAAGGATATAA
1 CAATTAAGGATATAA
3836 TCAGTTAGGC
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
29 20 0.23
30 6 0.07
31 61 0.70
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTTCGATTTCAAG
Found at i:4036 original size:29 final size:31
Alignment explanation
Indices: 3964--4030 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
3954 TCTAACGGAC
3964 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
*
3995 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
4024 TATATCC
1 TATATCC
4031 CAAATTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Found at i:4738 original size:124 final size:124
Alignment explanation
Indices: 4488--4738 Score: 396
Period size: 124 Copynumber: 2.0 Consensus size: 124
4478 ATGCGATTGC
* * * *
4488 TGAAAGATGCATGCTTGTTATAATCTGATGTTGAATTTAGTGTTTTTAAGCTATTTCACATCCTA
1 TGAAAGATGCATGCTTGTCATAATCTGACGTTGAATTCAGTGTTTTAAAGCTATTTCACATCCTA
*
4553 AAAGCTTATATACATTAGCCATAACCACCCAAGCTTTACACTTTGCCGTGGCTTAATGT
66 AAAGCTTATATACATTAGCCATAACCACCAAAGCTTTACACTTTGCCGTGGCTTAATGT
4612 TGAAAGATGCATGCTTGTCATAATCTGACGTTGAATTCAGTGTTTTAAAGCTATTTCACATCCTA
1 TGAAAGATGCATGCTTGTCATAATCTGACGTTGAATTCAGTGTTTTAAAGCTATTTCACATCCTA
* ** * *
4677 AAAGCTTGTATAGGTTAGCTATAACCACCAAAAGTTTTACACTTTGCCGTGGCTTAA-GT
66 AAAGCTTATATACATTAGCCATAACCACC-AAAGCTTTACACTTTGCCGTGGCTTAATGT
4736 TGA
1 TGA
4739 TTTATCCTAC
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
124 91 0.78
125 25 0.22
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (124 bp):
TGAAAGATGCATGCTTGTCATAATCTGACGTTGAATTCAGTGTTTTAAAGCTATTTCACATCCTA
AAAGCTTATATACATTAGCCATAACCACCAAAGCTTTACACTTTGCCGTGGCTTAATGT
Done.