Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024556.1 Corchorus olitorius cultivar O-4 contig24589, 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: 44111
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:433 original size:39 final size:40
Alignment explanation
Indices: 363--443 Score: 94
Period size: 39 Copynumber: 2.0 Consensus size: 40
353 ATACCTAAGA
*
363 ATTTAATTAATATAAGCATTTCAATT-TT-TATAGTATTAC
1 ATTTAATTAATATAAACATTTCAATTATTATATA-TATTAC
* * * *
402 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAACATTTCAATTATTATATATATTAC
442 AT
1 AT
444 AGGAATTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 21 0.60
40 10 0.29
41 4 0.11
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATATAAACATTTCAATTATTATATATATTAC
Found at i:1404 original size:33 final size:33
Alignment explanation
Indices: 1362--1427 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1352 CACCTTGTAA
1362 CCTTAACTTTTTTTATTCGTGAGAAGATTTATT
1 CCTTAACTTTTTTTATTCGTGAGAAGATTTATT
*
1395 CCTTAACTTTTTTTATTTGTGAGAAGATTTATT
1 CCTTAACTTTTTTTATTCGTGAGAAGATTTATT
1428 TTTGTAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.53
Consensus pattern (33 bp):
CCTTAACTTTTTTTATTCGTGAGAAGATTTATT
Found at i:1471 original size:58 final size:58
Alignment explanation
Indices: 1402--1517 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
1392 ATTCCTTAAC
*
1402 TTTTTTTATTTGTGAGAAGATTTATTTTTGTAAAAGAATAATAAAAATATATGAATAT
1 TTTTTTTATTTGTGAGAAAATTTATTTTTGTAAAAGAATAATAAAAATATATGAATAT
1460 TTTTTTTATTTGTGAGAAAATTTATTTTTGTAAAAGAATAATAAAAATATATGAATAT
1 TTTTTTTATTTGTGAGAAAATTTATTTTTGTAAAAGAATAATAAAAATATATGAATAT
1518 AAAAATACAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (58 bp):
TTTTTTTATTTGTGAGAAAATTTATTTTTGTAAAAGAATAATAAAAATATATGAATAT
Found at i:17989 original size:33 final size:34
Alignment explanation
Indices: 17922--18000 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
17912 TATTTCTAAA
17922 TTTAGACATAGGATATGGTGCAATAAAAAAAAAC
1 TTTAGACATAGGATATGGTGCAATAAAAAAAAAC
* *
17956 TTTAGATATAGGATATGGTGCAGT-AAAAAAAAC
1 TTTAGACATAGGATATGGTGCAATAAAAAAAAAC
17989 TTTAGACATAGG
1 TTTAGACATAGG
18001 GCGTTTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 20 0.48
34 22 0.52
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.27
Consensus pattern (34 bp):
TTTAGACATAGGATATGGTGCAATAAAAAAAAAC
Found at i:23856 original size:25 final size:25
Alignment explanation
Indices: 23822--23870 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
23812 GATTGGTTTG
23822 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
23847 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
23871 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:24278 original size:23 final size:23
Alignment explanation
Indices: 24252--24297 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
24242 GAACCTCTAC
24252 CCGTTTGTAATCCTGATTCGTGA
1 CCGTTTGTAATCCTGATTCGTGA
24275 CCGTTTGTAATCCTGATTCGTGA
1 CCGTTTGTAATCCTGATTCGTGA
24298 ATGAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (23 bp):
CCGTTTGTAATCCTGATTCGTGA
Found at i:26923 original size:31 final size:31
Alignment explanation
Indices: 26888--27006 Score: 175
Period size: 31 Copynumber: 3.8 Consensus size: 31
26878 GACATGTAGG
*
26888 ACGCCATGTGTACCAAAAAGTAACACATATC
1 ACGCCATGTGTACCAAAAAGTGACACATATC
26919 ACGCCATGTGTACCAAAAAGTGACACATATC
1 ACGCCATGTGTACCAAAAAGTGACACATATC
* **
26950 ACGCCATGTGTATCAAAAAGTGACACATGGC
1 ACGCCATGTGTACCAAAAAGTGACACATATC
* **
26981 ATGCCATGTGTTTCAAAAAGTGACAC
1 ACGCCATGTGTACCAAAAAGTGACAC
27007 GTGGCATGCC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (31 bp):
ACGCCATGTGTACCAAAAAGTGACACATATC
Found at i:28494 original size:4 final size:4
Alignment explanation
Indices: 28485--28519 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
28475 AGGATAGCAA
28485 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
28520 AAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:32993 original size:31 final size:32
Alignment explanation
Indices: 32957--33020 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
32947 GAGAGAAGAT
32957 TGGGAGGCTC-AAAAAATGTCCTGGGGTAGTA
1 TGGGAGGCTCAAAAAAATGTCCTGGGGTAGTA
32988 TGGGAGGCTCAAAAAAATGTCCTGGGGTAGTA
1 TGGGAGGCTCAAAAAAATGTCCTGGGGTAGTA
33020 T
1 T
33021 TGATTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 10 0.31
32 22 0.69
ACGTcount: A:0.30, C:0.12, G:0.34, T:0.23
Consensus pattern (32 bp):
TGGGAGGCTCAAAAAAATGTCCTGGGGTAGTA
Found at i:33272 original size:10 final size:10
Alignment explanation
Indices: 33259--33300 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
33249 ATTAGTATAT
33259 TCCATAAAAA
1 TCCATAAAAA
33269 TCCA-AAAAA
1 TCCATAAAAA
** *
33278 GACATAAACA
1 TCCATAAAAA
33288 TCCATAAAAA
1 TCCATAAAAA
33298 TCC
1 TCC
33301 CAGAATATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.57, C:0.24, G:0.02, T:0.17
Consensus pattern (10 bp):
TCCATAAAAA
Found at i:35448 original size:27 final size:27
Alignment explanation
Indices: 35411--35467 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
35401 CAGGCTCCCT
*
35411 CTCCATATACATCCGAGCAGCCTCAGC
1 CTCCATATACATCCGAGCAGCCTCAAC
*
35438 CTCCCTATACATCCGAGCAGCCTCAAC
1 CTCCATATACATCCGAGCAGCCTCAAC
35465 CTC
1 CTC
35468 TTTATCCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.44, G:0.12, T:0.19
Consensus pattern (27 bp):
CTCCATATACATCCGAGCAGCCTCAAC
Found at i:35625 original size:26 final size:27
Alignment explanation
Indices: 35571--35626 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
35561 CCTTCCAGCC
* **
35571 TAAATAAAAAATAATAATTAATTTTAG
1 TAAATAAAAAATAATAAGTAATTACAG
*
35598 TAAAT-AAAAATTATAAGTAATTACAG
1 TAAATAAAAAATAATAAGTAATTACAG
35624 TAA
1 TAA
35627 TATATAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (27 bp):
TAAATAAAAAATAATAAGTAATTACAG
Found at i:41235 original size:16 final size:16
Alignment explanation
Indices: 41210--41240 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41200 CAGATACTTA
41210 TGATGATTTGCATGAC
1 TGATGATTTGCATGAC
*
41226 TGATGTTTTGCATGA
1 TGATGATTTGCATGA
41241 ATGCATTCGG
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:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (16 bp):
TGATGATTTGCATGAC
Found at i:43141 original size:4 final size:4
Alignment explanation
Indices: 43129--43375 Score: 80
Period size: 4 Copynumber: 62.2 Consensus size: 4
43119 AAAAAAAAGT
* *
43129 AATA GATA AATA AATA AATA AATA AATA AATA GAA-A AATA AGTA AGA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA A-ATA
* ** * * * *
43177 TAATA GATA AATA AA-A AGATA AATA GGTA TATA GATA ATTA GATA AATA
1 -AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA
** ** * * * * ** *
43226 GGTA GGTA AA-A AAGTA GATA ATTGTA AATA AATA GAT- AATG GCTA AATT
1 AATA AATA AATA AA-TA AATA A--ATA AATA AATA AATA AATA AATA AATA
* * * ** *
43275 AATA AATA AATA GATA AAT- AGTA AATA AATA GAT- AATA GTTA AATT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * ** *
43321 AATA AATA AATA GATA AAT- AGTA AATA AATA GAT- AATA GTTA AATT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
43367 AATA AATA A
1 AATA AATA A
43376 TAATTTAAAA
Statistics
Matches: 170, Mismatches: 57, Indels: 32
0.66 0.22 0.12
Matches are distributed among these distances:
3 17 0.10
4 142 0.84
5 8 0.05
6 3 0.02
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:43278 original size:19 final size:18
Alignment explanation
Indices: 43230--43283 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
43220 TAAATAGGTA
43230 GGTAAA-AAAGTAGATAAT
1 GGTAAATAAA-TAGATAAT
*
43248 TGTAAATAAATAGATAAT
1 GGTAAATAAATAGATAAT
* *
43266 GGCTAAATTAATAAATAA
1 GG-TAAATAAATAGATAA
43284 ATAGATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.28
Consensus pattern (18 bp):
GGTAAATAAATAGATAAT
Found at i:43282 original size:27 final size:25
Alignment explanation
Indices: 43250--43375 Score: 96
Period size: 27 Copynumber: 5.3 Consensus size: 25
43240 TAGATAATTG
43250 TAAATAAATAGATAATGGCTAAATTAA
1 TAAATAAATAGATAAT-G-TAAATTAA
*
43277 TAAATAAATAG---A--TAAA-TAG
1 TAAATAAATAGATAATGTAAATTAA
43296 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAT-G-TAAATTAA
*
43323 TAAATAAATAG---A--TAAA-TAG
1 TAAATAAATAGATAATGTAAATTAA
43342 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAT-G-TAAATTAA
43369 TAAATAA
1 TAAATAA
43376 TAATTTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 32
0.69 0.03 0.28
Matches are distributed among these distances:
19 26 0.33
20 8 0.10
22 2 0.03
24 2 0.03
26 8 0.10
27 33 0.42
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (25 bp):
TAAATAAATAGATAATGTAAATTAA
Found at i:43309 original size:46 final size:46
Alignment explanation
Indices: 43232--43375 Score: 238
Period size: 46 Copynumber: 3.2 Consensus size: 46
43222 AATAGGTAGG
* * *
43232 TAAA-AAAGTAGAT-AATTGTAAATAAATAGATAATGGCTAAATTAA
1 TAAATAAA-TAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
43277 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
43323 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
43369 TAAATAA
1 TAAATAA
43376 TAATTTAAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
45 9 0.10
46 85 0.90
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.30
Consensus pattern (46 bp):
TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
Found at i:43376 original size:19 final size:19
Alignment explanation
Indices: 43277--43377 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 19
43267 GCTAAATTAA
* *
43277 TAAATAAATAGATAAATAG-
1 TAAATTAATAAAT-AATAGT
* *
43296 TAAATAAATAGATAATAGT
1 TAAATTAATAAATAATAGT
*
43315 TAAATTAATAAATAAATAGA
1 TAAATTAATAAAT-AATAGT
43335 TAAATAGTAAATAAATAGATAATAGT
1 TAAAT--T-AAT--A-A-ATAATAGT
43361 TAAATTAATAAATAATA
1 TAAATTAATAAATAATA
43378 ATTTAAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
18 5 0.07
19 30 0.43
20 11 0.16
21 1 0.01
22 1 0.01
23 6 0.09
24 1 0.01
25 1 0.01
26 11 0.16
27 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
TAAATTAATAAATAATAGT
Found at i:43817 original size:26 final size:26
Alignment explanation
Indices: 43785--43836 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
43775 TGAAATTAAA
43785 AACCTAAATTAATTAAACCATAACCC
1 AACCTAAATTAATTAAACCATAACCC
43811 AACCTAAATTAATTAAACCATAACCC
1 AACCTAAATTAATTAAACCATAACCC
43837 CAAGGTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (26 bp):
AACCTAAATTAATTAAACCATAACCC
Done.