Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022109.1 Corchorus olitorius cultivar O-4 contig22142, 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: 40932
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:5015 original size:31 final size:31
Alignment explanation
Indices: 4931--5032 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 31
4921 TGTCAACAAA
* *
4931 ATTTTGAAAGTTTAGGAGGTAAATTATCAAG
1 ATTTTGAAAGTTTAGGAGGCAAAATATCAAG
*
4962 ATTTT-AGAGTTTAGG-GGCAAAATATCAAG
1 ATTTTGAAAGTTTAGGAGGCAAAATATCAAG
* *
4991 ATTTTAAAAGTTTAGGAGGCAAAATGATTAA-
1 ATTTTGAAAGTTTAGGAGGCAAAAT-ATCAAG
5022 ATTTTGAAAGT
1 ATTTTGAAAGT
5033 AAATGTGTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
29 17 0.27
30 18 0.29
31 23 0.37
32 4 0.06
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (31 bp):
ATTTTGAAAGTTTAGGAGGCAAAATATCAAG
Found at i:9525 original size:124 final size:123
Alignment explanation
Indices: 9307--9543 Score: 314
Period size: 124 Copynumber: 1.9 Consensus size: 123
9297 CTGTCTAAAA
* * * *
9307 AAAGGTAATTTCATGATTTACAACTTTCATGAAGAACTTAGAAGCCAATTTTAATGTTTCAATTC
1 AAAGGTAATTGCATGATTTACAACTATCATGAAGAACTAAAAAGCCAATTTTAATGTTTCAATTC
** * * **
9372 TAAAAAATGCTTCCGAAATTTTGTGGTTTCGATTGCCGGTCTATTCAAGTGTCGGTTG
66 TAAAAAATGCTTCCGAAATTGGGTCGTTTCAATTGAAGGTCTATTCAAGTGTCGGTTG
* * * *
9430 AAAGGTTATTGCATGATTTGCAACTATCATGAATG-ACTCAAAAAGCTAATTTTTATGTTTCAAT
1 AAAGGTAATTGCATGATTTACAACTATCATGAA-GAACT-AAAAAGCCAATTTTAATGTTTCAAT
*
9494 TCTAAAAAATGCTTCCGAGATTGGGTCGTTTCAATTGAAGGTCTATTCAA
64 TCTAAAAAATGCTTCCGAAATTGGGTCGTTTCAATTGAAGGTCTATTCAA
9544 TATCATAGAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
123 32 0.33
124 65 0.67
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (123 bp):
AAAGGTAATTGCATGATTTACAACTATCATGAAGAACTAAAAAGCCAATTTTAATGTTTCAATTC
TAAAAAATGCTTCCGAAATTGGGTCGTTTCAATTGAAGGTCTATTCAAGTGTCGGTTG
Found at i:9602 original size:13 final size:13
Alignment explanation
Indices: 9586--9627 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
9576 TATTTTGTTG
9586 ATTATGTCTTTTA
1 ATTATGTCTTTTA
9599 ATTATG----TTA
1 ATTATGTCTTTTA
9608 ATTATGTCTTTTA
1 ATTATGTCTTTTA
9621 ATTATGT
1 ATTATGT
9628 ACAAGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 9 0.36
13 16 0.64
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.60
Consensus pattern (13 bp):
ATTATGTCTTTTA
Found at i:9611 original size:22 final size:22
Alignment explanation
Indices: 9581--9627 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9571 TGATTTATTT
*
9581 TGTTGATTATGTCTTTTAATTA
1 TGTTAATTATGTCTTTTAATTA
9603 TGTTAATTATGTCTTTTAATTA
1 TGTTAATTATGTCTTTTAATTA
9625 TGT
1 TGT
9628 ACAAGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (22 bp):
TGTTAATTATGTCTTTTAATTA
Found at i:10537 original size:18 final size:18
Alignment explanation
Indices: 10503--10541 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10493 TATTTTTTTC
*
10503 ATTATGTATTTTTGGTTG
1 ATTATGTATTTTGGGTTG
10521 ATTAT-TATTATTGGGTTG
1 ATTATGTATT-TTGGGTTG
10539 ATT
1 ATT
10542 TGGGCCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (18 bp):
ATTATGTATTTTGGGTTG
Found at i:12416 original size:28 final size:28
Alignment explanation
Indices: 12385--12442 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
12375 ATATATATTG
**
12385 AACTATAGAATTTCCTAAAAAAAAGGAA
1 AACTATAGAATTGACTAAAAAAAAGGAA
**
12413 AACTATAGAATTGACTAAATGAAAGGAA
1 AACTATAGAATTGACTAAAAAAAAGGAA
12441 AA
1 AA
12443 TTTATGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.21
Consensus pattern (28 bp):
AACTATAGAATTGACTAAAAAAAAGGAA
Found at i:18076 original size:49 final size:50
Alignment explanation
Indices: 18003--18106 Score: 176
Period size: 49 Copynumber: 2.1 Consensus size: 50
17993 TTGCCAGTTC
18003 TAATAGATACTTTGAATTACCTAAATCAGACATCCCAG-GCAAAAACTCTA
1 TAATAGATACTTTGAATTACCTAAATCAGACAT-CCAGAGCAAAAACTCTA
*
18053 TAATA-ATACTTTGAATTACCTAAATCAGACATCCTGAGCAAAAACTCTA
1 TAATAGATACTTTGAATTACCTAAATCAGACATCCAGAGCAAAAACTCTA
18102 TAATA
1 TAATA
18107 TTAATTAAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
48 3 0.06
49 44 0.85
50 5 0.10
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (50 bp):
TAATAGATACTTTGAATTACCTAAATCAGACATCCAGAGCAAAAACTCTA
Found at i:18717 original size:178 final size:178
Alignment explanation
Indices: 18341--18748 Score: 462
Period size: 178 Copynumber: 2.3 Consensus size: 178
18331 CAAATTTAGA
* * * * * *
18341 TTTCGGGTCCTTCATGAAAGTCGCAGATCATGGAACAACATTTTAACAGGCACTTGAATCATCTC
1 TTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTAAATCATCTC
* * * *
18406 AATCGGACATCTGGAGCAAAAATTATGTAATATTAAGTGGACTGTCCATTCTCGCTAACCGAAAC
66 AATCAGACATCTAGAGCAAAAATTATGTAATATTAAGTGGACTGTCCATTCCCACTAACCGAAAC
* * * *
18471 AACTAAATTTTTGGAAACATTTTTTATACTCAAAACATTAAATTTAGC
131 AACTAAATTTTTCGAAACATTTTTGATACTCAAAACATTAAATTCAAC
* * * * ** * * *
18519 TTTCGAATCATGT-GTGAAAGTTGTAGATAATAAAACAACCTTTTAAGAGATAGTTAAATCATCT
1 TTTCGAGTCCT-TCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTAAATCATCT
* * * *
18583 CAATCAGACGTCTAGAGCAAAAGTTATGTAATATTAAGTGGAAC-GTCCATTCCCATTAACTGAA
65 CAATCAGACATCTAGAGCAAAAATTATGTAATATTAAGTGG-ACTGTCCATTCCCACTAACCGAA
* ** *
18647 ACAACT-AATTTTTCGAAAGTATTTTTGATACTTTAAACATTAAATTCAAT
129 ACAACTAAATTTTTCGAAA-CATTTTTGATACTCAAAACATTAAATTCAAC
* * *
18697 TTTTGAGTCCTTCATGAAAGTTATAGATCATGGAACAACCTTTTAATAGACA
1 TTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACA
18749 TTTGAATTAC
Statistics
Matches: 185, Mismatches: 41, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
177 12 0.06
178 170 0.92
179 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (178 bp):
TTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAACAGACACTTAAATCATCTC
AATCAGACATCTAGAGCAAAAATTATGTAATATTAAGTGGACTGTCCATTCCCACTAACCGAAAC
AACTAAATTTTTCGAAACATTTTTGATACTCAAAACATTAAATTCAAC
Found at i:19003 original size:41 final size:41
Alignment explanation
Indices: 18940--19026 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
18930 CCTAAATTGT
*
18940 AGGCATGGGGTTGTGCCGTTCCTGAAATACAGGCACGGAGA
1 AGGCATGGGGTTGTGCCATTCCTGAAATACAGGCACGGAGA
*
18981 AGGCATGGGGTTGTGTCATTCCTGAAATACAGGCACGGAGA
1 AGGCATGGGGTTGTGCCATTCCTGAAATACAGGCACGGAGA
19022 AGGCA
1 AGGCA
19027 CAGAGAACGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (41 bp):
AGGCATGGGGTTGTGCCATTCCTGAAATACAGGCACGGAGA
Found at i:20421 original size:2 final size:2
Alignment explanation
Indices: 20380--20405 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20370 TAATATTTAA
20380 AT AT 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
20406 GTTATGCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20556 original size:34 final size:34
Alignment explanation
Indices: 20499--20564 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
20489 GACATGTAAA
* *
20499 ATGTGGCTAATTCTTAGTTCATTATAGGAGTTAT
1 ATGTGGCTAATTCGTAGTCCATTATAGGAGTTAT
*
20533 ATGTTGCTAATTCGTAGTCCATTATAGGAGTT
1 ATGTGGCTAATTCGTAGTCCATTATAGGAGTT
20565 CCTAACATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (34 bp):
ATGTGGCTAATTCGTAGTCCATTATAGGAGTTAT
Found at i:22349 original size:52 final size:52
Alignment explanation
Indices: 22266--22476 Score: 347
Period size: 52 Copynumber: 4.1 Consensus size: 52
22256 TGGGATCTTC
* * *
22266 CCTAAATTG-A-A-TTTGAAAACCTGATGGGAACTTTCTCGCTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
*
22315 CCTAAATTGAACACTTTGTAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
22367 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTAAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
22419 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
22471 CCTAAA
1 CCTAAA
22477 CTGGAGTTGG
Statistics
Matches: 150, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
49 9 0.06
50 1 0.01
51 1 0.01
52 139 0.93
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (52 bp):
CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
Found at i:22462 original size:28 final size:28
Alignment explanation
Indices: 22378--22468 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 28
22368 CTAAATCGAA
22378 CACTTTGAAAACTTGATGGGAACTTTCC
1 CACTTTGAAAACTTGATGGGAACTTTCC
* *** * ***
22406 CACTTT-AAAA--AGA-CCTAAATTGAA
1 CACTTTGAAAACTTGATGGGAACTTTCC
22430 CACTTTGAAAACTTGATGGGAACTTTCC
1 CACTTTGAAAACTTGATGGGAACTTTCC
22458 CACTTTGAAAA
1 CACTTTGAAAA
22469 GACCTAAACT
Statistics
Matches: 43, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
24 10 0.23
25 6 0.14
27 6 0.14
28 21 0.49
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (28 bp):
CACTTTGAAAACTTGATGGGAACTTTCC
Found at i:28370 original size:49 final size:49
Alignment explanation
Indices: 28292--28386 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
28282 AACACGCCCC
* ** *
28292 CTCACGTGTATCCCTGGTACACGTAGACAATTGAGTCTTGGGCAACCCA
1 CTCACGTGTATCCCTAGTACACGTAGACAACCGAGTCTGGGGCAACCCA
* *
28341 CTCATGTGTATCCCTAGTACACGTGGACAACCGAGTCTGGGGCAAC
1 CTCACGTGTATCCCTAGTACACGTAGACAACCGAGTCTGGGGCAAC
28387 GGGATAGACC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (49 bp):
CTCACGTGTATCCCTAGTACACGTAGACAACCGAGTCTGGGGCAACCCA
Found at i:29001 original size:30 final size:30
Alignment explanation
Indices: 28965--29027 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
28955 GTGCTCTCTA
* *
28965 TTGGTTTGGAATGCAAATGCAAAAATCTGT
1 TTGGTTTCGAATGCAAATGCAAAAATCAGT
*
28995 TTGGTTTCGAATGCGAATGCAAAAATCAGT
1 TTGGTTTCGAATGCAAATGCAAAAATCAGT
29025 TTG
1 TTG
29028 AAGTCCTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (30 bp):
TTGGTTTCGAATGCAAATGCAAAAATCAGT
Found at i:29229 original size:131 final size:131
Alignment explanation
Indices: 28995--29234 Score: 435
Period size: 131 Copynumber: 1.8 Consensus size: 131
28985 AAAAATCTGT
* *
28995 TTGGTTTCGAATGCGAATGCAAAAATCAGTTTGAAGTCCTGAGGGATAGAGTGAAAATATGGACT
1 TTGGTTTCGAATGCGAATGCAAAAAACAGTTTGAAGTCCTGAGGGATAGAGTGAAAAAATGGACT
29060 CGCCTGCGGTTTCCATGGAAGTTTACGTATCCAAATACTAACTATTGGTTTCGAATGTGCCCTCT
66 CGCCTGCGGTTTCCATGGAAGTTTACGTATCCAAATACTAACTATTGGTTTCGAATGTGCCCTCT
29125 A
131 A
* *
29126 TTGGTTTCGAATGCGAATGCAAAAAACAGTTTGAAGTCTTGAGGGATGGAGTGAAAAAATGGACT
1 TTGGTTTCGAATGCGAATGCAAAAAACAGTTTGAAGTCCTGAGGGATAGAGTGAAAAAATGGACT
*
29191 CGCCTGCGGTTTCCATGGAAGTTTACGTATCCAGATACTAACTA
66 CGCCTGCGGTTTCCATGGAAGTTTACGTATCCAAATACTAACTA
29235 CTTCGCATCT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 104 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (131 bp):
TTGGTTTCGAATGCGAATGCAAAAAACAGTTTGAAGTCCTGAGGGATAGAGTGAAAAAATGGACT
CGCCTGCGGTTTCCATGGAAGTTTACGTATCCAAATACTAACTATTGGTTTCGAATGTGCCCTCT
A
Found at i:38221 original size:28 final size:29
Alignment explanation
Indices: 38157--38229 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 29
38147 CAAATTGATA
38157 GACAAAATAGCCCTCAAACTTTGACAAATAAG
1 GACAAAATAGCCCT---ACTTTGACAAATAAG
*
38189 AACAAAATAGCCCT-CTTTGACAAA-ATAG
1 GACAAAATAGCCCTACTTTGACAAATA-AG
38217 GACAAAATAGCCC
1 GACAAAATAGCCC
38230 CTAAAGGAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.03
28 24 0.63
32 13 0.34
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.18
Consensus pattern (29 bp):
GACAAAATAGCCCTACTTTGACAAATAAG
Done.