Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021277.1 Corchorus olitorius cultivar O-4 contig21310, 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: 24895
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:800 original size:28 final size:27
Alignment explanation
Indices: 750--824 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
740 TATAGGCATA
* * *
750 AAATTACCGTCTTACACTAAGAATGAG-T
1 AAATTACCGTTTTACCCTTAGAA-G-GTT
778 AAATTACCGTTTTACCCTTAGAAGGTT
1 AAATTACCGTTTTACCCTTAGAAGGTT
*
805 AAATTTACAGTTTTACCCTT
1 AAA-TTACCGTTTTACCCTT
825 TTTAACCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.02
27 5 0.12
28 35 0.85
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (27 bp):
AAATTACCGTTTTACCCTTAGAAGGTT
Found at i:5660 original size:27 final size:26
Alignment explanation
Indices: 5610--5660 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
5600 TGAGTTGCCT
5610 AAATAAATAATAATATAAATAAAATA
1 AAATAAATAATAATATAAATAAAATA
* *
5636 AAATAAATATATATTTTAAATAAAA
1 AAATAAATA-ATAATATAAATAAAA
5661 ACTATGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAAATAATAATATAAATAAAATA
Found at i:11024 original size:22 final size:22
Alignment explanation
Indices: 10999--11191 Score: 156
Period size: 22 Copynumber: 8.8 Consensus size: 22
10989 TAATAGTGTT
* *
10999 GTTACCAAAATTTCGTATGAAG
1 GTTATCAAAATTTCATATGAAG
* *
11021 GTTATCAAAACTTCATAGTGTA-
1 GTTATCAAAATTTCATA-TGAAG
* *
11043 GTTATCAAAATTTCACATAAAG
1 GTTATCAAAATTTCATATGAAG
* * **
11065 GTTACCAAGATTTCATAAAAAG
1 GTTATCAAAATTTCATATGAAG
* * *
11087 GTTATCAAAATTTCTTAGGGAG
1 GTTATCAAAATTTCATATGAAG
* * *
11109 GTTAACAAAATTTCATACGAAA
1 GTTATCAAAATTTCATATGAAG
* * *
11131 GTTATCAGAATTTTATAGTG-TG
1 GTTATCAAAATTTCATA-TGAAG
* *
11153 ATTATCAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATATGAAG
*
11175 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
11192 GGGAGGAAAT
Statistics
Matches: 131, Mismatches: 36, Indels: 8
0.75 0.21 0.05
Matches are distributed among these distances:
21 3 0.02
22 124 0.95
23 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGAAG
Found at i:11080 original size:44 final size:44
Alignment explanation
Indices: 10984--11081 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
10974 AAGGCTAGCT
* * ** * *
10984 AAATTTAATAGTGTTGTTACCAAAATTTCGTATGAAGGTTATCA
1 AAATTTCATAGTGTAGTTACCAAAATTTCACATAAAGGTTACCA
* *
11028 AAACTTCATAGTGTAGTTATCAAAATTTCACATAAAGGTTACCA
1 AAATTTCATAGTGTAGTTACCAAAATTTCACATAAAGGTTACCA
*
11072 AGATTTCATA
1 AAATTTCATA
11082 AAAAGGTTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (44 bp):
AAATTTCATAGTGTAGTTACCAAAATTTCACATAAAGGTTACCA
Found at i:11444 original size:22 final size:22
Alignment explanation
Indices: 11396--11473 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
11386 CAAGATATGG
* *
11396 TTATCAAAACTTTCATAGTGCAG-
1 TTATCAAAA-TTCCATAG-GGAGA
11419 TTATCAAAATTCCATAGGGAGA
1 TTATCAAAATTCCATAGGGAGA
11441 TTATCAAAATTCCATAGGGAGA
1 TTATCAAAATTCCATAGGGAGA
11463 TTATCAAAATT
1 TTATCAAAATT
11474 TCACACTAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
21 3 0.06
22 40 0.77
23 9 0.17
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (22 bp):
TTATCAAAATTCCATAGGGAGA
Found at i:11489 original size:44 final size:44
Alignment explanation
Indices: 11363--11541 Score: 137
Period size: 44 Copynumber: 4.0 Consensus size: 44
11353 AGTTTCATTA
* *
11363 TCATAGGGAGGTTATCGAAATTTCA-AGATATGGTTATCAAAACTT
1 TCATAGGGAGGTTATCAAAATTTCACA-ATAAGGTTATCAAAA-TT
* * * *** *
11408 TCATAGTGCA-GTTATCAAAATTCCATAGGGAGATTATCAAAATT
1 TCATAG-GGAGGTTATCAAAATTTCACAATAAGGTTATCAAAATT
* * *
11452 CCATAGGGAGATTATCAAAATTTCACACTAAGGTTATCAAAATT
1 TCATAGGGAGGTTATCAAAATTTCACAATAAGGTTATCAAAATT
* * * * * ** *
11496 TCTTTGTGTGGTTATCAAAATTTCACAGTGTGGTTATCCAAATT
1 TCATAGGGAGGTTATCAAAATTTCACAATAAGGTTATCAAAATT
11540 TC
1 TC
11542 TATGTTGGAG
Statistics
Matches: 104, Mismatches: 27, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
43 2 0.02
44 70 0.67
45 29 0.28
46 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (44 bp):
TCATAGGGAGGTTATCAAAATTTCACAATAAGGTTATCAAAATT
Found at i:11508 original size:22 final size:22
Alignment explanation
Indices: 11463--11542 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
11453 CATAGGGAGA
* * **
11463 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTCTCAGTGTGG
**
11485 TTATCAAAATTTCTTTGTGTGG
1 TTATCAAAATTTCTCAGTGTGG
*
11507 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCTCAGTGTGG
*
11529 TTATCCAAATTTCT
1 TTATCAAAATTTCT
11543 ATGTTGGAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCTCAGTGTGG
Found at i:12463 original size:38 final size:38
Alignment explanation
Indices: 12409--12526 Score: 146
Period size: 38 Copynumber: 3.0 Consensus size: 38
12399 TTGACAAATG
* *
12409 ATATAATGAATGGTTTTAAATTTTTTGGTAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
*
12447 ATATAATAAATAGTTTTAAATTTTTTGATAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
* ** *
12485 ACTTTTTTCATAATGGTTTTAAATTTTTTGATGAATATATA
1 A-TATAAT-A-AATGGTTTTAAATTTTTTGATAAATATATA
12526 A
1 A
12527 CTTTTTTCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 36 0.52
39 3 0.04
40 1 0.01
41 29 0.42
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (38 bp):
ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
Found at i:12480 original size:22 final size:22
Alignment explanation
Indices: 12452--12521 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 22
12442 ATATAATATA
12452 ATAAATAGTTTTAAATTTTTTG
1 ATAAATAGTTTTAAATTTTTTG
* * *
12474 ATAAATA--TATAACTTTTTTC
1 ATAAATAGTTTTAAATTTTTTG
*
12494 AT-AATGGTTTTAAATTTTTTG
1 ATAAATAGTTTTAAATTTTTTG
*
12515 ATGAATA
1 ATAAATA
12522 TATAACTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 12 0.32
22 10 0.27
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (22 bp):
ATAAATAGTTTTAAATTTTTTG
Found at i:12485 original size:33 final size:34
Alignment explanation
Indices: 12398--12485 Score: 88
Period size: 38 Copynumber: 2.5 Consensus size: 34
12388 CTCAGAATAA
* * * *
12398 TTTGACAAATGATATAATGAATGGTTTTAAATTT
1 TTTGATAAATAATATAATAAATAGTTTTAAATTT
*
12432 TTTGGTAAATATATAATATAATAAATAGTTTTAAATTT
1 TTT-G---ATAAATAATATAATAAATAGTTTTAAATTT
12470 TTTGATAAAT-ATATAA
1 TTTGATAAATAATATAA
12486 CTTTTTTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
33 6 0.14
34 8 0.18
35 1 0.02
37 1 0.02
38 28 0.64
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.45
Consensus pattern (34 bp):
TTTGATAAATAATATAATAAATAGTTTTAAATTT
Found at i:12492 original size:20 final size:20
Alignment explanation
Indices: 12467--12538 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
12457 TAGTTTTAAA
*
12467 TTTTTTGATAAATATATAAC
1 TTTTTTCATAAATATATAAC
* * *
12487 TTTTTTCAT-AATGGTTTTAAA
1 TTTTTTCATAAAT--ATATAAC
* *
12508 TTTTTTGATGAATATATAAC
1 TTTTTTCATAAATATATAAC
12528 TTTTTTCATAA
1 TTTTTTCATAA
12539 CCATTACAAC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.08
20 21 0.54
21 12 0.31
22 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTTTTCATAAATATATAAC
Found at i:12511 original size:41 final size:41
Alignment explanation
Indices: 12417--12538 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
12407 TGATATAATG
* * **
12417 AATGGTTTTAAATTTTTTGGTAAATATATAA-TATAAT-A-
1 AATGGTTTTAAATTTTTTGATAAATATATAACTTTTTTCAT
*
12455 AATAGTTTTAAATTTTTTGATAAATATATAACTTTTTTCAT
1 AATGGTTTTAAATTTTTTGATAAATATATAACTTTTTTCAT
*
12496 AATGGTTTTAAATTTTTTGATGAATATATAACTTTTTTCAT
1 AATGGTTTTAAATTTTTTGATAAATATATAACTTTTTTCAT
12537 AA
1 AA
12539 CCATTACAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
38 29 0.39
39 3 0.04
40 1 0.01
41 41 0.55
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (41 bp):
AATGGTTTTAAATTTTTTGATAAATATATAACTTTTTTCAT
Found at i:12553 original size:41 final size:41
Alignment explanation
Indices: 12464--12553 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
12454 AAATAGTTTT
*** **
12464 AAATTTTTTGATAAATATATAACTTTTTTCATAATGGTTTT
1 AAATTTTTTGATAAATATATAACTTTTTTCATAACCATTAC
*
12505 AAATTTTTTGATGAATATATAACTTTTTTCATAACCATTAC
1 AAATTTTTTGATAAATATATAACTTTTTTCATAACCATTAC
*
12546 AACTTTTT
1 AAATTTTT
12554 CAGTAACTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (41 bp):
AAATTTTTTGATAAATATATAACTTTTTTCATAACCATTAC
Found at i:13338 original size:42 final size:40
Alignment explanation
Indices: 13279--13362 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 40
13269 ATTAATTCCT
13279 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
13319 ATGTAATAATACTATAATAACTTAAATACTTACATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
13361 AT
1 AT
13363 TCTTAGGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 7 0.17
41 3 0.07
42 31 0.76
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:13380 original size:24 final size:25
Alignment explanation
Indices: 13353--13399 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
13343 AATACTTACA
13353 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
13377 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
13400 GTGCAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTCAAATTCTTAGGTATTTTT
Found at i:17223 original size:20 final size:19
Alignment explanation
Indices: 17193--17233 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
17183 TTTTTTTTGG
17193 TTAAAAATAATATGCTAGT
1 TTAAAAATAATATGCTAGT
*
17212 TTAAACAATAATATGCTTGT
1 TTAAA-AATAATATGCTAGT
17232 TT
1 TT
17234 GTTTGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (19 bp):
TTAAAAATAATATGCTAGT
Found at i:17441 original size:4 final size:4
Alignment explanation
Indices: 17422--17454 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
17412 GACTCTATCG
*
17422 AATA ATTA AA-A AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
17455 GAAGAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:20893 original size:22 final size:22
Alignment explanation
Indices: 20861--20903 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20851 AAAAACTATA
20861 CATATACTCTGTTCCAATTTGT
1 CATATACTCTGTTCCAATTTGT
*
20883 CATATATTCTGTTCCAATTTG
1 CATATACTCTGTTCCAATTTG
20904 CCAGGAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (22 bp):
CATATACTCTGTTCCAATTTGT
Done.