Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020677.1 Corchorus olitorius cultivar O-4 contig20710, 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: 32080
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:194 original size:15 final size:14
Alignment explanation
Indices: 171--215 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
161 ATAACATTCA
*
171 ATATTTAATATATAT
1 ATATATAATATA-AT
186 ATATATAATATAAT
1 ATATATAATATAAT
200 ATAATATAATATAAT
1 AT-ATATAATATAAT
215 A
1 A
216 ACGCGAGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATAATATAAT
Found at i:198 original size:5 final size:5
Alignment explanation
Indices: 176--215 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
166 ATTCAATATT
176 TAATA T-ATA TATATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TA-ATA TAATA TAATA TAATA TAATA TAATA
216 ACGCGAGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:2379 original size:60 final size:60
Alignment explanation
Indices: 2268--2388 Score: 172
Period size: 60 Copynumber: 2.0 Consensus size: 60
2258 AACTCTATTT
* * **
2268 TTATTTAATTAAATCTAATATCCTTATAACTCTTTATTTTTTACAACTTACTATTTTAAA
1 TTATTTAATTAAATCTAATATCCTTATAAATATTTATAATTTACAACTTACTATTTTAAA
**
2328 TTATTTAATTAAATCTAATATCCTTATAAATATTTA-AATTTACCATTTTACTATTTTAAA
1 TTATTTAATTAAATCTAATATCCTTATAAATATTTATAATTTA-CAACTTACTATTTTAAA
2388 T
1 T
2389 AAAAAACTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (60 bp):
TTATTTAATTAAATCTAATATCCTTATAAATATTTATAATTTACAACTTACTATTTTAAA
Found at i:5781 original size:15 final size:15
Alignment explanation
Indices: 5735--5783 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
5725 AGGTAATTTT
5735 TTTAGGTCATTCGGG
1 TTTAGGTCATTCGGG
* *
5750 TTTCGTCTCA-TCTGGG
1 TTTAG-GTCATTC-GGG
5766 TTTAGGTCATTCGGG
1 TTTAGGTCATTCGGG
5781 TTT
1 TTT
5784 TGGGTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.10, C:0.16, G:0.29, T:0.45
Consensus pattern (15 bp):
TTTAGGTCATTCGGG
Found at i:7595 original size:129 final size:126
Alignment explanation
Indices: 7393--7648 Score: 338
Period size: 129 Copynumber: 2.0 Consensus size: 126
7383 TGATGAAGTG
* ** * *
7393 AATAAATAATACATGATTTTATGGTCAATAAATGTGTACATTGGATGGGTTAAAACCCCTTGTAA
1 AATAAATAATACATGATTTTATGGTCAATAAATGTATACATTCAATGGGTTAAAAACCCTTGCAA
*
7458 TTACAAAAAA-GGACCGGAGGAAAAAGGAATGGTGAGAAACTAATT-GAGGGCATTCTTAGTA
66 TTACAAAAAATGG-CCGGAGGAAAAAGGAATGATGAGAAACTAATTGGA-GGCATTCTTAGTA
* *
7519 AATAAATAATACATGATTTTATGTTTCAATAAATGCTATCACATTCAACT-GGTTAAAAACTCTT
1 AATAAATAATACATGATTTTATG-GTCAATAAATG-TAT-ACATTCAA-TGGGTTAAAAACCCTT
* * *
7583 GCAATTACAAAAAATGGCTGGAGGAGAAAGGAATGATGAGAAACTAATTGGAGGTATTCTTAGTA
62 GCAATTACAAAAAATGGCCGGAGGAAAAAGGAATGATGAGAAACTAATTGGAGGCATTCTTAGTA
7648 A
1 A
7649 TTAACCAAGT
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
126 23 0.20
127 10 0.09
128 2 0.02
129 73 0.65
130 5 0.04
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (126 bp):
AATAAATAATACATGATTTTATGGTCAATAAATGTATACATTCAATGGGTTAAAAACCCTTGCAA
TTACAAAAAATGGCCGGAGGAAAAAGGAATGATGAGAAACTAATTGGAGGCATTCTTAGTA
Found at i:7757 original size:2 final size:2
Alignment explanation
Indices: 7750--7781 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7740 AAATAACATA
7750 AT AT AT 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 AT AT AT
7782 TTACATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12292 original size:65 final size:65
Alignment explanation
Indices: 12219--12426 Score: 188
Period size: 65 Copynumber: 3.2 Consensus size: 65
12209 AAATCTCAGA
* * *
12219 TTATCAAAATTTATAAGAAGATTATCAAAATTTTATAGTGTTATTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTATAAGAAGATTATCAAAATTTTATAGTGTGATTATCAAAATTTCATAGAGAGG
* * * * * * * * * *
12284 TTATCAAAATTACATATG-TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAG
1 TTATCAAAATT-TATAAGAAGATTATCAAAATTTTATAGTGTGATTATCAAAATTTCATAGAGAG
12348 G
65 G
* * * * *
12349 TTATTAAAATTTCATAA-AGAGGTTATC-AAATTTTCAAAATGTGATTATCAAAATTTCATAGTG
1 TTATCAAAATTT-ATAAGA-AGATTATCAAAATTTT-ATAGTGTGATTATCAAAATTTCATAGAG
*
12412 GGG
63 AGG
12415 TTATCAAAATTT
1 TTATCAAAATTT
12427 CATAGTATGG
Statistics
Matches: 108, Mismatches: 30, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
65 66 0.61
66 42 0.39
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (65 bp):
TTATCAAAATTTATAAGAAGATTATCAAAATTTTATAGTGTGATTATCAAAATTTCATAGAGAGG
Found at i:12429 original size:22 final size:22
Alignment explanation
Indices: 12219--12813 Score: 296
Period size: 22 Copynumber: 27.5 Consensus size: 22
12209 AAATCTCAGA
* *
12219 TTATCAAAATTT-ATAAG-AAGA
1 TTATCAAAATTTCAT-AGTGAGG
* ***
12240 TTATCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAGTGAGG
* *
12262 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
12284 TTATCAAAATTACATATGTGA--
1 TTATCAAAATTTCATA-GTGAGG
* *
12305 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
12327 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* **
12349 TTATTAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
12371 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
12393 TTATCAAAATTTCATAGTGGGG
1 TTATCAAAATTTCATAGTGAGG
12415 TTATCAAAATTTCATAGT-ATGG
1 TTATCAAAATTTCATAGTGA-GG
* * *
12437 TTA-CCAAA--T--GAG-GAAAG
1 TTATCAAAATTTCATAGTG-AGG
* * *
12454 TTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
*
12476 TAATCAAAATTTC--AG-GCAGG
1 TTATCAAAATTTCATAGTG-AGG
*
12496 ATATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
12518 CTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* * *
12540 TTTTCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGAGG
* * *
12562 TTAACAAAATTTCATAATGCGG
1 TTATCAAAATTTCATAGTGAGG
** *
12584 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
12606 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
* ** *
12622 TTATCAAGATTTCATAACGAGT
1 TTATCAAAATTTCATAGTGAGG
* *
12644 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
12666 TTTATCAAAATTTTATAG-GAAGG
1 -TTATCAAAATTTCATAGTG-AGG
*
12689 TTATATCAAAATTTCATAGCGAGG
1 -T-TATCAAAATTTCATAGTGAGG
* *
12713 TTATCACAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
12735 TTATCAATATATT-ATA-TGGAGG
1 TTATCAAAAT-TTCATAGT-GAGG
*
12757 TTATCAACATCTT-ATAGT-ACTGG
1 TTATCAAAAT-TTCATAGTGA--GG
* *
12780 TTATCAAAATTTAATTAG-GAAG
1 TTATCAAAATTTCA-TAGTGAGG
12802 TTATCAAAATTT
1 TTATCAAAATTT
12814 GCTAGCTAGC
Statistics
Matches: 439, Mismatches: 92, Indels: 85
0.71 0.15 0.14
Matches are distributed among these distances:
16 9 0.02
17 9 0.02
18 4 0.01
19 5 0.01
20 15 0.03
21 39 0.09
22 290 0.66
23 44 0.10
24 23 0.05
25 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:12700 original size:24 final size:23
Alignment explanation
Indices: 12645--12716 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 23
12635 ATAACGAGTT
12645 TATCAAAATTTTATAGGGAGGTT-
1 TATCAAAATTTTATA-GGAGGTTA
12668 TATCAAAATTTTATAGGAAGGTTA
1 TATCAAAATTTTATAGG-AGGTTA
*
12692 TATCAAAATTTCATAGCGAGGTTA
1 TATCAAAATTTTATAG-GAGGTTA
12716 T
1 T
12717 CACAATTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
22 2 0.04
23 20 0.44
24 22 0.49
25 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
TATCAAAATTTTATAGGAGGTTA
Found at i:12916 original size:22 final size:22
Alignment explanation
Indices: 12891--12939 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12881 TTCCTTAGGG
* *
12891 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
*
12913 AGGTTAAAAAAATTTTATAAAA
1 AGGTTAAAAAAATTTCATAAAA
12935 AGGTT
1 AGGTT
12940 CTTGAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:14266 original size:12 final size:13
Alignment explanation
Indices: 14249--14286 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
14239 TTGTAATTTG
14249 TATAATATATA-A
1 TATAATATATATA
14261 TATAATATA-ATA
1 TATAATATATATA
14273 TAT-ATATATATA
1 TATAATATATATA
14285 TA
1 TA
14287 CTACTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATAATATATATA
Found at i:14270 original size:10 final size:11
Alignment explanation
Indices: 14253--14286 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
14243 AATTTGTATA
14253 ATATATAATAT
1 ATATATAATAT
14264 A-ATATAATAT
1 ATATATAATAT
14274 ATATAT-ATAT
1 ATATATAATAT
14284 ATA
1 ATA
14287 CTACTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATATAATAT
Found at i:18142 original size:43 final size:46
Alignment explanation
Indices: 18094--18196 Score: 140
Period size: 47 Copynumber: 2.3 Consensus size: 46
18084 TCAAATGAAA
* **
18094 ATTATA-TTATTTTTGTG-TTAT-ATTACAAATTAATATGTGATTT
1 ATTATATTTATTTTTATGATTATGATTACAAATTAATATGCAATTT
*
18137 ATTATATTTATTTTTATGATTTATGGTTACAAATTAATATGCAATTT
1 ATTATATTTATTTTTATGA-TTATGATTACAAATTAATATGCAATTT
18184 ATTATATTTATTT
1 ATTATATTTATTT
18197 ATTTACTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 6 0.12
44 10 0.19
46 4 0.08
47 32 0.62
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (46 bp):
ATTATATTTATTTTTATGATTATGATTACAAATTAATATGCAATTT
Found at i:18969 original size:26 final size:26
Alignment explanation
Indices: 18940--18992 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
18930 ATATGTAAAC
18940 ATACACTTGAATCTCATTTTTCACGA
1 ATACACTTGAATCTCATTTTTCACGA
18966 ATACACTTGAATCTCATTTTTCACGA
1 ATACACTTGAATCTCATTTTTCACGA
18992 A
1 A
18993 GTAGAGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (26 bp):
ATACACTTGAATCTCATTTTTCACGA
Found at i:20219 original size:119 final size:117
Alignment explanation
Indices: 20023--20266 Score: 375
Period size: 119 Copynumber: 2.1 Consensus size: 117
20013 TGAAACAAAA
*
20023 AAAAAAT-GGGCTCAATAAAAACCCAACACCTATTAGCAAATAGCCCAATTAAAATGGACCCATT
1 AAAAAATAGGGCTCAATAAAAACCCAACACCCATTAGCAAATAGCCCAATTAAAATGGACCCATT
*
20087 CACAAACTAAAATAATATTACAAAAATGAATAGTAT-AAAAAGGCAATTAAGATT
66 CACAAACTAAAAT-A-A-TACAAAAATGAATAGTATAAAAAAAGCAATTAAGATT
* * *
20141 AAAAAATAGGTCTCACTAAAAATCCAACACCCATTAGCAAATAGCCCAATTAAAATGGACCCATT
1 AAAAAATAGGGCTCAATAAAAACCCAACACCCATTAGCAAATAGCCCAATTAAAATGGACCCATT
* *
20206 CACAAGCTGAAATAATACAAAAATGAATAGTATAAAAAAAGCAATTAAGATT
66 CACAAACTAAAATAATACAAAAATGAATAGTATAAAAAAAGCAATTAAGATT
20258 AACAAAATA
1 AA-AAAATA
20267 ATCAAGAATC
Statistics
Matches: 116, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
116 18 0.16
117 20 0.17
118 14 0.12
119 64 0.55
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.20
Consensus pattern (117 bp):
AAAAAATAGGGCTCAATAAAAACCCAACACCCATTAGCAAATAGCCCAATTAAAATGGACCCATT
CACAAACTAAAATAATACAAAAATGAATAGTATAAAAAAAGCAATTAAGATT
Found at i:21362 original size:13 final size:13
Alignment explanation
Indices: 21344--21368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21334 AAATATAGTA
21344 AATATGATTTATT
1 AATATGATTTATT
21357 AATATGATTTAT
1 AATATGATTTAT
21369 GAGGTTATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AATATGATTTATT
Found at i:22099 original size:15 final size:16
Alignment explanation
Indices: 22074--22107 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
22064 ATAGTTGCTA
22074 ATAATATATAATAAAT
1 ATAATATATAATAAAT
*
22090 ATAA-ATATAATATAT
1 ATAATATATAATAAAT
22105 ATA
1 ATA
22108 TCAGTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATATATAATAAAT
Found at i:27660 original size:49 final size:49
Alignment explanation
Indices: 27598--27698 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
27588 TCATGATCAT
*
27598 AATAGTAATGATTCAATCCTAACTGAACTTTCAAGCAAGAAATTCAGAC
1 AATAGTAAGGATTCAATCCTAACTGAACTTTCAAGCAAGAAATTCAGAC
27647 AATAGTAAGGATTCAATCCTAACTGAACTTTCAAGCAAGAAATTCAGAC
1 AATAGTAAGGATTCAATCCTAACTGAACTTTCAAGCAAGAAATTCAGAC
27696 AAT
1 AAT
27699 TTAGCAGTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (49 bp):
AATAGTAAGGATTCAATCCTAACTGAACTTTCAAGCAAGAAATTCAGAC
Found at i:27722 original size:17 final size:17
Alignment explanation
Indices: 27700--27733 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27690 TCAGACAATT
27700 TAGCAGTATAAAACCTC
1 TAGCAGTATAAAACCTC
27717 TAGCAGTATAAAACCTC
1 TAGCAGTATAAAACCTC
27734 GCAAAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
TAGCAGTATAAAACCTC
Found at i:29599 original size:25 final size:25
Alignment explanation
Indices: 29571--29620 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29561 AACCAGAAAT
29571 GAGAAATCAAAAACCT-AATAATACC
1 GAGAAATCAAAAACCTGAA-AATACC
*
29596 GAGAAATCCAAAACCTGAAAATACC
1 GAGAAATCAAAAACCTGAAAATACC
29621 TAAAATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.14
Consensus pattern (25 bp):
GAGAAATCAAAAACCTGAAAATACC
Done.