Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013638.1 Corchorus olitorius cultivar O-4 contig13671, 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: 6207
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Found at i:228 original size:109 final size:107
Alignment explanation
Indices: 1--264 Score: 332
Period size: 109 Copynumber: 2.4 Consensus size: 107
* * * * * *
1 ACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTATAGGAATGACCGCACTGGGCCATC
1 ACTGGATCATCTGGGGATCAACTCTGATCTCTAAAAACTTCTTGAAATGACCGCACTAGACCATC
*
66 TGGAATCAACTCTGATCAACGAAAACTTCTTGGAATGACCGC
66 TGGAATCAACTCTAATCAACGAAAACTTCTTGGAATGACCGC
* * * *
108 ACTGGATCATCTGGGGATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATT
1 ACTGGATCATCTGGGGATCAACTCTGATCTCTAAAAACTTCTTGAAATGACCGCACTAGACCA-T
* * * * *
173 TTGGGGATCAACTCTAATCATTCG-AAACTTCTTGGAATGATCTC
65 CT-GGAATCAACTCTAATCA-ACGAAAACTTCTTGGAATGACCGC
*
217 ACTGGACCATCTGGGGATCAACTCTGATCTCTAAAAACTTCTATGAAA
1 ACTGGATCATCTGGGGATCAACTCTGATCTCTAAAAACTTCT-TGAAA
265 GACAACACCG
Statistics
Matches: 134, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
107 53 0.40
108 2 0.01
109 72 0.54
110 7 0.05
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (107 bp):
ACTGGATCATCTGGGGATCAACTCTGATCTCTAAAAACTTCTTGAAATGACCGCACTAGACCATC
TGGAATCAACTCTAATCAACGAAAACTTCTTGGAATGACCGC
Found at i:354 original size:106 final size:107
Alignment explanation
Indices: 233--430 Score: 301
Period size: 106 Copynumber: 1.9 Consensus size: 107
223 CCATCTGGGG
*
233 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAGATCAACTT-AT
1 ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAAATCAACTTAAT
*
297 CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
66 CTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAA
* ** * *
339 ATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAG
1 ATCAACTCT-GATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAAATCAACTTA-
403 ATCTCTGAAAACTTCTATGAAAGACCGC
64 ATCTCTGAAAACTTCTATGAAAGACCGC
431 CCAGGGCTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 1 0.01
106 54 0.66
108 27 0.33
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (107 bp):
ATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAACACCGAGTCATCTGAAAATCAACTTAAT
CTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAA
Found at i:419 original size:54 final size:54
Alignment explanation
Indices: 1--430 Score: 344
Period size: 54 Copynumber: 8.0 Consensus size: 54
* * * * *
1 ACTGGATCATCT-AGGGATCAACTCTGATCTCTAAAAACTTATAGGAATGACCGC
1 ACTGGGTCATCTGA-GGATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGC
* * * *
55 ACTGGGCCATCTG-GAATCAACTCTGATCAAC-GAAAACTTCT-TGGAATGACCGC
1 ACTGGGTCATCTGAGGATCAACTCTGATC-TCTGAAAACTTCTAT-GAAAGACCGC
* * * *
108 ACTGGATCATCTGGGGATCAACTCTGATCACTGAAAACTTCT-TGAAATGATCGC
1 ACTGGGTCATCTGAGGATCAACTCTGATCTCTGAAAACTTCTATGAAA-GACCGC
* * * * * * * *
162 ACTAGATCATTTTGGGGATCAACTCTAATCAT-TCG-AAACTTCT-TGGAATGATCTC
1 ACTGGGTCA-TCTGAGGATCAACTCTGATC-TCT-GAAAACTTCTAT-GAAAGACCGC
** * * **
217 ACTGGACCATCTGGGGATCAACTCTGATCTCTAAAAACTTCTATGAAAGACAAC
1 ACTGGGTCATCTGAGGATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGC
* * * *
271 ACCGAGTCATCTGAAGATCAACT-T-ATCTCTGAAAGCTTCTATGAAAGACCGC
1 ACTGGGTCATCTGAGGATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGC
** * **
323 ACAAGGTCATCTTAAAATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGC
1 ACTGGGTCATCTGAGGATCAACTCT-GATCTCTGAAAACTTCTATGAAAGACCGC
**
377 ACTGGGTCATCTGAAAATCAACT-TAGATCTCTGAAAACTTCTATGAAAGACCGC
1 ACTGGGTCATCTGAGGATCAACTCT-GATCTCTGAAAACTTCTATGAAAGACCGC
431 CCAGGGCTTA
Statistics
Matches: 315, Mismatches: 46, Indels: 30
0.81 0.12 0.08
Matches are distributed among these distances:
52 43 0.14
53 50 0.16
54 177 0.56
55 41 0.13
56 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (54 bp):
ACTGGGTCATCTGAGGATCAACTCTGATCTCTGAAAACTTCTATGAAAGACCGC
Found at i:528 original size:92 final size:93
Alignment explanation
Indices: 344--528 Score: 291
Period size: 92 Copynumber: 2.0 Consensus size: 93
334 TTAAAATCAA
** *
344 CTTAGATCTCTGAAAACTTCTATGAAAGACCGCACTGGGTCATCTGAAAATCAACTTAGATCTCT
1 CTTAGATCTCTGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCT
* *
409 GAAAACTTCTATGAAAGACCGCCCAGGG
66 GAAAACTTCTATGAAAGACCACACAGGG
* * *
437 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGCAAAGGGTC-TCTTAAGATCAACTTAAATCTCT
1 CTTAGATCTCTGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCT
501 GAAAACTTCTATGAAAGACCACACAGGG
66 GAAAACTTCTATGAAAGACCACACAGGG
529 TGCTTGAAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 46 0.55
93 38 0.45
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (93 bp):
CTTAGATCTCTGAAAACTTCTATGAAAGACCGCAAAGGGTCATCTGAAAATCAACTTAAATCTCT
GAAAACTTCTATGAAAGACCACACAGGG
Found at i:1707 original size:40 final size:39
Alignment explanation
Indices: 1628--1709 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
1618 ATCTTTTTGA
* * *
1628 AAAACATTTTTTCTCTTTTGAAAAGACTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGACTACACCTAGAGG
*
1667 AAAACATTTTTTTTTCTTTTGAAAAGA-TCACACCTAGAGG
1 AAAACA-TTTTTTCTCTTTTGAAAAGACT-ACACCTAGAGG
1707 AAA
1 AAA
1710 GTTTCATTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.19
40 30 0.81
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTGAAAAGACTACACCTAGAGG
Found at i:3610 original size:36 final size:36
Alignment explanation
Indices: 3565--3654 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
3555 TGACAATGAT
*
3565 AATGCATGATGGATGCATATATACAAGTGAATGACA
1 AATGCATGATGGATGCAAATATACAAGTGAATGACA
3601 AATGCATGATGGATGCAAATATACAAGTGAATGACA
1 AATGCATGATGGATGCAAATATACAAGTGAATGACA
3637 AATGCATGATGGATGCAA
1 AATGCATGATGGATGCAA
3655 TGTATGAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.23
Consensus pattern (36 bp):
AATGCATGATGGATGCAAATATACAAGTGAATGACA
Found at i:5101 original size:8 final size:8
Alignment explanation
Indices: 5088--5365 Score: 67
Period size: 8 Copynumber: 35.8 Consensus size: 8
5078 ATAGGTATAG
5088 AGATAAAT
1 AGATAAAT
5096 AGATAAAT
1 AGATAAAT
* *
5104 AGATACAG
1 AGATAAAT
5112 AGA-ATAAT
1 AGATA-AAT
*
5120 AAATAAAT
1 AGATAAAT
* **
5128 AGGTAGCT
1 AGATAAAT
5136 A-A-AAAT
1 AGATAAAT
5142 A-AT-AAT
1 AGATAAAT
5148 A-ATAACA-
1 AGATAA-AT
5155 A-ATAAAT
1 AGATAAAT
5162 AGAT-AAT
1 AGATAAAT
* *
5169 GGCTAAATT
1 AGATAAA-T
5178 A-ATAAAT
1 AGATAAAT
5185 --A-AAA-
1 AGATAAAT
5189 AGATAAAT
1 AGATAAAT
5197 AG-TAAAT
1 AGATAAAT
* *
5204 AAATATAT
1 AGATAAAT
*
5212 A-ATAATT
1 AGATAAAT
* *
5219 AAATTAAT
1 AGATAAAT
* *
5227 AAATAAAA
1 AGATAAAT
5235 AGATAAAT
1 AGATAAAT
5243 AGTAAATAAAT
1 AG---ATAAAT
5254 AGAT-AAT
1 AGATAAAT
*
5261 AGTTAAAAAT
1 AG--ATAAAT
* *
5271 AAATAAAA
1 AGATAAAT
5279 AGATAAAT
1 AGATAAAT
5287 AG-TAAAT
1 AGATAAAT
* *
5294 AAATAGAT
1 AGATAAAT
* *
5302 A-ACAATT
1 AGATAAAT
5309 A-A-AAAT
1 AGATAAAT
*
5315 AAATAAAT
1 AGATAAAT
*
5323 AAATAAAT
1 AGATAAAT
5331 AGTAAATAAAT
1 AG---ATAAAT
5342 AGATAATAGT
1 AGATAA-A-T
*
5352 AAATAAAT
1 AGATAAAT
5360 AGATAA
1 AGATAA
5366 TAGTTTAAAA
Statistics
Matches: 200, Mismatches: 41, Indels: 58
0.67 0.14 0.19
Matches are distributed among these distances:
5 3 0.01
6 17 0.09
7 45 0.22
8 104 0.52
9 5 0.03
10 10 0.05
11 16 0.08
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.26
Consensus pattern (8 bp):
AGATAAAT
Found at i:5103 original size:24 final size:24
Alignment explanation
Indices: 5075--5132 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
5065 TAAAAAAAGC
* *
5075 TAAATAGGTATAGAG-ATAAATAGA
1 TAAATAGGTACAGAGAAT-AATAAA
*
5099 TAAATAGATACAGAGAATAATAAA
1 TAAATAGGTACAGAGAATAATAAA
5123 TAAATAGGTA
1 TAAATAGGTA
5133 GCTAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (24 bp):
TAAATAGGTACAGAGAATAATAAA
Found at i:5187 original size:4 final size:4
Alignment explanation
Indices: 5172--5365 Score: 111
Period size: 4 Copynumber: 48.8 Consensus size: 4
5162 AGATAATGGC
* * * *
5172 TAAA TTAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TATA T-AA TAAT
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * *
5218 TAAA TTAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA
* * *
5267 -AAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA TAACAA TTAA -AAA
1 TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA T-A-AA TAAA TAAA
* * *
5314 TAAA TAAA TAAA TAAA T-AG TAAA TAAA TAGA TAATA GTAAA TAAA TAGA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA
5363 TAA
1 TAA
5366 TAGTTTAAAA
Statistics
Matches: 143, Mismatches: 28, Indels: 38
0.68 0.13 0.18
Matches are distributed among these distances:
3 20 0.14
4 105 0.73
5 11 0.08
6 7 0.05
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:5202 original size:19 final size:19
Alignment explanation
Indices: 5180--5369 Score: 98
Period size: 19 Copynumber: 9.1 Consensus size: 19
5170 GCTAAATTAA
5180 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
5199 TAAATAAATATATAATAATTAAATTAA
1 TAAAT--A-A-A-AA-GA-TAAA-TAG
5226 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
5245 TAAATAAATAGATAATAGTTAAAAA
1 TAAATAAAAAGATAA-A--T---AG
5270 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
5289 TAAATAAATAGATAACAATTAAAAA
1 TAAATAAAAAGAT-A-AA-T---AG
5314 TAAATAAATAA-ATAAATAG
1 TAAATAAA-AAGATAAATAG
*
5333 TAAATAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
*
5351 TAAATAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
5369 T
1 T
5370 TTAAAAAAAT
Statistics
Matches: 136, Mismatches: 13, Indels: 45
0.70 0.07 0.23
Matches are distributed among these distances:
18 25 0.18
19 45 0.33
20 6 0.04
21 4 0.03
22 7 0.05
23 4 0.03
24 5 0.04
25 28 0.21
26 5 0.04
27 7 0.05
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:5202 original size:27 final size:26
Alignment explanation
Indices: 5154--5259 Score: 82
Period size: 27 Copynumber: 4.2 Consensus size: 26
5144 TAATAATAAC
* *
5154 AAATAAATAGATAATGGCTAAATTAAT
1 AAATAAAAAGATAATAG-TAAATTAAT
5181 AAATAAAAAGATAAATAGT--A--AAT
1 AAATAAAAAGAT-AATAGTAAATTAAT
* *
5204 AAATATATA-ATAAT--TAAATTAAT
1 AAATAAAAAGATAATAGTAAATTAAT
*
5227 AAATAAAAAGATAAATAGTAAATAAAT
1 AAATAAAAAGAT-AATAGTAAATTAAT
*
5254 AGATAA
1 AAATAA
5260 TAGTTAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
21 4 0.06
22 2 0.03
23 20 0.32
24 2 0.03
25 4 0.06
27 25 0.40
28 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (26 bp):
AAATAAAAAGATAATAGTAAATTAAT
Found at i:5287 original size:44 final size:44
Alignment explanation
Indices: 5154--5365 Score: 291
Period size: 44 Copynumber: 4.7 Consensus size: 44
5144 TAATAATAAC
* *
5154 AAATAAATAGATAATGGCTAAATTAATAAATAAAAAGATAAATAGT
1 AAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATAAATAGT
* *
5200 AAATAAATATATAATAATTAAATTAATAAATAAAAAGATAAATAGT
1 AAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATAAATAGT
5246 AAATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGT
1 AAATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGT
* *
5290 AAATAAATAGATAACAATTAAAAATAAATAAATAA-ATAAATAGT
1 AAATAAATAGATAATAGTTAAAAATAAATAAA-AAGATAAATAGT
* *
5334 AAATAAATAGATAATAGTAAATAAATAGATAA
1 AAATAAATAGATAATAGTTAA-AAATAAATAA
5366 TAGTTTAAAA
Statistics
Matches: 152, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
44 79 0.52
45 11 0.07
46 62 0.41
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (44 bp):
AAATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGT
Found at i:5365 original size:62 final size:62
Alignment explanation
Indices: 5270--5408 Score: 192
Period size: 62 Copynumber: 2.2 Consensus size: 62
5260 TAGTTAAAAA
* *
5270 TAAATAAAAAGATAAATAGTAAATAAATAGATAACAATTAAAAATAAAT-AAATAAATAAATAG
1 TAAATAAATAGAT-AATAGTAAATAAATAGATAACAATTAAAAA-AAATAAAAAAAATAAATAG
* * *
5333 TAAATAAATAGATAATAGTAAATAAATAGATAATAGTTTAAAAAAATAAAAAAAATAAATAG
1 TAAATAAATAGATAATAGTAAATAAATAGATAACAATTAAAAAAAATAAAAAAAATAAATAG
*
5395 TGAATAAATA-ATAA
1 TAAATAAATAGATAA
5409 AAAAAATCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
61 8 0.12
62 49 0.71
63 12 0.17
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (62 bp):
TAAATAAATAGATAATAGTAAATAAATAGATAACAATTAAAAAAAATAAAAAAAATAAATAG
Found at i:5385 original size:106 final size:106
Alignment explanation
Indices: 5204--5408 Score: 299
Period size: 106 Copynumber: 1.9 Consensus size: 106
5194 AATAGTAAAT
* *
5204 AAATATATAATAATTAAATTAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAA
1 AAATAAATAATAAATAAATTAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAA
*
5269 ATAAATAAAAAGATAAATAGTAAATAAATAGATAACAATTAA
66 ATAAATAAAAAAATAAATAGTAAATAAATA-ATAACAATTAA
* * *
5311 AAATAAATAAATAAATAAA-TAGTAAATAAATAGAT-AATAGTAAATAAATAGATAATAGTTTAA
1 AAATAAAT-AATAAATAAATTAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAA
*
5374 AA-AAATAAAAAAAATAAATAGTGAATAAATAATAA
65 AATAAAT-AAAAAAATAAATAGTAAATAAATAATAA
5409 AAAAAATCTT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
105 8 0.09
106 51 0.57
107 21 0.24
108 9 0.10
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.26
Consensus pattern (106 bp):
AAATAAATAATAAATAAATTAATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAA
ATAAATAAAAAAATAAATAGTAAATAAATAATAACAATTAA
Found at i:5409 original size:18 final size:17
Alignment explanation
Indices: 5237--5409 Score: 63
Period size: 18 Copynumber: 10.3 Consensus size: 17
5227 AAATAAAAAG
5237 ATAAATAGTAAATAAATA
1 ATAAATAGT-AATAAATA
5255 GAT-AATAGTTAA-AAATAA
1 -ATAAATAG-TAATAAAT-A
* *
5273 ATAAAAAGATAA-ATAGTAA
1 ATAAATAG-TAATA-AAT-A
* *
5292 ATAAATAGATAACAATTA
1 ATAAATAG-TAATAAATA
5310 A-AAATA--AATAAATAA
1 ATAAATAGTAATAAAT-A
5325 ATAAATAGTAAATAAATA
1 ATAAATAGT-AATAAATA
5343 GAT-AATAGTAAATAAATA
1 -ATAAATAGT-AATAAATA
*
5361 GAT-AATAGT--TTAA-A
1 -ATAAATAGTAATAAATA
5375 A-AAATA--AA-AAA-A
1 ATAAATAGTAATAAATA
5387 ATAAATAGTGAATAAATA
1 ATAAATAGT-AATAAATA
5405 ATAAA
1 ATAAA
5410 AAAAATCTTT
Statistics
Matches: 125, Mismatches: 9, Indels: 41
0.71 0.05 0.23
Matches are distributed among these distances:
12 4 0.03
13 10 0.08
14 6 0.05
15 5 0.04
16 7 0.06
17 14 0.11
18 49 0.39
19 29 0.23
20 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (17 bp):
ATAAATAGTAATAAATA
Done.