Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003304.1 Corchorus capsularis cultivar CVL-1 contig03312, 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, 600
Length: 1000
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Found at i:40 original size:15 final size:15
Alignment explanation
Indices: 22--84 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
12 AGATAAAGGG
22 TAATCAGTAAAAAGA
1 TAATCAGTAAAAAGA
37 TAATCAGTAAAGAATGA
1 TAATCAGTAAA-AA-GA
*
54 -AAT-AGT-AAAAGG
1 TAATCAGTAAAAAGA
*
66 TAATCAATAATAAAGA
1 TAATCAGTAA-AAAGA
82 TAA
1 TAA
85 GAATAATCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
12 1 0.03
13 5 0.13
14 4 0.10
15 15 0.38
16 12 0.31
17 2 0.05
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (15 bp):
TAATCAGTAAAAAGA
Found at i:129 original size:21 final size:21
Alignment explanation
Indices: 101--383 Score: 125
Period size: 21 Copynumber: 14.3 Consensus size: 21
91 TCTGTAAAAG
101 GTAAAATAGTAATCAGTAAGA
1 GTAAAATAGTAATCAGTAAGA
* * *
122 GCAAAATAGTAATCAATGAGA
1 GTAAAATAGTAATCAGTAAGA
* *
143 GCAAAATGGTAATCAGTAAAGA
1 GTAAAATAGTAATCAGT-AAGA
* *
165 GTAAAATAGTAATCATTAAAAA
1 GTAAAATAGTAATCAGT-AAGA
*
187 G-AAAGA-GGTAATCAGTAAAGA
1 GTAAA-ATAGTAATCAGT-AAGA
* *
208 GTAAAATAGTAATCAGCAAAA
1 GTAAAATAGTAATCAGTAAGA
229 GGT--AATCAGT-A--AG----A
1 -GTAAAAT-AGTAATCAGTAAGA
243 GTAAAATAGTAATCAGT-AGAA
1 GTAAAATAGTAATCAGTAAG-A
264 GGT--AATCAG---T-A--AAGA
1 -GTAAAAT-AGTAATCAGTAAGA
279 GTAAAATAGTAATC------A
1 GTAAAATAGTAATCAGTAAGA
*
294 GTAAAAGA-TAATCAGTAAGA
1 GTAAAATAGTAATCAGTAAGA
* *
314 GTAAAACAGTAACCAGTAAGA
1 GTAAAATAGTAATCAGTAAGA
* * * *
335 GCAAAGTGGTAATTAGTAAGA
1 GTAAAATAGTAATCAGTAAGA
*
356 GTCAAATAGTAATCAGTAAAGA
1 GTAAAATAGTAATCAGT-AAGA
378 GTAAAA
1 GTAAAA
384 GGTGATCAGT
Statistics
Matches: 199, Mismatches: 31, Indels: 63
0.68 0.11 0.22
Matches are distributed among these distances:
13 2 0.01
14 11 0.06
15 15 0.08
16 5 0.03
17 3 0.02
18 4 0.02
20 15 0.08
21 97 0.49
22 47 0.24
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (21 bp):
GTAAAATAGTAATCAGTAAGA
Found at i:135 original size:43 final size:44
Alignment explanation
Indices: 88--395 Score: 198
Period size: 43 Copynumber: 7.7 Consensus size: 44
78 AAGATAAGAA
* * *
88 TAATCTGTAAAAGGTAAAATAGTAATCAGT-AAGAGCAAAATAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
* * * *
131 TAATCAATGAGA-GCAAAATGGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
* *
174 TAATCATTAAAAAG-AAAGA-GGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAGGTAAA-ATGGTAATCAGTAAAGAGTAAAATAG
*
217 TAATC------A-GCAAAA-GGTAATCAGT-AAGAGTAAAATAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
252 TAATCAGT---A-G---AA-GGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
*
288 TAATCAGTAAAA-G----A---TAATCAGT-AAGAGTAAAACAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
* * * * * *
323 TAACCAGTAAGA-GCAAAGTGGTAATTAGT-AAGAGTCAAATAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
*
365 TAATCAGT-AAAGAGTAAAA-GGTGATCAGTAA
1 TAATCAGTAAAAG-GTAAAATGGTAATCAGTAA
396 TTCAAAGAGT
Statistics
Matches: 221, Mismatches: 23, Indels: 42
0.77 0.08 0.15
Matches are distributed among these distances:
35 53 0.24
36 41 0.19
37 4 0.02
38 3 0.01
39 2 0.01
41 2 0.01
42 48 0.22
43 66 0.30
44 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.21
Consensus pattern (44 bp):
TAATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATAG
Found at i:218 original size:15 final size:15
Alignment explanation
Indices: 157--219 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
147 AATGGTAATC
157 AGTAAAGAGTAAAAT
1 AGTAAAGAGTAAAAT
** *
172 AGTAATCATTAAAA-
1 AGTAAAGAGTAAAAT
186 AG-AAAGAGGT--AAT
1 AGTAAAGA-GTAAAAT
199 CAGTAAAGAGTAAAAT
1 -AGTAAAGAGTAAAAT
215 AGTAA
1 AGTAA
220 TCAGCAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
12 2 0.06
13 3 0.08
14 7 0.19
15 21 0.58
16 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.19, T:0.21
Consensus pattern (15 bp):
AGTAAAGAGTAAAAT
Found at i:232 original size:36 final size:35
Alignment explanation
Indices: 192--375 Score: 224
Period size: 35 Copynumber: 5.0 Consensus size: 35
182 AAAAAGAAAG
*
192 AGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAA
1 AGGTAATCAGT-AAGAGTAAAATAGTAATCAGTAAA
*
228 AGGTAATCAGTAAGAGTAAAATAGTAATCAGTAGA
1 AGGTAATCAGTAAGAGTAAAATAGTAATCAGTAAA
263 AGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAA
1 AGGTAATCAGT-AAGAGTAAAATAGTAATCAGTAAA
* * *
299 AGATAATCAGTAAGAGTAAAACAGTAACCAGTAAGAGCAA
1 AGGTAATCAGTAAGAGTAAAATAGTAATCAGT---A--AA
* *
339 AGTGGTAATTAGTAAGAGTCAAATAGTAATCAGTAAA
1 A--GGTAATCAGTAAGAGTAAAATAGTAATCAGTAAA
376 GAGTAAAAGG
Statistics
Matches: 129, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
35 52 0.40
36 44 0.34
37 2 0.02
38 1 0.01
39 1 0.01
40 3 0.02
42 26 0.20
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (35 bp):
AGGTAATCAGTAAGAGTAAAATAGTAATCAGTAAA
Found at i:270 original size:71 final size:71
Alignment explanation
Indices: 192--331 Score: 244
Period size: 71 Copynumber: 2.0 Consensus size: 71
182 AAAAAGAAAG
* * *
192 AGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
1 AGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTAACC
257 AGTAGA
66 AGTAGA
*
263 AGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAGTAAGAGTAAAACAGTAACC
1 AGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTAACC
328 AGTA
66 AGTA
332 AGAGCAAAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.21
Consensus pattern (71 bp):
AGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTAACC
AGTAGA
Found at i:282 original size:14 final size:15
Alignment explanation
Indices: 250--282 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
240 AGAGTAAAAT
250 AGTAATCAGTAGAAG
1 AGTAATCAGTAGAAG
265 -GTAATCAGTA-AAG
1 AGTAATCAGTAGAAG
278 AGTAA
1 AGTAA
283 AATAGTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.21
Consensus pattern (15 bp):
AGTAATCAGTAGAAG
Found at i:307 original size:14 final size:15
Alignment explanation
Indices: 278--311 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
268 ATCAGTAAAG
*
278 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
293 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
307 AGTAA
1 AGTAA
312 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:395 original size:42 final size:41
Alignment explanation
Indices: 293--395 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
283 AATAGTAATC
*
293 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
* * * * * *
334 AGCAAAGTGGTAATTAGTAAGAGTCAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAACAGTAACCAGT-AAG
*
377 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
396 TTCAAAGAGT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 5 0.10
42 36 0.73
43 8 0.16
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
Found at i:474 original size:13 final size:13
Alignment explanation
Indices: 458--504 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
448 GGTAATAAAT
458 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
471 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
485 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
498 AAAAGAG
1 AAAAGAG
505 TAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:475 original size:29 final size:28
Alignment explanation
Indices: 449--511 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
439 GTAAAAAGTG
449 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
* *
477 GTAATTAGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
504 GTAA-AAAT
1 GTAATAAAT
512 GATAAAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 18 0.58
28 11 0.35
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Done.