Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006599.1 Corchorus capsularis cultivar CVL-1 contig06620, 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: 1998
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:48 original size:26 final size:26
Alignment explanation
Indices: 12--78 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
2 CTATCAATTA
12 TTATTAATTTATATTAGTTTTAGTTG
1 TTATTAATTTATATTAGTTTTAGTTG
38 TTATTAATTTATATTAGTTTTAGTTG
1 TTATTAATTTATATTAGTTTTAGTTG
*
64 TTATTAATTTCTATT
1 TTATTAATTTATATT
79 TTTATTCTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.27, C:0.01, G:0.09, T:0.63
Consensus pattern (26 bp):
TTATTAATTTATATTAGTTTTAGTTG
Found at i:181 original size:27 final size:30
Alignment explanation
Indices: 151--208 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 30
141 TTCTATTCGA
*
151 TTTATAAATCTAT-TT-TATATT-TTATAT
1 TTTATAAATCTATATTAGATATTATTATAT
178 TTTATAAATCTATATTAGATATTATTATAT
1 TTTATAAATCTATATTAGATATTATTATAT
208 T
1 T
209 AGATATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.48
28 2 0.07
29 5 0.19
30 7 0.26
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTATAAATCTATATTAGATATTATTATAT
Found at i:206 original size:15 final size:15
Alignment explanation
Indices: 188--221 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
178 TTTATAAATC
*
188 TATATTAGATATTAT
1 TATATTAGATATAAT
203 TATATTAGATATAAT
1 TATATTAGATATAAT
218 TATA
1 TATA
222 ATATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATTAGATATAAT
Found at i:270 original size:25 final size:25
Alignment explanation
Indices: 249--357 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
239 ATCTAATATT
249 ATTATAATAATAATTTAGTAATTTA
1 ATTATAATAATAATTTAGTAATTTA
274 ATTATAATAATAATTTAGTAATTTAA
1 ATTATAATAATAATTTAGTAATTT-A
*
300 ATT-TAAT-A-AA-TTA-TAACTTA
1 ATTATAATAATAATTTAGTAATTTA
* * *
320 ATAAT-ATAATAACTTAATAATCTTA
1 ATTATAATAATAATTTAGTAAT-TTA
345 ATT-TAATAATAAT
1 ATTATAATAATAAT
358 ATATTATTAG
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
20 5 0.07
21 7 0.10
22 5 0.07
23 5 0.07
24 5 0.07
25 40 0.56
26 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTATAATAATAATTTAGTAATTTA
Found at i:352 original size:14 final size:13
Alignment explanation
Indices: 259--354 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 13
249 ATTATAATAA
*
259 TAATTTAGTAATT
1 TAATTTAATAATT
272 TAATTATAATAA--
1 TAATT-TAATAATT
*
284 TAATTTAGTAATT
1 TAATTTAATAATT
297 TAAATTTAATAAATT
1 T-AATTTAAT-AATT
*
312 ATAACTTAATAATAT
1 -TAATTTAATAAT-T
*
327 AATAACTTAATAATCT
1 --TAATTTAATAAT-T
343 TAATTTAATAAT
1 TAATTTAATAAT
355 AATATATTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
11 5 0.07
12 5 0.07
13 6 0.09
14 26 0.38
15 12 0.17
16 15 0.22
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (13 bp):
TAATTTAATAATT
Found at i:354 original size:8 final size:8
Alignment explanation
Indices: 256--354 Score: 73
Period size: 8 Copynumber: 12.9 Consensus size: 8
246 ATTATTATAA
256 TAATAATT
1 TAATAATT
*
264 TAGTAATT
1 TAATAATT
* *
272 TAATTATAA
1 TAATAAT-T
281 TAATAATT
1 TAATAATT
*
289 TAGTAATT
1 TAATAATT
297 T-A-AATT
1 TAATAATT
*
303 TAATAAAT
1 TAATAATT
*
311 T-ATAACT
1 TAATAATT
*
318 TAATAATA
1 TAATAATT
*
326 TAATAACT
1 TAATAATT
*
334 TAATAATC
1 TAATAATT
342 T--TAATT
1 TAATAATT
348 TAATAAT
1 TAATAAT
355 AATATATTAT
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
6 10 0.15
7 7 0.10
8 45 0.66
9 6 0.09
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (8 bp):
TAATAATT
Found at i:388 original size:17 final size:16
Alignment explanation
Indices: 371--445 Score: 91
Period size: 15 Copynumber: 4.7 Consensus size: 16
361 TTATTAGATA
*
371 ATTTATAAATAGATAT
1 ATTTATAAATAGAAAT
387 AATTTATAAATAGAAAT
1 -ATTTATAAATAGAAAT
*
404 A-TTCTAAATAGAAAT
1 ATTTATAAATAGAAAT
419 ATTT-TAAATAGAAAT
1 ATTTATAAATAGAAAT
*
434 ATATATATAATA
1 ATTTATA-AATA
446 TAATTTCTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
15 28 0.54
16 5 0.10
17 19 0.37
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (16 bp):
ATTTATAAATAGAAAT
Found at i:389 original size:32 final size:32
Alignment explanation
Indices: 353--449 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 32
343 TAATTTAATA
* *
353 ATAATATATTATTAGATAAT-TTATAAATAGAT
1 ATAATATATAAATAGA-AATATTATAAATAGAT
* * *
385 ATAATTTATAAATAGAAATATTCTAAATAGAA
1 ATAATATATAAATAGAAATATTATAAATAGAT
* *
417 AT-AT-TTTAAATAGAAATA-TATATATA-AT
1 ATAATATATAAATAGAAATATTATAAATAGAT
445 ATAAT
1 ATAAT
450 TTCTAATTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
28 3 0.06
29 8 0.15
30 13 0.24
31 5 0.09
32 25 0.46
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (32 bp):
ATAATATATAAATAGAAATATTATAAATAGAT
Found at i:1536 original size:13 final size:13
Alignment explanation
Indices: 1518--1544 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1508 GTCACCGGAT
1518 TCCTTCAATTCAA
1 TCCTTCAATTCAA
1531 TCCTTCAATTCAA
1 TCCTTCAATTCAA
1544 T
1 T
1545 ATGTATGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (13 bp):
TCCTTCAATTCAA
Done.