Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004682.1 Corchorus capsularis cultivar CVL-1 contig04698, 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, 699
Length: 1165
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Found at i:193 original size:18 final size:18
Alignment explanation
Indices: 170--205 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
160 AATTAAAATG
170 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
188 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
206 CAATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATCAATTCTTACTAT
Found at i:241 original size:26 final size:26
Alignment explanation
Indices: 212--278 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
202 CTATCAATTA
212 TTATTAATTTATATTAGTTTTAGTTG
1 TTATTAATTTATATTAGTTTTAGTTG
238 TTATTAATTTATATTAGTTTTAGTTG
1 TTATTAATTTATATTAGTTTTAGTTG
*
264 TTATTAATTTCTATT
1 TTATTAATTTATATT
279 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:381 original size:27 final size:30
Alignment explanation
Indices: 351--408 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 30
341 TTCTATTCGA
*
351 TTTATAAATCTAT-TT-TATATT-TTATAT
1 TTTATAAATCTATATTAGATATTATTATAT
378 TTTATAAATCTATATTAGATATTATTATAT
1 TTTATAAATCTATATTAGATATTATTATAT
408 T
1 T
409 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:406 original size:15 final size:15
Alignment explanation
Indices: 388--421 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
378 TTTATAAATC
*
388 TATATTAGATATTAT
1 TATATTAGATATAAT
403 TATATTAGATATAAT
1 TATATTAGATATAAT
418 TATA
1 TATA
422 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:470 original size:25 final size:25
Alignment explanation
Indices: 449--557 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
439 ATCTAATATT
449 ATTATAATAATAATTTAGTAATTTA
1 ATTATAATAATAATTTAGTAATTTA
474 ATTATAATAATAATTTAGTAATTTAA
1 ATTATAATAATAATTTAGTAATTT-A
*
500 ATT-TAAT-A-AA-TTA-TAACTTA
1 ATTATAATAATAATTTAGTAATTTA
* * *
520 ATAAT-ATAATAACTTAATAATCTTA
1 ATTATAATAATAATTTAGTAAT-TTA
545 ATT-TAATAATAAT
1 ATTATAATAATAAT
558 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:552 original size:14 final size:13
Alignment explanation
Indices: 459--554 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 13
449 ATTATAATAA
*
459 TAATTTAGTAATT
1 TAATTTAATAATT
472 TAATTATAATAA--
1 TAATT-TAATAATT
*
484 TAATTTAGTAATT
1 TAATTTAATAATT
497 TAAATTTAATAAATT
1 T-AATTTAAT-AATT
*
512 ATAACTTAATAATAT
1 -TAATTTAATAAT-T
*
527 AATAACTTAATAATCT
1 --TAATTTAATAAT-T
543 TAATTTAATAAT
1 TAATTTAATAAT
555 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:554 original size:8 final size:8
Alignment explanation
Indices: 456--554 Score: 73
Period size: 8 Copynumber: 12.9 Consensus size: 8
446 ATTATTATAA
456 TAATAATT
1 TAATAATT
*
464 TAGTAATT
1 TAATAATT
* *
472 TAATTATAA
1 TAATAAT-T
481 TAATAATT
1 TAATAATT
*
489 TAGTAATT
1 TAATAATT
497 T-A-AATT
1 TAATAATT
*
503 TAATAAAT
1 TAATAATT
*
511 T-ATAACT
1 TAATAATT
*
518 TAATAATA
1 TAATAATT
*
526 TAATAACT
1 TAATAATT
*
534 TAATAATC
1 TAATAATT
542 T--TAATT
1 TAATAATT
548 TAATAAT
1 TAATAAT
555 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:588 original size:17 final size:16
Alignment explanation
Indices: 571--645 Score: 91
Period size: 15 Copynumber: 4.7 Consensus size: 16
561 TTATTAGATA
*
571 ATTTATAAATAGATAT
1 ATTTATAAATAGAAAT
587 AATTTATAAATAGAAAT
1 -ATTTATAAATAGAAAT
*
604 A-TTCTAAATAGAAAT
1 ATTTATAAATAGAAAT
619 ATTT-TAAATAGAAAT
1 ATTTATAAATAGAAAT
*
634 ATATATATAATA
1 ATTTATA-AATA
646 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:589 original size:32 final size:32
Alignment explanation
Indices: 553--649 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 32
543 TAATTTAATA
* *
553 ATAATATATTATTAGATAAT-TTATAAATAGAT
1 ATAATATATAAATAGA-AATATTATAAATAGAT
* * *
585 ATAATTTATAAATAGAAATATTCTAAATAGAA
1 ATAATATATAAATAGAAATATTATAAATAGAT
* *
617 AT-AT-TTTAAATAGAAATA-TATATATA-AT
1 ATAATATATAAATAGAAATATTATAAATAGAT
645 ATAAT
1 ATAAT
650 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
Done.