Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009394.1 Corchorus capsularis cultivar CVL-1 contig09415, 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: 3997
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:457 original size:11 final size:12
Alignment explanation
Indices: 434--489 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
424 TTTTTTTAAA
434 AAAAATAATAAT
1 AAAAATAATAAT
446 AAAAATAA-AAT
1 AAAAATAATAAT
457 --AAAT-ATAAT
1 AAAAATAATAAT
* *
466 AAATATAATAAA
1 AAAAATAATAAT
478 AAAAATATATAA
1 AAAAATA-ATAA
490 ATTGCTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
8 1 0.03
9 7 0.19
11 6 0.17
12 18 0.50
13 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:460 original size:9 final size:9
Alignment explanation
Indices: 430--490 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
420 CGTTTTTTTT
*
430 TAAAAAAAA
1 TAAATAAAA
439 T-AATAATAA
1 TAAATAA-AA
448 -AAATAAAA
1 TAAATAAAA
*
456 TAAATATAA
1 TAAATAAAA
*
465 TAAATATAA
1 TAAATAAAA
*
474 TAAAAAAAA
1 TAAATAAAA
*
483 TATATAAA
1 TAAATAAA
491 TTGCTGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.14
9 37 0.86
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
TAAATAAAA
Found at i:464 original size:20 final size:21
Alignment explanation
Indices: 430--490 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
420 CGTTTTTTTT
430 TAAAAAAAATAATAATAAAAA
1 TAAAAAAAATAATAATAAAAA
* *
451 TAAAATAAAT-ATAATAAATA
1 TAAAAAAAATAATAATAAAAA
471 TAATAAAAAA-AATATATAAA
1 TAA-AAAAAATAATA-ATAAA
491 TTGCTGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 12 0.35
21 17 0.50
22 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAAAATAATAATAAAAA
Found at i:475 original size:23 final size:22
Alignment explanation
Indices: 430--491 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
420 CGTTTTTTTT
*
430 TAAAAAAAATA-AT-AATAAAAA
1 TAAAAAAAATATATAAAT-ATAA
*
451 TAAAATAAATATAATAAATATAA
1 TAAAAAAAATAT-ATAAATATAA
474 TAAAAAAAATATATAAAT
1 TAAAAAAAATATATAAAT
492 TGCTGAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 10 0.29
22 6 0.17
23 16 0.46
24 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAAAAAATATATAAATATAA
Found at i:483 original size:14 final size:14
Alignment explanation
Indices: 430--490 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
420 CGTTTTTTTT
430 TAAAAAAAATAATAA
1 TAAAAAAAAT-ATAA
445 TAAAAATAAA-ATAAA
1 TAAAAA-AAATAT-AA
* *
460 TATAATAAATATAA
1 TAAAAAAAATATAA
474 TAAAAAAAATAT-A
1 TAAAAAAAATATAA
487 TAAA
1 TAAA
491 TTGCTGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.13
14 17 0.44
15 14 0.36
16 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAAAAAATATAA
Found at i:3307 original size:2 final size:2
Alignment explanation
Indices: 3300--3334 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3290 AGGTTTTAGG
3300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3335 CTAAGTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.