Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003251.1 Corchorus capsularis cultivar CVL-1 contig03259, 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, 850
Length: 1417
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Found at i:377 original size:15 final size:15
Alignment explanation
Indices: 360--413 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
350 ATTGCCATTT
*
360 TACTCTTTTACTGAT
1 TACTCTTTTACTGAC
*
375 TACTATTTT-CTG-C
1 TACTCTTTTACTGAC
*
388 T-CTTTTTTACTGAC
1 TACTCTTTTACTGAC
*
402 TACCCTTTTACT
1 TACTCTTTTACT
414 TTCTACAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 6 0.19
13 4 0.13
14 5 0.16
15 16 0.52
ACGTcount: A:0.17, C:0.24, G:0.06, T:0.54
Consensus pattern (15 bp):
TACTCTTTTACTGAC
Found at i:441 original size:43 final size:45
Alignment explanation
Indices: 391--499 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 45
381 TTTCTGCTCT
**
391 TTTTTACTGACTACCCTTTTACTTTC-TACAGATTGCCT-TT-AGC
1 TTTTTACTGACTACCCTTTTACTTTCTTACAGATTAACTATTCA-C
* *
434 TTTTTACTGATTA-CCTTTTAC-TTCTTACTGATTAACTATTCAC
1 TTTTTACTGACTACCCTTTTACTTTCTTACAGATTAACTATTCAC
**
477 TTTTTACTGACTACTATTTTACT
1 TTTTTACTGACTACCCTTTTACT
500 CTTGTTGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
41 3 0.06
42 17 0.31
43 27 0.50
44 7 0.13
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.50
Consensus pattern (45 bp):
TTTTTACTGACTACCCTTTTACTTTCTTACAGATTAACTATTCAC
Found at i:461 original size:21 final size:21
Alignment explanation
Indices: 394--550 Score: 81
Period size: 21 Copynumber: 7.4 Consensus size: 21
384 CTGCTCTTTT
*
394 TTACTGACTACCCTTTTACTT-
1 TTACTGATTA-CCTTTTACTTC
* * *
415 TCTACAGATTGCC-TTTAGCTTT
1 T-TACTGATTACCTTTTA-CTTC
437 TTACTGATTACCTTTTACTTC
1 TTACTGATTACCTTTTACTTC
* * *
458 TTACTGATTAACTATTCACTTT
1 TTACTGATTACCT-TTTACTTC
* *
480 TTACTGACTACTATTTTAC-TC
1 TTACTGATTAC-CTTTTACTTC
** * *
501 TTGTTGATTACCATTTAC-CC
1 TTACTGATTACCTTTTACTTC
* * *
521 TTTCAGA-TACCATTTTACTTT
1 TTACTGATTACC-TTTTACTTC
542 TTACTGATT
1 TTACTGATT
551 GCATTTTATA
Statistics
Matches: 99, Mismatches: 28, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.04
20 19 0.19
21 44 0.44
22 31 0.31
23 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTTC
Found at i:556 original size:21 final size:21
Alignment explanation
Indices: 337--569 Score: 93
Period size: 22 Copynumber: 10.6 Consensus size: 21
327 GATCATCTTC
* *
337 TTACTTTTTATTGATTGCCATT
1 TTACTTTTTACTGATT-ACATT
359 TTACTCTTTTACTGATTACTATTT
1 TTACT-TTTTACTGATTAC-A-TT
* * *
383 TCTGCTCTTTTTTACTGACTACCCTT
1 T-T--AC-TTTTTACTGATTA-CATT
* * * *
409 TTACTTTCTACAGATTGC-CT
1 TTACTTTTTACTGATTACATT
*
429 TTAGCTTTTTACTGATTACCTT
1 TTA-CTTTTTACTGATTACATT
*
451 TTACTTCTTACTGATTA-ACTAT
1 TTACTTTTTACTGATTACA-T-T
* *
473 TCACTTTTTACTGACTACTATT
1 TTACTTTTTACTGATTAC-ATT
*
495 TTACTCTTGT--TGATTACCA-T
1 TTACT-TTTTACTGATTA-CATT
** *
515 TTACCCTTT-CAGA-TACCATT
1 TTACTTTTTACTGATTA-CATT
*
535 TTACTTTTTACTGATTGCATTT
1 TTACTTTTTACTGATTACA-TT
557 TATACTTTTTACT
1 T-TACTTTTTACT
570 CTTCATTACT
Statistics
Matches: 158, Mismatches: 31, Indels: 43
0.68 0.13 0.19
Matches are distributed among these distances:
19 7 0.04
20 19 0.12
21 38 0.24
22 44 0.28
23 27 0.17
24 4 0.03
25 2 0.01
26 3 0.02
27 12 0.08
28 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (21 bp):
TTACTTTTTACTGATTACATT
Found at i:807 original size:55 final size:55
Alignment explanation
Indices: 746--1053 Score: 445
Period size: 55 Copynumber: 5.6 Consensus size: 55
736 TATCAATTTA
* * * * * * * *
746 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACCATTACATTGACT
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
* * * *
801 CTGATTAATCTCGTTTTACTTAATTACCGGTTTACTGATTACTACTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
*
856 CTGATTAATCTCTTTTTACTTAATTACCGATTTATTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
*
911 CTTGATTAATCTCTTTTTACTTAATTACCAATTTACTGATTACTATTACCTTAACT
1 C-TGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
*
967 CTAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
* * *
1022 CTAATTAATCCCTTTTTACTTAATTACTGATT
1 CTGATTAATCTCTTTTTACTTAATTACCGATT
1054 GCCCCCTTTC
Statistics
Matches: 231, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 178 0.77
56 53 0.23
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACT
Found at i:947 original size:166 final size:166
Alignment explanation
Indices: 747--1053 Score: 461
Period size: 166 Copynumber: 1.8 Consensus size: 166
737 ATCAATTTAC
* * ** * *
747 TGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACCATTACATTGACTCTGATTAATCT
1 TGATTAATATCTTTTTACCTAATTACCAATTTACTGATTACCATTACATTAACTCTAATTAATCT
* * * *
812 CGTTTTACTTAATTACCGGTTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTTACTT
66 CGTTTTACTTAATTACCGATTTACTGATTACTACTACCTTAACTCTAATTAATCCCTTTTTACTT
877 AATTACCGATTTATTGATTACTATTACCTTAACTCT
131 AATTACCGATTTATTGATTACTATTACCTTAACTCT
* * * *
913 TGATTAATCTCTTTTTACTTAATTACCAATTTACTGATTACTATTACCTTAACTCTAATTAATCT
1 TGATTAATATCTTTTTACCTAATTACCAATTTACTGATTACCATTACATTAACTCTAATTAATCT
* *
978 CTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACTCTAATTAATCCCTTTTTACTT
66 CGTTTTACTTAATTACCGATTTACTGATTACTACTACCTTAACTCTAATTAATCCCTTTTTACTT
*
1043 AATTACTGATT
131 AATTACCGATT
1054 GCCCCCTTTC
Statistics
Matches: 124, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
166 124 1.00
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (166 bp):
TGATTAATATCTTTTTACCTAATTACCAATTTACTGATTACCATTACATTAACTCTAATTAATCT
CGTTTTACTTAATTACCGATTTACTGATTACTACTACCTTAACTCTAATTAATCCCTTTTTACTT
AATTACCGATTTATTGATTACTATTACCTTAACTCT
Found at i:961 original size:111 final size:110
Alignment explanation
Indices: 746--1048 Score: 444
Period size: 111 Copynumber: 2.7 Consensus size: 110
736 TATCAATTTA
* * * * * * * *
746 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACCATTACATTGACTCTGATTAATC
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACTCTGATTAATC
* ** *
811 TCGTTTTACTTAATTACCGGTTTACTGATTACTACTACCTTGACT
66 TCTTTTTACTTAATTACCAATTTACTGATTACTACTACCTTAACT
*
856 CTGATTAATCTCTTTTTACTTAATTACCGATTTATTGATTACTATTACCTTAACTCTTGATTAAT
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACTC-TGATTAAT
*
921 CTCTTTTTACTTAATTACCAATTTACTGATTACTATTACCTTAACT
65 CTCTTTTTACTTAATTACCAATTTACTGATTACTACTACCTTAACT
* *
967 CTAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACTCTAATTAATC
1 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACTCTGATTAATC
*
1032 CCTTTTTACTTAATTAC
66 TCTTTTTACTTAATTAC
1049 TGATTGCCCC
Statistics
Matches: 174, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
110 71 0.41
111 103 0.59
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (110 bp):
CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTAACTCTGATTAATC
TCTTTTTACTTAATTACCAATTTACTGATTACTACTACCTTAACT
Done.