Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013829.1 Corchorus capsularis cultivar CVL-1 contig13850, 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: 3863
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Found at i:3119 original size:23 final size:23
Alignment explanation
Indices: 3044--3134 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
3034 CTGATTATTC
*
3044 TTTA-TCTTGTACTGATTACTAT
1 TTTACTCTTGTACTGATTACCAT
* *
3066 TTTACTCTGGT--TGATTACCTT
1 TTTACTCTTGTACTGATTACCAT
*
3087 TTTACT-TTTTACTGATTACCAT
1 TTTACTCTTGTACTGATTACCAT
* *
3109 TTTACTCTTTTACTGATTACTAT
1 TTTACTCTTGTACTGATTACCAT
3132 TTT
1 TTT
3135 CTGCTCCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.03
21 14 0.24
22 19 0.33
23 23 0.40
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTACTCTTGTACTGATTACCAT
Found at i:3128 original size:15 final size:15
Alignment explanation
Indices: 3110--3165 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
3100 GATTACCATT
3110 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
3125 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
3138 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
*
3153 TTACTCTTCTACT
1 TTACTCTTTTACT
3166 TCTTACTGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
15 18 0.58
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.55
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:3192 original size:21 final size:21
Alignment explanation
Indices: 3146--3233 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
3136 TGCTCCTTTT
*
3146 TTACTGATTACTCTTCT-ACTTC
1 TTACTGATTACTATT-TGAC-TC
3168 TTACTGATTACTATTTGACTC
1 TTACTGATTACTATTTGACTC
* *
3189 TTACTAATTACCACTTTG-CTC
1 TTACTGATTACTA-TTTGACTC
* * * *
3210 TCATTGATTACTGTTTTACTC
1 TTACTGATTACTATTTGACTC
3231 TTA
1 TTA
3234 ATGACTACCT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.06
21 30 0.57
22 20 0.38
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.49
Consensus pattern (21 bp):
TTACTGATTACTATTTGACTC
Found at i:3262 original size:35 final size:35
Alignment explanation
Indices: 3214--3302 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
3204 TTGCTCTCAT
*
3214 TGATTACTGTTTTACTCTTAATGACTACCTTCTAC
1 TGATTACTATTTTACTCTTAATGACTACCTTCTAC
* * ** * *
3249 TGATCACTATTTTACTCTTAATGGCTGTCTTTTGC
1 TGATTACTATTTTACTCTTAATGACTACCTTCTAC
3284 TGATTACTATTTTACTCTT
1 TGATTACTATTTTACTCTT
3303 TACTGATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (35 bp):
TGATTACTATTTTACTCTTAATGACTACCTTCTAC
Found at i:3513 original size:31 final size:31
Alignment explanation
Indices: 3457--3522 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
3447 AATTACTGAT
*
3457 TTACTGATTACTATTTTTACCTTGACTCTTAA
1 TTACTGATTAC-ATTTTAACCTTGACTCTTAA
3489 TTACTGATTA-ATTTCTAACCTTGACTCTTAA
1 TTACTGATTACATTT-TAACCTTGACTCTTAA
3520 TTA
1 TTA
3523 TCAATTTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 18 0.56
32 10 0.31
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (31 bp):
TTACTGATTACATTTTAACCTTGACTCTTAA
Found at i:3592 original size:55 final size:53
Alignment explanation
Indices: 3532--3664 Score: 136
Period size: 47 Copynumber: 2.5 Consensus size: 53
3522 ATCAATTTAC
3532 TGATTACTATGTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
1 TGATTA-TAT-TTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
* * *
3587 TGATTA-A---TCT-CTT-TTTACTGATTTACTGATTACCATCACTTTGATTT
1 TGATTATATTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
*
3634 TGATTAATCTCTTTTTAC-TGATTTACTGATT
1 TGATT-ATAT-TTTTTACTTGA-TTACTGATT
3665 ACCATCACCG
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
47 37 0.59
48 4 0.06
49 2 0.03
53 4 0.06
54 1 0.02
55 15 0.24
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (53 bp):
TGATTATATTTTTTACTTGATTACTGATTTACTGATTACCATCACTTTGACTT
Found at i:3617 original size:26 final size:26
Alignment explanation
Indices: 3587--3665 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
3577 ACTTTGACTT
3587 TGATTAATCTCTTTTTACTGATTTAC
1 TGATTAATCTCTTTTTACTGATTTAC
*
3613 TGATTACCATCAC---TT--TGATTT--
1 TGATTA--ATCTCTTTTTACTGATTTAC
3634 TGATTAATCTCTTTTTACTGATTTAC
1 TGATTAATCTCTTTTTACTGATTTAC
3660 TGATTA
1 TGATTA
3666 CCATCACCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
19 4 0.10
21 6 0.14
22 2 0.05
23 6 0.14
24 6 0.14
25 2 0.05
26 12 0.29
28 4 0.10
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (26 bp):
TGATTAATCTCTTTTTACTGATTTAC
Found at i:3623 original size:47 final size:47
Alignment explanation
Indices: 3554--3713 Score: 259
Period size: 47 Copynumber: 3.4 Consensus size: 47
3544 TTTTACTTGA
3554 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
*
3601 TTACTGATTTACTGATTACCATCACTTTGATTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
** * * *
3648 TTACTGATTTACTGATTACCATCACCGTGACTCTGTTTAAGCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
3695 TTACTGA-TTACTGATTACC
1 TTACTGATTTACTGATTACC
3714 CCTTTTTACT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 12 0.11
47 94 0.89
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
Done.