Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010098.1 Corchorus capsularis cultivar CVL-1 contig10119, 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: 54573
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1108 original size:24 final size:24
Alignment explanation
Indices: 1055--1108 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1045 TTATTTGTGT
*
1055 TTTAATTTTTAAATTTGATTTTTA
1 TTTAAATTTTAAATTTGATTTTTA
** *
1079 AATAAATTTT-AATTATTATTTTTA
1 TTTAAATTTTAAATT-TGATTTTTA
1103 TTTAAA
1 TTTAAA
1109 AAATTAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTAAATTTTAAATTTGATTTTTA
Found at i:8098 original size:2 final size:2
Alignment explanation
Indices: 8091--8118 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8081 TGAGAAATGC
8091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8119 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12125 original size:61 final size:63
Alignment explanation
Indices: 12021--12149 Score: 183
Period size: 62 Copynumber: 2.1 Consensus size: 63
12011 TTTCGCACAC
*
12021 ATATGTCAATGGAAAATGAATAACAAATGCTCTTAAAGATACTCTTCAG-CCTTAAGGTTACT
1 ATATATCAATGGAAAATGAATAACAAATGCTCTTAAAGATACTCTTCAGTCCTTAAGGTTACT
** * *
12083 -TATATCAATGGAAAAATGAATAATGAATGCTCTT-AAGATACTCTTTAGTCTTTAAGGTTACT
1 ATATATCAATGG-AAAATGAATAACAAATGCTCTTAAAGATACTCTTCAGTCCTTAAGGTTACT
12145 ATATA
1 ATATA
12150 ACTTGATCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 23 0.39
62 32 0.54
63 4 0.07
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (63 bp):
ATATATCAATGGAAAATGAATAACAAATGCTCTTAAAGATACTCTTCAGTCCTTAAGGTTACT
Found at i:19338 original size:2 final size:2
Alignment explanation
Indices: 19331--19362 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19321 AAGTACTGGT
19331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19363 ATTAAGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20630 original size:2 final size:2
Alignment explanation
Indices: 20623--20650 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20613 GAATCAATAA
20623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20651 TATGAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24272 original size:107 final size:107
Alignment explanation
Indices: 24118--24383 Score: 408
Period size: 107 Copynumber: 2.5 Consensus size: 107
24108 AGTTTAGCCT
* * * *
24118 TAATTTCATTAAGTTTAGCCCCAAATTAAAATTTTAGTTTTACTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAATTCCAAAATT
*
24183 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAAAACAAAAC
*
24225 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAATTCCAAAATT
* *
24290 AATAATTTATTGTTATAGGGTTTTAGAAATAAAAAATATAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAAAACAAAAC
* * **
24332 TAAAATTCACTAAGTTTAG-TCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 T-AATTTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGT
24384 TAGAAAAATT
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
107 130 0.89
108 16 0.11
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAATTCCAAAATT
AATAATTTATTGTTATAGGGTTTTAGAAATAAAAAACAAAAC
Found at i:25969 original size:15 final size:15
Alignment explanation
Indices: 25945--25976 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25935 AGAGGAAAAA
*
25945 CTGAATTTTTGGGTT
1 CTGAAATTTTGGGTT
25960 CTGAAATTTTGGGTT
1 CTGAAATTTTGGGTT
25975 CT
1 CT
25977 TGCAATGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (15 bp):
CTGAAATTTTGGGTT
Found at i:28048 original size:7 final size:7
Alignment explanation
Indices: 28036--28071 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
28026 CGTAGTAATT
28036 TTTCTTC
1 TTTCTTC
28043 TTTCTTC
1 TTTCTTC
28050 TTTCTTC
1 TTTCTTC
*
28057 TCTCTTC
1 TTTCTTC
28064 TTTCTTC
1 TTTCTTC
28071 T
1 T
28072 ATTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTCTTC
Found at i:30640 original size:16 final size:16
Alignment explanation
Indices: 30602--30643 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
30592 TTATTTACAA
**
30602 GTGAAATTT-TTTTTG
1 GTGAAATTTATTAGTG
30617 GTGAAAATTTATTAGTG
1 GTG-AAATTTATTAGTG
30634 GTGAAATTTA
1 GTGAAATTTA
30644 CAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 13 0.57
17 7 0.30
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (16 bp):
GTGAAATTTATTAGTG
Found at i:41791 original size:10 final size:9
Alignment explanation
Indices: 41775--41800 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41765 GTACCACTCA
41775 ATTTTTTTT
1 ATTTTTTTT
41784 ATTTTTTTT
1 ATTTTTTTT
41793 ATTTTTTT
1 ATTTTTTT
41801 GGCAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:44397 original size:51 final size:51
Alignment explanation
Indices: 44337--44435 Score: 198
Period size: 51 Copynumber: 1.9 Consensus size: 51
44327 GCCAACACAA
44337 TGTTCAGACAAGGGTTCTCTTTCCCCGTCTTTAACACCACTGGAGCTCTGC
1 TGTTCAGACAAGGGTTCTCTTTCCCCGTCTTTAACACCACTGGAGCTCTGC
44388 TGTTCAGACAAGGGTTCTCTTTCCCCGTCTTTAACACCACTGGAGCTC
1 TGTTCAGACAAGGGTTCTCTTTCCCCGTCTTTAACACCACTGGAGCTC
44436 CCAGCAGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31
Consensus pattern (51 bp):
TGTTCAGACAAGGGTTCTCTTTCCCCGTCTTTAACACCACTGGAGCTCTGC
Done.