Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012542.1 Corchorus capsularis cultivar CVL-1 contig12563, 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: 10172
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Found at i:37 original size:27 final size:27
Alignment explanation
Indices: 2--54 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1 C
* **
2 TTTTTAAAATATATTCTTTTACAATTT
1 TTTTTAAAAAATAAACTTTTACAATTT
29 TTTTTAAAAAATAAACTTTTACAATT
1 TTTTTAAAAAATAAACTTTTACAATT
55 ATTCTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTTAAAAAATAAACTTTTACAATTT
Found at i:65 original size:29 final size:30
Alignment explanation
Indices: 17--96 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 30
7 AAAATATATT
**
17 CTTTTACAATT-TT-TTTTAAAAAAT-AAA
1 CTTTTACAATTATTCTACTAAAAAATCAAA
* * *
44 CTTTTACAATTATTCTACT-AAAACTCTAT
1 CTTTTACAATTATTCTACTAAAAAATCAAA
73 CTTTTACAATTATTCTACTAAAAA
1 CTTTTACAATTATTCTACTAAAAA
97 CTCTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.25
28 7 0.16
29 22 0.50
30 4 0.09
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (30 bp):
CTTTTACAATTATTCTACTAAAAAATCAAA
Found at i:106 original size:29 final size:29
Alignment explanation
Indices: 44--107 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
34 AAAAAATAAA
44 CTTTTACAATTATTCTACTAAAACTCTAT
1 CTTTTACAATTATTCTACTAAAACTCTAT
73 CTTTTACAATTATTCTACTAAAAACTCTAT
1 CTTTTACAATTATTCTACT-AAAACTCTAT
103 -TTTTA
1 CTTTTA
108 TTCGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (29 bp):
CTTTTACAATTATTCTACTAAAACTCTAT
Found at i:1253 original size:108 final size:110
Alignment explanation
Indices: 981--1274 Score: 425
Period size: 109 Copynumber: 2.7 Consensus size: 110
971 ACTATTATAG
* * *
981 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA-T---TCTAATATCTTTATAATTACTT
**
1046 TATTTTTA-CAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
62 TATTTTTACCAAAAAATTTGGATATACTAAAAAATTTTCTAATATACAA
*
1094 TTTTATTATACTAAAAACTCTATTTTCATTTAATTAAA-TCTAATATCTTTATAATTACTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
*
1158 TTTACCAAAAAATTTGGATATATTAAAAAATTTTCTAATATACAA
66 TTTACCAAAAAATTTGGATATACTAAAAAATTTTCTAATATACAA
**
1203 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-AATAT-TTTATATGATTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATA--ATTACTTTA
1266 TTTTTACCA
64 TTTTTACCA
1275 TTTTAATTTA
Statistics
Matches: 167, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
108 36 0.22
109 79 0.47
110 18 0.11
113 34 0.20
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (110 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCTAATATCTTTATAATTACTTTATT
TTTACCAAAAAATTTGGATATACTAAAAAATTTTCTAATATACAA
Found at i:2236 original size:25 final size:23
Alignment explanation
Indices: 2208--2262 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
2198 AACCCTAAAT
*
2208 TTCATTTCTAACAACTTCTTCAAA
1 TTCATTTCTAACAA-ATCTTCAAA
*
2232 CTTCATTTTTAACAAATCTTCAAA
1 -TTCATTTCTAACAAATCTTCAAA
2256 TTCATTT
1 TTCATTT
2263 TCCTTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 8 0.29
25 13 0.46
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (23 bp):
TTCATTTCTAACAAATCTTCAAA
Found at i:2301 original size:26 final size:26
Alignment explanation
Indices: 2272--2339 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
2262 TTCCTTCATT
2272 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * *
2298 TTAATAATAAACTAATTAGATATTAA
1 TTAATCATAAACTAATTAAATACTAA
*
2324 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
2340 AAACTAAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:2302 original size:15 final size:15
Alignment explanation
Indices: 2272--2315 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2262 TTCCTTCATT
*
2272 TTAATCATAAACTAA
1 TTAATAATAAACTAA
2287 TT-A-AAT--ACTAA
1 TTAATAATAAACTAA
2298 TTAATAATAAACTAA
1 TTAATAATAAACTAA
2313 TTA
1 TTA
2316 GATATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 7 0.29
12 1 0.04
13 5 0.21
14 1 0.04
15 10 0.42
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATAATAAACTAA
Found at i:2706 original size:2 final size:2
Alignment explanation
Indices: 2699--2732 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2689 ACACCACCAG
2699 AT AT AT 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 AT AT AT
2733 TTTAAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5056 original size:13 final size:13
Alignment explanation
Indices: 5040--5066 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5030 AATTCATTGC
5040 TTTAATTACAAGT
1 TTTAATTACAAGT
5053 TTTAATTACAAGT
1 TTTAATTACAAGT
5066 T
1 T
5067 ATGCAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTAATTACAAGT
Found at i:6846 original size:5 final size:5
Alignment explanation
Indices: 6836--6862 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6826 TATTTGGGAA
6836 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
6863 GAAGTTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:9764 original size:2 final size:2
Alignment explanation
Indices: 9757--9790 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9747 ATTGCATACG
9757 AT AT AT 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 AT AT AT
9791 GAGTCCCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.