Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015462.1 Corchorus capsularis cultivar CVL-1 contig15483, 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: 4973
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Found at i:946 original size:6 final size:6
Alignment explanation
Indices: 930--966 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
920 GAAAACAAAA
930 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
967 TGGCAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:1022 original size:6 final size:6
Alignment explanation
Indices: 1004--1041 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
994 AAAAGCATAC
1004 TTAGGG TTTAGGG TTAGGG TTAGGG TTAGGG TTTAGGG
1 TTAGGG -TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG
1042 CTCCAAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:1028 original size:12 final size:13
Alignment explanation
Indices: 1004--1041 Score: 69
Period size: 12 Copynumber: 3.0 Consensus size: 13
994 AAAAGCATAC
1004 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
1017 TTAGGG-TTAGGG
1 TTAGGGTTTAGGG
1029 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
1042 CTCCAAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:4223 original size:12 final size:12
Alignment explanation
Indices: 4206--4330 Score: 67
Period size: 12 Copynumber: 10.6 Consensus size: 12
4196 GAAATAGCTA
*
4206 CTGTTTTTATTG
1 CTGTTTTTGTTG
4218 CTGTTTTTTGTTG
1 CTG-TTTTTGTTG
* *
4231 ATGTTTTTGTTA
1 CTGTTTTTGTTG
* *
4243 CT-ATTTTATTG
1 CTGTTTTTGTTG
* *
4254 ATGTTTCTGTTG
1 CTGTTTTTGTTG
* *
4266 CTGGTATTGTTG
1 CTGTTTTTGTTG
* *
4278 CTGTTTTAG-GG
1 CTGTTTTTGTTG
* *
4289 TTGTTATTGTTG
1 CTGTTTTTGTTG
* *
4301 CTGTTTTAGGT-
1 CTGTTTTTGTTG
* *
4312 CTGGTATTGTTG
1 CTGTTTTTGTTG
4324 CTGTTTT
1 CTGTTTT
4331 AGGGCTAGTG
Statistics
Matches: 76, Mismatches: 33, Indels: 8
0.65 0.28 0.07
Matches are distributed among these distances:
11 21 0.28
12 45 0.59
13 10 0.13
ACGTcount: A:0.09, C:0.07, G:0.24, T:0.60
Consensus pattern (12 bp):
CTGTTTTTGTTG
Found at i:4276 original size:35 final size:36
Alignment explanation
Indices: 4210--4285 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 36
4200 TAGCTACTGT
* * * *
4210 TTTTATTGCTGTTTTTTGTTGATGTTTTTGTTACTA
1 TTTTATTGATGTTTTCTGTTGATGGTATTGTTACTA
* * *
4246 TTTTATTGATG-TTTCTGTTGCTGGTATTGTTGCTG
1 TTTTATTGATGTTTTCTGTTGATGGTATTGTTACTA
4281 TTTTA
1 TTTTA
4286 GGGTTGTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.11, C:0.07, G:0.20, T:0.63
Consensus pattern (36 bp):
TTTTATTGATGTTTTCTGTTGATGGTATTGTTACTA
Found at i:4324 original size:46 final size:46
Alignment explanation
Indices: 4265--4381 Score: 173
Period size: 46 Copynumber: 2.5 Consensus size: 46
4255 TGTTTCTGTT
*
4265 GCTGGTATTGTTGCTGTTTTAGGG-TTGTTATTGTTGCTGTTTTAGG
1 GCTGGTATTGTTGCTGTTTTAGGGCTAG-TATTGTTGCTGTTTTAGG
* *
4311 TCTGGTATTGTTGCTGTTTTAGGGCTAGTGTTGTTGCTGTTTTAGG
1 GCTGGTATTGTTGCTGTTTTAGGGCTAGTATTGTTGCTGTTTTAGG
**
4357 GCTGCAATTGTTGCTGTTTTAGGGC
1 GCTGGTATTGTTGCTGTTTTAGGGC
4382 CGATTTTGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 62 0.97
47 2 0.03
ACGTcount: A:0.09, C:0.09, G:0.32, T:0.49
Consensus pattern (46 bp):
GCTGGTATTGTTGCTGTTTTAGGGCTAGTATTGTTGCTGTTTTAGG
Found at i:4390 original size:23 final size:23
Alignment explanation
Indices: 4265--4398 Score: 155
Period size: 23 Copynumber: 5.8 Consensus size: 23
4255 TGTTTCTGTT
*
4265 GCTGGTATTGTTGCTGTTTTAGG
1 GCTGATATTGTTGCTGTTTTAGG
* *
4288 GTTGTTATTGTTGCTGTTTTAGG
1 GCTGATATTGTTGCTGTTTTAGG
* *
4311 TCTGGTATTGTTGCTGTTTTAGG
1 GCTGATATTGTTGCTGTTTTAGG
*
4334 GCT-AGTGTTGTTGCTGTTTTAGG
1 GCTGA-TATTGTTGCTGTTTTAGG
4357 GCTGCA-ATTGTTGCTGTTTTAGG
1 GCTG-ATATTGTTGCTGTTTTAGG
* * *
4380 GCCGATTTTGTTGTTGTTT
1 GCTGATATTGTTGCTGTTT
4399 AATGGATTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.01
23 93 0.98
25 1 0.01
ACGTcount: A:0.09, C:0.09, G:0.31, T:0.51
Consensus pattern (23 bp):
GCTGATATTGTTGCTGTTTTAGG
Found at i:4417 original size:69 final size:69
Alignment explanation
Indices: 4275--4422 Score: 163
Period size: 69 Copynumber: 2.1 Consensus size: 69
4265 GCTGGTATTG
* ** * * * * * *
4275 TTGCTGTTTTAGGGTTGTTATTGTTGCTGTTTTAGGTCTGGTATTGTTGCTGTTTTAGGGCTAGT
1 TTGCTGTTTTAGGGCTGCAATTGTTGCTGTTTTAGGGCCGATATTGTTGCTGTTTAAGGACTAAT
*
4340 GTTG
66 GTTC
* * *
4344 TTGCTGTTTTAGGGCTGCAATTGTTGCTGTTTTAGGGCCGATTTTGTTGTTGTTTAATGGATTAA
1 TTGCTGTTTTAGGGCTGCAATTGTTGCTGTTTTAGGGCCGATATTGTTGCTGTTTAA-GGACTAA
4409 T-TTC
65 TGTTC
4413 TTGCTGTTTT
1 TTGCTGTTTT
4423 TATATTGTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
69 60 0.92
70 5 0.08
ACGTcount: A:0.11, C:0.09, G:0.28, T:0.52
Consensus pattern (69 bp):
TTGCTGTTTTAGGGCTGCAATTGTTGCTGTTTTAGGGCCGATATTGTTGCTGTTTAAGGACTAAT
GTTC
Done.