Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015864.1 Corchorus capsularis cultivar CVL-1 contig15885, 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: 49137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9336 original size:19 final size:20
Alignment explanation
Indices: 9309--9347 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
9299 AAGCCAGCCC
9309 AAAGTAAAAAAAAATGGAAA
1 AAAGTAAAAAAAAATGGAAA
* *
9329 AAAG-AAAAAGAAATTGAAA
1 AAAGTAAAAAAAAATGGAAA
9348 CCTTTCGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAGTAAAAAAAAATGGAAA
Found at i:10442 original size:18 final size:19
Alignment explanation
Indices: 10419--10457 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
10409 GTAAAAAGGT
10419 TTTTTTTATT-CATTTTTC
1 TTTTTTTATTGCATTTTTC
* *
10437 TTTTTTTGTTGGATTTTTC
1 TTTTTTTATTGCATTTTTC
10456 TT
1 TT
10458 ACTGGGCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (19 bp):
TTTTTTTATTGCATTTTTC
Found at i:11245 original size:31 final size:31
Alignment explanation
Indices: 11210--11332 Score: 122
Period size: 31 Copynumber: 4.0 Consensus size: 31
11200 AACATTGGGT
* *
11210 ACTGA-TTTATGCCGATTTTGCAACGTTAGGG
1 ACTGATTTTA-GCCGATTTTGCAACGTTATGA
* * * * *
11241 ACTGATTTGAACCGATTTTGCAATGTCAAGA
1 ACTGATTTTAGCCGATTTTGCAACGTTATGA
* * *
11272 ACTAATTTTAGCCAATTTTGCAACGTTATAA
1 ACTGATTTTAGCCGATTTTGCAACGTTATGA
* *
11303 ATTGATTTTAGCCGATTTTGCAATGTTATG
1 ACTGATTTTAGCCGATTTTGCAACGTTATG
11333 GACTTAATGA
Statistics
Matches: 72, Mismatches: 19, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
31 69 0.96
32 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (31 bp):
ACTGATTTTAGCCGATTTTGCAACGTTATGA
Found at i:14016 original size:16 final size:15
Alignment explanation
Indices: 13992--14025 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
13982 GAGCTAGCAA
*
13992 TTTTCCTTTTTTCGTT
1 TTTTACTTTTTT-GTT
14008 TTTTACTTTTTTGTT
1 TTTTACTTTTTTGTT
14023 TTT
1 TTT
14026 GTTCGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTACTTTTTTGTT
Found at i:17871 original size:18 final size:18
Alignment explanation
Indices: 17842--17905 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
17832 TGTCCCGCCC
*
17842 ATGGTGGAGTTGGTTGGT
1 ATGGTGGTGTTGGTTGGT
* *
17860 ATTGTGGTGTTGCTTGGT
1 ATGGTGGTGTTGGTTGGT
*
17878 ATGGTGGTGTGGGTTGGT
1 ATGGTGGTGTTGGTTGGT
*
17896 AAGGTGGTGT
1 ATGGTGGTGT
17906 AGCTTGATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.09, C:0.02, G:0.48, T:0.41
Consensus pattern (18 bp):
ATGGTGGTGTTGGTTGGT
Found at i:17882 original size:36 final size:36
Alignment explanation
Indices: 17842--17911 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
17832 TGTCCCGCCC
* ** *
17842 ATGGTGGAGTTGGTTGGTATTGTGGTGTTGCTTGGT
1 ATGGTGGAGTGGGTTGGTAAGGTGGTGTAGCTTGGT
*
17878 ATGGTGGTGTGGGTTGGTAAGGTGGTGTAGCTTG
1 ATGGTGGAGTGGGTTGGTAAGGTGGTGTAGCTTG
17912 ATAAGTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.10, C:0.03, G:0.47, T:0.40
Consensus pattern (36 bp):
ATGGTGGAGTGGGTTGGTAAGGTGGTGTAGCTTGGT
Found at i:17916 original size:18 final size:18
Alignment explanation
Indices: 17863--17916 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
17853 GGTTGGTATT
* *
17863 GTGGTGTTGCTTGGTATG
1 GTGGTGTAGCTTGGTAAG
* *
17881 GTGGTGTGGGTTGGTAAG
1 GTGGTGTAGCTTGGTAAG
*
17899 GTGGTGTAGCTTGATAAG
1 GTGGTGTAGCTTGGTAAG
17917 TTGGCCATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.13, C:0.04, G:0.46, T:0.37
Consensus pattern (18 bp):
GTGGTGTAGCTTGGTAAG
Found at i:21370 original size:109 final size:109
Alignment explanation
Indices: 21174--21461 Score: 449
Period size: 109 Copynumber: 2.6 Consensus size: 109
21164 ACTATTATAG
* *
21174 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
21239 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
21288 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
21353 TTACCAAAAAATTTGGATATATTAAAAATTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
*
21397 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTAT-ATTAATTT-TT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATAATTACTTTATT
21458 TTTA
65 TTTA
21462 ATTTTTACCA
Statistics
Matches: 168, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
106 6 0.04
107 7 0.04
108 6 0.04
109 123 0.73
110 3 0.02
111 2 0.01
114 21 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:25176 original size:59 final size:60
Alignment explanation
Indices: 25095--25217 Score: 205
Period size: 59 Copynumber: 2.1 Consensus size: 60
25085 TAGTATGAAA
* *
25095 ATTTAGACATTCAATTGGTTGTCTGAT-ATGGTATCTATATGAGTCTCATATGAAAATGG
1 ATTTAGACATTCAATTGGTTGTCTGATAATGGCACCTATATGAGTCTCATATGAAAATGG
*
25154 ATTTAGACATTCAATTGGTTGTCTGATAATTGCACCTATATGAGTCTCATATGAAAATGG
1 ATTTAGACATTCAATTGGTTGTCTGATAATGGCACCTATATGAGTCTCATATGAAAATGG
25214 -TTTA
1 ATTTA
25218 TATGTATGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 31 0.52
60 29 0.48
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (60 bp):
ATTTAGACATTCAATTGGTTGTCTGATAATGGCACCTATATGAGTCTCATATGAAAATGG
Found at i:29530 original size:19 final size:19
Alignment explanation
Indices: 29506--29543 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29496 TTTACAAAAG
29506 CTTAAAGATTTAGGTCATT
1 CTTAAAGATTTAGGTCATT
29525 CTTAAAGATTTAGGTCATT
1 CTTAAAGATTTAGGTCATT
29544 TAATGAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
CTTAAAGATTTAGGTCATT
Found at i:32970 original size:17 final size:17
Alignment explanation
Indices: 32945--32980 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
32935 TTTTTGTTAA
32945 ATCTATATTAATATTTT
1 ATCTATATTAATATTTT
* *
32962 ATCTGTATTTATATTTT
1 ATCTATATTAATATTTT
32979 AT
1 AT
32981 GTTGTGTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (17 bp):
ATCTATATTAATATTTT
Found at i:37429 original size:1 final size:1
Alignment explanation
Indices: 37423--37458 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
37413 GATATATATC
37423 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37459 ACTTTAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.