Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007049.1 Corchorus capsularis cultivar CVL-1 contig07070, 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: 17833
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:6434 original size:21 final size:22
Alignment explanation
Indices: 6389--6436 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
6379 CTTGATGATG
*
6389 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAAA
6411 AGGTTAA-AGAAATTT-ATAAAA
1 AGGTTAACA-AAATTTCATAAAA
6432 AGGTT
1 AGGTT
6437 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAAA
Found at i:15454 original size:11 final size:11
Alignment explanation
Indices: 15411--15448 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15401 TTTCTATATA
*
15411 AAATAAATTAT
1 AAATTAATTAT
15422 CAAA-TAATTAT
1 -AAATTAATTAT
15433 AAATTAATTAT
1 AAATTAATTAT
15444 AAATT
1 AAATT
15449 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:15683 original size:24 final size:24
Alignment explanation
Indices: 15653--15700 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
15643 CTTTTTTATA
15653 GTTGTTATAGAATAACAACAATTT
1 GTTGTTATAGAATAACAACAATTT
15677 GTTGTTATAGAATAACAACAATTT
1 GTTGTTATAGAATAACAACAATTT
15701 CACCCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
GTTGTTATAGAATAACAACAATTT
Found at i:15750 original size:16 final size:16
Alignment explanation
Indices: 15725--15759 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15715 ATTTTCTTCT
15725 TCTCTATATTCTATTG
1 TCTCTATATTCTATTG
* *
15741 TCTCTCTATTCTCTTG
1 TCTCTATATTCTATTG
15757 TCT
1 TCT
15760 TTTACATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (16 bp):
TCTCTATATTCTATTG
Found at i:17062 original size:2 final size:2
Alignment explanation
Indices: 17049--17094 Score: 74
Period size: 2 Copynumber: 22.0 Consensus size: 2
17039 GTTAAAAATA
17049 AT AT AT AGT AT AT AT AT AT AT AT ACT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
17093 AT
1 AT
17095 GTGTGTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17069 original size:17 final size:16
Alignment explanation
Indices: 17049--17094 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 16
17039 GTTAAAAATA
17049 ATATATAGTATATATAT
1 ATATATA-TATATATAT
17066 ATATATACTATATATAT
1 ATATATA-TATATATAT
17083 ATATATATATAT
1 ATATATATATAT
17095 GTGTGTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 5 0.18
17 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATATATATATAT
Found at i:17104 original size:21 final size:23
Alignment explanation
Indices: 17050--17094 Score: 81
Period size: 23 Copynumber: 1.9 Consensus size: 23
17040 TTAAAAATAA
17050 TATATAGTATATATATATATATAC
1 TATATA-TATATATATATATATAC
17074 TATATATATATATATATATAT
1 TATATATATATATATATATAT
17095 GTGTGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATATATATATATATATATAC
Done.