Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010164.1 Corchorus capsularis cultivar CVL-1 contig10185, 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: 15699
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Found at i:901 original size:31 final size:31
Alignment explanation
Indices: 863--928 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
853 TGTCAATTTA
** *
863 GAAATATATATTAAAATAAAGGGTACAATTG
1 GAAATATATACGAAAATAAAGGGTACAATCG
894 GAAATATATACGAAAATAAAGGGTACAATCG
1 GAAATATATACGAAAATAAAGGGTACAATCG
925 GAAA
1 GAAA
929 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.23
Consensus pattern (31 bp):
GAAATATATACGAAAATAAAGGGTACAATCG
Found at i:2895 original size:2 final size:2
Alignment explanation
Indices: 2888--2916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2878 ATTTATAGCT
2888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2917 CTTCAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5035 original size:30 final size:30
Alignment explanation
Indices: 5000--5062 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
4990 TATATTAAAT
5000 ACACAAACAAATAAATTACAAAGAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAACTC
5030 ACACAAACAAATAAATTACAAAGAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAACTC
5060 ACA
1 ACA
5063 TTCCGTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.63, C:0.21, G:0.03, T:0.13
Consensus pattern (30 bp):
ACACAAACAAATAAATTACAAAGAAAACTC
Found at i:7022 original size:2 final size:2
Alignment explanation
Indices: 7015--7039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7005 CTTTTACTAG
7015 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7040 TGCACGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9972 original size:25 final size:26
Alignment explanation
Indices: 9943--9995 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
9933 ACTAATATTC
*
9943 TTATTCAATGTCACTAAAAA-TGCAG
1 TTATTCAAGGTCACTAAAAAGTGCAG
*
9968 TTATTCAAGGTTACTAAAAAGTGCAG
1 TTATTCAAGGTCACTAAAAAGTGCAG
9994 TT
1 TT
9996 GTTATTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (26 bp):
TTATTCAAGGTCACTAAAAAGTGCAG
Found at i:10332 original size:20 final size:22
Alignment explanation
Indices: 10299--10338 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
10289 AAAGTTATAT
10299 ATATATATATATATTATAAATA
1 ATATATATATATATTATAAATA
10321 ATAT-TATA-ATATTATAAA
1 ATATATATATATATTATAAA
10339 CAAATTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATATATATATTATAAATA
Found at i:13679 original size:78 final size:76
Alignment explanation
Indices: 13597--13825 Score: 260
Period size: 70 Copynumber: 3.1 Consensus size: 76
13587 TTGTTTAGGT
* *
13597 TTTTATAGCTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACTA
1 TTTTATA-CTTTAC-TAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
*
13662 TTTTATTTTA-C-
64 TTATATTTTATCA
*
13673 ---TAT--TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
1 TTTTATACTTTACT-AACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTAT
13733 TATATTTTATCA
65 TATATTTTATCA
* * ** * *
13745 TTTTACTATTTTACTCAACTAAAAGCTCTATTTTTATATAATTAAATCCAACATCCTTATTAC--
1 TTTTA-TACTTTACT-AACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
13808 TTATATTTTATCA
64 TTATATTTTATCA
13821 TTTTA
1 TTTTA
13826 CTATTTTAAT
Statistics
Matches: 136, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
69 1 0.01
70 60 0.44
71 1 0.01
73 3 0.02
75 2 0.01
76 19 0.14
78 50 0.37
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.50
Consensus pattern (76 bp):
TTTTATACTTTACTAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTATT
ATATTTTATCA
Found at i:13681 original size:70 final size:74
Alignment explanation
Indices: 13606--13833 Score: 293
Period size: 78 Copynumber: 3.1 Consensus size: 74
13596 TTTTTATAGC
* * *
13606 TTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAAC-TA-TTT-T-A
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTTATTTTATCA
13667 TTTTACTAT
66 TTTTACTAT
*
13676 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAAC---T-TATTTT
13741 ATCATTTTACTAT
62 ATCATTTTACTAT
* ** * *
13754 TTTACTCAACTAAAAGCTCTATTTTTATATAATTAAATCCAACATCCTTATTACTTATATTTTAT
1 TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAAC-T-TATTTTAT
13819 CATTTTACTAT
64 CATTTTACTAT
13830 TTTA
1 TTTA
13834 ATTAAAAAAC
Statistics
Matches: 142, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
70 50 0.35
75 2 0.01
76 29 0.20
77 1 0.01
78 60 0.42
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (74 bp):
TTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTTATTTTATCA
TTTTACTAT
Found at i:15606 original size:3 final size:3
Alignment explanation
Indices: 15598--15641 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
15588 TATAGTATAT
15598 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
15642 AAGTTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.