Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005773.1 Corchorus capsularis cultivar CVL-1 contig05791, 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: 23691
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:938 original size:21 final size:20
Alignment explanation
Indices: 896--939 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
886 TCTTGTAATT
*
896 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
916 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
937 TAA
1 TAA
940 TGCTTTCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:5001 original size:2 final size:2
Alignment explanation
Indices: 4994--5031 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4984 GAGAATAAAG
* *
4994 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5032 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12013 original size:24 final size:24
Alignment explanation
Indices: 11980--12025 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
11970 GAATGAATCT
11980 ATAGACACCATTAATTAAAGATCA
1 ATAGACACCATTAATTAAAGATCA
*
12004 ATAGATACCATTAATTAAAGAT
1 ATAGACACCATTAATTAAAGAT
12026 ATCAATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (24 bp):
ATAGACACCATTAATTAAAGATCA
Found at i:13861 original size:15 final size:14
Alignment explanation
Indices: 13843--13873 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
13833 TTTTCTAATG
13843 TTTTATTTATTATAT
1 TTTTATTTATT-TAT
13858 TTTTATTTATTTAT
1 TTTTATTTATTTAT
13872 TT
1 TT
13874 AGTTTGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:13959 original size:11 final size:11
Alignment explanation
Indices: 13916--13953 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13906 TTCCTATATA
*
13916 AAATAAATTAT
1 AAATTAATTAT
13927 CAAA-TAATTAT
1 -AAATTAATTAT
13938 AAATTAATTAT
1 AAATTAATTAT
13949 AAATT
1 AAATT
13954 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:14172 original size:17 final size:17
Alignment explanation
Indices: 14150--14212 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
14140 CAATTTCTCA
*
14150 TCTTCTTCATATTTTCT
1 TCTTCTCCATATTTTCT
* *
14167 TCTTCTCCATATTCTAT
1 TCTTCTCCATATTTTCT
* *
14184 T-GTCTTCATATTTTCT
1 TCTTCTCCATATTTTCT
14200 TCTTCTCCATATT
1 TCTTCTCCATATT
14213 CTATTGTCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 12 0.33
17 24 0.67
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (17 bp):
TCTTCTCCATATTTTCT
Found at i:14195 original size:16 final size:16
Alignment explanation
Indices: 14174--14238 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
14164 TCTTCTTCTC
14174 CATATTCTATTGTCTT
1 CATATTCTATTGTCTT
* * * *
14190 CATATTTTCTTCTTCTC
1 CATATTCTATT-GTCTT
14207 CATATTCTATTGTCTCT
1 CATATTCTATTGTCT-T
*
14224 C-TATTCTTTTGTCTT
1 CATATTCTATTGTCTT
14239 TTCCATGCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 24 0.63
17 13 0.34
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (16 bp):
CATATTCTATTGTCTT
Found at i:14195 original size:33 final size:33
Alignment explanation
Indices: 14153--14221 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
14143 TTTCTCATCT
14153 TCTTCATATTTTCTTCTTCTCCATATTCTATTG
1 TCTTCATATTTTCTTCTTCTCCATATTCTATTG
14186 TCTTCATATTTTCTTCTTCTCCATATTCTATTG
1 TCTTCATATTTTCTTCTTCTCCATATTCTATTG
14219 TCT
1 TCT
14222 CTCTATTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.14, C:0.25, G:0.03, T:0.58
Consensus pattern (33 bp):
TCTTCATATTTTCTTCTTCTCCATATTCTATTG
Found at i:14372 original size:41 final size:42
Alignment explanation
Indices: 14300--14548 Score: 477
Period size: 41 Copynumber: 6.0 Consensus size: 42
14290 GCAAAATTTC
14300 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14342 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14383 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14425 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14466 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14508 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
14549 GCAACCGCAC
Statistics
Matches: 205, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
41 109 0.53
42 96 0.47
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:14431 original size:83 final size:83
Alignment explanation
Indices: 14300--14548 Score: 498
Period size: 83 Copynumber: 3.0 Consensus size: 83
14290 GCAAAATTTC
14300 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
14365 AAGAATTTATAAAATAAA
66 AAGAATTTATAAAATAAA
14383 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
14448 AAGAATTTATAAAATAAA
66 AAGAATTTATAAAATAAA
14466 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
14531 AAGAATTTATAAAATAAA
66 AAGAATTTATAAAATAAA
14549 GCAACCGCAC
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 166 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (83 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAATTTCTTAACTGAATTTTCTTAA
AAGAATTTATAAAATAAA
Found at i:15661 original size:14 final size:14
Alignment explanation
Indices: 15642--15669 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15632 TACGTGTGAT
15642 TTAACCTCGATTAC
1 TTAACCTCGATTAC
15656 TTAACCTCGATTAC
1 TTAACCTCGATTAC
15670 GTGGTAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
TTAACCTCGATTAC
Found at i:16887 original size:17 final size:17
Alignment explanation
Indices: 16838--16889 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
16828 TTGTATAATT
16838 TAAGGATTTATATACAA
1 TAAGGATTTATATACAA
*
16855 TAATGG--TTAAATACAA
1 TAA-GGATTTATATACAA
16871 TAAGGATTTATATACAA
1 TAAGGATTTATATACAA
16888 TA
1 TA
16890 CATCGTCAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
17 14 0.47
18 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
TAAGGATTTATATACAA
Found at i:18947 original size:29 final size:29
Alignment explanation
Indices: 18914--19020 Score: 113
Period size: 29 Copynumber: 3.9 Consensus size: 29
18904 GTATGCCACG
*
18914 TGTCACTTTTTAGTACACGTGGCGTGACA
1 TGTCACTTTTTGGTACACGTGGCGTGACA
18943 TGTCACTTTTTGGTACA--T---GTGACA
1 TGTCACTTTTTGGTACACGTGGCGTGACA
* *
18967 CG--ACTTTTTGGTACATGTGGCGTGCCACA
1 TGTCACTTTTTGGTACACGTGGCGTG--ACA
18996 TGTCAC-TTTTGGTACACGTGGCGTG
1 TGTCACTTTTTGGTACACGTGGCGTG
19021 CCACGTCGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
22 13 0.20
24 8 0.12
27 4 0.06
29 20 0.31
30 18 0.28
31 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (29 bp):
TGTCACTTTTTGGTACACGTGGCGTGACA
Done.