Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008783.1 Corchorus capsularis cultivar CVL-1 contig08804, 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: 25160
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:5408 original size:27 final size:27
Alignment explanation
Indices: 5370--5423 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5360 ATGGCTTGGG
5370 CTAAATTATTGCTAACACTTTTTCTTT
1 CTAAATTATTGCTAACACTTTTTCTTT
5397 CTAAATTATTGCTAACACTTTTTCTTT
1 CTAAATTATTGCTAACACTTTTTCTTT
5424 TATAAGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.52
Consensus pattern (27 bp):
CTAAATTATTGCTAACACTTTTTCTTT
Found at i:7609 original size:28 final size:29
Alignment explanation
Indices: 7542--7612 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
7532 GAAAGGGGGT
7542 AAAACGTCACAAAATTAAAAGTTCAGCAGGC
1 AAAACGTC-CAAAATTAAAAGTTCAG-AGGC
*
7573 AAAATGTCCAAAATT-AAAGTTCATG-GGC
1 AAAACGTCCAAAATTAAAAGTTCA-GAGGC
*
7601 AAAAGGTCCAAA
1 AAAACGTCCAAA
7613 TCCTATAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 14 0.38
29 8 0.22
30 8 0.22
31 7 0.19
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (29 bp):
AAAACGTCCAAAATTAAAAGTTCAGAGGC
Found at i:9889 original size:72 final size:72
Alignment explanation
Indices: 9803--9952 Score: 185
Period size: 72 Copynumber: 2.1 Consensus size: 72
9793 AAGATCTTGA
* * * *
9803 TTTGTGGGATTCTAGTTTTGATGCAAAATTTTCTACTGAAGTCATGAGATTGTCAAAAATT-GTC
1 TTTGTTGGATTCTAGTTTGGATGCAAAATTTTCTACTGAAATCATGAGATTGTCAAAAATTAAT-
9867 TTTGAAGG
65 TTTGAAGG
* * * ** *
9875 TTTGTTGGATTCTAGTTTGGATGCGAAATTTTTTGCTGAAATTTTTAGATTGTCAAAAATTAATT
1 TTTGTTGGATTCTAGTTTGGATGCAAAATTTTCTACTGAAATCATGAGATTGTCAAAAATTAATT
*
9940 TTGATGG
66 TTGAAGG
9947 TTTGTT
1 TTTGTT
9953 TGCAAAAGCA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
72 65 0.98
73 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.45
Consensus pattern (72 bp):
TTTGTTGGATTCTAGTTTGGATGCAAAATTTTCTACTGAAATCATGAGATTGTCAAAAATTAATT
TTGAAGG
Found at i:13989 original size:14 final size:14
Alignment explanation
Indices: 13970--13996 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13960 GTCCAACGGG
13970 TCGGGTCGGTCCTT
1 TCGGGTCGGTCCTT
13984 TCGGGTCGGTCCT
1 TCGGGTCGGTCCT
13997 ACTCTAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.30, G:0.37, T:0.33
Consensus pattern (14 bp):
TCGGGTCGGTCCTT
Found at i:14959 original size:6 final size:7
Alignment explanation
Indices: 14903--14961 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
14893 TAAAAAAACA
*
14903 TATATAA
1 TATATAT
*
14910 TATATAA
1 TATATAT
14917 TATATAT
1 TATATAT
14924 TAT-T-T
1 TATATAT
*
14929 TAAATATT
1 TATATA-T
14937 TATATAT
1 TATATAT
14944 ATATATAT
1 -TATATAT
14952 TATA-AT
1 TATATAT
14958 TATA
1 TATA
14962 CAATCGGTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
5 3 0.07
6 8 0.18
7 21 0.47
8 13 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:18562 original size:16 final size:16
Alignment explanation
Indices: 18541--18581 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
18531 CTTGGGTTAT
18541 TCGGGTTTCAGGTCAC
1 TCGGGTTTCAGGTCAC
* *
18557 TCGGGTTACAGGTCAT
1 TCGGGTTTCAGGTCAC
*
18573 TCGGATTTC
1 TCGGGTTTC
18582 GGGTAGGGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (16 bp):
TCGGGTTTCAGGTCAC
Found at i:18815 original size:20 final size:18
Alignment explanation
Indices: 18768--18814 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
18758 CGGTTTGAAT
18768 ATATTACAT-ATATATTAC
1 ATATTA-ATAATATATTAC
*
18786 ATATTAATAATATATTAT
1 ATATTAATAATATATTAC
18804 ATATTAA-AATA
1 ATATTAATAATA
18815 AAATTCTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTAATAATATATTAC
Found at i:18859 original size:22 final size:22
Alignment explanation
Indices: 18831--18873 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
18821 TTTCATGTAT
18831 ATATATATATATTCTTATTTAC
1 ATATATATATATTCTTATTTAC
18853 ATATATATATATTCTTATTTA
1 ATATATATATATTCTTATTTA
18874 ATAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATATATATATTCTTATTTAC
Found at i:18882 original size:22 final size:22
Alignment explanation
Indices: 18835--18882 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
18825 ATGTATATAT
*
18835 ATATATATTCTTATTTACATAT
1 ATATATATTCTTATTTACATAA
18857 ATATATATTCTTATTTA-ATAA
1 ATATATATTCTTATTTACATAA
18878 A-ATAT
1 ATATAT
18883 TTTACATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.16
21 4 0.16
22 17 0.68
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATATATTCTTATTTACATAA
Found at i:18940 original size:6 final size:7
Alignment explanation
Indices: 18913--18960 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
18903 CGATTTTTGG
18913 ATATATA
1 ATATATA
18920 ATATATA
1 ATATATA
18927 TATATATA
1 -ATATATA
18935 AT-TATA
1 ATATATA
* *
18941 ATTAAAAA
1 A-TATATA
18949 ATATATA
1 ATATATA
18956 ATATA
1 ATATA
18961 ACTAAACCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.15
7 19 0.56
8 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:18952 original size:21 final size:20
Alignment explanation
Indices: 18928--18966 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18918 TAATATATAT
*
18928 ATATATAATTATAATTAAAAA
1 ATATATAA-TATAACTAAAAA
18949 ATATATAATATAACTAAA
1 ATATATAATATAACTAAA
18967 CCCTATGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATATAATATAACTAAAAA
Found at i:19259 original size:14 final size:16
Alignment explanation
Indices: 19240--19271 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19230 TCTGGTCAAA
19240 TCGGGTT-G-ACGGGT
1 TCGGGTTCGAACGGGT
19254 TCGGGTTCGAACGGGT
1 TCGGGTTCGAACGGGT
19270 TC
1 TC
19272 TCAGGTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.09, C:0.19, G:0.44, T:0.28
Consensus pattern (16 bp):
TCGGGTTCGAACGGGT
Found at i:22996 original size:20 final size:19
Alignment explanation
Indices: 22953--23000 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
22943 AATTAGTGAT
*
22953 TAAA-TTTTATTTTTAAAA
1 TAAATTTTTAATTTTAAAA
22971 TAAATTGTTTAATTTTAAAA
1 TAAATT-TTTAATTTTAAAA
22991 CT-AATTTTTA
1 -TAAATTTTTA
23001 TTGATGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 5 0.19
20 16 0.62
21 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TAAATTTTTAATTTTAAAA
Done.