Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005348.1 Corchorus capsularis cultivar CVL-1 contig05366, 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: 7434
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Found at i:3883 original size:10 final size:10
Alignment explanation
Indices: 3868--3902 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3858 AAATCTTTTT
3868 AAAAAATTTA
1 AAAAAATTTA
*
3878 AAAAAAATT-
1 AAAAAATTTA
3887 AAAAAATTTA
1 AAAAAATTTA
3897 AAAAAA
1 AAAAAA
3903 AAAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:3890 original size:8 final size:9
Alignment explanation
Indices: 3865--3901 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
3855 AAAAAATCTT
3865 TTTAAAAAA
1 TTTAAAAAA
3874 TTTAAAAAAA
1 TTT-AAAAAA
*
3884 ATTAAAAAA
1 TTTAAAAAA
3893 TTTAAAAAA
1 TTTAAAAAA
3902 AAAAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:3890 original size:19 final size:19
Alignment explanation
Indices: 3866--3903 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3856 AAAAATCTTT
3866 TTAAAAAATTTAAAAAAAA
1 TTAAAAAATTTAAAAAAAA
3885 TTAAAAAATTTAAAAAAAA
1 TTAAAAAATTTAAAAAAAA
3904 AAAAAGAAAA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
TTAAAAAATTTAAAAAAAA
Found at i:3964 original size:33 final size:33
Alignment explanation
Indices: 3925--4080 Score: 269
Period size: 33 Copynumber: 4.8 Consensus size: 33
3915 GGTCGAGCCA
*
3925 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCA
1 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCT
*
3958 TGGCTAGCTGCCCAGCGTGGGCGGCCTTGCCCT
1 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCT
3991 TGGCTAG-CGCCCAGCGTGGGCGGCCTTGCCCT
1 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCT
4023 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCT
1 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCT
* *
4056 TGGCTAGCCGCCCAGCTTGAGCGGC
1 TGGCTAGCCGCCCAGCGTGGGCGGC
4081 TCGGCCATTT
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 31 0.26
33 86 0.74
ACGTcount: A:0.08, C:0.38, G:0.37, T:0.18
Consensus pattern (33 bp):
TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCT
Found at i:4030 original size:65 final size:66
Alignment explanation
Indices: 3925--4080 Score: 269
Period size: 65 Copynumber: 2.4 Consensus size: 66
3915 GGTCGAGCCA
*
3925 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCTAGCTGCCCAGCGTGGGCGGCCTTGCCC
1 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCC
3990 T
66 T
*
3991 TGGCTAG-CGCCCAGCGTGGGCGGCCTTGCCCTTGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCC
1 TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCC
4055 T
66 T
* *
4056 TGGCTAGCCGCCCAGCTTGAGCGGC
1 TGGCTAGCCGCCCAGCGTGGGCGGC
4081 TCGGCCATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
65 63 0.74
66 22 0.26
ACGTcount: A:0.08, C:0.38, G:0.37, T:0.18
Consensus pattern (66 bp):
TGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCTAGCCGCCCAGCGTGGGCGGCCTTGCCC
T
Found at i:4199 original size:26 final size:26
Alignment explanation
Indices: 4170--4237 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
4160 TACTTAGTTT
* *
4170 ATTAGTTTA-TATTTAATTTGTATCTA
1 ATTAGTTTATTA-TTAATTAGCATCTA
*
4196 ATTAGTTTATTATTAATTAGCATTTA
1 ATTAGTTTATTATTAATTAGCATCTA
*
4222 ATTAGTTTATGATTAA
1 ATTAGTTTATTATTAA
4238 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 35 0.95
27 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATTATTAATTAGCATCTA
Found at i:4281 original size:24 final size:25
Alignment explanation
Indices: 4247--4305 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
4237 AAATGAAGGA
4247 AAATGAA-TTTGAAG-A-TTCGTTAG
1 AAATGAAGTTTGAAGAAGTT-GTTAG
4270 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
4295 AAATGAAGTTT
1 AAATGAAGTTT
4306 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 17 0.52
26 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.34
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:4639 original size:32 final size:32
Alignment explanation
Indices: 4601--4687 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
4591 CGGGTTTAAG
4601 TCGGGTTCGGGTTGAATTTGGGTCAAGTCAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAAGTCAAT
* * *
4633 TCGGGTTCTGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAAGTCAAT
* *
4665 TCGGGTTCGGGTTCAGTTTGGGT
1 TCGGGTTCGGGTTGAATTTGGGT
4688 TTTAGCCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAAGTCAAT
Found at i:4881 original size:16 final size:16
Alignment explanation
Indices: 4862--4904 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4852 GGTTCTGAAA
4862 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTTGAGCT
* * * *
4878 TTTTCGGATTCGGGTT
1 TTTTCGGGTTTGAGCT
4894 TTTTCGGGTTT
1 TTTTCGGGTTT
4905 AGATAGGTTC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.05, C:0.12, G:0.30, T:0.53
Consensus pattern (16 bp):
TTTTCGGGTTTGAGCT
Found at i:4916 original size:48 final size:48
Alignment explanation
Indices: 4836--4931 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
4826 TTTGGATTCA
**
4836 GATTCGGGTTTTTTCGGGTTCTGAAATTTTCGGG-TTTGAGCTTTTTCG
1 GATTCGGGTTTTTTCGGGTTCTGAAAGGTTCGGGATTTGA-CTTTTTCG
*
4884 GATTCGGGTTTTTTCGGGTT-TAGATAGGTTCGGGTATTTGACTTTTTC
1 GATTCGGGTTTTTTCGGGTTCT-GAAAGGTTCGGG-ATTTGACTTTTTC
4932 TGGTCAATCG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 1 0.02
48 29 0.69
49 7 0.17
50 5 0.12
ACGTcount: A:0.11, C:0.11, G:0.29, T:0.48
Consensus pattern (48 bp):
GATTCGGGTTTTTTCGGGTTCTGAAAGGTTCGGGATTTGACTTTTTCG
Done.