Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007292.1 Corchorus capsularis cultivar CVL-1 contig07313, 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: 22904
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:3720 original size:43 final size:43
Alignment explanation
Indices: 3673--3774 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 43
3663 GGGGAAAGCC
*
3673 AAAAAA-AAAAAACCTTAGCCTAAAATAGAAAGAGGTCGGAAA
1 AAAAAATAAAAAAACTTAGCCTAAAATAGAAAGAGGTCGGAAA
* * * *
3715 AAAAAATAGATAAACTTGGCCTAAAATATAAAGAGGTCGGAAA
1 AAAAAATAAAAAAACTTAGCCTAAAATAGAAAGAGGTCGGAAA
3758 AAGATAAATAAATAAAA
1 AA-A-AAATAAA-AAAA
3775 GGAGGGGTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
42 6 0.12
43 33 0.67
44 1 0.02
45 6 0.12
46 3 0.06
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.16
Consensus pattern (43 bp):
AAAAAATAAAAAAACTTAGCCTAAAATAGAAAGAGGTCGGAAA
Found at i:4886 original size:18 final size:18
Alignment explanation
Indices: 4863--4897 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4853 TGAGGGTTTC
4863 TTGTTTCAATTCCAAATT
1 TTGTTTCAATTCCAAATT
*
4881 TTGTTTCATTTCCAAAT
1 TTGTTTCAATTCCAAAT
4898 CCTAATCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (18 bp):
TTGTTTCAATTCCAAATT
Found at i:4910 original size:64 final size:63
Alignment explanation
Indices: 4795--5067 Score: 331
Period size: 63 Copynumber: 4.3 Consensus size: 63
4785 TCTGGTCGAA
* * * *
4795 GTTTCTTGTTTCATTTCCAGAATTTTG-TTCTTTTCAAATCCTAATCGAGGTCTCTAATTGAGG
1 GTTTCTTGTTTCAATTCCA-AATCTTGTTTCATTTCAAATCCTAATCGAGGTCTCTAATCGAGG
*
4858 GTTTCTTGTTTCAATTCCAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGG
1 GTTTCTTGTTTCAATTCCAAATCTTGTTTCATTT-CAAATCCTAATCGAGGTCTCTAATCGAGG
* * * *
4922 GTTT-TCTGTTTCAGTTCTAAATCTTGTTGCGA-TTCAAATCCTAATCGAGGTCTCTAGTCGAGG
1 GTTTCT-TGTTTCAATTCCAAATCTTGTTTC-ATTTCAAATCCTAATCGAGGTCTCTAATCGAGG
* * * *
4985 GTTTCCTGTTTCAA-TCTAAAGTCTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGG
1 GTTTCTTGTTTCAATTCCAAA-TCTTGTTTCATTTCAAATCCTAATCGAGGTCTCTAATCGAGG
5048 GTTTTCTTGCTTT-AATTCCA
1 G-TTTCTTG-TTTCAATTCCA
5068 GGTTTTGCTT
Statistics
Matches: 186, Mismatches: 14, Indels: 18
0.85 0.06 0.08
Matches are distributed among these distances:
62 13 0.07
63 104 0.56
64 62 0.33
65 7 0.04
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (63 bp):
GTTTCTTGTTTCAATTCCAAATCTTGTTTCATTTCAAATCCTAATCGAGGTCTCTAATCGAGG
Found at i:4969 original size:127 final size:126
Alignment explanation
Indices: 4827--5054 Score: 368
Period size: 127 Copynumber: 1.8 Consensus size: 126
4817 TTTTGTTCTT
* * *
4827 TTCAAATCCTAATCGAGGTCTCTAATTGAGGGTTTCTTGTTTCAATTCCAAA-TTTTGTTTCATT
1 TTCAAATCCTAATCGAGGTCTCTAATCGAGGGTTTCCTGTTTCAA-TCCAAAGTCTTGTTTCATT
4891 TCCAAATCCTAATCGAGGTCTCTAATCGAGGGTTTTCTGTTTCAGTTCTAAATCTTGTTGCGA
65 T-CAAATCCTAATCGAGGTCTCTAATCGAGGGTTTTCTGTTTCAGTTCTAAATCTTGTTGCGA
* * *
4954 TTCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCCTGTTTCAATCTAAAGTCTTGTTTCGTTT
1 TTCAAATCCTAATCGAGGTCTCTAATCGAGGGTTTCCTGTTTCAATCCAAAGTCTTGTTTCATTT
*
5019 CAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTTCT
66 CAAATCCTAATCGAGGTCTCTAATCGAGGGTTTTCT
5055 TGCTTTAATT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
126 40 0.43
127 53 0.57
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (126 bp):
TTCAAATCCTAATCGAGGTCTCTAATCGAGGGTTTCCTGTTTCAATCCAAAGTCTTGTTTCATTT
CAAATCCTAATCGAGGTCTCTAATCGAGGGTTTTCTGTTTCAGTTCTAAATCTTGTTGCGA
Found at i:5423 original size:28 final size:27
Alignment explanation
Indices: 5364--5422 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
5354 AGGGTCACCT
*
5364 AGGGGCATTTTGGTCATTTTTACATTC
1 AGGGGCATTTTGGTCATTCTTACATTC
* * *
5391 AGGGGCATTTTTGTCATTCTTGCATTT
1 AGGGGCATTTTGGTCATTCTTACATTC
5418 AGGGG
1 AGGGG
5423 GGTATATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTCTTACATTC
Found at i:22312 original size:21 final size:21
Alignment explanation
Indices: 22273--22321 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
22263 TCAATGCTTT
*
22273 AGGAATGCAAGAGGAATTTCAA
1 AGGAA-GCAAGAGCAATTTCAA
* *
22295 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCAATTTCAA
22316 A-GAAGC
1 AGGAAGC
22322 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCAATTTCAA
Done.