Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021119.1 Corchorus olitorius cultivar O-4 contig21152, 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: 7960
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1203 original size:15 final size:15
Alignment explanation
Indices: 1176--1224 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
1166 AATCTTGGAT
1176 GTTTGAG-CAGTTTA
1 GTTTGAGTCAGTTTA
1190 GTTTGAGTCAGTTTA
1 GTTTGAGTCAGTTTA
*
1205 GTTTGAGTCAGTTGA
1 GTTTGAGTCAGTTTA
1220 GTTTG
1 GTTTG
1225 TTGAGTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 7 0.21
15 26 0.79
ACGTcount: A:0.18, C:0.06, G:0.31, T:0.45
Consensus pattern (15 bp):
GTTTGAGTCAGTTTA
Found at i:1789 original size:27 final size:28
Alignment explanation
Indices: 1735--1789 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1725 ATTAATAAAC
*
1735 AAAAATCTTATTATTATATTACTCAAAAAA
1 AAAAATCTTATTATTATATGA--CAAAAAA
1765 AAAAATCTTATTATTATATGA-AAAA
1 AAAAATCTTATTATTATATGACAAAA
1790 CATACGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
30 20 0.83
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAAATCTTATTATTATATGACAAAAAA
Found at i:3571 original size:16 final size:15
Alignment explanation
Indices: 3539--3568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3529 AGGTTAATCA
*
3539 AAATAATTAAATTTT
1 AAATAAATAAATTTT
3554 AAATAAATAAATTTT
1 AAATAAATAAATTTT
3569 TAACTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATAAATAAATTTT
Found at i:4065 original size:123 final size:127
Alignment explanation
Indices: 3833--4087 Score: 419
Period size: 123 Copynumber: 2.0 Consensus size: 127
3823 ATTTAAGAAA
3833 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT--AATAAAA
* * *
3898 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAGTGTAAAA
64 T--GTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
3963 G
127 G
3964 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
4025 TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
4087 T
1 T
4088 TTAAACAATG
Statistics
Matches: 121, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
123 60 0.50
126 5 0.04
127 1 0.01
130 26 0.21
131 29 0.24
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
TATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:5673 original size:19 final size:18
Alignment explanation
Indices: 5635--5673 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5625 ATTCACATAA
* *
5635 TTCTCTTTAGATTTATTT
1 TTCTCTTTAGATCTAGTT
5653 TTCTCTTCTAGATCTAGTT
1 TTCTCTT-TAGATCTAGTT
5672 TT
1 TT
5674 TAGGGCTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (18 bp):
TTCTCTTTAGATCTAGTT
Found at i:6758 original size:17 final size:17
Alignment explanation
Indices: 6736--6769 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6726 ATAGATTAAA
6736 TGGAAGTTTGCCACCAG
1 TGGAAGTTTGCCACCAG
6753 TGGAAGTTTGCCACCAG
1 TGGAAGTTTGCCACCAG
6770 AACTTGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (17 bp):
TGGAAGTTTGCCACCAG
Done.