Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014599.1 Corchorus capsularis cultivar CVL-1 contig14620, 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: 5815
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:194 original size:21 final size:20
Alignment explanation
Indices: 170--217 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
160 TAGATTTAGA
* *
170 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTACTT
* *
191 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTACTT
211 TTTAATT
1 TTTAATT
218 GATAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTACTT
Found at i:1385 original size:25 final size:25
Alignment explanation
Indices: 1357--1406 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1347 TTCAACCGAC
* *
1357 CCAGGGCGGTCTTTCTTCATTTTAT
1 CCAGGGCGATCTTTCTTCAGTTTAT
1382 CCAGGGCGATCTTTCTTCAGTTTAT
1 CCAGGGCGATCTTTCTTCAGTTTAT
1407 GTCAGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (25 bp):
CCAGGGCGATCTTTCTTCAGTTTAT
Found at i:1493 original size:70 final size:70
Alignment explanation
Indices: 1400--2101 Score: 815
Period size: 70 Copynumber: 10.0 Consensus size: 70
1390 ATCTTTCTTC
* * * * *
1400 AGTTTATGTCAGAATAATTGATTCAGTCGA-CCAGGGCGGTCTTTCCTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
1464 ATTCGA
66 A-TCCA
* * ** *
1470 AGTTTATGTTAGAATGATCGATTCAGTCGACCTAGGGCCGTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
1535 ATCCA
66 ATCCA
* * * *
1540 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
1605 ATCAA
66 ATCCA
*
1610 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
1675 ATTCCA
66 A-TCCA
* *
1681 AGTTTATGTCAGAATGATCGATTCAGTCGACCAAGGGTGGTCTTTCTTCAGTTATTT-CAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
1745 ATCTA
66 ATCCA
* * * *
1750 AGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTT-TATGTCGGAA-
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGT-T-TC-CAAG
* *
1813 -TGATCGA
63 TTTATCCA
* * * * *** ** * * *
1820 GGGTGGTCTTTCTTTA-G-TTTATTTCGGTTGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAG
1 -AGT-TTATGTCAGAATGATCGA-TTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAG
*
1883 TTTATTCGA
63 TTTA-TCCA
** * *
1892 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGACGTTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
1957 ATCCA
66 ATCCA
* * * *
1962 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCATGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2027 ATCCA
66 ATCCA
* * * *
2032 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGAGGTTTTTCATCAGTTGTTTCCAAGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2097 ATCCA
66 ATCCA
2102 GGGTGGTCTT
Statistics
Matches: 534, Mismatches: 83, Indels: 30
0.83 0.13 0.05
Matches are distributed among these distances:
68 1 0.00
69 56 0.10
70 300 0.56
71 163 0.31
72 14 0.03
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:1865 original size:35 final size:35
Alignment explanation
Indices: 1775--1873 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 35
1765 GATCGATTCA
* *
1775 GTTGACCTAGGGTGGTTTTTCTTCAGTTTATGTCG
1 GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
* * * * *
1810 GAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCG
1 G-TTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
1846 GTTGACCCAGGGTGGTCTTTCTTCAGTT
1 GTTGACCCAGGGTGGTCTTTCTTCAGTT
1874 GTTTTCAAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 24 0.45
36 29 0.55
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.43
Consensus pattern (35 bp):
GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
Found at i:5731 original size:21 final size:20
Alignment explanation
Indices: 5692--5733 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5682 TCATTTGCCT
*
5692 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
5712 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
5733 A
1 A
5734 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Done.