Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021357.1 Corchorus olitorius cultivar O-4 contig21390, 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: 21813
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1579 original size:29 final size:29
Alignment explanation
Indices: 1534--1591 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1524 ATGCCCAATT
1534 TTTTTCCTTGAAATTTTAGAAAAGAGACA
1 TTTTTCCTTGAAATTTTAGAAAAGAGACA
*
1563 TTTTTCCTT-AAACTTTTAGGAAAGAGACA
1 TTTTTCCTTGAAA-TTTTAGAAAAGAGACA
1592 AAATCTCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (29 bp):
TTTTTCCTTGAAATTTTAGAAAAGAGACA
Found at i:2268 original size:17 final size:17
Alignment explanation
Indices: 2236--2283 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
2226 GTAAGTATAA
*
2236 ATTATAT-TTAATAAAT
1 ATTATATATTAACAAAT
2252 ATTATATATTAACAAAT
1 ATTATATATTAACAAAT
** *
2269 AAAAAATATTAACAA
1 ATTATATATTAACAA
2284 GCATATTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTATATATTAACAAAT
Found at i:8375 original size:16 final size:16
Alignment explanation
Indices: 8354--8387 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
8344 CTTATGTGTC
8354 TTTCTTGTGGATATTA
1 TTTCTTGTGGATATTA
8370 TTTCTTGTGGATATTA
1 TTTCTTGTGGATATTA
8386 TT
1 TT
8388 GTTTTGCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.59
Consensus pattern (16 bp):
TTTCTTGTGGATATTA
Found at i:9653 original size:29 final size:30
Alignment explanation
Indices: 9612--9668 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9602 CAAATTGACG
* *
9612 TTTGCTCTCTAAA-TTTTAATTTGAGACTT
1 TTTGCTCTCTAAACTTATAATTTAAGACTT
9641 TTTGCTC-CATAAACTTATAATTTAAGAC
1 TTTGCTCTC-TAAACTTATAATTTAAGAC
9669 CATGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 11 0.46
30 12 0.50
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.46
Consensus pattern (30 bp):
TTTGCTCTCTAAACTTATAATTTAAGACTT
Found at i:10716 original size:101 final size:101
Alignment explanation
Indices: 10541--10742 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
10531 CAGCCAATGT
10541 CTACATGTATGTCCACGTCAGCATTAAAGCCTGGACTTAACACAATCGTCGGTCACGTGAACATT
1 CTACATGTATGTCCACGTCAGCATTAAAGCCTGGACTTAACACAATCGTCGGTCACGTGAACATT
10606 TTCCGTTAACAAAAGGACCAACCAACATGGTCTTAA
66 TTCCGTTAACAAAAGGACCAACCAACATGGTCTTAA
10642 CTACATGTATGTCCACGTCAGCATTAAAGCCTGGACTTAACACAATCGTCGGTCACGTGAACATT
1 CTACATGTATGTCCACGTCAGCATTAAAGCCTGGACTTAACACAATCGTCGGTCACGTGAACATT
10707 TTCCGTTAACAAAAGGACCAACCAACATGGTCTTAA
66 TTCCGTTAACAAAAGGACCAACCAACATGGTCTTAA
10743 ATTGCAAGCT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
CTACATGTATGTCCACGTCAGCATTAAAGCCTGGACTTAACACAATCGTCGGTCACGTGAACATT
TTCCGTTAACAAAAGGACCAACCAACATGGTCTTAA
Found at i:11164 original size:22 final size:24
Alignment explanation
Indices: 11134--11191 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
11124 GCTGCAAACT
*
11134 AAACATTAATG-G-CAAAGAGAGG
1 AAACCTTAATGTGACAAAGAGAGG
11156 AAACCTTAATGTATGACAAAGAGAGG
1 AAACCTTAATG--TGACAAAGAGAGG
11182 AAACCTTAAT
1 AAACCTTAAT
11192 AAATAACTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 10 0.32
25 1 0.03
26 20 0.65
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (24 bp):
AAACCTTAATGTGACAAAGAGAGG
Found at i:18846 original size:28 final size:28
Alignment explanation
Indices: 18810--18868 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
18800 CATATTTTGC
*
18810 ATATTTTCTTCCAATACATTCATACATA
1 ATATTTTCTTCCAATACATTCATACACA
*
18838 ATATTTTCTTCTAATACATTCATACACA
1 ATATTTTCTTCCAATACATTCATACACA
18866 ATA
1 ATA
18869 CATAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTTTCTTCCAATACATTCATACACA
Found at i:19571 original size:49 final size:49
Alignment explanation
Indices: 19514--19614 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
19504 TCGCTTTCGG
19514 CTGTTACCCTTATGTCCCCAAAAATTGTCATTCCAGAATTCACGGGAAA
1 CTGTTACCCTTATGTCCCCAAAAATTGTCATTCCAGAATTCACGGGAAA
*
19563 CTGTTACCCTTATGTCCCCAAAAATTGTCATTCCAGAATTCACTGGAAA
1 CTGTTACCCTTATGTCCCCAAAAATTGTCATTCCAGAATTCACGGGAAA
19612 CTG
1 CTG
19615 AATTCCACCG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (49 bp):
CTGTTACCCTTATGTCCCCAAAAATTGTCATTCCAGAATTCACGGGAAA
Done.