Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023824.1 Corchorus olitorius cultivar O-4 contig23857, 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: 16438
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1822 original size:14 final size:14
Alignment explanation
Indices: 1797--1835 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1787 AATTTGTCAT
1797 GAGAAA-TAAAAAA
1 GAGAAATTAAAAAA
*
1810 GATAAATTAAAAAA
1 GAGAAATTAAAAAA
*
1824 GAGAAATGAAAA
1 GAGAAATTAAAA
1836 TTTGTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
GAGAAATTAAAAAA
Found at i:4984 original size:13 final size:13
Alignment explanation
Indices: 4966--4990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4956 ACTCACAATC
4966 AAAACAATTTATT
1 AAAACAATTTATT
4979 AAAACAATTTAT
1 AAAACAATTTAT
4991 AACAAAACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAACAATTTATT
Found at i:7641 original size:21 final size:20
Alignment explanation
Indices: 7605--7644 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
7595 CACCCATGAG
*
7605 CATATGTGAGACATATGGTA
1 CATATGTGACACATATGGTA
7625 CATATGTGTACACATATGGT
1 CATATGTG-ACACATATGGT
7645 CACTTGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
CATATGTGACACATATGGTA
Found at i:8970 original size:45 final size:47
Alignment explanation
Indices: 8919--9010 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 47
8909 TTATCTTTTA
* *
8919 TTTAATAAAATCTACATTA-TTATAGTTTTACCTATT-TAAATTATC
1 TTTAATAAAATCTACATTAGTTATAATTTCACCTATTATAAATTATC
* *
8964 TTTAATAAAATTTATATTAGTGTTATAATTTCACCTATTATAAATTA
1 TTTAATAAAATCTACATTA--GTTATAATTTCACCTATTATAAATTA
9011 ATATTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 17 0.44
48 15 0.38
49 7 0.18
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (47 bp):
TTTAATAAAATCTACATTAGTTATAATTTCACCTATTATAAATTATC
Found at i:10629 original size:22 final size:21
Alignment explanation
Indices: 10582--10634 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
10572 ATTGTTAGCA
* *
10582 AAAAAAAAACAGAGAAATACC
1 AAAAAAAAACAGAAAAAAACC
* *
10603 GAAAAAATACAAGAAAAAAACC
1 AAAAAAAAAC-AGAAAAAAACC
10625 AAAAACAAAA
1 AAAAA-AAAA
10635 AACCGAGAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 8 0.33
22 13 0.54
23 3 0.12
ACGTcount: A:0.75, C:0.13, G:0.08, T:0.04
Consensus pattern (21 bp):
AAAAAAAAACAGAAAAAAACC
Found at i:14679 original size:4 final size:4
Alignment explanation
Indices: 14634--14665 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
14624 GGGTTTAGTA
*
14634 GTTT ATTT GTTT GTTT GTTT GTTT GTTT GTTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT
14666 AGTTAGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.22, T:0.75
Consensus pattern (4 bp):
GTTT
Found at i:15052 original size:32 final size:31
Alignment explanation
Indices: 14992--15052 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
14982 AATACCAAAA
* *
14992 TCGAAAATACCGAACCCGACAGATCCCGAGC
1 TCGAAAATACCGAACCCGACAAAGCCCGAGC
* *
15023 TCGAAAATATCTGAATCCGACAAAGCCCGA
1 TCGAAAATA-CCGAACCCGACAAAGCCCGA
15053 ACATGAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (31 bp):
TCGAAAATACCGAACCCGACAAAGCCCGAGC
Found at i:15431 original size:22 final size:21
Alignment explanation
Indices: 15381--15437 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
15371 ATATATAAAA
*
15381 TAAATTAT-ATTTTATTTAAT
1 TAAATTATAATTTTACTTAAT
* *
15401 AAAATTTATAATTTTACTTATT
1 TAAA-TTATAATTTTACTTAAT
*
15423 CTAAATTATATTTTT
1 -TAAATTATAATTTT
15438 TTAGAAACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 19 0.66
23 3 0.10
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TAAATTATAATTTTACTTAAT
Found at i:15467 original size:22 final size:22
Alignment explanation
Indices: 15423--15477 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
15413 TTTACTTATT
* *
15423 CTAAATTATATTTTTTTAGAAA
1 CTAAATTATATTTTATTAAAAA
15445 CTAAATTATCA-TTTATTAAAAA
1 CTAAATTAT-ATTTTATTAAAAA
*
15467 C-AATTTATATT
1 CTAAATTATATT
15478 ATTGTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.04
21 7 0.25
22 19 0.68
23 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (22 bp):
CTAAATTATATTTTATTAAAAA
Done.