Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022472.1 Corchorus olitorius cultivar O-4 contig22505, 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: 36032
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6392 original size:21 final size:21
Alignment explanation
Indices: 6368--6407 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6358 CTGAAAGGAA
*
6368 CATCTCAACGTATAGAAAAAG
1 CATCACAACGTATAGAAAAAG
* *
6389 CATCACAATGTATGGAAAA
1 CATCACAACGTATAGAAAA
6408 TCAGTGTCCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (21 bp):
CATCACAACGTATAGAAAAAG
Found at i:9010 original size:28 final size:30
Alignment explanation
Indices: 8948--9003 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
8938 ACATTATATT
8948 AAGAGTGACACTAAAAAGTTTATAAAAAAAA
1 AAGAGTGACACTAAAAAG-TTATAAAAAAAA
8979 AAGAGTGACACT-AAAA-TTATAAAAA
1 AAGAGTGACACTAAAAAGTTATAAAAA
9004 GTGAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 9 0.36
30 4 0.16
31 12 0.48
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (30 bp):
AAGAGTGACACTAAAAAGTTATAAAAAAAA
Found at i:10384 original size:13 final size:13
Alignment explanation
Indices: 10360--10408 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
10350 AAAAACTTGG
10360 TTTTGAAAAAGTGC
1 TTTTG-AAAAGTGC
10374 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
10387 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
10400 TTTTTAAAA
1 TTTTGAAAA
10409 TTAAGGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 29 0.85
14 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:12114 original size:18 final size:18
Alignment explanation
Indices: 12091--12130 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
12081 TCACCGGACA
12091 AATGTCCAACACTCTACC
1 AATGTCCAACACTCTACC
12109 AATGTCCAACACTCTACC
1 AATGTCCAACACTCTACC
12127 AATG
1 AATG
12131 ACTATTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (18 bp):
AATGTCCAACACTCTACC
Found at i:22568 original size:51 final size:51
Alignment explanation
Indices: 22510--22613 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
22500 AACCCTTAAC
*
22510 CCCCACATGTGTAGTCTGCTAAACTATACTGTCGATGTATTGTATACTTTT
1 CCCCACATGTGTAGTCTGCTAAACTATACTGTCGATGTATTATATACTTTT
* * *
22561 CCCCACATGTGTAGTCTGCTAAATTATATTGTCGGTGTATTATATACTTTT
1 CCCCACATGTGTAGTCTGCTAAACTATACTGTCGATGTATTATATACTTTT
22612 CC
1 CC
22614 TTGCATTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (51 bp):
CCCCACATGTGTAGTCTGCTAAACTATACTGTCGATGTATTATATACTTTT
Found at i:32504 original size:30 final size:30
Alignment explanation
Indices: 32470--32544 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
32460 TACCGTACAA
32470 GTCCCTCTACTTACAAAAAAGGACAATTTG
1 GTCCCTCTACTTACAAAAAAGGACAATTTG
* ** *
32500 GTCCCTCTAC-TATAAAAACTGTCAATTTG
1 GTCCCTCTACTTACAAAAAAGGACAATTTG
32529 GTCCCTCTACTTACAA
1 GTCCCTCTACTTACAA
32545 TTTGGTGTCG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.31
Consensus pattern (30 bp):
GTCCCTCTACTTACAAAAAAGGACAATTTG
Found at i:32590 original size:31 final size:31
Alignment explanation
Indices: 32469--32588 Score: 106
Period size: 31 Copynumber: 3.9 Consensus size: 31
32459 ATACCGTACA
*** *
32469 AGTCCCTCTACTTACAAAAAAGGACAATTTG
1 AGTCCCTCTACTTACAAAATCTGTCAATTTG
32500 -GTCCCTCTACTATA-AAAA-CTGTCAATTTG
1 AGTCCCTCTACT-TACAAAATCTGTCAATTTG
** * *
32529 -GTCCCTCTACTTACAATTTGGTGTCGA-TTG
1 AGTCCCTCTACTTACAAAAT-CTGTCAATTTG
32559 AGTCCCTCTACTTAACAAAATCTGTCAATT
1 AGTCCCTCTACTT-ACAAAATCTGTCAATT
32589 GATTATATAT
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
28 2 0.03
29 21 0.30
30 18 0.25
31 24 0.34
32 6 0.08
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (31 bp):
AGTCCCTCTACTTACAAAATCTGTCAATTTG
Found at i:32898 original size:30 final size:30
Alignment explanation
Indices: 32837--32911 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
32827 TGACACCAAA
* *
32837 TTGTAAGTAAAGGGACCAAATTGACAGTTT
1 TTGTAAGTAGAGGGACCAAATTGACACTTT
* *
32867 TTGTAA-TAGGGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGA-CACTTT
32897 TTGTAAGTAGAGGGA
1 TTGTAAGTAGAGGGA
32912 TATATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 15 0.39
30 16 0.42
31 7 0.18
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.31
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACCAAATTGACACTTT
Found at i:34754 original size:16 final size:15
Alignment explanation
Indices: 34723--34752 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34713 CATGTCCACA
*
34723 ACCTTCTTGCTTTTT
1 ACCTCCTTGCTTTTT
34738 ACCTCCTTGCTTTTT
1 ACCTCCTTGCTTTTT
34753 TAGGTGTTCC
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:0.07, C:0.30, G:0.07, T:0.57
Consensus pattern (15 bp):
ACCTCCTTGCTTTTT
Found at i:36011 original size:2 final size:2
Alignment explanation
Indices: 36004--36032 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35994 CTCGTATTGA
36004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.