Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022040.1 Corchorus olitorius cultivar O-4 contig22073, 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: 17620
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:2085 original size:21 final size:21
Alignment explanation
Indices: 2052--2100 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2042 AAGAATTGTA
**
2052 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
2072 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
2093 GCATTCCT
1 GC-TTCCT
2101 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:5060 original size:25 final size:25
Alignment explanation
Indices: 5032--5091 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
5022 ACATGTCTTC
5032 TTGCCTTGAACTTGTCTTTGCTCCT
1 TTGCCTTGAACTTGTCTTTGCTCCT
5057 TTGCCTTGAACTTGTCTTTGCTCCT
1 TTGCCTTGAACTTGTCTTTGCTCCT
*
5082 TTGGCTTGAA
1 TTGCCTTGAA
5092 AACACCAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.10, C:0.25, G:0.18, T:0.47
Consensus pattern (25 bp):
TTGCCTTGAACTTGTCTTTGCTCCT
Found at i:5444 original size:41 final size:41
Alignment explanation
Indices: 5399--5513 Score: 178
Period size: 41 Copynumber: 2.8 Consensus size: 41
5389 ACCAAATTGA
*
5399 ATCAAATAGTAAATAGAATCCTAAATCAAGGG-CTAAATTAC
1 ATCAAATAGTAAATAGAATCCTAAATC-AGGGACAAAATTAC
*
5440 ATCAAATAGTAAATAGAATCCTAAATCAGGGACAAAATTGC
1 ATCAAATAGTAAATAGAATCCTAAATCAGGGACAAAATTAC
* *
5481 ATCAAATAGTAAATAGAACCCTAAATTAGGGAC
1 ATCAAATAGTAAATAGAATCCTAAATCAGGGAC
5514 CATATTGAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.06
41 65 0.94
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (41 bp):
ATCAAATAGTAAATAGAATCCTAAATCAGGGACAAAATTAC
Found at i:6065 original size:2 final size:2
Alignment explanation
Indices: 6058--6087 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6048 TAAAGCGTCC
6058 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6088 TCGAATCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6665 original size:18 final size:17
Alignment explanation
Indices: 6630--6665 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6620 TATCGCCCCT
*
6630 TTTTTTTTCTTTTCTCC
1 TTTTTTTTCTTTTATCC
6647 TTTTTTTTCTTCTTATCC
1 TTTTTTTTCTT-TTATCC
6665 T
1 T
6666 CTATTTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTTTCTTTTATCC
Found at i:6807 original size:16 final size:17
Alignment explanation
Indices: 6774--6808 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6764 GGTAAACCTC
6774 CTTTCTCTCCCTTGTAA
1 CTTTCTCTCCCTTGTAA
*
6791 CTTTCTCTCTC-TGTAA
1 CTTTCTCTCCCTTGTAA
6807 CT
1 CT
6809 GCTCAGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.11, C:0.34, G:0.06, T:0.49
Consensus pattern (17 bp):
CTTTCTCTCCCTTGTAA
Found at i:10863 original size:24 final size:23
Alignment explanation
Indices: 10812--10861 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
10802 ATGTTTTGTG
10812 TTTTGCGTCAAAGAAAAAAAAAA
1 TTTTGCGTCAAAGAAAAAAAAAA
10835 TTTTGCGTCATAA-AAAAAAAAAA
1 TTTTGCGTCA-AAGAAAAAAAAAA
10858 TTTT
1 TTTT
10862 TGTCCCTGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (23 bp):
TTTTGCGTCAAAGAAAAAAAAAA
Found at i:13682 original size:22 final size:21
Alignment explanation
Indices: 13657--13702 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13647 CTAAACCATT
*
13657 ACCGCCCATTCATCGTGCCACC
1 ACCGCCCATGC-TCGTGCCACC
* *
13679 ACCGGCCATGCTCGTGCCATC
1 ACCGCCCATGCTCGTGCCACC
13700 ACC
1 ACC
13703 ATTCCATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (21 bp):
ACCGCCCATGCTCGTGCCACC
Found at i:14294 original size:16 final size:16
Alignment explanation
Indices: 14270--14302 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
14260 CATGCATCAT
14270 AATCCTAATATATGCC
1 AATCCTAATATATGCC
*
14286 AATCTTAATATATGCC
1 AATCCTAATATATGCC
14302 A
1 A
14303 TAATTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (16 bp):
AATCCTAATATATGCC
Found at i:16180 original size:11 final size:11
Alignment explanation
Indices: 16164--16189 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16154 AGATAATTTC
16164 TTTTCTTCTAG
1 TTTTCTTCTAG
16175 TTTTCTTCTAG
1 TTTTCTTCTAG
16186 TTTT
1 TTTT
16190 TTAGACAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:17505 original size:50 final size:49
Alignment explanation
Indices: 17444--17619 Score: 201
Period size: 50 Copynumber: 3.6 Consensus size: 49
17434 CGATCAACTT
* * * * * *
17444 CTTTGAGCTGTCTTTCAATTCAATCTTCAGGGTATCGTCTTCCGCTTACC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAGG-ACCGTCTTCCGCTTATC
* *
17494 CTTTGAACTGTCTTCCAATTCAACCTTAAAAGGACCATCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAGGACCGTCTTCCGCTTATC
* * *
17544 TTTTGAACTGTCTTCCAATTCAATCTTAAAAGCACCGTCTTTCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAGGACCGTCTTCCGCTTATC
* *
17594 CTTTGGACTGTCTTAC-ATTCAATCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT
17620 T
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
49 10 0.09
50 96 0.88
51 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (49 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAGGACCGTCTTCCGCTTATC
Done.