Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016480.1 Corchorus olitorius cultivar O-4 contig16513, 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: 50282
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:15738 original size:24 final size:23
Alignment explanation
Indices: 15703--15747 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
15693 CAAATTCGGT
15703 AACCCTAACAGAAACAGGCAAAAC
1 AACCCTAACAG-AACAGGCAAAAC
* *
15727 AACCCTAGCAGAAGAGGCAAA
1 AACCCTAACAGAACAGGCAAA
15748 TTTGGTGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.51, C:0.27, G:0.18, T:0.04
Consensus pattern (23 bp):
AACCCTAACAGAACAGGCAAAAC
Found at i:21899 original size:2 final size:2
Alignment explanation
Indices: 21894--21922 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21884 ATAAGATGCG
21894 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21923 TAGTGCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22101 original size:2 final size:2
Alignment explanation
Indices: 22094--22118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22084 GATATTGCAT
22094 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22119 GCAGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26572 original size:6 final size:6
Alignment explanation
Indices: 26561--26596 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
26551 TCACTTGTCT
* *
26561 ATGGGA ATGGGA ATGGGT ATGGGG ATGGGA ATGGGA
1 ATGGGA ATGGGA ATGGGA ATGGGA ATGGGA ATGGGA
26597 CGAAACTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.53, T:0.19
Consensus pattern (6 bp):
ATGGGA
Found at i:26583 original size:18 final size:18
Alignment explanation
Indices: 26560--26595 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
26550 ATCACTTGTC
26560 TATGGGAATGGGAATGGG
1 TATGGGAATGGGAATGGG
*
26578 TATGGGGATGGGAATGGG
1 TATGGGAATGGGAATGGG
26596 ACGAAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.53, T:0.22
Consensus pattern (18 bp):
TATGGGAATGGGAATGGG
Found at i:37193 original size:13 final size:13
Alignment explanation
Indices: 37175--37199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37165 CAAAATGACA
37175 AAAAAATAAAAAT
1 AAAAAATAAAAAT
37188 AAAAAATAAAAA
1 AAAAAATAAAAA
37200 ATCAATCTAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:37798 original size:17 final size:17
Alignment explanation
Indices: 37772--37805 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37762 AAGATCAAAA
37772 CGCCCCCTAATATTATC
1 CGCCCCCTAATATTATC
*
37789 CGCCCTCTAATATTATC
1 CGCCCCCTAATATTATC
37806 AATTGGTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.38, G:0.06, T:0.32
Consensus pattern (17 bp):
CGCCCCCTAATATTATC
Found at i:37901 original size:16 final size:17
Alignment explanation
Indices: 37873--37905 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
37863 AATATCAAAA
37873 CGCCCCTTAATATTATC
1 CGCCCCTTAATATTATC
37890 CGCCCC-TAATATTATC
1 CGCCCCTTAATATTATC
37906 AATTGGTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.36, G:0.06, T:0.33
Consensus pattern (17 bp):
CGCCCCTTAATATTATC
Found at i:48448 original size:2 final size:2
Alignment explanation
Indices: 48436--48478 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
48426 ATGTGTACTG
48436 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48477 AT
1 AT
48479 GAGGATCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48717 original size:57 final size:57
Alignment explanation
Indices: 48618--48733 Score: 189
Period size: 57 Copynumber: 2.0 Consensus size: 57
48608 TATTCGTTTC
* * *
48618 CTTTCATACAATAAATGTTATAATAAATCTTATACCCTCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATACCCCCTATCTCTACTTAATTATT
48675 CTTTCACACAATAAATGTTATAATAAATCATAT-CCTCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATACC-CCCTATCTCTACTTAATTATT
48732 CT
1 CT
48734 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 2 0.04
57 53 0.96
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCATATACCCCCTATCTCTACTTAATTATT
Found at i:48862 original size:42 final size:42
Alignment explanation
Indices: 48799--48879 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
48789 TAAGCCTTAG
48799 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
* *
48841 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTC
48880 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (42 bp):
GATTTGAGTTGAGTATGTCTTAATTTACAAAGAATTTTCTAT
Found at i:50094 original size:2 final size:2
Alignment explanation
Indices: 50087--50123 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
50077 ACGTAGCATC
50087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50124 GCTACTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.