Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017129.1 Corchorus olitorius cultivar O-4 contig17162, 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: 12175
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:983 original size:16 final size:15
Alignment explanation
Indices: 945--986 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
935 ACAGAGATTG
*
945 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
960 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
975 ACTAGAAAACAA
1 AC-AGAAAACAA
987 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4161 original size:37 final size:37
Alignment explanation
Indices: 4117--4187 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
4107 CTTGATCAAC
* *
4117 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
*
4154 ATACATGTCTTTCCAAATAGACATAATTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
4188 ATACTTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:4829 original size:29 final size:30
Alignment explanation
Indices: 4768--4830 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
4758 AAATTGCAAA
**
4768 AAAAAAAAAAAAAAGAAAGAAGAAGAAGGT
1 AAAAAAAAAAAAAAGAAAGAAGAAGAACAT
** *
4798 AAAAAAAAAACGAA-AAAGAATAAGAACAT
1 AAAAAAAAAAAAAAGAAAGAAGAAGAACAT
4827 AAAA
1 AAAA
4831 TAACTTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (30 bp):
AAAAAAAAAAAAAAGAAAGAAGAAGAACAT
Found at i:7578 original size:74 final size:71
Alignment explanation
Indices: 7466--7655 Score: 280
Period size: 74 Copynumber: 2.7 Consensus size: 71
7456 TCACATTTTC
*
7466 TCAAGTATTAGTTCATGAGTATAGGCATTTATCATATATGCTGTTGATTCCTTGATATTTCGGTA
1 TCAAGTATTAGTTGATGAGTATAGGCATTTATCATATATGCTGTTGATTCCTTGATATTTCGGTA
7531 CACATGTGG
66 CAC-T-T-G
*
7540 TCAAGTATTAGTTGATGAGTATAGGCATTTATAATATATGCTGTTGATTCCTTGATATTTCGGTA
1 TCAAGTATTAGTTGATGAGTATAGGCATTTATCATATATGCTGTTGATTCCTTGATATTTCGGTA
7605 CACTTG
66 CACTTG
* *
7611 ---AGTATTAGTTGATGAGTAAAGG-ATCTTCTCATATATGCTGTTGAT
1 TCAAGTATTAGTTGATGAGTATAGGCAT-TTATCATATATGCTGTTGAT
7656 GCATTCAATG
Statistics
Matches: 110, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
67 2 0.02
68 39 0.35
71 1 0.01
72 1 0.01
73 1 0.01
74 66 0.60
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.41
Consensus pattern (71 bp):
TCAAGTATTAGTTGATGAGTATAGGCATTTATCATATATGCTGTTGATTCCTTGATATTTCGGTA
CACTTG
Found at i:11256 original size:63 final size:64
Alignment explanation
Indices: 11160--11478 Score: 398
Period size: 63 Copynumber: 5.0 Consensus size: 64
11150 AAGAAGGTAG
* * *
11160 AAACCACCAAGGAGGAT-GTGATTTCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAG
1 AAACCACCAATGAGGATAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAA
* * * *
11223 AAACCAGCAATGAGGATA-TGATTCCGAGAAGTAAACTTTTTGAAGAACTGCAGCAGCGATTAAA
1 AAACCACCAATGAGGATAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATT-AA
* *
11287 AAGCACCACAAATGAGG-TAGTGATTCCGAGAGGTAAACTTGTTGAGGAACTGCAGCAGCGT-TT
1 AA--ACCACCAATGAGGATAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGC-TATT
11350 AA
63 AA
* * *
11352 AAAGCACCCATGAGGA-AGTGATTCTGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAA
1 AAACCACCAATGAGGATAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAA
* * * * * *
11415 AAAGCACCAATAAGGA-AGTGATTCCGAGAAGTGAACTTGTGGAGGAATTGCAGCAACTATTAA
1 AAACCACCAATGAGGATAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAA
11478 A
1 A
11479 GCCATGAAAG
Statistics
Matches: 223, Mismatches: 25, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
62 1 0.00
63 164 0.74
64 3 0.01
65 6 0.03
66 49 0.22
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (64 bp):
AAACCACCAATGAGGATAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAA
Found at i:11400 original size:129 final size:126
Alignment explanation
Indices: 11172--11478 Score: 402
Period size: 129 Copynumber: 2.4 Consensus size: 126
11162 ACCACCAAGG
* * * *
11172 AGGATGTGATTTCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAGAAACCAGCAATGAG
1 AGGAAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAAAAACCACCAATGAG
* *
11237 GATATGATTCCGAGAAGTAAACTTTTTGAAGAACTGCAGCAGCGATTAAAAAGCACCACAAATG
66 GATATGATTCCGAGAAGTAAACTTGTTGAAGAACTGCAGCAGCGATTAAAAAGCA-C-C-AATA
* * * *
11301 AGGTAGTGATTCCGAGAGGTAAACTTGTTGAGGAACTGCAGCAGCGT-TTAAAAAGCACCCATGA
1 AGGAAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGC-TATTAAAAACCACCAATGA
* * *
11365 GGA-AGTGATTCTGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAAAAAGCACCAATA
65 GGATA-TGATTCCGAGAAGTAAACTTGTTGAAGAACTGCAGCAGCGATTAAAAAGCACCAATA
* * * *
11427 AGGAAGTGATTCCGAGAAGTGAACTTGTGGAGGAATTGCAGCAACTATTAAA
1 AGGAAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAAA
11479 GCCATGAAAG
Statistics
Matches: 156, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
125 1 0.01
126 47 0.30
127 1 0.01
128 2 0.01
129 104 0.67
130 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (126 bp):
AGGAAGTGATTCCGAGAAGTAAACTTGTTGAGGAACTGCAGCAGCTATTAAAAACCACCAATGAG
GATATGATTCCGAGAAGTAAACTTGTTGAAGAACTGCAGCAGCGATTAAAAAGCACCAATA
Done.