Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018261.1 Corchorus olitorius cultivar O-4 contig18294, 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: 37008
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:243 original size:125 final size:126
Alignment explanation
Indices: 16--266 Score: 357
Period size: 125 Copynumber: 2.0 Consensus size: 126
6 AAGAAATATA
*
16 ATTTAAAAAATTCTAATATATATAAGTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAATAGG
1 ATTTAAAAAATTCTAATATATATAAGTTTTAAAATAAAATAGTAAAATGGTAAAAAT---ACA-G
* *
81 TATAAGGATGTTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAATTAT
62 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATTAT
* *
146 ATTTAAAAAATTCTAATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-T
1 ATTTAAAAAATTCT-A-ATATATATAAG-TTTTAAAATAAAATAGTAAAATGGTAAAAATACAGT
*
209 A-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAA
63 ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
267 GTTTAAACAA
Statistics
Matches: 112, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
125 52 0.46
126 2 0.02
127 2 0.02
129 1 0.01
130 14 0.12
131 1 0.01
132 11 0.10
133 29 0.26
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (126 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTAAAATAAAATAGTAAAATGGTAAAAATACAGTATA
AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAATTAT
Found at i:1499 original size:13 final size:13
Alignment explanation
Indices: 1481--1505 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1471 TCTTACCCTA
1481 AACTTTCACTAAT
1 AACTTTCACTAAT
1494 AACTTTCACTAA
1 AACTTTCACTAA
1506 AAAAAATAAC
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
AACTTTCACTAAT
Found at i:2935 original size:61 final size:61
Alignment explanation
Indices: 2840--2962 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
2830 CTTATTTAAG
2840 ATATGGTGTACGTATGAATTATATTTAATATATATTATATATCAACAAATAAAAAATAAAA
1 ATATGGTGTACGTATGAATTATATTTAATATATATTATATATCAACAAATAAAAAATAAAA
2901 ATATGGTGTACGTATGAATTATATTTAATATATATTATATATCAACAAATAAAAAATAAAA
1 ATATGGTGTACGTATGAATTATATTTAATATATATTATATATCAACAAATAAAAAATAAAA
2962 A
1 A
2963 ACATGTATAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (61 bp):
ATATGGTGTACGTATGAATTATATTTAATATATATTATATATCAACAAATAAAAAATAAAA
Found at i:15271 original size:69 final size:69
Alignment explanation
Indices: 15156--15290 Score: 261
Period size: 69 Copynumber: 2.0 Consensus size: 69
15146 TGGTGCCTCT
15156 CGGGAAAAAGAGCGGGTTTCTGAGCGTGAGTGGTCAGGCAACTCTGATAGGAGGCATCGTGATGA
1 CGGGAAAAAGAGCGGGTTTCTGAGCGTGAGTGGTCAGGCAACTCTGATAGGAGGCATCGTGATGA
15221 GGAG
66 GGAG
*
15225 CGGGAAAAAGAGCGGGTTTCTGAGCGTGAGTGGTCAGGCAATTCTGATAGGAGGCATCGTGATGA
1 CGGGAAAAAGAGCGGGTTTCTGAGCGTGAGTGGTCAGGCAACTCTGATAGGAGGCATCGTGATGA
15290 G
66 G
15291 AAGGAGCGGG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.26, C:0.14, G:0.40, T:0.20
Consensus pattern (69 bp):
CGGGAAAAAGAGCGGGTTTCTGAGCGTGAGTGGTCAGGCAACTCTGATAGGAGGCATCGTGATGA
GGAG
Found at i:19377 original size:15 final size:16
Alignment explanation
Indices: 19354--19386 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
19344 TTGAGTTTGG
19354 TTGGTTTTGGTTTTTT
1 TTGGTTTTGGTTTTTT
19370 TTGG-TTTGGTTTTTT
1 TTGGTTTTGGTTTTTT
19385 TT
1 TT
19387 ATCTCACGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (16 bp):
TTGGTTTTGGTTTTTT
Done.