Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019498.1 Corchorus olitorius cultivar O-4 contig19531, 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: 18444
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:2383 original size:15 final size:15
Alignment explanation
Indices: 2353--2392 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
2343 TTACTTTGTT
*
2353 TTGTTTTCCAGTTTAA
1 TTGTTTT-CTGTTTAA
2369 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
2384 TTGTTTTCT
1 TTGTTTTCT
2393 ATCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:9819 original size:36 final size:36
Alignment explanation
Indices: 9777--9864 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
9767 TGTGAATGCA
9777 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
1 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
*
9813 ATGCCTAATTACTAATAATTACTAATGTGAATGATG
1 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
9849 ATGCCTAATTACTAAT
1 ATGCCTAATTACTAAT
9865 GTGGATACTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (36 bp):
ATGCCTAATTACTAATAATTACTAATGTGAACGATG
Found at i:13631 original size:22 final size:22
Alignment explanation
Indices: 13603--13649 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
13593 TAAATTACTT
*
13603 CACGTAAATTATGGTAGAAACC
1 CACGTAAATTATAGTAGAAACC
13625 CACGTAAATTATAGTAGAAACC
1 CACGTAAATTATAGTAGAAACC
13647 CAC
1 CAC
13650 TTGTTTCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (22 bp):
CACGTAAATTATAGTAGAAACC
Found at i:14294 original size:245 final size:245
Alignment explanation
Indices: 13864--14413 Score: 1082
Period size: 245 Copynumber: 2.2 Consensus size: 245
13854 TACTTTATTT
13864 AAAATAAGGATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGTTTGAG
1 AAAATAAGGATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGTTTGAG
13929 TAAAACTATAAAAGTATATTTAAAAATTCTAATATAAAAGTATAATTAAATAGTTATAAGGATAT
66 TAAAACTATAAAAGTATATTTAAAAATTCTAATATAAAAGTATAATTAAATAGTTATAAGGATAT
13994 TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCA
131 TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCA
14059 TATAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATATACGA
196 TATAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATATACGA
*
14109 AAAATAAGGATATAATAGATGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGTTTGAG
1 AAAATAAGGATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGTTTGAG
14174 TAAAACTATAAAAGTATATTTAAAAATTCTAATATAAAAGTATAATTAAATAGTTATAAGGATAT
66 TAAAACTATAAAAGTATATTTAAAAATTCTAATATAAAAGTATAATTAAATAGTTATAAGGATAT
14239 TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCA
131 TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCA
*
14304 TTTAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATATACGA
196 TATAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATATACGA
14354 AAAATAAGGATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGT
1 AAAATAAGGATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGT
14414 ATAGATAAGG
Statistics
Matches: 302, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 302 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (245 bp):
AAAATAAGGATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGTTTGAG
TAAAACTATAAAAGTATATTTAAAAATTCTAATATAAAAGTATAATTAAATAGTTATAAGGATAT
TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATGGCA
TATAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATATACGA
Found at i:14661 original size:74 final size:74
Alignment explanation
Indices: 14567--14704 Score: 258
Period size: 74 Copynumber: 1.9 Consensus size: 74
14557 CGGTGGTAAG
*
14567 TGGTAACTTTAAGGGTCATTTTGTCTCGTTTTGTAGTTCATGGGGCTAAATGTCTTTAATGCAAA
1 TGGTAACTTTAAGGGTCATTTTCTCTCGTTTTGTAGTTCATGGGGCTAAATGTCTTTAATGCAAA
14632 AGTGGCAAC
66 AGTGGCAAC
*
14641 TGGTAACTTTAGGGGTCATTTTCTCTCGTTTTGTAGTTCATGGGGCTAAATGTCTTTAATGCAA
1 TGGTAACTTTAAGGGTCATTTTCTCTCGTTTTGTAGTTCATGGGGCTAAATGTCTTTAATGCAA
14705 TAGTTCGGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (74 bp):
TGGTAACTTTAAGGGTCATTTTCTCTCGTTTTGTAGTTCATGGGGCTAAATGTCTTTAATGCAAA
AGTGGCAAC
Done.