Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021217.1 Corchorus olitorius cultivar O-4 contig21250, 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: 5252
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:264 original size:27 final size:28
Alignment explanation
Indices: 217--291 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
207 CCCTTATTGG
*
217 TAAAATTA-CGATTTTACCCCTATCAT-GAA
1 TAAAATTACCG-TTTT-GCCCT-TCATCGAA
**
246 -AAAATTACCGTTTTGCCCTTTGTCGAA
1 TAAAATTACCGTTTTGCCCTTCATCGAA
273 TAAAATTACCGTTTTGCCC
1 TAAAATTACCGTTTTGCCC
292 CTGTAGACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.05
27 7 0.17
28 29 0.73
29 2 0.05
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (28 bp):
TAAAATTACCGTTTTGCCCTTCATCGAA
Found at i:306 original size:28 final size:28
Alignment explanation
Indices: 246--298 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
236 CTATCATGAA
* *
246 AAAATTACCGTTTTGCCCTTTGTCGAAT
1 AAAATTACCGTTTTGCCCTCTGTAGAAT
274 AAAATTACCGTTTTGCCC-CTGTAGA
1 AAAATTACCGTTTTGCCCTCTGTAGA
299 CCTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (28 bp):
AAAATTACCGTTTTGCCCTCTGTAGAAT
Found at i:4489 original size:21 final size:21
Alignment explanation
Indices: 4442--4489 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4432 TAAAATCATA
*
4442 AAAAACTTTAATAAGCTTACT
1 AAAAAGTTTAATAAGCTTACT
4463 AAAAAGTTTAATAATGC-TACT
1 AAAAAGTTTAATAA-GCTTACT
*
4484 ATAAAG
1 AAAAAG
4490 CATATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (21 bp):
AAAAAGTTTAATAAGCTTACT
Found at i:5188 original size:200 final size:200
Alignment explanation
Indices: 4562--5251 Score: 931
Period size: 198 Copynumber: 3.5 Consensus size: 200
4552 CTCAATAAAT
* ** * ** * *
4562 TAATAATCCTACAAGAAAAATTATACAATACAATGTCAGTAGAGTTTAATATACTGCATGTGCGG
1 TAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGG
* *
4627 GGTTTAAGGGTCAACATGTGT-CCCATAGGGGAATATGTATTAATATTAAATATATTTATTTAAT
66 GGTTTAAGGGTCGACATGTGTCCCCTTA-GGGAATATGTATTAATATTAAATATATTT-TTTAAT
*
4691 TAAGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTG
129 TACGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTG
*
4756 TATTGTA
194 TATTATA
* *
4763 TAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGAAGTTTAGCAGACTGCACATGCGG
1 TAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGG
* * * * **
4828 GGTTCAATGGTTGACATGTGACCCCTTAGGGAATAT-TATTAATATTAAATAT-TTAATTAATTA
66 GGTTTAAGGGTCGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTTTTAATTA
* * * * * *
4891 TC-AAATGGGGTATGTGTCAACATCTTAATCCACTTACGGAGTCTAAAATTTACACTGACAGTGA
131 -CGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGT
4955 ATTATA
195 ATTATA
* * *
4961 TAATAATCCTATAAGAAAAAGTATACAATACACCATCAGTGGAGTTTAGCAGACTGCACGTTCGG
1 TAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGG
* *
5026 GGTTTAA-GGTTGACACGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTTCTTAATT
66 GGTTTAAGGGTCGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTT-TTAATT
* * * * * *
5090 ACGAAATGGGGCATGTTTCAACTTATTAACCCGCTTATTGAGTCCAAATTTTACACTGATAGTGT
130 ACGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGT
5155 ATTATA
195 ATTATA
* * * *
5161 TAATAATCCTATAAGAAAAATTATACAATACACTGTAAGTGGAGTTTAGCATATTGCACGTGCGG
1 TAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGG
*
5226 GGCTTAAGGGTCGACATGTGTCCCCT
66 GGTTTAAGGGTCGACATGTGTCCCCT
5252 A
Statistics
Matches: 424, Mismatches: 58, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
197 26 0.06
198 150 0.35
199 5 0.01
200 143 0.34
201 95 0.22
202 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (200 bp):
TAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGG
GGTTTAAGGGTCGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTTTTAATTA
CGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTA
TTATA
Done.