Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017511.1 Corchorus olitorius cultivar O-4 contig17544, 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: 48490
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6611 original size:4 final size:4
Alignment explanation
Indices: 6604--6635 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
6594 AAAAAAAAGG
6604 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
6636 AGGGTCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:8318 original size:21 final size:19
Alignment explanation
Indices: 8294--8350 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
8284 CTGCTCTAAA
8294 AATCTCATATGTACAGTACCT
1 AATCTCATATGTACAGT--CT
* * *
8315 AATCTAATTTGTACAGTGT
1 AATCTCATATGTACAGTCT
8334 AATCTCATATGTACAGT
1 AATCTCATATGTACAGT
8351 TGCTAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTCATATGTACAGTCT
Found at i:20552 original size:17 final size:17
Alignment explanation
Indices: 20529--20562 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20519 CGAAAAAAGT
*
20529 AAAAAAAAAAATGGAACG
1 AAAAAAAGAAA-GGAACG
20547 AAAAAAAGAAAGGAAC
1 AAAAAAAGAAAGGAAC
20563 TGTTTTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.06, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAGGAACG
Found at i:26209 original size:17 final size:17
Alignment explanation
Indices: 26187--26219 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
26177 CTTCCTTCTT
26187 TTTCTTGTTT-TTTTTTC
1 TTTCTT-TTTGTTTTTTC
26204 TTTCTTTTTGTTTTTT
1 TTTCTTTTTGTTTTTT
26220 AGGAGATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTCTTTTTGTTTTTTC
Found at i:30764 original size:188 final size:188
Alignment explanation
Indices: 30447--30825 Score: 758
Period size: 188 Copynumber: 2.0 Consensus size: 188
30437 TTCATTGTCA
30447 AATCATTATAATTCTTTACATGGCTAATCACCTAGATGGTGAAGTCAGGTTTGTCCACAACAAAA
1 AATCATTATAATTCTTTACATGGCTAATCACCTAGATGGTGAAGTCAGGTTTGTCCACAACAAAA
30512 CATTTGCTTTACTTTAGCCAAAACTATGAAATCTAGTGAAGTCATGCATAAGAGAGAATCTGGGG
66 CATTTGCTTTACTTTAGCCAAAACTATGAAATCTAGTGAAGTCATGCATAAGAGAGAATCTGGGG
30577 GGAGTTCCACTAAATATAAAATTAACTAACTTAGTACTTCATATCAACAAATACTACC
131 GGAGTTCCACTAAATATAAAATTAACTAACTTAGTACTTCATATCAACAAATACTACC
30635 AATCATTATAATTCTTTACATGGCTAATCACCTAGATGGTGAAGTCAGGTTTGTCCACAACAAAA
1 AATCATTATAATTCTTTACATGGCTAATCACCTAGATGGTGAAGTCAGGTTTGTCCACAACAAAA
30700 CATTTGCTTTACTTTAGCCAAAACTATGAAATCTAGTGAAGTCATGCATAAGAGAGAATCTGGGG
66 CATTTGCTTTACTTTAGCCAAAACTATGAAATCTAGTGAAGTCATGCATAAGAGAGAATCTGGGG
30765 GGAGTTCCACTAAATATAAAATTAACTAACTTAGTACTTCATATCAACAAATACTACC
131 GGAGTTCCACTAAATATAAAATTAACTAACTTAGTACTTCATATCAACAAATACTACC
30823 AAT
1 AAT
30826 TCACTCATTT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 191 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (188 bp):
AATCATTATAATTCTTTACATGGCTAATCACCTAGATGGTGAAGTCAGGTTTGTCCACAACAAAA
CATTTGCTTTACTTTAGCCAAAACTATGAAATCTAGTGAAGTCATGCATAAGAGAGAATCTGGGG
GGAGTTCCACTAAATATAAAATTAACTAACTTAGTACTTCATATCAACAAATACTACC
Found at i:39306 original size:88 final size:88
Alignment explanation
Indices: 39203--39379 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
39193 GACACATGTC
*
39203 ATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCATAGTCTTTAGAAGACAAATGTCATTTTT
1 ATTTTTTGAATTAATTAAATTTTAAATATTTCAATCATAGTCTTTAGAAGACAAATGTCATTTTT
*
39268 CAGGACCTTTATGTAGTCTGCTA
66 CAGGACCTTTATGTAATCTGCTA
39291 ATTTTTTGAATTAATTAAATTTTAAATATTTCAATCATAGTCTTTAGAAGACAAATGTCATTTTT
1 ATTTTTTGAATTAATTAAATTTTAAATATTTCAATCATAGTCTTTAGAAGACAAATGTCATTTTT
39356 CAGGACCTTTATGTAATCTGCTA
66 CAGGACCTTTATGTAATCTGCTA
39379 A
1 A
39380 ACTCACCGCC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (88 bp):
ATTTTTTGAATTAATTAAATTTTAAATATTTCAATCATAGTCTTTAGAAGACAAATGTCATTTTT
CAGGACCTTTATGTAATCTGCTA
Done.