Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024457.1 Corchorus olitorius cultivar O-4 contig24490, 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: 27279
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:8794 original size:19 final size:20
Alignment explanation
Indices: 8765--8828 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
8755 TTGATACTAT
8765 TTAGCAACTGTACAGATGAGA
1 TTAG-AACTGTACAGATGAGA
* *
8786 TTA-AACTGTACATATTTA-A
1 TTAGAACTGTACAGA-TGAGA
*
8805 TTAGGTACTGTACAGATGAGA
1 TTA-GAACTGTACAGATGAGA
8826 TTA
1 TTA
8829 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.41
20 4 0.12
21 16 0.47
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
TTAGAACTGTACAGATGAGA
Found at i:8828 original size:21 final size:19
Alignment explanation
Indices: 8770--8828 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
8760 ACTATTTAGC
8770 AACTGTACAGATGAGATTA
1 AACTGTACAGATGAGATTA
* *
8789 AACTGTACATATTTA-ATTA
1 AACTGTACAGA-TGAGATTA
*
8808 GGTACTGTACAGATGAGATTA
1 --AACTGTACAGATGAGATTA
8829 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 13 0.42
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (19 bp):
AACTGTACAGATGAGATTA
Found at i:14143 original size:44 final size:44
Alignment explanation
Indices: 14093--14176 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
14083 TTGGCACAAA
14093 TTCCTACTTGTCCATGTTTAAGATGTACACTATGATCTGCCAAG
1 TTCCTACTTGTCCATGTTTAAGATGTACACTATGATCTGCCAAG
14137 TTCCTACTTGTCCATGTTTAAGATGTACACTATGATCTGC
1 TTCCTACTTGTCCATGTTTAAGATGTACACTATGATCTGC
14177 AGAAGATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (44 bp):
TTCCTACTTGTCCATGTTTAAGATGTACACTATGATCTGCCAAG
Found at i:25938 original size:168 final size:174
Alignment explanation
Indices: 25658--26004 Score: 526
Period size: 168 Copynumber: 2.0 Consensus size: 174
25648 GGGTTCCAAT
* *
25658 ATATTCTTACATTAGTTTTTCACATTAACAAAGGGAGCCATTAAATGTTTTTACATAAATTTTTG
1 ATATTCTTACATTAGTTTTTCACATTAACAAAGAGAGCCATTAAATGTGTTTACATAAATTTTTG
*
25723 TTTGATTTGGAAAGAGGACAATTCAAACTCATATGTCACTCTCCATGGTTTGATTCTTC-CACTT
66 TTTGATTTGGAAAGAGGACAATTCAAACTCATATGTCACTCTCCATGGTTTGATTCTTCAAACTT
* *
25787 GCTTATATGACATAA-CA-AACTAATAATTTTCCACAAA-TATA
131 GCTTATATCACATAATAACAACTAATAATTTTCCACAAACTATA
*** * *
25828 ATATTCTTACATTAGTTTTTCACATTTGGAAAGAGATCCATT-AA-GTGTTTCCATAAATTTTTG
1 ATATTCTTACATTAGTTTTTCACATTAACAAAGAGAGCCATTAAATGTGTTTACATAAATTTTTG
* *
25891 TTTGATTTGGGAAGATGACAATTCAAACTCATATGTCACTCTCCATGGTTTGATTCTTCATGAAC
66 TTTGATTTGGAAAGAGGACAATTCAAACTCATATGTCACTCTCCATGGTTTGATTCTTCA--AAC
25956 TTGCTTATATCACATAATAACAACTAATAATTTTCCACAAACTATA
129 TTGCTTATATCACATAATAACAACTAATAATTTTCCACAAACTATA
26002 ATA
1 ATA
26005 AACACCTTTA
Statistics
Matches: 159, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
168 74 0.47
169 2 0.01
170 37 0.23
171 18 0.11
172 1 0.01
173 20 0.13
174 7 0.04
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (174 bp):
ATATTCTTACATTAGTTTTTCACATTAACAAAGAGAGCCATTAAATGTGTTTACATAAATTTTTG
TTTGATTTGGAAAGAGGACAATTCAAACTCATATGTCACTCTCCATGGTTTGATTCTTCAAACTT
GCTTATATCACATAATAACAACTAATAATTTTCCACAAACTATA
Done.