Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021751.1 Corchorus olitorius cultivar O-4 contig21784, 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: 16199
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:6979 original size:2 final size:2
Alignment explanation
Indices: 6972--7001 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6962 TTTTATGAAA
6972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7002 GCACCATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8274 original size:2 final size:2
Alignment explanation
Indices: 8269--8295 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8259 AAAATATAAA
8269 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8296 ATTGTCGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9375 original size:84 final size:84
Alignment explanation
Indices: 9279--9644 Score: 572
Period size: 84 Copynumber: 4.3 Consensus size: 84
9269 CCAATAACCA
* * * *
9279 AAAGTCTCCAAACACATATATAACACAAGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
9344 ACACAGAGACACCTATATTC
66 ACACAGAGACATCTAT-TAC
9364 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
9428 ACACAGAGTCATCTATTAC
66 ACACAGAGACATCTATTAC
9447 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
9512 ACACAGAGCCAACTATTAC
66 ACACAGAGACATCTATTAC
*
9531 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
9596 ACACAGGGGCATCTCTATTAC
66 ACACAGAGACA--TCTATTAC
**
9617 AAAGTCCTTAAACACATATATAACACAG
1 AAAGTCCCCAAACACATATATAACACAG
9645 AGGTACTTCT
Statistics
Matches: 263, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
83 2 0.01
84 228 0.87
86 33 0.13
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGACATCTATTAC
Found at i:9644 original size:43 final size:43
Alignment explanation
Indices: 9279--9644 Score: 521
Period size: 43 Copynumber: 8.7 Consensus size: 43
9269 CCAATAACCA
* * *
9279 AAAGT-CTCCAAACACATATATAACACAAGGGCATCTCTATTCC
1 AAAGTCCT-CAAACACATATATAACACAGGGGCACCTCTATTAC
* * *
9322 AAAGTCCTCAAACACATATATAACACAGAGACACCTATATT-C
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
9364 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
* *
9406 AAAGTCCTCAAACACATATATAACACAGAGTCA--TCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
9447 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
* **
9490 AAAGTCCTCAAACACATATATAACACA-GAGC-CAACTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
* *
9531 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
9574 AAAGTCCTCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
9617 AAAGTCCTTAAACACATATATAACACAG
1 AAAGTCCTCAAACACATATATAACACAG
9645 AGGTACTTCT
Statistics
Matches: 290, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
41 108 0.37
42 8 0.03
43 172 0.59
44 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
Found at i:16067 original size:29 final size:30
Alignment explanation
Indices: 16018--16117 Score: 130
Period size: 29 Copynumber: 3.3 Consensus size: 30
16008 AAGTACCTAA
16018 TTAGTCCCTCTACTATTGAAAAAGATCAAT
1 TTAGTCCCTCTACTATTGAAAAAGATCAAT
* ****
16048 TTAGTCCCTCTATTA-TGAAATCTTTCAAT
1 TTAGTCCCTCTACTATTGAAAAAGATCAAT
16077 TTAGTCCCTCTACTATTGAAAAGAGATCAAT
1 TTAGTCCCTCTACTATTGAAAA-AGATCAAT
*
16108 TTAATCCCTC
1 TTAGTCCCTC
16118 CGTTAAATTG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
29 24 0.42
30 19 0.33
31 14 0.25
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (30 bp):
TTAGTCCCTCTACTATTGAAAAAGATCAAT
Done.