Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018971.1 Corchorus olitorius cultivar O-4 contig19004, 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: 19760
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:318 original size:66 final size:66
Alignment explanation
Indices: 166--361 Score: 301
Period size: 66 Copynumber: 3.0 Consensus size: 66
156 CCGCATTAAC
* * *
166 TTGATTCACCGAACCATCCTGAACTGTTCGAAAATGTGCTGCACCGAGCT--CCGAATTCCAAT-
1 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC
228 T
66 T
***
229 TCTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTATGCCGAGCTCACCGAAATCCAAT
1 T-TGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAAT
294 CT
65 CT
296 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCG-AATCCAATC
1 TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC
360 T
66 T
361 T
1 T
362 GAAGATGTAA
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
63 1 0.01
64 44 0.37
65 11 0.09
66 62 0.52
67 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (66 bp):
TTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAAATCCAATC
T
Found at i:6799 original size:11 final size:11
Alignment explanation
Indices: 6783--6807 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6773 AGAAAATTGT
6783 TTGTTTTTGGA
1 TTGTTTTTGGA
6794 TTGTTTTTGGA
1 TTGTTTTTGGA
6805 TTG
1 TTG
6808 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:15060 original size:23 final size:23
Alignment explanation
Indices: 15034--15106 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
15024 CATATTAAAA
15034 ACTTATATTGGTCCCACTTATTC
1 ACTTATATTGGTCCCACTTATTC
* ** ** ***
15057 ACTTTTACTTCATCATA-TTAAAA
1 ACTTATA-TTGGTCCCACTTATTC
15080 ACTTATATTGGTCCCACTTATTC
1 ACTTATATTGGTCCCACTTATTC
15103 ACTT
1 ACTT
15107 TTATCGAATT
Statistics
Matches: 32, Mismatches: 16, Indels: 4
0.62 0.31 0.08
Matches are distributed among these distances:
22 5 0.16
23 22 0.69
24 5 0.16
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.44
Consensus pattern (23 bp):
ACTTATATTGGTCCCACTTATTC
Found at i:15081 original size:46 final size:46
Alignment explanation
Indices: 15014--15109 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
15004 ATAACTGGCA
15014 TTTACTTCATCATATTAAAAACTTATATTGGTCCCACTTATTCACT
1 TTTACTTCATCATATTAAAAACTTATATTGGTCCCACTTATTCACT
15060 TTTACTTCATCATATTAAAAACTTATATTGGTCCCACTTATTCACT
1 TTTACTTCATCATATTAAAAACTTATATTGGTCCCACTTATTCACT
15106 TTTA
1 TTTA
15110 TCGAATTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (46 bp):
TTTACTTCATCATATTAAAAACTTATATTGGTCCCACTTATTCACT
Found at i:17172 original size:30 final size:30
Alignment explanation
Indices: 17116--17172 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
17106 GGAAGAAAAT
* *
17116 GGTTAAAGTCTTATTCTATTAGTTTTCAAC
1 GGTTAAAGTCTTATTCTATCAATTTTCAAC
*
17146 GGTTAAATTCTTATTCTATCAATTTTC
1 GGTTAAAGTCTTATTCTATCAATTTTC
17173 TTTTGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (30 bp):
GGTTAAAGTCTTATTCTATCAATTTTCAAC
Found at i:17544 original size:86 final size:85
Alignment explanation
Indices: 17382--17544 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 85
17372 AGGTTTCATG
* * * * *
17382 TAAAAAATTATAAAGTTGAATATTAGTGAGAATATTTTTTTAAATCTTGCCAAATTGTGGAAGGT
1 TAAAAAATTATAAAGTTGAATAATAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGAAGAT
*
17447 TTAGGAGATATTTTAAGAAA
66 TTAGGAAATATTTTAAGAAA
* *
17467 TAAATAAATTATAAAGATTGAATAATAATGAGAATA-TTCTCTAAATCTTGTCAAATTGTGGGAG
1 TAAA-AAATTATAAAG-TTGAATAATAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGAAG
17531 ATTT-GGAAAATATT
64 ATTTAGG-AAATATT
17545 AAATAAAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
85 6 0.09
86 44 0.66
87 17 0.25
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (85 bp):
TAAAAAATTATAAAGTTGAATAATAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGAAGAT
TTAGGAAATATTTTAAGAAA
Done.