Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008563.1 Corchorus olitorius cultivar O-4 contig08590, 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, 913
Length: 1522
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Found at i:288 original size:30 final size:30
Alignment explanation
Indices: 226--288 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
216 TACGCTAAAA
* * *
226 AAAGATATAATAATGTTTTCTACAAATTAT
1 AAAGATATAATAATATTTTCAACAAATCAT
* * *
256 AAAGATTTAGTAATATTTTCAACGAATCAT
1 AAAGATATAATAATATTTTCAACAAATCAT
286 AAA
1 AAA
289 AGTTTTACAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (30 bp):
AAAGATATAATAATATTTTCAACAAATCAT
Found at i:773 original size:4 final size:4
Alignment explanation
Indices: 764--794 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
754 ATGATATTAA
764 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
795 TGAATATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:780 original size:69 final size:69
Alignment explanation
Indices: 634--859 Score: 302
Period size: 65 Copynumber: 3.2 Consensus size: 69
624 TATATATTAA
634 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATT-A
1 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
698 A---
66 ATTG
699 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
764 ATTG
66 ATTG
**
768 ATTGATTGATTGATTGATTGATTGATTTGAATATCATGATCCAATTAGAATCAATTAGTACT--A
1 ATTGATTGATTGA-T--TTGA---A--T--ATATTTTGATCCAATTAGAATCAATTAGTACTAAA
831 ATGATATTAAATTG
56 ATGATATTAAATTG
845 ATTGATTGATTGATT
1 ATTGATTGATTGATT
860 GATTGATTGA
Statistics
Matches: 145, Mismatches: 2, Indels: 19
0.87 0.01 0.11
Matches are distributed among these distances:
65 63 0.43
66 2 0.01
69 13 0.09
70 1 0.01
72 4 0.03
74 1 0.01
75 1 0.01
76 1 0.01
77 29 0.20
79 30 0.21
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (69 bp):
ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
ATTG
Found at i:790 original size:77 final size:77
Alignment explanation
Indices: 699--899 Score: 270
Period size: 77 Copynumber: 2.6 Consensus size: 77
689 ATGATATTAA
**
699 ATTGATTGATTGATTTGA-AT-ATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATT
1 ATTGATTGATTGATTTGATATAATATCATGATCCAATTAGAATCAATTAGTACT--AATGATATT
762 AAATTGATTGATTG
64 AAATTGATTGATTG
*
776 ATTGATTGATTGA-TTGATTTGAATATCATGATCCAATTAGAATCAATTAGTACTAATGATATTA
1 ATTGATTGATTGATTTGATAT-AATATCATGATCCAATTAGAATCAATTAGTACTAATGATATTA
840 AATTGATTGATTG
65 AATTGATTGATTG
* * *
853 ATTGATTGATTGA-TTGATTTGAATAT--TGATCAAATTAAAATCAATTA
1 ATTGATTGATTGATTTGATAT-AATATCATGATCCAATTAGAATCAATTA
900 AAATCAATTA
Statistics
Matches: 116, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
75 19 0.16
76 4 0.03
77 63 0.54
79 30 0.26
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.42
Consensus pattern (77 bp):
ATTGATTGATTGATTTGATATAATATCATGATCCAATTAGAATCAATTAGTACTAATGATATTAA
ATTGATTGATTG
Found at i:793 original size:65 final size:65
Alignment explanation
Indices: 627--778 Score: 304
Period size: 65 Copynumber: 2.3 Consensus size: 65
617 CAATTTATAT
627 ATATTAAATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATG
1 ATATTAAATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATG
692 ATATTAAATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATG
1 ATATTAAATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATG
757 ATATTAAATTGATTGATTGATT
1 ATATTAAATTGATTGATTGATT
779 GATTGATTGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 87 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.43
Consensus pattern (65 bp):
ATATTAAATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATG
Found at i:850 original size:4 final size:4
Alignment explanation
Indices: 841--871 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
831 ATGATATTAA
841 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
872 TGAATATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:900 original size:10 final size:10
Alignment explanation
Indices: 885--909 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
875 ATATTGATCA
885 AATTAAAATC
1 AATTAAAATC
895 AATTAAAATC
1 AATTAAAATC
905 AATTA
1 AATTA
910 GTATTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAAAATC
Done.