Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011691.1 Corchorus capsularis cultivar CVL-1 contig11712, 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, 609
Length: 1015
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Found at i:556 original size:55 final size:55
Alignment explanation
Indices: 490--884 Score: 626
Period size: 55 Copynumber: 7.3 Consensus size: 55
480 AGAAAGATGC
* * * * *
490 AATCAGTAAGTCAGTATTTAAGTAAAAAGAGATTAATCAAATTCAAAGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* *
545 AATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
*
600 AATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-----AAT-GT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
649 AAT-AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
*
703 -ATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
*
757 AATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* *
812 AATCAGTAAATCATTAATTAAGTAAAAACAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
867 AATCAGTAAATCAGTAAT
1 AATCAGTAAATCAGTAAT
885 CAGGAGTAAT
Statistics
Matches: 325, Mismatches: 7, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
48 39 0.12
49 5 0.02
50 3 0.01
53 5 0.02
54 52 0.16
55 221 0.68
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (55 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
Found at i:656 original size:40 final size:44
Alignment explanation
Indices: 604--747 Score: 135
Period size: 48 Copynumber: 3.0 Consensus size: 44
594 AATAGTAATC
* *
604 AGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAATGTAAT
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-A---AAG
652 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-----AA-AG
*
702 TATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAGAGTCAA
1 ----AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
748 GGTAATAGTA
Statistics
Matches: 83, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
48 39 0.47
49 3 0.04
50 1 0.01
52 1 0.01
54 39 0.47
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (44 bp):
AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAG
Found at i:865 original size:212 final size:211
Alignment explanation
Indices: 491--875 Score: 644
Period size: 212 Copynumber: 1.8 Consensus size: 211
481 GAAAGATGCA
* * * * *
491 ATCAGTAAGTCAGTATTTAAGTAAAAAGAGATTAATCAAATTCAAAGTAATAGTAATCAGTAAGT
1 ATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAAT
* *
556 CAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAGTCAGTAATTAA
66 CAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAA
* *
621 GTAAAAAGAGATTAATCAGAGTCAATGTAATAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
131 GTAAAAACAGATTAATCAGAGTCAAGGTAATAGT-AATCAGTAATTAAGTAAAAAGAGATTAATC
686 AGAGTCAAGGTAATAGT
195 AGAGTCAAGGTAATAGT
* *
703 ATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAAT
1 ATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAAT
* *
768 CAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCATTAATTAA
66 CAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAA
833 GTAAAAACAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAA
131 GTAAAAACAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAA
876 ATCAGTAATC
Statistics
Matches: 160, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
211 9 0.06
212 151 0.94
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (211 bp):
ATCAGTAAATCAGTAATTAAGTAAAAACAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAAT
CAGTAATTAAGTAAAAACAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAA
GTAAAAACAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAATTAAGTAAAAAGAGATTAATCA
GAGTCAAGGTAATAGT
Found at i:966 original size:37 final size:35
Alignment explanation
Indices: 913--1015 Score: 152
Period size: 36 Copynumber: 2.8 Consensus size: 35
903 AGTAAAAATG
*
913 AAAAGAAGTAAAAGTAATCAGCAAAAGAAGAATAGGT
1 AAAA-AAGTAAAAGTAATCAGTAAAAGAAGAAT-GGT
950 AAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
1 AAAAAAGTAAA-AGTAATCAGTAAAAGAAGAATGGT
*
986 AAAAAAGAAAAAAGTAATCAGTAAAAGAAG
1 AAAAAAG-TAAAAGTAATCAGTAAAAGAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
36 35 0.56
37 27 0.44
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.14
Consensus pattern (35 bp):
AAAAAAGTAAAAGTAATCAGTAAAAGAAGAATGGT
Done.