Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012523.1 Corchorus capsularis cultivar CVL-1 contig12544, 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: 83677
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:10935 original size:1 final size:1
Alignment explanation
Indices: 10929--10964 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
10919 ATACCGGATG
10929 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10965 CCAAATAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19730 original size:29 final size:30
Alignment explanation
Indices: 19697--19762 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
19687 CGTTCAAGGT
*
19697 GCAAAATGTCCAAAAT-TA-AAGTTTAGGGG
1 GCAAAACGT-CAAAATATACAAGTTTAGGGG
19726 GCAAAACGTCAAAATCATACAAGTTTAGGGG
1 GCAAAACGTCAAAAT-ATACAAGTTTAGGGG
*
19757 GTAAAA
1 GCAAAA
19763 AGGGCATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 8 0.25
30 2 0.06
31 16 0.50
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (30 bp):
GCAAAACGTCAAAATATACAAGTTTAGGGG
Found at i:24862 original size:16 final size:16
Alignment explanation
Indices: 24838--24878 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 16
24828 AGTTATAATT
24838 CATACTAATAATTAAC
1 CATACTAATAATTAAC
*
24854 C--A-TAGTAATTAAC
1 CATACTAATAATTAAC
24867 CATACTAATAAT
1 CATACTAATAAT
24879 CTACTGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 6
0.71 0.07 0.21
Matches are distributed among these distances:
13 11 0.55
14 1 0.05
15 1 0.05
16 7 0.35
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (16 bp):
CATACTAATAATTAAC
Found at i:27594 original size:2 final size:2
Alignment explanation
Indices: 27587--27619 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27577 AAATTAATAC
*
27587 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27620 TCTCTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27865 original size:40 final size:40
Alignment explanation
Indices: 27807--27883 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
27797 TTTATGACTA
*
27807 GGGGCTAAATCTGGATTTAATTTCTTACCTTAATTATCAG
1 GGGGCTAAATCTGAATTTAATTTCTTACCTTAATTATCAG
* *
27847 GGGGCTAAA-CTTGAATTTAATTTGTTTCCTTAATTAT
1 GGGGCTAAATC-TGAATTTAATTTCTTACCTTAATTAT
27884 TTAGGAGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (40 bp):
GGGGCTAAATCTGAATTTAATTTCTTACCTTAATTATCAG
Found at i:39299 original size:2 final size:2
Alignment explanation
Indices: 39292--39325 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39282 AAAGAGGTAG
39292 AT AT 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 AT AT
39326 CATTCATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46607 original size:2 final size:2
Alignment explanation
Indices: 46600--46624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46590 ATCATTTTCC
46600 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46625 TAATTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49083 original size:2 final size:2
Alignment explanation
Indices: 49076--49107 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49066 TGGAAGAAAG
49076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49108 CAATGAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54074 original size:36 final size:36
Alignment explanation
Indices: 54034--54106 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
54024 ACCGCTAATC
54034 TATGAGCCAACAAACCCCTTCCCCATCTAATTACAA
1 TATGAGCCAACAAACCCCTTCCCCATCTAATTACAA
54070 TATGAGCCAACAAACCCCTTCCCCATCTAATTACAA
1 TATGAGCCAACAAACCCCTTCCCCATCTAATTACAA
54106 T
1 T
54107 TTAAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.36, G:0.05, T:0.23
Consensus pattern (36 bp):
TATGAGCCAACAAACCCCTTCCCCATCTAATTACAA
Found at i:55137 original size:2 final size:2
Alignment explanation
Indices: 55130--55163 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55120 AAGACCATAG
55130 AT AT 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 AT AT
55164 CTACAGCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63195 original size:18 final size:19
Alignment explanation
Indices: 63163--63198 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
63153 GTGAAATTGT
*
63163 AAAGAAAAAGCAAAGAAAA
1 AAAGAAAAAGAAAAGAAAA
63182 AAAG-AAAAGAAAAGAAA
1 AAAGAAAAAGAAAAGAAA
63199 TCTCTTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAGAAAAGAAAA
Found at i:63325 original size:3 final size:3
Alignment explanation
Indices: 63317--63353 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
63307 TTTGAACACC
63317 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
63354 AACCTTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:66736 original size:42 final size:42
Alignment explanation
Indices: 66673--66756 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
66663 ATTCTAATTT
* *
66673 CGGCTCAAATAAGGGTTTGACGTGATTGTTAACCATTGTGAA
1 CGGCTCAAATAAGGGTCTGACGTAATTGTTAACCATTGTGAA
66715 CGGCTCAAATAAGGGTCTGACGTAATTGTTAACCATTGTGAA
1 CGGCTCAAATAAGGGTCTGACGTAATTGTTAACCATTGTGAA
66757 ACCGAGTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
CGGCTCAAATAAGGGTCTGACGTAATTGTTAACCATTGTGAA
Found at i:71949 original size:21 final size:21
Alignment explanation
Indices: 71925--71969 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
71915 AACCAAGCTA
*
71925 AAATGGAAGCAAAG-AATCAAG
1 AAATGGAACCAAAGAAATC-AG
*
71946 AAATGGACCCAAAGAAATCAG
1 AAATGGAACCAAAGAAATCAG
71967 AAA
1 AAA
71970 CAACAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.13, G:0.20, T:0.09
Consensus pattern (21 bp):
AAATGGAACCAAAGAAATCAG
Found at i:80736 original size:2 final size:2
Alignment explanation
Indices: 80702--80728 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80692 TCATTATTTC
80702 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
80729 CTTATATAAA
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
Done.