Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014538.1 Corchorus capsularis cultivar CVL-1 contig14559, 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: 46266
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:7812 original size:24 final size:24
Alignment explanation
Indices: 7781--7846 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
7771 AAATTAGGGT
7781 AAGAAGAAAAAGAAGAAGTTGGGG
1 AAGAAGAAAAAGAAGAAGTTGGGG
*
7805 AAGAAGAAAAGGAAGAAGTTGGGG
1 AAGAAGAAAAAGAAGAAGTTGGGG
* * *
7829 AGGAAGGAGAAGAAGAAG
1 AAGAAGAAAAAGAAGAAG
7847 AAGAAGAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (24 bp):
AAGAAGAAAAAGAAGAAGTTGGGG
Found at i:7844 original size:3 final size:3
Alignment explanation
Indices: 7831--7864 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
7821 AGTTGGGGAG
* *
7831 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAT GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
7865 CACTTTTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:9703 original size:33 final size:32
Alignment explanation
Indices: 9666--9730 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
9656 TAACTCTATG
*
9666 TTTGTTTCTTATGTAAAGTTTAAAAGTTTGAGT
1 TTTGTTT-TTATGTAAAGATTAAAAGTTTGAGT
* * *
9699 TTTGTTTTTTTTTTAAGATTAAAAGTTTGAGT
1 TTTGTTTTTATGTAAAGATTAAAAGTTTGAGT
9731 ATTATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (32 bp):
TTTGTTTTTATGTAAAGATTAAAAGTTTGAGT
Found at i:10270 original size:33 final size:33
Alignment explanation
Indices: 10140--10330 Score: 246
Period size: 32 Copynumber: 5.9 Consensus size: 33
10130 ATTGCTCATA
10140 CCGCCCTAGTGGGGCGG-TTAGCCGTGGCAGAG
1 CCGCCCTAGTGGGGCGGCTTAGCCGTGGCAGAG
*
10172 CCGCCCTAGTGGGGCGGC-TAGCCGTGGTAGAG
1 CCGCCCTAGTGGGGCGGCTTAGCCGTGGCAGAG
*
10204 CCGTCCTAGTGGGGCGGC-TAGCCGTGGCAGAG
1 CCGCCCTAGTGGGGCGGCTTAGCCGTGGCAGAG
* *
10236 CCGTCCTAGTGGGGCGGCTTCA-CCATGGCAGAG
1 CCGCCCTAGTGGGGCGGCTT-AGCCGTGGCAGAG
* ** *
10269 CCGCCCTAGTGGGGAGGCTCCGTCGTGGCAGAG
1 CCGCCCTAGTGGGGCGGCTTAGCCGTGGCAGAG
* **
10302 CCGCCCTAGTGGGGAGGCTCCGCCGTGGC
1 CCGCCCTAGTGGGGCGGCTTAGCCGTGGC
10331 TAAGGGCAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
32 78 0.54
33 65 0.45
34 1 0.01
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (33 bp):
CCGCCCTAGTGGGGCGGCTTAGCCGTGGCAGAG
Found at i:14733 original size:2 final size:2
Alignment explanation
Indices: 14679--14713 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14669 TTTTACTCTC
14679 AT AT AT AT 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 AT AT AT AT A
14714 GTTCTTGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32618 original size:13 final size:13
Alignment explanation
Indices: 32600--32625 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32590 CTTTCCAATT
32600 AGGACAATTATAA
1 AGGACAATTATAA
32613 AGGACAATTATAA
1 AGGACAATTATAA
32626 GAGGGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
AGGACAATTATAA
Found at i:34580 original size:19 final size:20
Alignment explanation
Indices: 34556--34596 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
34546 TTTCTCTTTT
*
34556 TCCAAATGG-ATTCAACCCC
1 TCCAAATGGAATCCAACCCC
34575 TCCAAATGGAATCCAACCCC
1 TCCAAATGGAATCCAACCCC
34595 TC
1 TC
34597 TCTTCATTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.32, C:0.39, G:0.10, T:0.20
Consensus pattern (20 bp):
TCCAAATGGAATCCAACCCC
Found at i:35002 original size:76 final size:76
Alignment explanation
Indices: 34867--35008 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 76
34857 TATAGGAAAC
* * * * *
34867 AACATGGGGTTGGAGTCTAAACAAAGACCCGAAATCCAAAACAAACCAATGAAGAACAGCAACAC
1 AACATGGGGTTGGACTCAAAACAAAGACCCCAAATCCAAAACAAACCAACGAAAAACAGCAACAC
34932 AAAAAATTAAG
66 AAAAAATTAAG
* *
34943 AACA-GGGGATTGGACTCAAAACAGAGACCCCAAATCC-AAACAAACCCAACGAAAAACAGCAGC
1 AACATGGGG-TTGGACTCAAAACAAAGACCCCAAATCCAAAACAAA-CCAACGAAAAACAGCAAC
35006 ACA
64 ACA
35009 GTTAAGATCA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
75 11 0.19
76 46 0.81
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (76 bp):
AACATGGGGTTGGACTCAAAACAAAGACCCCAAATCCAAAACAAACCAACGAAAAACAGCAACAC
AAAAAATTAAG
Found at i:36362 original size:21 final size:21
Alignment explanation
Indices: 36293--36367 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
36283 GGAAAGCAAT
36293 AAATTAAT-T-AAATAAGTAA
1 AAATTAATATAAAATAAGTAA
*
36312 AAATTAATATAAAATCAACT--
1 AAATTAATATAAAAT-AAGTAA
* * *
36332 ACATTGATATTAAATAAGTAA
1 AAATTAATATAAAATAAGTAA
36353 AAATTAATATAAAAT
1 AAATTAATATAAAAT
36368 CATGCCCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 11 0.26
20 13 0.30
21 16 0.37
22 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
AAATTAATATAAAATAAGTAA
Found at i:41256 original size:39 final size:39
Alignment explanation
Indices: 41203--41281 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
41193 ACTTGTGTTG
* *
41203 TATACGATAGAAGAATGCATAAGGTGAATAAAAAGGAGA
1 TATACAATACAAGAATGCATAAGGTGAATAAAAAGGAGA
*
41242 TATACAATACAAGAATGCATAAGGTGAATAGAAAGGAGA
1 TATACAATACAAGAATGCATAAGGTGAATAAAAAGGAGA
41281 T
1 T
41282 GATGGTTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.24, T:0.19
Consensus pattern (39 bp):
TATACAATACAAGAATGCATAAGGTGAATAAAAAGGAGA
Found at i:43745 original size:10 final size:9
Alignment explanation
Indices: 43728--43763 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
43718 CCCAAAACCA
43728 AGGAAACAG
1 AGGAAACAG
43737 AGAGAAACAG
1 AG-GAAACAG
43747 AGGAAAACAG
1 AGG-AAACAG
43757 AGGAAAC
1 AGGAAAC
43764 GAGTGCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.58, C:0.11, G:0.31, T:0.00
Consensus pattern (9 bp):
AGGAAACAG
Found at i:44978 original size:2 final size:2
Alignment explanation
Indices: 44971--44999 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44961 CTCTTATTGC
44971 AT 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 AT A
45000 AAGCAAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45790 original size:33 final size:33
Alignment explanation
Indices: 45747--45834 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
45737 GCCGTGGCGA
* * **
45747 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCGTCCCAGTGGGGAGGCTCCGCCATGACTG
*
45780 AGCCTTCCCAGTGGGGAGGCTCCGCCATGACTG
1 AGCCGTCCCAGTGGGGAGGCTCCGCCATGACTG
* *
45813 AGCCGTCCTAGTGAGGAGGCTC
1 AGCCGTCCCAGTGGGGAGGCTC
45835 AGTGTAAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.14, C:0.32, G:0.38, T:0.17
Consensus pattern (33 bp):
AGCCGTCCCAGTGGGGAGGCTCCGCCATGACTG
Done.