Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011080.1 Corchorus capsularis cultivar CVL-1 contig11101, 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: 51038
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:604 original size:32 final size:35
Alignment explanation
Indices: 568--635 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
558 CTAATATATT
568 AACTTACTTTC-T-TATTTA-TTATAAGTAATAAG
1 AACTTACTTTCTTATATTTATTTATAAGTAATAAG
600 AACTTACTTTCTTATATTTATTTTATAAGTAATAAG
1 AACTTACTTTCTTATATTTA-TTTATAAGTAATAAG
636 GGAAGAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 6 0.19
36 14 0.44
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (35 bp):
AACTTACTTTCTTATATTTATTTATAAGTAATAAG
Found at i:5979 original size:2 final size:2
Alignment explanation
Indices: 5974--6053 Score: 58
Period size: 2 Copynumber: 40.0 Consensus size: 2
5964 GCCCCAAAAA
* * * * *
5974 AT AT AT AT AT AT AT AT ACT AT -T TT TT TT AT AC AT A- AA AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
6015 AT AT ACT AT AT AT CT AT AT AT AT AT AT AT -T AGT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
6054 GTTTTTTTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
1 3 0.05
2 57 0.86
3 6 0.09
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6086 original size:60 final size:57
Alignment explanation
Indices: 5974--6087 Score: 126
Period size: 60 Copynumber: 1.9 Consensus size: 57
5964 GCCCCAAAAA
* *
5974 ATATATATATATATATACTATTTTTTTTATACATAAAATATATATACTATATATCTAT
1 ATATATATATATATATACTATTTTTTTTATACAAAAAAAATATATAC-ATATATCTAT
6032 ATATATATATATTAGTATA-TATGTTTTTTTACTACAAAACAAGAATAT-TA-ATATAT
1 ATATATATATA-TA-TATACTAT-TTTTTTTA-TACAAAA-AA-AATATATACATATAT
6088 ATGTTAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
58 11 0.23
59 5 0.10
60 18 0.38
61 6 0.12
62 4 0.08
63 4 0.08
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (57 bp):
ATATATATATATATATACTATTTTTTTTATACAAAAAAAATATATACATATATCTAT
Found at i:6149 original size:20 final size:18
Alignment explanation
Indices: 6124--6168 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6114 ACATATGTTT
6124 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
6144 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
6162 TACTAAT
1 TACTAAT
6169 TTTACTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:10180 original size:2 final size:2
Alignment explanation
Indices: 10173--10200 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10163 ATCAGTAATG
10173 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
10201 TAAGAGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15053 original size:27 final size:27
Alignment explanation
Indices: 15023--15080 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
15013 TCAATGCGTA
*
15023 TATCTTTAAATCTATCACTTTCACGAT
1 TATCTTTAAATCCATCACTTTCACGAT
*
15050 TATCTTTAAATCCATCATTTTCACGAT
1 TATCTTTAAATCCATCACTTTCACGAT
15077 TATC
1 TATC
15081 ATCTACAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.45
Consensus pattern (27 bp):
TATCTTTAAATCCATCACTTTCACGAT
Found at i:18807 original size:24 final size:24
Alignment explanation
Indices: 18780--18832 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
18770 CTTCTCTCGA
18780 TCCTTAAGT-TTCTCTCTCTCCTTT
1 TCCTT-AGTCTTCTCTCTCTCCTTT
* * *
18804 TCCTTTGTCTTGTCTCTTTCCTTT
1 TCCTTAGTCTTCTCTCTCTCCTTT
18828 TCCTT
1 TCCTT
18833 TTCTCTATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.04, C:0.32, G:0.06, T:0.58
Consensus pattern (24 bp):
TCCTTAGTCTTCTCTCTCTCCTTT
Found at i:21636 original size:40 final size:40
Alignment explanation
Indices: 21577--21656 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 40
21567 AATAAAGTCT
* *
21577 TAATTGGCAAAATATTTCAAT-ACTCTCCACGTAAAAAAC
1 TAATTGGCAAAACATTTCAATAACTCTCCACATAAAAAAC
*
21616 TAATTGGAGAAAACATTTCAATAGACTCTCCACATAAAAAA
1 TAATTGG-CAAAACATTTCAATA-ACTCTCCACATAAAAAA
21657 ATTAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 7 0.20
40 12 0.34
42 16 0.46
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (40 bp):
TAATTGGCAAAACATTTCAATAACTCTCCACATAAAAAAC
Found at i:30186 original size:20 final size:21
Alignment explanation
Indices: 30148--30186 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
30138 ATAGAAGAGA
*
30148 ACCTTATATAAATTATCAATC
1 ACCTTATATAAAATATCAATC
30169 ACCTTATA-AAAATATCAA
1 ACCTTATATAAAATATCAA
30187 CTTCCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (21 bp):
ACCTTATATAAAATATCAATC
Found at i:40492 original size:25 final size:24
Alignment explanation
Indices: 40457--40515 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
40447 TTCAAACCCT
* *
40457 AAACTTAATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAAATT-TTC
*
40482 AAACTTCATTTTTAACAAATTTTC
1 AAACTTCATTTCTAACAAATTTTC
40506 AAA-TTCATTT
1 AAACTTCATTT
40516 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 6 0.19
25 18 0.58
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATTTTC
Found at i:40561 original size:26 final size:26
Alignment explanation
Indices: 40525--40628 Score: 108
Period size: 26 Copynumber: 4.0 Consensus size: 26
40515 TTCCTTCATT
*
40525 TTAATCATAAACTAATTAAATACTAA
1 TTAATAATAAACTAATTAAATACTAA
*
40551 TTAATAATAAACTAATTAGATACTAA
1 TTAATAATAAACTAATTAAATACTAA
*
40577 TTAA-ACATAAACTAA-TAAACTAAGTAA
1 TTAATA-ATAAACTAATTAAA-T-ACTAA
* *
40604 TT-TTAATTAACTAATTAAA-ACTAA
1 TTAATAATAAACTAATTAAATACTAA
40628 T
1 T
40629 CATAAACTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
24 5 0.08
25 4 0.06
26 46 0.70
27 11 0.17
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (26 bp):
TTAATAATAAACTAATTAAATACTAA
Found at i:40616 original size:52 final size:51
Alignment explanation
Indices: 40525--40642 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
40515 TTCCTTCATT
* *
40525 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
40577 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
40628 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
40643 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:40950 original size:22 final size:22
Alignment explanation
Indices: 40925--40971 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40915 AAAATTATAA
**
40925 AAAAAAAGGGACGGTATTTAGC
1 AAAAAAAGGGACGGTAAATAGC
* *
40947 AAAAAAGGGGGCGGTAAATAGC
1 AAAAAAAGGGACGGTAAATAGC
40969 AAA
1 AAA
40972 CCCCTATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.30, T:0.13
Consensus pattern (22 bp):
AAAAAAAGGGACGGTAAATAGC
Found at i:46316 original size:88 final size:87
Alignment explanation
Indices: 46167--46462 Score: 443
Period size: 88 Copynumber: 3.5 Consensus size: 87
46157 GCTGCCTCAG
*
46167 AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACACAAGGTGGAAACAAGTA
1 AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACACAAGGTGGAAACAAGCA
46232 AGAGTCTATGACTCCATGGCGAA
66 AGAGTCTATGACTCCATGGCG-A
* * *
46255 AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTAGATCTTAACACAAGATAGAAACAAGCA
1 AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACACAAGGTGGAAACAAGCA
46320 AGAGTCTATGACTCCAT-----
66 AGAGTCTATGACTCCATGGCGA
*
46337 -GG--C-G--GCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACAGAAGGTGGAAACAAGCA
1 AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACACAAGGTGGAAACAAGCA
*
46396 AGAGTTTATGACTCCATGGCGA
66 AGAGTCTATGACTCCATGGCGA
46418 GAGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTT
1 -AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTT
46463 TTCTCGGCAC
Statistics
Matches: 187, Mismatches: 9, Indels: 24
0.85 0.04 0.11
Matches are distributed among these distances:
76 67 0.36
78 1 0.01
79 1 0.01
81 2 0.01
83 2 0.01
85 1 0.01
86 1 0.01
88 112 0.60
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (87 bp):
AGGCACAGCTGCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACACAAGGTGGAAACAAGCA
AGAGTCTATGACTCCATGGCGA
Found at i:46353 original size:76 final size:76
Alignment explanation
Indices: 46265--46416 Score: 259
Period size: 76 Copynumber: 2.0 Consensus size: 76
46255 AGGCACAGCT
46265 GCAGGTAGTAGTGGGGTGTGCCAAACTAGATCTTAACACAAGATAGAAACAAGCAAGAGTCTATG
1 GCAGGTAGTAGTGGGGTGTGCCAAACTAGATCTTAACACAAGATAGAAACAAGCAAGAGTCTATG
46330 ACTCCATGGCG
66 ACTCCATGGCG
* * * * *
46341 GCAGGTAGTAGTGGGGTGTGCCAAACTGGATCTTAACAGAAGGTGGAAACAAGCAAGAGTTTATG
1 GCAGGTAGTAGTGGGGTGTGCCAAACTAGATCTTAACACAAGATAGAAACAAGCAAGAGTCTATG
46406 ACTCCATGGCG
66 ACTCCATGGCG
46417 AGAGGCACAG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.20
Consensus pattern (76 bp):
GCAGGTAGTAGTGGGGTGTGCCAAACTAGATCTTAACACAAGATAGAAACAAGCAAGAGTCTATG
ACTCCATGGCG
Done.