Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013060.1 Corchorus capsularis cultivar CVL-1 contig13081, 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: 33827
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:15400 original size:6 final size:6
Alignment explanation
Indices: 15389--15415 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15379 ATTAATCTGC
15389 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
15416 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:22315 original size:6 final size:6
Alignment explanation
Indices: 22304--22330 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22294 ATTAATCTGC
22304 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
22331 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:28909 original size:41 final size:41
Alignment explanation
Indices: 28852--28998 Score: 206
Period size: 41 Copynumber: 3.6 Consensus size: 41
28842 GAAAAGTAAA
*
28852 GTCTTAATCCAGGGCGATTAAGAAGGTCAAACATAGTTAAG
1 GTCTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTTAAG
*
28893 GTCTTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAG
1 GTCTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTTAAG
* * * *
28934 GTTTTAATCCAGGGCGATTAAGAAAGTCAGA-TTAGTTAAA
1 GTCTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTTAAG
* * *
28974 GTTTTAATCCATGGTGATTAAGAAA
1 GTCTTAATCCAGGGCGATTAAGAAA
28999 AGAGCAGTCA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 29 0.30
41 68 0.70
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (41 bp):
GTCTTAATCCAGGGCGATTAAGAAAGTCAAACATAGTTAAG
Found at i:29048 original size:37 final size:36
Alignment explanation
Indices: 28990--29313 Score: 324
Period size: 37 Copynumber: 8.4 Consensus size: 36
28980 ATCCATGGTG
* * *
28990 ATTAAGAAAAGAGCAGTCAAAGAACTTAATTCATGATA
1 ATTAAGTAAA-AGCAGT-AAAGAACTTAATTCAGGGTA
29028 ATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGT-AAAGAACTTAATTCAGGGTA
*
29065 ATTAAGTAAGAGCAGTTAAAGAACTTAATTCAGGACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAG-TAAAG----------A--ACTTAATTCAGGGTA
* *
29114 ATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGGGCA
1 ATTAAGTAAAAGCA-GTAAAGAACTTAATTCAGGGTA
*
29151 ATTAAGTAAAAGCAGGTAAAGAATTTAATTCAGGGTA
1 ATTAAGTAAAAGCA-GTAAAGAACTTAATTCAGGGTA
* * **
29188 ATTAAGTAAAGAACAGTTAAGAACTTAATTCAGGACA
1 ATTAAGTAAA-AGCAGTAAAGAACTTAATTCAGGGTA
*
29225 ATTAAGTAAAAGCAGTGAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTAAAGAACTTAATTCAGGGTA
* * *
29261 ATTAAGTAAAAGCAGTTGAAGGACTTAATTCAGGCTA
1 ATTAAGTAAAAGCAG-TAAAGAACTTAATTCAGGGTA
*
29298 ATTAAGTAAAAACAGT
1 ATTAAGTAAAAGCAGT
29314 TAAAAGGTAA
Statistics
Matches: 248, Mismatches: 22, Indels: 34
0.82 0.07 0.11
Matches are distributed among these distances:
36 38 0.15
37 162 0.65
38 13 0.05
39 1 0.00
47 1 0.00
49 32 0.13
50 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (36 bp):
ATTAAGTAAAAGCAGTAAAGAACTTAATTCAGGGTA
Found at i:29107 original size:49 final size:49
Alignment explanation
Indices: 29050--29147 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
29040 CAGTCAAAGA
*
29050 ACTTAATTCAGGGTAATTAAGTAAGAGCA-GTTAAAGAACTTAATTCAGG
1 ACTTAATTCAGGGTAATTAAGTAAAAGCAGGTT-AAGAACTTAATTCAGG
29099 ACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGG
1 ACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGG
29148 GCAATTAAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 44 0.94
50 3 0.06
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (49 bp):
ACTTAATTCAGGGTAATTAAGTAAAAGCAGGTTAAGAACTTAATTCAGG
Found at i:29158 original size:86 final size:86
Alignment explanation
Indices: 29013--29184 Score: 265
Period size: 86 Copynumber: 2.0 Consensus size: 86
29003 CAGTCAAAGA
* * *
29013 ACTTAATTCATGATAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAGAGC
1 ACTTAATTCAGGATAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
*
29078 AGTTAAAGAACTTAATTCAGG
66 AGGTAAAGAACTTAATTCAGG
* *
29099 ACTTAATTCAGGGTAATTAAGTAAAAGCAGGT-TAAGAACTTAATTCAGGGCAATTAAGTAAAAG
1 ACTTAATTCAGGATAATTAAGTAAAAGCA-GTCAAAGAACTTAATTCAGGGCAATTAAGTAAAAG
*
29163 CAGGTAAAGAATTTAATTCAGG
65 CAGGTAAAGAACTTAATTCAGG
29185 GTAATTAAGT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 76 0.97
87 2 0.03
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (86 bp):
ACTTAATTCAGGATAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGCAATTAAGTAAAAGC
AGGTAAAGAACTTAATTCAGG
Found at i:29375 original size:41 final size:40
Alignment explanation
Indices: 29330--29505 Score: 220
Period size: 41 Copynumber: 4.5 Consensus size: 40
29320 GTAAGGATAG
29330 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAA
* * *
29371 GCACAGACTTAA-TTCA-G--GGTAATTAAGTAAAG-TAA
1 GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAA
29406 GCACAGACTTAATTTCAGTGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTCAG-GAAGGAAATTAGGTAAAGACAA
* * *
29447 GCATAGACTTAATTTCAAGGAAGGAAATTAGCTAAAGGCAA
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAA
*
29488 GCACATACTTAA-TTCAGG
1 GCACAGACTTAATTTCAGG
29506 GTAATTAAGT
Statistics
Matches: 117, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
35 14 0.12
36 17 0.15
38 2 0.02
39 4 0.03
40 19 0.16
41 59 0.50
42 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAA
Found at i:29715 original size:37 final size:37
Alignment explanation
Indices: 29626--29747 Score: 160
Period size: 37 Copynumber: 3.4 Consensus size: 37
29616 TAAGTAAAGA
* *
29626 AAGGACTTAGTTCCAAGGAA-GGAATTAAGTAGA-AT
1 AAGGACTTAATTCCAAGGAAGGGAATTAAGTAGAGTT
*
29661 AAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGGAATTAAGTAGAGTT
* *
29698 AAGGACTTAATTTCAAGGAAGGAAATTAAGTCA-AGTT
1 AAGGACTTAATTCCAAGGAAGGGAATTAAGT-AGAGTT
*
29735 AGGGACTTAATTC
1 AAGGACTTAATTC
29748 AGGGTAATGA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 18 0.24
36 13 0.17
37 44 0.58
38 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (37 bp):
AAGGACTTAATTCCAAGGAAGGGAATTAAGTAGAGTT
Found at i:29766 original size:32 final size:32
Alignment explanation
Indices: 29725--29792 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
29715 GAAGGAAATT
29725 AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
1 AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
*
29757 AAGTCAAGTTAGGGACTTAATTCAGGGTAATT
1 AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
29789 AAGT
1 AAGT
29793 AGTGTCAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (32 bp):
AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
Found at i:29817 original size:36 final size:35
Alignment explanation
Indices: 29738--29920 Score: 171
Period size: 36 Copynumber: 5.2 Consensus size: 35
29728 TCAAGTTAGG
* **
29738 GACTTAATTCAGGGTAATGAAGTCA-AGT---TAGG
1 GACTTAATTCAGGGTAATTAAGT-AGAGTCAATAAA
*
29770 GACTTAATTCAGGGTAATTAAGTAGTGTCAATAAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAAT-AAA
*
29806 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
* ** **
29841 GAACTTAATCTAAAAG-AGATTAAGTA-AAACAATAAA
1 G-ACTTAAT-TCAGGGTA-ATTAAGTAGAGTCAATAAA
*
29877 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
29912 GAACTTAAT
1 G-ACTTAAT
29921 CTAAAAATAG
Statistics
Matches: 122, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
31 1 0.01
32 24 0.20
34 10 0.08
35 22 0.18
36 55 0.45
37 10 0.08
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (35 bp):
GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
Found at i:29891 original size:71 final size:72
Alignment explanation
Indices: 29798--29948 Score: 277
Period size: 71 Copynumber: 2.1 Consensus size: 72
29788 TAAGTAGTGT
29798 CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCT-AAAAGAGATT
1 CAAT-AAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
29862 AAGTAAAA
65 AAGTAAAA
*
29870 CAATAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAATAGATTA
1 CAATAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
29935 AGTAAAA
66 AGTAAAA
29942 CAATAAA
1 CAATAAA
29949 AGGACTTGAT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 49 0.64
72 28 0.36
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (72 bp):
CAATAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
AGTAAAA
Done.