Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012295.1 Corchorus capsularis cultivar CVL-1 contig12316, 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: 10319
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Found at i:98 original size:36 final size:36
Alignment explanation
Indices: 2--143 Score: 187
Period size: 36 Copynumber: 4.0 Consensus size: 36
1 A
* * *
2 GTAAAGAAAAGACTGGCTTAACTTCAAGGGAATTAA
1 GTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAG
* * *
38 GTAAA-AAAGGACTGGCTTAGTTTCAAGGAAACTAG
1 GTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAG
*
73 GTAAAGAAAAGACTGGCCTAATTTCAAGGAAATTAG
1 GTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAG
* * *
109 GTAAAGGAAAGATTGGCTTAATTTTAAGGAAATTA
1 GTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
144 AGTGAAAAGA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 29 0.32
36 62 0.68
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (36 bp):
GTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAG
Found at i:237 original size:36 final size:34
Alignment explanation
Indices: 188--306 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 34
178 AATTAAGTAA
*
188 AATAAAGAACTTAATTCAGGTCAATTAAGTGAAGT
1 AATAAAGAGCTTAATTCAGGT-AATTAAGTGAAGT
223 CAATAAA-AGGCTTAATTCAGGGTAATTAAGT--AG-
1 -AATAAAGA-GCTTAATTCA-GGTAATTAAGTGAAGT
*
256 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTT
1 AATAAAGAGCTTAATTC-AGGTAATTAAGTGAAG-T
292 AATAAAGAGCTTAAT
1 AATAAAGAGCTTAAT
307 CTAGAAAAGA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
32 25 0.35
33 2 0.03
34 4 0.06
35 1 0.01
36 37 0.51
37 3 0.04
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.29
Consensus pattern (34 bp):
AATAAAGAGCTTAATTCAGGTAATTAAGTGAAGT
Found at i:260 original size:68 final size:68
Alignment explanation
Indices: 178--306 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 68
168 TAGGAAAGGA
178 AATTAAGTAAAATAAAGAACTTAATTC-AGGTCAATTAAGTGAAGTCAATAAA-AGGCTTAATTC
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGT-AATTAAGTGAAGTCAATAAAGA-GCTTAATTC
241 AGGGT
64 AGGGT
* *
246 AATTAAGTAGAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTTAATAAAGAGCTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAAT
307 CTAGAAAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
68 52 0.91
69 5 0.09
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTCAATAAAGAGCTTAATTCAG
GGT
Found at i:269 original size:32 final size:31
Alignment explanation
Indices: 178--285 Score: 119
Period size: 32 Copynumber: 3.3 Consensus size: 31
168 TAGGAAAGGA
*
178 AATTAAGTAAAATAAAGAACTTAATTCAGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGT
*
209 CAATTAAGTGAAGTCAATAAA-AGGCTTAATTCAGGGT
1 -AATTAAGT--AG--AATAAAGA-ACTTAATTCA-GGT
246 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAGAATAAAGAACTTAATTC-AGGT
278 AATTAAGT
1 AATTAAGT
286 GAAGTTAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
32 33 0.51
33 2 0.03
34 3 0.05
35 1 0.02
36 23 0.35
37 3 0.05
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (31 bp):
AATTAAGTAGAATAAAGAACTTAATTCAGGT
Found at i:5667 original size:60 final size:60
Alignment explanation
Indices: 5573--5844 Score: 350
Period size: 60 Copynumber: 4.5 Consensus size: 60
5563 GCGTCCCAAG
**
5573 GTATCAGTTGGCTATAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAA
1 GTATCAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAA
* * ** *
5633 ATATCAGTTGGGC-ACGGACTAGCCTACTTAAAGTGTCAACCACAGATTGGTCTCTTTCAG
1 GTATCAGTT-GGCTACGGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAA
* * * * *
5693 GTATTAGTTGGCTACAGACTAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCATTCAA
1 GTATCAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAA
* *
5753 GTATCAGTTGGCTACGGACTGGCCTACTTC-AGTGTTGACCACAGATTGGTCTCTTCCAA
1 GTATCAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAA
** ** *
5812 GCGTCAGTAAGCTACAGACTAGCCTACTTCAAG
1 GTATCAGTTGGCTACGGACTAGCCTACTTCAAG
5845 CATCGACCAC
Statistics
Matches: 179, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
59 52 0.29
60 124 0.69
61 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (60 bp):
GTATCAGTTGGCTACGGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAA
Found at i:5872 original size:119 final size:120
Alignment explanation
Indices: 5583--5862 Score: 357
Period size: 119 Copynumber: 2.3 Consensus size: 120
5573 GTATCAGTTG
* * * *
5583 GCTATAGACTAGCCTACTTCAAGTGTTGACCACAGATTGGTCTCTTTCAAATATCAGTTGGGCAC
1 GCTACAGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCATTCAAGTATCAGTTGGGCAC
* * * * **
5648 GGACTAGCCTACTTAAAGTGTCAACCACAGATTGGTCTCTTTCAGGTATTAGTTG
66 GGACTAGCCTACTTAAAGTGTCAACCACAGATTGGTCTCTTCCAAGCATCAGTAA
*
5703 GCTACAGACTAGCCTACTTCAAGTGTTGACCACGGGTTGGTCTCATTCAAGTATCAGTT-GGCTA
1 GCTACAGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCATTCAAGTATCAGTTGGGC-A
* * ** *
5767 CGGACTGGCCTACTT-CAGTGTTGACCACAGATTGGTCTCTTCCAAGCGTCAGTAA
65 CGGACTAGCCTACTTAAAGTGTCAACCACAGATTGGTCTCTTCCAAGCATCAGTAA
** * *
5822 GCTACAGACTAGCCTACTTCAAGCATCGACCACGGACTGGT
1 GCTACAGACTAGCCTACTTCAAGTGTTGACCACGGATTGGT
5863 TTTCTTCAAG
Statistics
Matches: 138, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
119 69 0.50
120 69 0.50
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (120 bp):
GCTACAGACTAGCCTACTTCAAGTGTTGACCACGGATTGGTCTCATTCAAGTATCAGTTGGGCAC
GGACTAGCCTACTTAAAGTGTCAACCACAGATTGGTCTCTTCCAAGCATCAGTAA
Found at i:5889 original size:27 final size:29
Alignment explanation
Indices: 5838--5895 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
5828 GACTAGCCTA
*
5838 CTTCAAGCATCGACCACGGACTGGT-TTT
1 CTTCAAGAATCGACCACGGACTGGTCTTT
* *
5866 CTTCAAGAAT-GACCATGGATTGGTCTTT
1 CTTCAAGAATCGACCACGGACTGGTCTTT
5894 CT
1 CT
5896 CTAAGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (29 bp):
CTTCAAGAATCGACCACGGACTGGTCTTT
Found at i:9978 original size:11 final size:11
Alignment explanation
Indices: 9814--9992 Score: 180
Period size: 11 Copynumber: 16.1 Consensus size: 11
9804 TTAGGCAAAA
9814 GAAAGAAGACT
1 GAAAGAAGACT
9825 GAAAAGAAGACT
1 G-AAAGAAGACT
*
9837 GAAATTAA-ACT
1 GAAA-GAAGACT
**
9848 GAAATTAGACT
1 GAAAGAAGACT
**
9859 GAAATTAGACT
1 GAAAGAAGACT
9870 GAAAGAAGACT
1 GAAAGAAGACT
**
9881 GAAATTAGACT
1 GAAAGAAGACT
**
9892 GAAATTAGACT
1 GAAAGAAGACT
**
9903 GAAATTAGACT
1 GAAAGAAGACT
9914 GAAAGAAGACT
1 GAAAGAAGACT
9925 GAAAAGAAGACT
1 G-AAAGAAGACT
**
9937 GAAATTAGACT
1 GAAAGAAGACT
9948 GAAAGAAGACT
1 GAAAGAAGACT
* *
9959 AAAATAAGACT
1 GAAAGAAGACT
*
9970 GAGAGAAGACT
1 GAAAGAAGACT
9981 GAAAGAAGACT
1 GAAAGAAGACT
9992 G
1 G
9993 GCTTAGTTTC
Statistics
Matches: 146, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
10 2 0.01
11 120 0.82
12 24 0.16
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.17
Consensus pattern (11 bp):
GAAAGAAGACT
Found at i:10039 original size:36 final size:36
Alignment explanation
Indices: 9987--10308 Score: 464
Period size: 36 Copynumber: 8.9 Consensus size: 36
9977 GACTGAAAGA
* * *
9987 AGACTGGCTTAGTTTCAAGGAAACTAGGTAAAAAAT
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
* *
10023 AGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAA
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
* * *
10059 AGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
*
10095 AGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
* *
10131 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAG
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
* * *
10167 AGATTGGCTTAATTTCAAGGAAATTAAGTAAAGAAA
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
* * * *
10203 AGATTGGCTTAGTTTCTAGGAAACTAGGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
*
10239 AGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
10275 AGACTGGCTTAATTTACAAGGAAATTAGGTAAAG
1 AGACTGGCTTAATTT-CAAGGAAATTAGGTAAAG
10309 GAAAGATTGG
Statistics
Matches: 253, Mismatches: 32, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
36 236 0.93
37 17 0.07
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (36 bp):
AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAT
Found at i:10071 original size:72 final size:72
Alignment explanation
Indices: 9986--10308 Score: 520
Period size: 72 Copynumber: 4.5 Consensus size: 72
9976 AGACTGAAAG
*
9986 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAAAATAGACTGGCTTAATTTCAAGGAAATTAAG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
10051 TAAAGAA
66 TAAAGAA
*
10058 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
10123 TAAAGAA
66 TAAAGAA
* * * * * *
10130 TAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAGAGATTGGCTTAATTTCAAGGAAATTAAG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
10195 TAAAGAA
66 TAAAGAA
* *
10202 AAGATTGGCTTAGTTTCTAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
10267 TAAAGAA
66 TAAAGAA
* * *
10274 TAGACTGGCTTAATTTACAAGGAAATTAGGTAAAG
1 AAGACTGGCTTAGTTT-CAAGGAAACTAGGTAAAG
10309 GAAAGATTGG
Statistics
Matches: 228, Mismatches: 22, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
72 212 0.93
73 16 0.07
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (72 bp):
AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
TAAAGAA
Done.