Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015674.1 Corchorus capsularis cultivar CVL-1 contig15695, 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: 3535
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Found at i:281 original size:16 final size:15
Alignment explanation
Indices: 251--298 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
241 CAAAGTAAAG
251 AAGAAAAACAAA-AAA
1 AAGAAAAA-AAAGAAA
*
266 AGGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAA
281 AAGAAAAGAAAAGAAA
1 AAGAAAA-AAAAGAAA
297 AA
1 AA
299 CCTTGGCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 3 0.10
15 16 0.55
16 10 0.34
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:876 original size:12 final size:11
Alignment explanation
Indices: 860--939 Score: 58
Period size: 11 Copynumber: 7.3 Consensus size: 11
850 AAGTGCATGT
860 AAAAAATGAAA
1 AAAAAATGAAA
*
871 TAAAAA-GAAA
1 AAAAAATGAAA
*
881 AAGAAA-GAAA
1 AAAAAATGAAA
* *
891 TAAAAAAAGAGA
1 -AAAAAATGAAA
*
903 GAAAAATG-AA
1 AAAAAATGAAA
*
913 AGAAAATGAAA
1 AAAAAATGAAA
924 AAAAGAATGAAGA
1 AAAA-AATGAA-A
937 AAA
1 AAA
940 GAAGCTCTAG
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
10 19 0.36
11 21 0.40
12 9 0.17
13 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:886 original size:16 final size:16
Alignment explanation
Indices: 859--906 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
849 CAAGTGCATG
* *
859 TAAAAAATGAAATAAA
1 TAAAAAAAGAAAGAAA
875 -AAGAAAAAGAAAGAAA
1 TAA-AAAAAGAAAGAAA
*
891 TAAAAAAAGAGAGAAA
1 TAAAAAAAGAAAGAAA
907 AATGAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (16 bp):
TAAAAAAAGAAAGAAA
Found at i:913 original size:27 final size:28
Alignment explanation
Indices: 862--929 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
852 GTGCATGTAA
*
862 AAAATGAAATAAA-A-AGAAAAAGAAAG
1 AAAATGAAAAAAAGAGAGAAAAAGAAAG
888 -AAAT-AAAAAAAGAGAGAAAAATGAAAG
1 AAAATGAAAAAAAGAGAGAAAAA-GAAAG
915 AAAATGAAAAAAAGA
1 AAAATGAAAAAAAGA
930 ATGAAGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 6 0.17
25 5 0.14
26 7 0.19
27 5 0.14
28 4 0.11
29 9 0.25
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (28 bp):
AAAATGAAAAAAAGAGAGAAAAAGAAAG
Found at i:1862 original size:70 final size:69
Alignment explanation
Indices: 1773--2292 Score: 638
Period size: 70 Copynumber: 7.6 Consensus size: 69
1763 AATGCTTCGA
* * * * *
1773 CTTTTCCATAAGTCTAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
1838 AGGGG
65 AGGGG
* * ** **
1843 CTTTTCCACAAGCCAAACTCGTTCCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAAAATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
1908 AGGGG
65 AGGGG
*
1913 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
**
1978 ACGG
66 GGGG
1982 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
2047 GCGG
66 GGGG
* * **
2051 CTTTTCCACAAACCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
2116 AGGGG
65 AGGGG
* * * *
2121 CTTTTCCACAAGCCAAACTCATTTCCACACGAGTCCA-TT-TAGCCTTTGTTCCATCCAAGCAGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGT-CAGTTCAAGCCTTGGTTCCATCCAAGCAGC
**
2184 AAAGG
65 AGGGG
* * * * *
2189 TTTTTCCACTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCC-A--AGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
2250 GGGG
66 GGGG
* ** * *
2254 CTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
2293 CTTCCAAGAC
Statistics
Matches: 397, Mismatches: 49, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
65 31 0.08
66 6 0.02
67 2 0.01
68 50 0.13
69 149 0.38
70 157 0.40
71 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGG
Found at i:2109 original size:138 final size:139
Alignment explanation
Indices: 1773--2292 Score: 660
Period size: 138 Copynumber: 3.8 Consensus size: 139
1763 AATGCTTCGA
* * *
1773 CTTTTCCATAAGTCTAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
* * *
1838 AGGGGCTTTTCCACAAGCCAAACTCGTTCCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAA
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
* ** *
1903 AATTTAGGGG
131 CA-GCAGAGG
*
1913 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
**
1977 AACGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
2042 CAGCAGCGG
131 CAGCAGAGG
* * * *
2051 CTTTTCCACAAACCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
* * * *
2116 AGGGGCTTTTCCACAAGCCAAACTCATTTCCACACGAGTCCA-TT-TAGCCTTTGTTCCATCCAA
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGT-CAGTTCAAGCCTTGGTTCCATCCAA
*
2179 GCAGCAAAGG
130 GCAGCAGAGG
* * * * *
2189 TTTTTCCACTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAG----C
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
* ** * *
2249 AGGGGCTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
66 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
2293 CTTCCAAGAC
Statistics
Matches: 337, Mismatches: 39, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
133 33 0.10
134 4 0.01
137 18 0.05
138 122 0.36
139 99 0.29
140 61 0.18
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (139 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGTATTC
AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
CAGCAGAGG
Found at i:3267 original size:20 final size:20
Alignment explanation
Indices: 3229--3267 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3219 AAATACAAGG
* *
3229 CATTTGATTTACGAGTTGGA
1 CATTTGATTTACAAATTGGA
*
3249 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
3268 TGCTCTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Done.