Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022740.1 Corchorus olitorius cultivar O-4 contig22773, 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: 43745
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:223 original size:6 final size:6
Alignment explanation
Indices: 206--234 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
196 CTCGGAAATT
206 TCGAGC -CGAGC TCGAGC TCGAGC TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC
235 CCAAGTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.14
Consensus pattern (6 bp):
TCGAGC
Found at i:11047 original size:25 final size:25
Alignment explanation
Indices: 11017--11067 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11007 GGGTTGCTGC
11017 AGAAAGTGGCGCAGGGCCTGAGAGA
1 AGAAAGTGGCGCAGGGCCTGAGAGA
11042 AGAAAGTGGCGCAGGGCCTGAGAGA
1 AGAAAGTGGCGCAGGGCCTGAGAGA
11067 A
1 A
11068 AATAAGCACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.43, T:0.08
Consensus pattern (25 bp):
AGAAAGTGGCGCAGGGCCTGAGAGA
Found at i:12174 original size:17 final size:17
Alignment explanation
Indices: 12133--12165 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12123 TTATTTACTG
12133 AAATAATAATAATTATA
1 AAATAATAATAATTATA
*
12150 AAATAATAATTATTAT
1 AAATAATAATAATTAT
12166 TCAATAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAATAATAATTATA
Found at i:19281 original size:14 final size:15
Alignment explanation
Indices: 19262--19291 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19252 CAATCAAAGC
19262 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
19276 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
19291 A
1 A
19292 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:19670 original size:21 final size:21
Alignment explanation
Indices: 19646--19718 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
19636 GGCACTGAAT
*
19646 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATGGCC
* **
19667 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATGGCC
*
19688 GGTGGTGGCACGGTGAATGGCC
1 GGTGGTGGCACGG-GCATGGCC
*
19710 GGTTGTGGC
1 GGTGGTGGC
19719 TTGGTAGTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 30 0.71
22 12 0.29
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATGGCC
Found at i:22903 original size:21 final size:22
Alignment explanation
Indices: 22878--22920 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
22868 TTTTTTTTAG
*
22878 AAAAACGCAAACACAA-AAATT
1 AAAAACGCAAAAACAACAAATT
22899 AAAAACGCAAAAACAACAAATT
1 AAAAACGCAAAAACAACAAATT
22921 TTTTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAACGCAAAAACAACAAATT
Found at i:27484 original size:223 final size:223
Alignment explanation
Indices: 27096--27541 Score: 883
Period size: 223 Copynumber: 2.0 Consensus size: 223
27086 ATACACAACG
27096 ACTGAAGAACTTAGAGTATCAACTTCTAGATTACTATGGATATATTATCAAATTATAAATATAAA
1 ACTGAAGAACTTAGAGTATCAACTTCTAGATTACTATGGATATATTATCAAATTATAAATATAAA
27161 TATGCAGTGGCATCATATTTCAAAAGCAAATAAGCAAACCAAAGTAGAAGCATCATTTCAGTAAA
66 TATGCAGTGGCATCATATTTCAAAAGCAAATAAGCAAACCAAAGTAGAAGCATCATTTCAGTAAA
27226 GTTTTGAAGTTTTGATCCACCAATTAACTGCATATGAACCATACACCAAGAATAGAATAATTTAA
131 GTTTTGAAGTTTTGATCCACCAATTAACTGCATATGAACCATACACCAAGAATAGAATAATTTAA
27291 AACAATTTGGCTAAAAATATAAACCTCA
196 AACAATTTGGCTAAAAATATAAACCTCA
27319 ACTGAAGAACTTAGAGTATCAACTTCTAGATTACTATGGATATATTATCAAATTATAAATATAAA
1 ACTGAAGAACTTAGAGTATCAACTTCTAGATTACTATGGATATATTATCAAATTATAAATATAAA
27384 TATGCAGTGGCATCATATTTCAAAAGCAAATAAGCAAACCAAAGTAGAAGCATCATTTCAGTAAA
66 TATGCAGTGGCATCATATTTCAAAAGCAAATAAGCAAACCAAAGTAGAAGCATCATTTCAGTAAA
*
27449 GTTTTGAATTTTTGATCCACCAATTAACTGCATATGAACCATACACCAAGAATAGAATAATTTAA
131 GTTTTGAAGTTTTGATCCACCAATTAACTGCATATGAACCATACACCAAGAATAGAATAATTTAA
27514 AACAATTTGGCTAAAAATATAAACCTCA
196 AACAATTTGGCTAAAAATATAAACCTCA
27542 TATATCTAAC
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
223 222 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (223 bp):
ACTGAAGAACTTAGAGTATCAACTTCTAGATTACTATGGATATATTATCAAATTATAAATATAAA
TATGCAGTGGCATCATATTTCAAAAGCAAATAAGCAAACCAAAGTAGAAGCATCATTTCAGTAAA
GTTTTGAAGTTTTGATCCACCAATTAACTGCATATGAACCATACACCAAGAATAGAATAATTTAA
AACAATTTGGCTAAAAATATAAACCTCA
Found at i:42629 original size:100 final size:100
Alignment explanation
Indices: 42456--42656 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
42446 ATTAAGTTCA
42456 AACCTGATTGAAGAAGGAAATTGGCGGATTGAAGTTGAGTAGGATTAAAAATCCTAGTCCAATTC
1 AACCTGATTGAAGAAGGAAATTGGCGGATTGAAGTTGAGTAGGATTAAAAATCCTAGTCCAATTC
42521 GGGTAAGGAGTCTTATTGTCCAGCGTCAGGGATCG
66 GGGTAAGGAGTCTTATTGTCCAGCGTCAGGGATCG
42556 AACCTGATTGAAGAAGGAAATTGGCGGATTGAAGTTGAGTAGGATTAAAAATCCTAGTCCAATTC
1 AACCTGATTGAAGAAGGAAATTGGCGGATTGAAGTTGAGTAGGATTAAAAATCCTAGTCCAATTC
42621 GGGTAAGGAGTCTTATTGTCCAGCGTCAGGGATCG
66 GGGTAAGGAGTCTTATTGTCCAGCGTCAGGGATCG
42656 A
1 A
42657 GCTGGGCGCT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (100 bp):
AACCTGATTGAAGAAGGAAATTGGCGGATTGAAGTTGAGTAGGATTAAAAATCCTAGTCCAATTC
GGGTAAGGAGTCTTATTGTCCAGCGTCAGGGATCG
Found at i:42684 original size:21 final size:21
Alignment explanation
Indices: 42658--42707 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
42648 AGGGATCGAG
*
42658 CTGGGCGCTGA-GCCTTGTCGC
1 CTGGGCGCTGAGGCATT-TCGC
42679 CTGGGCGCTGAGGCATTTCGC
1 CTGGGCGCTGAGGCATTTCGC
*
42700 TTGGGCGC
1 CTGGGCGC
42708 CCAGCGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.06, C:0.30, G:0.40, T:0.24
Consensus pattern (21 bp):
CTGGGCGCTGAGGCATTTCGC
Done.