Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021226.1 Corchorus olitorius cultivar O-4 contig21259, 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: 17919
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:588 original size:21 final size:20
Alignment explanation
Indices: 549--588 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
539 AAAAAAATCC
* *
549 TTAATTAGGTTTCTTAAAAA
1 TTAATTAGGGTTATTAAAAA
569 TTAATTAGGGTTATTAAAAA
1 TTAATTAGGGTTATTAAAAA
589 GTTTATAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (20 bp):
TTAATTAGGGTTATTAAAAA
Found at i:874 original size:46 final size:47
Alignment explanation
Indices: 821--913 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 47
811 CATTACCTAA
*
821 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATAT
867 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
914 TAATTGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
46 6 0.14
49 37 0.86
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (47 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATAT
Found at i:1250 original size:66 final size:66
Alignment explanation
Indices: 1168--1298 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
1158 CTTAGCATTG
*
1168 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTTAATAA
1 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
1233 T
66 T
1234 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
1 GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
1299 AAAGGAAGTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (66 bp):
GCTAACTGTGCTTTTGGAAATGTGAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATAA
T
Found at i:2142 original size:22 final size:21
Alignment explanation
Indices: 2091--2152 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
2081 AATATTAATA
*
2091 AAGTCACTAAAAAACTTAAAG
1 AAGTCACTATAAAACTTAAAG
*
2112 AAGTTACTATAAAACTTAAAG
1 AAGTCACTATAAAACTTAAAG
2133 AAGGTCACTATAAAACTTAA
1 AA-GTCACTATAAAACTTAA
2153 TAAGATTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (21 bp):
AAGTCACTATAAAACTTAAAG
Found at i:2393 original size:19 final size:19
Alignment explanation
Indices: 2371--2424 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
2361 TACGAATTAT
* *
2371 TAAAGTTACTAAAAATCTC
1 TAAAGTTACTAAAAACCTA
*
2390 TAAAATTACTGAAAAACCTA
1 TAAAGTTACT-AAAAACCTA
*
2410 TAAAGTTATTAAAAA
1 TAAAGTTACTAAAAA
2425 AGCTTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.30
Consensus pattern (19 bp):
TAAAGTTACTAAAAACCTA
Found at i:2491 original size:21 final size:22
Alignment explanation
Indices: 2465--2513 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2455 TGAAATCCAC
*
2465 AATAAGATTA-CTAAAAATCTT
1 AATAAGATTAGCTAAAAAACTT
* *
2486 AATAAGGTTAGGTAAAAAACTT
1 AATAAGATTAGCTAAAAAACTT
2508 AATAAG
1 AATAAG
2514 GTGACCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (22 bp):
AATAAGATTAGCTAAAAAACTT
Found at i:5566 original size:27 final size:27
Alignment explanation
Indices: 5535--5588 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5525 GAATATGCTC
*
5535 GACTTTGCTAGCTCCTCTTTCGTGCAT
1 GACTTTGCTAGCTCCTCTTTCATGCAT
* **
5562 GACTTTGGTATTTCCTCTTTCATGCAT
1 GACTTTGCTAGCTCCTCTTTCATGCAT
5589 TGTAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.44
Consensus pattern (27 bp):
GACTTTGCTAGCTCCTCTTTCATGCAT
Found at i:6152 original size:191 final size:191
Alignment explanation
Indices: 5825--6169 Score: 611
Period size: 192 Copynumber: 1.8 Consensus size: 191
5815 TCTCAACTCA
*
5825 GTATTCTTTTGTGGTTTGCTCTGCCAAGTGAAAGATGGCTGTTGAAAATTTGCTGGCAGATTTTA
1 GTATTCTTTTGTGGTTTGCCCTGCCAAGTGAAAGATGGCTGTTGAAAATTTGCTGGCAGATTTTA
* *
5890 TGCCAATGATATTTAATTAATGTTAAGTCAGTCAGATTGCTGTAGCTTAGATGCTTCCAGTTGAC
66 TGCCAATGATATCTAATTAATGTTAAGTCAGTCAGATTGCTGTAGCTTAGACGCTTCCAGTTGAC
*
5955 ATGTTGCATATTTTTATATTCTCACTGTTCGCATAGTTACATGTTTATGTTGCATAGTTTT
131 ATGTTGCATAGTTTTATATTCTCACTGTTCGCATAGTTACATGTTTATGTTGCATAGTTTT
*
6016 GTATTCTTTATGTGGTTTGCCCTGCCAAGTTAAAGATGGCTGTTGAAAATTTGCTGGCAGATTTT
1 GTATTCTTT-TGTGGTTTGCCCTGCCAAGTGAAAGATGGCTGTTGAAAATTTGCTGGCAGATTTT
* *
6081 ATGCCAATGGTATCTAATTAATGTT-AGTCAGTCGGATTGCTGTAGCTTAGACGCTTCCAGTTGA
65 ATGCCAATGATATCTAATTAATGTTAAGTCAGTCAGATTGCTGTAGCTTAGACGCTTCCAGTTGA
6145 CATGTTGCATAGTTTTATATTCTCA
130 CATGTTGCATAGTTTTATATTCTCA
6170 TTGGCACATT
Statistics
Matches: 146, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
191 70 0.48
192 76 0.52
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (191 bp):
GTATTCTTTTGTGGTTTGCCCTGCCAAGTGAAAGATGGCTGTTGAAAATTTGCTGGCAGATTTTA
TGCCAATGATATCTAATTAATGTTAAGTCAGTCAGATTGCTGTAGCTTAGACGCTTCCAGTTGAC
ATGTTGCATAGTTTTATATTCTCACTGTTCGCATAGTTACATGTTTATGTTGCATAGTTTT
Found at i:8092 original size:30 final size:30
Alignment explanation
Indices: 8051--8109 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
8041 GCAAGGTTAT
* *
8051 TAAGCTGAATGTTACAGTAGCATTTTCAAG
1 TAAGCTGAATGTTAAAGCAGCATTTTCAAG
*
8081 TAAGCTTAATGTTAAAGCAGCATTTTCAA
1 TAAGCTGAATGTTAAAGCAGCATTTTCAA
8110 ATCTAACTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (30 bp):
TAAGCTGAATGTTAAAGCAGCATTTTCAAG
Found at i:9949 original size:13 final size:13
Alignment explanation
Indices: 9933--9960 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9923 AAAACATGAA
9933 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
9946 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
9959 AA
1 AA
9961 GAGCGAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Done.