Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012109.1 Corchorus olitorius cultivar O-4 contig12142, 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: 7884
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3152 original size:29 final size:29
Alignment explanation
Indices: 3093--3156 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
3083 AAAAGGTCTA
*
3093 ATTTGGCCAAAATTGGGAGTTCATGGGTTT
1 ATTTGGCCAAAATTGGAAGTT-ATGGGTTT
3123 ATTTGGCCAAAATT-GAAGTT-TGGAGGTTT
1 ATTTGGCCAAAATTGGAAGTTAT-G-GGTTT
3152 ATTTG
1 ATTTG
3157 AGCGTTGCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 15 0.48
30 14 0.45
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.39
Consensus pattern (29 bp):
ATTTGGCCAAAATTGGAAGTTATGGGTTT
Found at i:3271 original size:9 final size:8
Alignment explanation
Indices: 3254--3286 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3244 ATATAACTTA
3254 TATTATTT
1 TATTATTT
3262 TATTATTTT
1 TATTA-TTT
3271 TATTATTT
1 TATTATTT
3279 TA-TATTT
1 TATTATTT
3286 T
1 T
3287 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.25
8 10 0.42
9 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:3276 original size:17 final size:16
Alignment explanation
Indices: 3254--3288 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
3244 ATATAACTTA
3254 TATTATTTTATTATTTT
1 TATTATTTTA-TATTTT
3271 TATTATTTTATATTTT
1 TATTATTTTATATTTT
3287 TA
1 TA
3289 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTATTTTATATTTT
Found at i:3511 original size:302 final size:303
Alignment explanation
Indices: 2960--3560 Score: 1168
Period size: 302 Copynumber: 2.0 Consensus size: 303
2950 GATTAAAGGA
*
2960 ATTAGTTTTTATTATTTTATATTTTTTAAAAAAAATTCTAAAAATTTAGCTTTTGCTGACGTGAC
1 ATTAGTTTTTATTATTTTATATTTTTAAAAAAAAATTCTAAAAATTTAGCTTTTGCTGACGTGAC
3025 ATTTTTTGGTCACGTGGCGTGCTTACATGGCACTATTTAACGGAAGTGAACCGTTTGCAAAAGGT
66 ATTTTTTGGTCACGTGGCGTGCTTACATGGCACTATTTAACGGAAGTGAACCGTTTGCAAAAGGT
*
3090 CTAATTTGGCCAAAATTGGGAGTTCATGGGTTTATTTGGCCAAAATTGAAGTTTGGAGGTTTATT
131 CTAATTTGGCCAAAATTGGGAGTTCATGGGTTTATTTGGCCAAAATTAAAGTTTGGAGGTTTATT
*
3155 TGAGCGTTGCCGGAAAGTTCAGGGGTCTTTTTTGCCATTAAGCCATTATAATTATTATTATAATT
196 TGAGCGTTGCCGAAAAGTTCAGGGGTCTTTTTTGCCATTAAGCCATTATAATTATTATTATAATT
3220 ATGGTTGGTACTTGGTAGACCAATATATAACTTATATTATTTT
261 ATGGTTGGTACTTGGTAGACCAATATATAACTTATATTATTTT
3263 ATTA-TTTTTATTATTTTATATTTTTAAAAAAAAATTCTAAAAATTTAGCTTTTGCTGACGTGAC
1 ATTAGTTTTTATTATTTTATATTTTTAAAAAAAAATTCTAAAAATTTAGCTTTTGCTGACGTGAC
3327 ATTTTTTGGTCACGTGGCGTGCTTACATGGCACTATTTAACGGAAGTGAACCGTTTGCAAAAGGT
66 ATTTTTTGGTCACGTGGCGTGCTTACATGGCACTATTTAACGGAAGTGAACCGTTTGCAAAAGGT
3392 CTAATTTGGCCAAAATTGGGAGTTCATGGGTTTATTTGGCCAAAATTAAAGTTTGGAGGTTTATT
131 CTAATTTGGCCAAAATTGGGAGTTCATGGGTTTATTTGGCCAAAATTAAAGTTTGGAGGTTTATT
3457 TGAGCGTTGCCGAAAAGTTCAGGGGTCTTTTTTGCCATTAAGCCATTATAATTATTATTATAATT
196 TGAGCGTTGCCGAAAAGTTCAGGGGTCTTTTTTGCCATTAAGCCATTATAATTATTATTATAATT
3522 ATGGTTGGTACTTGGTAGACCAATATATAACTTATATTA
261 ATGGTTGGTACTTGGTAGACCAATATATAACTTATATTA
3561 AGGTTAAGGC
Statistics
Matches: 295, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
302 291 0.99
303 4 0.01
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (303 bp):
ATTAGTTTTTATTATTTTATATTTTTAAAAAAAAATTCTAAAAATTTAGCTTTTGCTGACGTGAC
ATTTTTTGGTCACGTGGCGTGCTTACATGGCACTATTTAACGGAAGTGAACCGTTTGCAAAAGGT
CTAATTTGGCCAAAATTGGGAGTTCATGGGTTTATTTGGCCAAAATTAAAGTTTGGAGGTTTATT
TGAGCGTTGCCGAAAAGTTCAGGGGTCTTTTTTGCCATTAAGCCATTATAATTATTATTATAATT
ATGGTTGGTACTTGGTAGACCAATATATAACTTATATTATTTT
Found at i:5391 original size:18 final size:18
Alignment explanation
Indices: 5337--5383 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
5327 TCTTTTTTTT
5337 TTAAATAAAAATAAA-AT-
1 TTAAATAAAAA-AAATATA
*
5354 TTCAATAAAAAAAATATA
1 TTAAATAAAAAAAATATA
5372 TTAAATAAAAAA
1 TTAAATAAAAAA
5384 TATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 12 0.46
18 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TTAAATAAAAAAAATATA
Done.