Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017896.1 Corchorus olitorius cultivar O-4 contig17929, 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: 18593
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--43 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TTACTTA
8 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44 AATGCTAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:293 original size:20 final size:20
Alignment explanation
Indices: 268--305 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
258 TATATATACT
*
268 TTTTAATGAGTTGTTTTTGC
1 TTTTAATGAGTAGTTTTTGC
288 TTTTAATGAGTAGTTTTT
1 TTTTAATGAGTAGTTTTT
306 ATTTTCTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (20 bp):
TTTTAATGAGTAGTTTTTGC
Found at i:310 original size:19 final size:20
Alignment explanation
Indices: 268--310 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
258 TATATATACT
* *
268 TTTTAATGAGTTGTTTTTGC
1 TTTTAATGAGTAGTTTTTGA
288 TTTTAATGAGTAGTTTTT-A
1 TTTTAATGAGTAGTTTTTGA
307 TTTT
1 TTTT
311 CTGTTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.02, G:0.16, T:0.63
Consensus pattern (20 bp):
TTTTAATGAGTAGTTTTTGA
Found at i:547 original size:57 final size:56
Alignment explanation
Indices: 456--570 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 56
446 TATCCGTTTC
* *
456 CTTTCACACAATAAATATTATAATAAATCCTATCCCCTCTATCTCTACTTTATTATT
1 CTTTCACACAATAAATATTATAATAAATCATAT-CCCTCTATCTCTACTTAATTATT
*
513 CTTTCACACAATAAATGTTATAATAAATCATATCCCTCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCTCTATCTCTACTTAATTATT
569 CT
1 CT
571 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 24 0.44
57 31 0.56
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.42
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCATATCCCTCTATCTCTACTTAATTATT
Found at i:583 original size:57 final size:57
Alignment explanation
Indices: 465--576 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 57
455 CCTTTCACAC
* * * * *
465 AATAAATATTATAATAAATCCTATCCCCTCTATCTCTACTTTATTATTCTTTCACAC
1 AATAAATATTATAATAAATCATATCCCCTCTATCTCTACTTAATTATTCTTACAAAA
*
522 AATAAATGTTATAATAAATCATAT-CCCTCTATCTCTACTTAATTATTC-TACAAAA
1 AATAAATATTATAATAAATCATATCCCCTCTATCTCTACTTAATTATTCTTACAAAA
577 TAAATAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 4 0.08
56 23 0.47
57 22 0.45
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (57 bp):
AATAAATATTATAATAAATCATATCCCCTCTATCTCTACTTAATTATTCTTACAAAA
Found at i:9383 original size:15 final size:15
Alignment explanation
Indices: 9363--9397 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9353 ATAATTTAAA
9363 AAAAATAAAAAAAAT
1 AAAAATAAAAAAAAT
*
9378 AAAAATAATAAAAAT
1 AAAAATAAAAAAAAT
9393 AAAAA
1 AAAAA
9398 CCAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:9394 original size:9 final size:9
Alignment explanation
Indices: 9359--9391 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
9349 AATAATAATT
9359 TAAAAAAAA
1 TAAAAAAAA
9368 TAAAAAAAA
1 TAAAAAAAA
*
9377 TAAAAATAA
1 TAAAAAAAA
9386 TAAAAA
1 TAAAAA
9392 TAAAAACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:17839 original size:21 final size:22
Alignment explanation
Indices: 17804--17844 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
17794 AATTTTAAGT
17804 TTTTAACGTTTGGTTTGTTGAA
1 TTTTAACGTTTGGTTTGTTGAA
17826 TTTTAACG-TTGGTTTGTTG
1 TTTTAACGTTTGGTTTGTTG
17845 TAAGCTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.15, C:0.05, G:0.24, T:0.56
Consensus pattern (22 bp):
TTTTAACGTTTGGTTTGTTGAA
Found at i:17853 original size:22 final size:22
Alignment explanation
Indices: 17806--17853 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
17796 TTTTAAGTTT
**
17806 TTAACGTTTGGTTTGTTGAATT
1 TTAACGTTTGGTTTGTTGAAGC
17828 TTAACG-TTGGTTTGTTGTAAGC
1 TTAACGTTTGGTTTGTTG-AAGC
17850 TTAA
1 TTAA
17854 GGGAAGTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.21, C:0.06, G:0.23, T:0.50
Consensus pattern (22 bp):
TTAACGTTTGGTTTGTTGAAGC
Done.