Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1836
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: 25992
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:1808 original size:29 final size:29
Alignment explanation
Indices: 1775--1834 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1765 GGTGAAAGTT
1775 AGAAAGCTCACATCATTTGTTTTAATGAA
1 AGAAAGCTCACATCATTTGTTTTAATGAA
1804 AGAAAGCTCACATCATTTGTTTTAATGAA
1 AGAAAGCTCACATCATTTGTTTTAATGAA
1833 AG
1 AG
1835 TCTTACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (29 bp):
AGAAAGCTCACATCATTTGTTTTAATGAA
Found at i:10120 original size:5 final size:5
Alignment explanation
Indices: 10110--10138 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
10100 CTTTCACTAT
10110 TATAG TATAG TATAG TATAG TATAG TATA
1 TATAG TATAG TATAG TATAG TATAG TATA
10139 TGACAACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
TATAG
Found at i:10189 original size:27 final size:27
Alignment explanation
Indices: 10151--10204 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
10141 ACAACTGAAG
10151 GAGATTTTCATCTTCCTATGTGTTTTT
1 GAGATTTTCATCTTCCTATGTGTTTTT
10178 GAGATTTTCATCTTCCTATGTGTTTTT
1 GAGATTTTCATCTTCCTATGTGTTTTT
10205 TTCTGATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (27 bp):
GAGATTTTCATCTTCCTATGTGTTTTT
Found at i:12390 original size:2 final size:2
Alignment explanation
Indices: 12383--12418 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12373 GTTACTAAAA
12383 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
12419 TATAACTTCA
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:17633 original size:9 final size:9
Alignment explanation
Indices: 17619--17727 Score: 76
Period size: 9 Copynumber: 11.6 Consensus size: 9
17609 GACTTTATAA
17619 AATTTTTAT
1 AATTTTTAT
17628 AATTTTTAT
1 AATTTTTAT
*
17637 AATTTCTAT
1 AATTTTTAT
17646 ATATTTTTAT
1 A-ATTTTTAT
*
17656 AATATTTTAC
1 AAT-TTTTAT
*
17666 GATTTTTAT
1 AATTTTTAT
** *
17675 AAAATTTAC
1 AATTTTTAT
17684 ATATTTTT-T
1 A-ATTTTTAT
*
17693 ACTATTTTAT
1 AAT-TTTTAT
* *
17703 ATTTTTTCCT
1 AATTTTT-AT
17713 AATTTTTAAT
1 AATTTTT-AT
17723 AATTT
1 AATTT
17728 ATTTTTATTA
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
8 1 0.01
9 40 0.53
10 35 0.46
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:17664 original size:38 final size:38
Alignment explanation
Indices: 17612--17709 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
17602 TTCTTATGAC
* * *
17612 TTTATAAAATTTTTATAATTTTTAT-AATTTCTATATATT
1 TTTATAATA-TTTTATAATTTTTATAAAATT-TACATATT
**
17651 TTTATAATATTTTACGATTTTTATAAAATTTACATATT
1 TTTATAATATTTTATAATTTTTATAAAATTTACATATT
* *
17689 TTT-TACTATTTTATATTTTTT
1 TTTATAATATTTTATAATTTTT
17710 CCTAATTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 14 0.29
38 23 0.47
39 12 0.24
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (38 bp):
TTTATAATATTTTATAATTTTTATAAAATTTACATATT
Found at i:17681 original size:11 final size:10
Alignment explanation
Indices: 17612--17663 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
17602 TTCTTATGAC
17612 TTTATAAAATT
1 TTTAT-AAATT
17623 TTTAT-AATT
1 TTTATAAATT
17632 TTTAT-AATT
1 TTTATAAATT
* *
17641 TCTATATATT
1 TTTATAAATT
17651 TTTATAATATT
1 TTTATAA-ATT
17662 TT
1 TT
17664 ACGATTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 17 0.49
10 8 0.23
11 10 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTATAAATT
Found at i:17689 original size:19 final size:19
Alignment explanation
Indices: 17612--17691 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
17602 TTCTTATGAC
**
17612 TTTATAAAATTTTTATAATT
1 TTTATAAAATTTACAT-ATT
* *
17632 TTTAT-AATTTCTATATATT
1 TTTATAAAATT-TACATATT
* *
17651 TTTATAATATTTTAC-GATT
1 TTTATAA-AATTTACATATT
17670 TTTATAAAATTTACATATT
1 TTTATAAAATTTACATATT
17689 TTT
1 TTT
17692 TACTATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.12
19 28 0.56
20 12 0.24
21 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTATAAAATTTACATATT
Found at i:17945 original size:92 final size:92
Alignment explanation
Indices: 17821--18017 Score: 227
Period size: 92 Copynumber: 2.1 Consensus size: 92
17811 AAGGGTTTAA
* * * * * * *
17821 TTGCTTTTTTTTGAAAAATTTTGAGGGTTTTTTTGATATATTTTGAAAGTTCAAGTATTCAAATG
1 TTGCTTTTTTTTAAAAAAGTTTGAAGGCTTTTTTGATACATTTTGAAAATTCAAGTACTCAAATG
*
17886 AGTGTAAAAAAAAGAGCAGGGGCTTAT
66 AGTGCAAAAAAAAGAGCAGGGGCTTAT
* * *
17913 TTGC-TTTTTTTAAAAAAGGTTTGAAGGCTTTTTTTATGCATTTTGAAAATTTAAGTACTCAAAT
1 TTGCTTTTTTTTAAAAAA-GTTTGAAGGCTTTTTTGATACATTTTGAAAATTCAAGTACTCAAAT
**
17977 GAGTGCAAAAAAAA-AATAGGGGCTTAAT
65 GAGTGCAAAAAAAAGAGCAGGGGCTT-AT
**
18005 TTTTTTTTTTTTA
1 TTGCTTTTTTTTA
18018 TGTTTGAGGG
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
91 21 0.24
92 58 0.67
93 8 0.09
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (92 bp):
TTGCTTTTTTTTAAAAAAGTTTGAAGGCTTTTTTGATACATTTTGAAAATTCAAGTACTCAAATG
AGTGCAAAAAAAAGAGCAGGGGCTTAT
Found at i:18257 original size:35 final size:35
Alignment explanation
Indices: 18210--18280 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
18200 TCCATGTTAC
18210 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
1 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
*
18245 TGTTAAGTTACATTCTTCAAATTCTCACTGATTGT
1 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
18280 T
1 T
18281 ATTTTTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (35 bp):
TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
Done.