Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2381
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: 44680
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Found at i:12987 original size:2 final size:2
Alignment explanation
Indices: 12980--13009 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12970 CTTATTGTTA
12980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13010 GGAAGATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13236 original size:23 final size:22
Alignment explanation
Indices: 13204--13246 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
13194 ATATTTTTAT
*
13204 TTAATTTTAATTATAAAAATATA
1 TTAATATTAA-TATAAAAATATA
13227 TTAATATTAATATAAAAATA
1 TTAATATTAATATAAAAATA
13247 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATATTAATATAAAAATATA
Found at i:13616 original size:2 final size:2
Alignment explanation
Indices: 13609--13644 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13599 TTTATTTTAT
13609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13645 ACATCTAATC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14095 original size:13 final size:13
Alignment explanation
Indices: 14077--14102 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14067 TTAACAGAGA
14077 TATATTTAATTTT
1 TATATTTAATTTT
14090 TATATTTAATTTT
1 TATATTTAATTTT
14103 AAACCCAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATTTAATTTT
Found at i:20766 original size:13 final size:13
Alignment explanation
Indices: 20748--20772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20738 ACAGAGATAA
20748 ATTCAATTTTTAT
1 ATTCAATTTTTAT
20761 ATTCAATTTTTA
1 ATTCAATTTTTA
20773 ACCTAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTCAATTTTTAT
Found at i:21300 original size:38 final size:38
Alignment explanation
Indices: 21229--21301 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
21219 AGCTCAAGTT
* *
21229 AATCGAATTTAACATTTAAGTTAATTAAATTTAATATC
1 AATCAAATTTAACATTTAAGTTAATCAAATTTAATATC
* * *
21267 AATCAAATTTATCATTTAAGTTTATCAAGTTTAAT
1 AATCAAATTTAACATTTAAGTTAATCAAATTTAAT
21302 CATTTTAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (38 bp):
AATCAAATTTAACATTTAAGTTAATCAAATTTAATATC
Found at i:22429 original size:17 final size:17
Alignment explanation
Indices: 22407--22478 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
22397 TTAAATTGTT
*
22407 ATATTAATTAGATTTGA
1 ATATTAATTAGATTTAA
*
22424 ATATTAATTATATTTAA
1 ATATTAATTAGATTTAA
*
22441 ATA-T-ATTATGTAATTAA
1 ATATTAATTA-G-ATTTAA
*
22458 ATATTAATTATATTTAA
1 ATATTAATTAGATTTAA
22475 ATAT
1 ATAT
22479 GTTATATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 4 0.09
16 1 0.02
17 35 0.78
18 1 0.02
19 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
ATATTAATTAGATTTAA
Found at i:22485 original size:15 final size:15
Alignment explanation
Indices: 22430--22486 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
22420 TTGAATATTA
22430 ATTATATTTAAATAT
1 ATTATATTTAAATAT
*
22445 ATTATGTAATTAAATATT
1 ATTA--TATTTAAATA-T
22463 AATTATATTTAAATAT
1 -ATTATATTTAAATAT
*
22479 GTTATATT
1 ATTATATT
22487 ATATTTATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 11 0.31
16 1 0.03
17 18 0.51
18 1 0.03
19 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
ATTATATTTAAATAT
Found at i:25639 original size:15 final size:15
Alignment explanation
Indices: 25619--25652 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25609 AAACAAATGC
* *
25619 TCATCATTTTCATTA
1 TCATCATCTTCATAA
25634 TCATCATCTTCATAA
1 TCATCATCTTCATAA
25649 TCAT
1 TCAT
25653 ATTCATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATCATCTTCATAA
Found at i:26935 original size:16 final size:16
Alignment explanation
Indices: 26914--26951 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
26904 AATAATGCTT
26914 ATATTAACTTTTTTAA
1 ATATTAACTTTTTTAA
**
26930 ATATTATTTTTTTTAA
1 ATATTAACTTTTTTAA
26946 A-ATTAA
1 ATATTAA
26952 TATTATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTAACTTTTTTAA
Found at i:27595 original size:16 final size:16
Alignment explanation
Indices: 27574--27608 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
27564 TATGTATAAT
27574 ATCTAAATTATGACGA
1 ATCTAAATTATGACGA
27590 ATCTAAATTATGACGA
1 ATCTAAATTATGACGA
27606 ATC
1 ATC
27609 ATGTTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (16 bp):
ATCTAAATTATGACGA
Found at i:32226 original size:13 final size:12
Alignment explanation
Indices: 32207--32253 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
32197 AACAGAGATA
32207 AATTCAATTTTT
1 AATTCAATTTTT
32219 ATATTCAATTTTT
1 A-ATTCAATTTTT
**
32232 AACCCAATTTTT
1 AATTCAATTTTT
32244 AAGTTCAATT
1 AA-TTCAATT
32254 AAAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (12 bp):
AATTCAATTTTT
Found at i:32709 original size:38 final size:38
Alignment explanation
Indices: 32655--32727 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
32645 TTACGAGCTC
* * *
32655 AATCGAATTTAACATTTAAGTTAATTAAATTTAATATA
1 AATCAAATTTAACATTTAAATTAATCAAATTTAATATA
* *
32693 AATCAAATTTATCATTTAAATTTATCAAATTTAAT
1 AATCAAATTTAACATTTAAATTAATCAAATTTAAT
32728 CATTTTAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.44
Consensus pattern (38 bp):
AATCAAATTTAACATTTAAATTAATCAAATTTAATATA
Found at i:32710 original size:23 final size:23
Alignment explanation
Indices: 32683--32732 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
32673 AGTTAATTAA
32683 ATTTAATATAAATCAAATTT-ATC
1 ATTTAA-ATAAATCAAATTTAATC
**
32706 ATTTAAATTTATCAAATTTAATC
1 ATTTAAATAAATCAAATTTAATC
32729 ATTT
1 ATTT
32733 TAAACTCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAAATAAATCAAATTTAATC
Found at i:33876 original size:10 final size:10
Alignment explanation
Indices: 33858--33887 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
33848 ATTTGAATAA
33858 TAAATATATT
1 TAAATATATT
*
33868 TAAAAATATT
1 TAAATATATT
33878 TAAATATATT
1 TAAATATATT
33888 ATGTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAAATATATT
Found at i:33914 original size:17 final size:17
Alignment explanation
Indices: 33873--33933 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
33863 ATATTTAAAA
33873 ATATTTAAATA-T-ATT
1 ATATTTAAATATTAATT
*
33888 ATGTAATTAAATATTAATT
1 A--TATTTAAATATTAATT
33907 ATATTTAAATATGTTATATT
1 ATATTTAAATA--TTA-ATT
33927 ATATTTA
1 ATATTTA
33934 TCAAATACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 1 0.03
17 18 0.49
18 1 0.03
19 7 0.19
20 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATATTTAAATATTAATT
Found at i:37079 original size:15 final size:15
Alignment explanation
Indices: 37059--37092 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
37049 AAACAAATGC
* *
37059 TCATCATTTTCATTA
1 TCATCATCTTCATAA
37074 TCATCATCTTCATAA
1 TCATCATCTTCATAA
37089 TCAT
1 TCAT
37093 ATTCATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATCATCTTCATAA
Found at i:38375 original size:16 final size:16
Alignment explanation
Indices: 38354--38391 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38344 AATAATGCTT
38354 ATATTAACTTTTTTAA
1 ATATTAACTTTTTTAA
**
38370 ATATTATTTTTTTTAA
1 ATATTAACTTTTTTAA
38386 A-ATTAA
1 ATATTAA
38392 TATTATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTAACTTTTTTAA
Found at i:39035 original size:16 final size:16
Alignment explanation
Indices: 39014--39048 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
39004 TATGTATAAT
39014 ATCTAAATTATGACGA
1 ATCTAAATTATGACGA
39030 ATCTAAATTATGACGA
1 ATCTAAATTATGACGA
39046 ATC
1 ATC
39049 ATGTTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (16 bp):
ATCTAAATTATGACGA
Found at i:43699 original size:13 final size:12
Alignment explanation
Indices: 43653--43699 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
43643 AACAGAGATA
43653 AATTCAATTTTT
1 AATTCAATTTTT
43665 ATATTCAATTTTT
1 A-ATTCAATTTTT
*
43678 AA-CCTAATTTTT
1 AATTC-AATTTTT
43690 AAGTTCAATT
1 AA-TTCAATT
43700 AAAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 11 0.38
13 16 0.55
14 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (12 bp):
AATTCAATTTTT
Done.