Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2590
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: 15295
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Found at i:4355 original size:37 final size:37
Alignment explanation
Indices: 4296--4394 Score: 137
Period size: 37 Copynumber: 2.6 Consensus size: 37
4286 TTACGACAAG
*
4296 TAATATTTGGGTGGCTTGGCCAATCCACTATGATTGT
1 TAATATTTGGGTGGCTAGGCCAATCCACTATGATTGT
*
4333 TAGTATTTGGGTGG-TAGTGCCAATCCACTATGATTGT
1 TAATATTTGGGTGGCTAG-GCCAATCCACTATGATTGT
* *
4370 TAAAATTTGGGTGGCCAGCGCCAAT
1 TAATATTTGGGTGGCTAG-GCCAAT
4395 TCACGAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
36 2 0.04
37 44 0.81
38 8 0.15
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (37 bp):
TAATATTTGGGTGGCTAGGCCAATCCACTATGATTGT
Found at i:6460 original size:102 final size:103
Alignment explanation
Indices: 6341--6549 Score: 334
Period size: 103 Copynumber: 2.0 Consensus size: 103
6331 ATTCAATTAG
6341 TTTTTATTATAAAATT-GGTAGTTTTTCATAA-TTTTTAAATAATAAATTTTAAAAGATATAAAT
1 TTTTTATTATAAAATTGGGTAGTTTTT-ATAATTTTTTAAATAATAAATTTTAAAAGATATAAAT
6404 ACCGTTTT-CAGTTTTTTTGTTATAATTTCAATTTTGAGT
65 A-CGTTTTCCAGTTTTTTTGTTATAATTTCAATTTTGAGT
*
6443 TTTTTATTATAAAATTGGGTAGTTTTTATAATTTTTTAAATACTAAATTTTAAAAGATATAAATA
1 TTTTTATTATAAAATTGGGTAGTTTTTATAATTTTTTAAATAATAAATTTTAAAAGATATAAATA
** * *
6508 CGTTTTCCTTTTTTTTTGTTATTATTTCAATTTTGGGT
66 CGTTTTCCAGTTTTTTTGTTATAATTTCAATTTTGAGT
6546 TTTT
1 TTTT
6550 GATAATTTCA
Statistics
Matches: 99, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
102 26 0.26
103 73 0.74
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (103 bp):
TTTTTATTATAAAATTGGGTAGTTTTTATAATTTTTTAAATAATAAATTTTAAAAGATATAAATA
CGTTTTCCAGTTTTTTTGTTATAATTTCAATTTTGAGT
Found at i:10315 original size:2 final size:2
Alignment explanation
Indices: 10310--10352 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
10300 ACACACACTC
*
10310 AT AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10350 AT A
1 AT A
10353 GCACTTGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10332 original size:16 final size:16
Alignment explanation
Indices: 10310--10352 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
10300 ACACACACTC
10310 ATATATATATATATA-
1 ATATATATATATATAG
10325 ATTATATATATATATAG
1 A-TATATATATATATAG
10342 ATATATATATA
1 ATATATATATA
10353 GCACTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATATATATATATAG
Found at i:12268 original size:4 final size:4
Alignment explanation
Indices: 12259--12287 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
12249 TGACTGCTAA
12259 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
12288 TATAATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:13369 original size:14 final size:13
Alignment explanation
Indices: 13348--13400 Score: 74
Period size: 14 Copynumber: 4.1 Consensus size: 13
13338 ATTTTTTCGG
13348 TTTTAAATATATT
1 TTTTAAATATATT
13361 TTATTAAATATA-T
1 TT-TTAAATATATT
13374 TTTT-AATATATT
1 TTTTAAATATATT
13386 TTGTTAAATATATT
1 TT-TTAAATATATT
13400 T
1 T
13401 ATAGTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.17
12 5 0.14
13 7 0.19
14 18 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTTAAATATATT
Found at i:13382 original size:25 final size:25
Alignment explanation
Indices: 13348--13400 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
13338 ATTTTTTCGG
13348 TTTTAAATATATTTTATTAAATATA
1 TTTTAAATATATTTTATTAAATATA
* *
13373 TTTTTAATATATTTTGTTAAATATA
1 TTTTAAATATATTTTATTAAATATA
13398 TTT
1 TTT
13401 ATAGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTAAATATATTTTATTAAATATA
Found at i:13403 original size:20 final size:19
Alignment explanation
Indices: 13380--13434 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
13370 ATATTTTTAA
13380 TATATTTTGTTAAATATATT
1 TATATTTT-TTAAATATATT
*
13400 TATAGTTTATTAAA-ATATT
1 TATA-TTTTTTAAATATATT
* *
13419 TAAATATTTTAAATAT
1 TATATTTTTTAAATAT
13435 TAATTCGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 7 0.24
19 10 0.34
20 9 0.31
21 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
TATATTTTTTAAATATATT
Found at i:13684 original size:11 final size:11
Alignment explanation
Indices: 13662--13699 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
13652 AATCATATTC
13662 ATATAT-TTAA
1 ATATATATTAA
13672 ATATATATTAA
1 ATATATATTAA
13683 ATATAAATATTAA
1 ATAT--ATATTAA
13696 ATAT
1 ATAT
13700 TAAATATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.24
11 8 0.32
13 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATTAA
Found at i:13694 original size:13 final size:13
Alignment explanation
Indices: 13668--13706 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
13658 ATTCATATAT
13668 TTAAATAT--ATA
1 TTAAATATAAATA
13679 TTAAATATAAATA
1 TTAAATATAAATA
13692 TTAAATATTAAATA
1 TTAAATA-TAAATA
13706 T
1 T
13707 GATTATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.32
13 10 0.40
14 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:13696 original size:7 final size:7
Alignment explanation
Indices: 13676--13706 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
13666 ATTTAAATAT
13676 ATATTAA
1 ATATTAA
13683 ATA-TAA
1 ATATTAA
13689 ATATTAA
1 ATATTAA
13696 ATATTAA
1 ATATTAA
13703 ATAT
1 ATAT
13707 GATTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATTAA
Done.