Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2749
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: 20571
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:6952 original size:21 final size:22
Alignment explanation
Indices: 6922--6962 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6912 TATTTTAATA
*
6922 TTATA-ATTTTAATTTAATTTT
1 TTATATATTTTAATTAAATTTT
*
6943 TTATATTTTTTAATTAAATT
1 TTATATATTTTAATTAAATT
6963 GTGTCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATATTTTAATTAAATTTT
Found at i:7351 original size:10 final size:9
Alignment explanation
Indices: 7331--7394 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
7321 ATTTAATTTA
7331 ATTTTATAT
1 ATTTTATAT
7340 ATTTTATA-
1 ATTTTATAT
7348 ATATTTATAT
1 AT-TTTATAT
*
7358 GATTATT-TTT
1 -ATT-TTATAT
* *
7368 ATTTAATTT
1 ATTTTATAT
*
7377 AATTTATAT
1 ATTTTATAT
7386 ATTTTATAT
1 ATTTTATAT
7395 TTAATTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 3 0.07
9 34 0.77
10 3 0.07
11 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTATAT
Found at i:7382 original size:14 final size:15
Alignment explanation
Indices: 7348--7397 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
7338 ATATTTTATA
*
7348 ATATTTATATGA-TT
1 ATATTTATATAATTT
* *
7362 ATTTTTATTTAATTT
1 ATATTTATATAATTT
*
7377 A-ATTTATATATTTT
1 ATATTTATATAATTT
7391 ATATTTA
1 ATATTTA
7398 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
ATATTTATATAATTT
Found at i:7412 original size:20 final size:20
Alignment explanation
Indices: 7373--7412 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7363 TTTTTATTTA
**
7373 ATTTAATTTATATATTTTAT
1 ATTTAATTTATATAAATTAT
*
7393 ATTTAATTTTTATAAATTAT
1 ATTTAATTTATATAAATTAT
7413 TCATACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATTTATATAAATTAT
Found at i:7413 original size:25 final size:24
Alignment explanation
Indices: 7359--7413 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
7349 TATTTATATG
*
7359 ATTATTTTTATTTAATTTAATTTAT
1 ATTATTTTTATTTAATTT-ATTTAA
7384 A-TATTTTATATTTAATTT-TTATAA
1 ATTATTTT-TATTTAATTTATT-TAA
7408 ATTATT
1 ATTATT
7414 CATACAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
25 15 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTATTTTTATTTAATTTATTTAA
Found at i:7612 original size:16 final size:16
Alignment explanation
Indices: 7569--7612 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
7559 TTATTATTAA
*
7569 ATTAAAAAATAAATTT
1 ATTAAAAAATTAATTT
*
7585 ATTAAAATATTAA-TT
1 ATTAAAAAATTAATTT
7600 ATATAAAAAATTA
1 AT-TAAAAAATTA
7613 TATAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAAAAATTAATTT
Found at i:9178 original size:3 final size:3
Alignment explanation
Indices: 9170--9208 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
9160 TAATTGGTTC
* *
9170 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA CTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
9209 CTGCAGTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.03, G:0.31, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:10097 original size:21 final size:21
Alignment explanation
Indices: 10071--10114 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10061 AATAAATAAG
10071 TATTATGTAAT-TATTTTAATT
1 TATTAT-TAATATATTTTAATT
*
10092 TATTATTAATATTTTTTAATT
1 TATTATTAATATATTTTAATT
10113 TA
1 TA
10115 AATAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTATTAATATATTTTAATT
Found at i:10120 original size:19 final size:20
Alignment explanation
Indices: 10084--10123 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
10074 TATGTAATTA
*
10084 TTTTAATTTATTATTAATATT
1 TTTTAATTTA-TAATAATATT
10105 TTTTAATTTA-AATAATATT
1 TTTTAATTTATAATAATATT
10124 ATTATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAATTTATAATAATATT
Found at i:10165 original size:26 final size:26
Alignment explanation
Indices: 10127--10187 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
10117 TAATATTATT
10127 ATATTTGATA-TTTATAATTTA-TAAAA
1 ATATTT-ATATTTTAT-ATTTATTAAAA
*
10153 ATATTTATCATTTTATTTTTATTAAAA
1 ATATTTAT-ATTTTATATTTATTAAAA
*
10180 TTATTTAT
1 ATATTTAT
10188 TATAATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 2 0.07
26 11 0.37
27 17 0.57
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATATTTATATTTTATATTTATTAAAA
Found at i:10174 original size:33 final size:33
Alignment explanation
Indices: 10101--10174 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
10091 TTATTATTAA
*
10101 TATTTTT-TAATTTAAATAATATTATTATATTT
1 TATTTTTATAATTTAAAAAATATTATTATATTT
* *
10133 GATATTTATAATTTATAAAAATA-T-TTATCATTT
1 TATTTTTATAATTTA-AAAAATATTATTAT-ATTT
10166 TATTTTTAT
1 TATTTTTAT
10175 TAAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
32 9 0.26
33 19 0.56
34 6 0.18
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTTTTATAATTTAAAAAATATTATTATATTT
Found at i:10262 original size:14 final size:15
Alignment explanation
Indices: 10243--10272 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10233 TATTTAATTT
10243 TATT-AAAATATTGA
1 TATTAAAAATATTGA
10257 TATTAAAAATATTGA
1 TATTAAAAATATTGA
10272 T
1 T
10273 GAGATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TATTAAAAATATTGA
Found at i:11300 original size:15 final size:14
Alignment explanation
Indices: 11266--11304 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
11256 AAAATAACTA
*
11266 TAAATTTTAAAATT
1 TAAATATTAAAATT
*
11280 TGAATATTAAATATT
1 TAAATATTAAA-ATT
11295 TAAATATTAA
1 TAAATATTAA
11305 TTGATTGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
TAAATATTAAAATT
Found at i:11768 original size:2 final size:2
Alignment explanation
Indices: 11761--11803 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
11751 AGATATGGGT
11761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11801 TA T
1 TA T
11804 TCTTTGGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15246 original size:1 final size:1
Alignment explanation
Indices: 15242--15278 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
15232 TTTTTTTTTT
15242 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
15279 AAGGGAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Done.