Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1186
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: 12571
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:340 original size:24 final size:25
Alignment explanation
Indices: 286--340 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
276 GGTTGAGGGT
*
286 TTAAATT-TTTAATTTAATTTATTA
1 TTAAATTATTTAATTTAATTTATAA
* *
310 TT-TATTATTTAATTTATTTTA-AA
1 TTAAATTATTTAATTTAATTTATAA
333 TTAAATTA
1 TTAAATTA
341 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTAAATTATTTAATTTAATTTATAA
Found at i:397 original size:22 final size:21
Alignment explanation
Indices: 372--412 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
362 TATTTTAAAA
372 ATAT-TTTTA-AATTAATATTT
1 ATATATTTTATAATTAA-ATTT
392 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
413 TAATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:672 original size:17 final size:18
Alignment explanation
Indices: 627--674 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
617 TTAATATTTT
*
627 ATTAATTTTTAAGTTATTAA
1 ATTAA-TTTTAA-TTAATAA
647 ATTAA-TTTAATTAATAA
1 ATTAATTTTAATTAATAA
664 A-TAATTTTAAT
1 ATTAATTTTAAT
675 ATATTTACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 13 0.50
18 5 0.19
20 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTAATTTTAATTAATAA
Found at i:2041 original size:20 final size:19
Alignment explanation
Indices: 2002--2041 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1992 TTTGCCTGAT
**
2002 TTTAAATATAATTTTTTAA
1 TTTAAATATAATTTAATAA
2021 TTTAAATTATAATTTAATAA
1 TTTAAA-TATAATTTAATAA
2041 T
1 T
2042 AAAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAATATAATTTAATAA
Found at i:2076 original size:32 final size:33
Alignment explanation
Indices: 2006--2076 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1996 CCTGATTTTA
* ***
2006 AATATAATTTTTTAATTTAAATTATAATTTAAT
1 AATAAAATTTTTTAATTTAAATTATAAAAAAAT
2039 AATAAAATTTTTT-ATTTAAATTTATAAAAAAAT
1 AATAAAATTTTTTAATTTAAA-TTATAAAAAAAT
2072 -ATAAA
1 AATAAA
2077 TATTAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AATAAAATTTTTTAATTTAAATTATAAAAAAAT
Found at i:2996 original size:13 final size:12
Alignment explanation
Indices: 2946--2995 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2936 CCTAGATCAA
*
2946 ATAATTTTAAAT
1 ATAATATTAAAT
*
2958 ATGATATTATAAT
1 ATAATATTA-AAT
*
2971 AAAATA-TAAAT
1 ATAATATTAAAT
2982 ATAATATT-AAT
1 ATAATATTAAAT
2993 ATA
1 ATA
2996 TTAAATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 14 0.45
12 10 0.32
13 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:4349 original size:21 final size:22
Alignment explanation
Indices: 4316--4384 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 22
4306 ATATTTATAT
4316 ATTTTTATAATTAAATTATA-TAA
1 ATTTTT-T-ATTAAATTATATTAA
4339 ATTTTTTATT-AATTA-ATTAA
1 ATTTTTTATTAAATTATATTAA
* ** *
4359 AATTTAAATTAAATTAAATTAA
1 ATTTTTTATTAAATTATATTAA
4381 ATTT
1 ATTT
4385 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 8 0.21
22 9 0.23
23 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTTTATTAAATTATATTAA
Found at i:4367 original size:6 final size:6
Alignment explanation
Indices: 4353--4393 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
4343 TTTATTAATT
*
4353 AATTAA AATTTA AA-TTA AA-TTA AA-TTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
4394 ATATTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
5 15 0.45
6 18 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:4377 original size:16 final size:16
Alignment explanation
Indices: 4349--4395 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4339 ATTTTTTATT
4349 AATT-AATTAAAATTTA
1 AATTAAATTAAAA-TTA
4365 AATTAAATT-AAATTA
1 AATTAAATTAAAATTA
4380 AATTTAAATTTAAAAT
1 AA-TTAAA-TTAAAAT
4396 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.19
16 12 0.44
17 6 0.22
18 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAAATTAAAATTA
Found at i:4385 original size:21 final size:21
Alignment explanation
Indices: 4319--4389 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
4309 TTTATATATT
*
4319 TTTATAATTAAATTATA-TAAA
1 TTTA-AATTAAATTAAATTAAA
**
4340 TTTTTTATT-AATT-AATTAAAA
1 -TTTAAATTAAATTAAATT-AAA
4361 TTTAAATTAAATTAAATTAAA
1 TTTAAATTAAATTAAATTAAA
4382 TTTAAATT
1 TTTAAATT
4390 TAAAATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.28
21 21 0.52
22 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAATTAAATTAAATTAAA
Found at i:5313 original size:16 final size:16
Alignment explanation
Indices: 5261--5313 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
5251 CATATTATGC
*
5261 TTTTATAATTT-ATTT
1 TTTTAAAATTTAATTT
*
5276 TTTTAAAAATATATATTT
1 TTTT-AAAATTTA-ATTT
5294 TTTTAAAATTTAATTAT
1 TTTTAAAATTTAATT-T
5311 TTT
1 TTT
5314 CTTTTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 11 0.35
18 8 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTAAAATTTAATTT
Found at i:5393 original size:27 final size:29
Alignment explanation
Indices: 5361--5415 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
5351 ATTTTTAATA
*
5361 TTTATATTAT-AATATTACAT-ATATATT
1 TTTATATTATAAAAATTACATAATATATT
5388 TTTATATTATAAAAATTACATAATATAT
1 TTTATATTATAAAAATTACATAATATAT
5416 AATATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 9 0.36
29 6 0.24
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTATATTATAAAAATTACATAATATATT
Found at i:5991 original size:16 final size:15
Alignment explanation
Indices: 5954--6034 Score: 51
Period size: 16 Copynumber: 5.3 Consensus size: 15
5944 GATTTACATA
5954 AAATAAAATATAAA--
1 AAAT-AAATATAAATT
5968 AAATATAATTATTAAATT
1 AAATA-AA-TA-TAAATT
5986 AAATAAATATAAATT
1 AAATAAATATAAATT
* * *
6001 ATATACAAAATTAATT
1 AAATA-AATATAAATT
* *
6017 AAATATATA-AAAAT
1 AAATAAATATAAATT
6031 AAAT
1 AAAT
6035 TATTTTATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
13 1 0.02
14 13 0.25
15 14 0.26
16 18 0.34
17 2 0.04
18 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAATATAAATT
Found at i:5993 original size:22 final size:23
Alignment explanation
Indices: 5959--6002 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5949 ACATAAAATA
5959 AAATATAAAAAATAT-AATTATT
1 AAATATAAAAAATATAAATTATT
5981 AAAT-TAAATAAATATAAATTAT
1 AAATATAAA-AAATATAAATTAT
6003 ATACAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAAAAAATATAAATTATT
Found at i:5997 original size:31 final size:31
Alignment explanation
Indices: 5954--6038 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 31
5944 GATTTACATA
5954 AAATAAAATATAAAAAATATAATTATTAAATT
1 AAAT-AAATATAAAAAATATAATTATTAAATT
* **
5986 AAATAAATAT--AAATTAT-A-TACAAAATT
1 AAATAAATATAAAAAATATAATTATTAAATT
*
6013 AATTAAATATATAAAAATA-AATTATT
1 AAATAAATATA-AAAAATATAATTATT
6039 TTATTTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
27 16 0.39
28 1 0.02
29 6 0.15
30 6 0.15
31 8 0.20
32 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (31 bp):
AAATAAATATAAAAAATATAATTATTAAATT
Done.