Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2092
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: 11628
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:2123 original size:2 final size:2
Alignment explanation
Indices: 2116--2142 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2106 TTATTATTAT
2116 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2143 TTTTGGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2249 original size:39 final size:39
Alignment explanation
Indices: 2199--2295 Score: 176
Period size: 39 Copynumber: 2.5 Consensus size: 39
2189 ACACACACAC
2199 ACATATATATATATATATATAATCACCTGATATTTACAT
1 ACATATATATATATATATATAATCACCTGATATTTACAT
*
2238 ACATACATATATATATATATAATCACCTGATATTTACAT
1 ACATATATATATATATATATAATCACCTGATATTTACAT
*
2277 TCATATATATATATATATA
1 ACATATATATATATATATA
2296 AACAGCTAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (39 bp):
ACATATATATATATATATATAATCACCTGATATTTACAT
Found at i:9734 original size:18 final size:18
Alignment explanation
Indices: 9708--9748 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
9698 TTTTAAAAAA
* *
9708 TTTAATATTTAAATTTTT
1 TTTATTATTTAAATTATT
*
9726 TTTATTATTTATATTATT
1 TTTATTATTTAAATTATT
9744 TTTAT
1 TTTAT
9749 GATTACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTATTTAAATTATT
Found at i:9758 original size:18 final size:18
Alignment explanation
Indices: 9714--9761 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
9704 AAAATTTAAT
* * *
9714 ATTTAAATTTTTTTTATT
1 ATTTATATTATTTTTATG
9732 ATTTATATTATTTTTATG
1 ATTTATATTATTTTTATG
9750 A-TTACTATTATT
1 ATTTA-TATTATT
9762 AGTCAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTATATTATTTTTATG
Found at i:9860 original size:11 final size:10
Alignment explanation
Indices: 9844--9886 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
9834 AATTTTAAAA
9844 TTTTATTATTT
1 TTTTATT-TTT
*
9855 TTTTATTTTA
1 TTTTATTTTT
9865 TTTTATTCTTAT
1 TTTTATT-TT-T
9877 TTTTATTTTT
1 TTTTATTTTT
9887 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 10 0.36
11 11 0.39
12 7 0.25
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:9862 original size:16 final size:16
Alignment explanation
Indices: 9843--9885 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
9833 AAATTTTAAA
*
9843 ATTTTATTATT-TTTTT
1 ATTTTATT-TTATTCTT
9859 ATTTTATTTTATTCTT
1 ATTTTATTTTATTCTT
9875 ATTTTTATTTT
1 A-TTTTATTTT
9886 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTATTTTATTCTT
Found at i:9869 original size:21 final size:22
Alignment explanation
Indices: 9843--9885 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
9833 AAATTTTAAA
9843 ATTTTATTATT-TTTTTATTTT
1 ATTTTATTATTATTTTTATTTT
*
9864 ATTTTATTCTTATTTTTATTTT
1 ATTTTATTATTATTTTTATTTT
9886 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (22 bp):
ATTTTATTATTATTTTTATTTT
Found at i:9876 original size:6 final size:5
Alignment explanation
Indices: 9843--9885 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
9833 AAATTTTAAA
*
9843 ATTTT ATTATT TTTTT ATTTT ATTTT ATTCTT ATTTTT ATTTT
1 ATTTT ATT-TT ATTTT ATTTT ATTTT ATT-TT A-TTTT ATTTT
9886 TAATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 21 0.64
6 10 0.30
7 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:9886 original size:6 final size:6
Alignment explanation
Indices: 9844--9893 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
9834 AATTTTAAAA
* *
9844 TTTTAT TATT-T TTTTA- TTTTA- TTTTAT TCTTAT TTTTAT TTTTAAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT
9890 TTTT
1 TTTT
9894 TAATTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 14 0.38
6 17 0.46
7 6 0.16
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:11328 original size:11 final size:12
Alignment explanation
Indices: 11314--11427 Score: 75
Period size: 11 Copynumber: 9.9 Consensus size: 12
11304 TATTTTTTTT
11314 ATTTTAA-TTAA
1 ATTTTAATTTAA
11325 ATTTTAATTTAA
1 ATTTTAATTTAA
*
11337 A-TTTAA-ATAA
1 ATTTTAATTTAA
11347 ACTTTTAATTTAA
1 A-TTTTAATTTAA
*
11360 A-TTTAA-ATAA
1 ATTTTAATTTAA
11370 A-TTTAATTTAA
1 ATTTTAATTTAA
* *
11381 ATATATATTTTAA
1 AT-TTTAATTTAA
*
11394 A---TATTTTAA
1 ATTTTAATTTAA
*
11403 ATATTAATTTAA
1 ATTTTAATTTAA
11415 TTATTTTAATTTA
1 --ATTTTAATTTA
11428 TTTAATTTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
9 9 0.11
10 13 0.16
11 21 0.25
12 17 0.20
13 13 0.16
14 10 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTTAATTTAA
Found at i:11335 original size:5 final size:5
Alignment explanation
Indices: 11311--11443 Score: 56
Period size: 5 Copynumber: 25.2 Consensus size: 5
11301 TGATATTTTT
* * * *
11311 TTTAT TTTAA TTAAA TTTTAA TTTAAA TTTAA ATAAA CTTTTAA TTTAAA
1 TTTAA TTTAA TTTAA -TTTAA TTT-AA TTTAA TTTAA --TTTAA TTT-AA
* * * * *
11361 TTTAA ATAAA TTTAA TTTAAA TATATAT TTTAA -ATAT TTTAAA TATTAA
1 TTTAA TTTAA TTTAA TTT-AA T-T-TAA TTTAA TTTAA TTT-AA T-TTAA
* *
11410 TTTAA -TTAT TTTAA TTT-A TTTAA TTTAT TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
11444 AAAAAAATCA
Statistics
Matches: 94, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
4 9 0.10
5 53 0.56
6 23 0.24
7 8 0.09
8 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:11340 original size:23 final size:22
Alignment explanation
Indices: 11316--11382 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 22
11306 TTTTTTTTAT
*
11316 TTTAATTAAATTTTAATTTAAA
1 TTTAAATAAATTTTAATTTAAA
11338 TTTAAATAAACTTTTAATTTAAA
1 TTTAAATAAA-TTTTAATTTAAA
11361 TTTAAATAAA-TTTAATTTAAA
1 TTTAAATAAATTTTAATTTAAA
11382 T
1 T
11383 ATATATTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
21 12 0.28
22 9 0.21
23 22 0.51
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAATAAATTTTAATTTAAA
Found at i:11341 original size:6 final size:6
Alignment explanation
Indices: 11321--11382 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
11311 TTTATTTTAA
* *
11321 TTAAAT TTTAAT TTAAAT TTAAA- -TAAACT TTTAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT
11367 -TAAAT TT-AAT TTAAAT
1 TTAAAT TTAAAT TTAAAT
11383 ATATATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
4 8 0.17
5 5 0.11
6 30 0.65
7 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:11399 original size:21 final size:20
Alignment explanation
Indices: 11375--11432 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
11365 AATAAATTTA
*
11375 ATTTAAATATATATTTTAAAT
1 ATTTAAATAT-TAATTTAAAT
*
11396 ATTTTAAATATTAATTTAATT
1 A-TTTAAATATTAATTTAAAT
*
11417 ATTTTAAT-TT-ATTTAA
1 ATTTAAATATTAATTTAA
11433 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 6 0.18
21 10 0.30
22 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAAATATTAATTTAAAT
Found at i:11403 original size:22 final size:21
Alignment explanation
Indices: 11376--11423 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
11366 ATAAATTTAA
*
11376 TTTAAATATATATTTTAAATAT
1 TTTAAATAT-TAATTTAAATAT
*
11398 TTTAAATATTAATTTAATTAT
1 TTTAAATATTAATTTAAATAT
11419 TTTAA
1 TTTAA
11424 TTTATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAAATATTAATTTAAATAT
Found at i:11513 original size:14 final size:13
Alignment explanation
Indices: 11494--11536 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
11484 AATCGATAAA
11494 AATAAATTAAATT
1 AATAAATTAAATT
*
11507 AACTAAATTAATTT
1 AA-TAAATTAAATT
11521 AATCAAATT-AATT
1 AAT-AAATTAAATT
11534 AAT
1 AAT
11537 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (13 bp):
AATAAATTAAATT
Done.