Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1332
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: 16007
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:293 original size:17 final size:17
Alignment explanation
Indices: 271--308 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
261 TATTTGAATA
271 TTACAGGAACGGCATGC
1 TTACAGGAACGGCATGC
288 TTACAGGAACGGCATGC
1 TTACAGGAACGGCATGC
305 TTAC
1 TTAC
309 TCTTCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (17 bp):
TTACAGGAACGGCATGC
Found at i:3002 original size:29 final size:24
Alignment explanation
Indices: 2943--2991 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2933 TGTGCTATAT
2943 ATATCAATAGTATATGAAATTTAA
1 ATATCAATAGTATATGAAATTTAA
*
2967 ATATCAATAGTGTATGAAATTTAA
1 ATATCAATAGTATATGAAATTTAA
2991 A
1 A
2992 GCTTGAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (24 bp):
ATATCAATAGTATATGAAATTTAA
Found at i:3360 original size:2 final size:2
Alignment explanation
Indices: 3353--3386 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3343 CAGTCGCCCA
3353 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3387 ACTGAAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5066 original size:24 final size:23
Alignment explanation
Indices: 5022--5066 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5012 TATTTTAAAA
**
5022 TTTGAATTATTTTAATGTTATTT
1 TTTGAATTATTTTAAAATTATTT
*
5045 TTTGTATTATATTTAAAATTAT
1 TTTGAATTAT-TTTAAAATTAT
5067 CAAATTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTGAATTATTTTAAAATTATTT
Found at i:5801 original size:14 final size:14
Alignment explanation
Indices: 5782--5815 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5772 TTATATCGAG
**
5782 ATTTATATTTTTAT
1 ATTTATATTTAAAT
5796 ATTTATATTTAAAT
1 ATTTATATTTAAAT
5810 ATTTAT
1 ATTTAT
5816 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTATATTTAAAT
Found at i:6222 original size:24 final size:24
Alignment explanation
Indices: 6195--6244 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
6185 TTTTGGAAAG
*
6195 AAGAGATTGTAATTTTA-AAATTAA
1 AAGAGATT-AAATTTTATAAATTAA
* *
6219 AAGATATTAAATTTTATAATTTAA
1 AAGAGATTAAATTTTATAAATTAA
6243 AA
1 AA
6245 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
AAGAGATTAAATTTTATAAATTAA
Found at i:6232 original size:23 final size:24
Alignment explanation
Indices: 6205--6254 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6195 AAGAGATTGT
6205 AATTTTA-AAATTAAAAGATATTA
1 AATTTTATAAATTAAAAGATATTA
* **
6228 AATTTTATAATTTAAAATTTATTA
1 AATTTTATAAATTAAAAGATATTA
6252 AAT
1 AAT
6255 AATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATTTTATAAATTAAAAGATATTA
Found at i:6834 original size:13 final size:13
Alignment explanation
Indices: 6816--6881 Score: 53
Period size: 14 Copynumber: 5.0 Consensus size: 13
6806 AAACTAAAAG
6816 ATAATAAAAATTA
1 ATAATAAAAATTA
*
6829 ATAAT-AAAATTT
1 ATAATAAAAATTA
* *
6841 TTAATAAAAAATTT
1 ATAAT-AAAAATTA
*
6855 ATAATACAAAATAA
1 ATAATA-AAAATTA
* *
6869 AAAATTAAAATTA
1 ATAATAAAAATTA
6882 TTAAAATTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 10 0.24
13 12 0.29
14 20 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATAAAAATTA
Found at i:6853 original size:14 final size:14
Alignment explanation
Indices: 6826--6866 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6816 ATAATAAAAA
6826 TTAATAATAAAATTT
1 TTAATAA-AAAATTT
6841 TTAATAAAAAATTT
1 TTAATAAAAAATTT
* *
6855 ATAATACAAAAT
1 TTAATAAAAAAT
6867 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAATAAAAAATTT
Found at i:6889 original size:15 final size:14
Alignment explanation
Indices: 6869--6900 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
6859 TACAAAATAA
6869 AAAATTAAAATTATT
1 AAAATTAAAATT-TT
6884 AAAATTAAAATTTT
1 AAAATTAAAATTTT
6898 AAA
1 AAA
6901 TTTATTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTAAAATTTT
Found at i:7518 original size:20 final size:21
Alignment explanation
Indices: 7475--7529 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
7465 TCTCAAATAA
*
7475 AATTAAAAAAAATAAATTATTT
1 AATTAAATAAAATAAA-TATTT
7497 AATTAAATAAAATAAA-ATTT
1 AATTAAATAAAATAAATATTT
* *
7517 AAATAAATTAAAT
1 AATTAAATAAAAT
7530 TTAATTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 15 0.50
22 15 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTAAATAAAATAAATATTT
Found at i:7524 original size:15 final size:16
Alignment explanation
Indices: 7499--7533 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
7489 AATTATTTAA
7499 TTAAATAAAATAAAAT
1 TTAAATAAAATAAAAT
*
7515 TTAAAT-AAATTAAAT
1 TTAAATAAAATAAAAT
7530 TTAA
1 TTAA
7534 TTACATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATAAAATAAAAT
Found at i:7542 original size:35 final size:32
Alignment explanation
Indices: 7484--7552 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
7474 AAATTAAAAA
7484 AAATAAATTATTTAATTAAATAAAATAAAATTT
1 AAATAAATTATTTAATTAAAT-AAATAAAATTT
* *
7517 AAATAAATTAAATTTAATTACATAAATTAAATTT
1 AAATAAATT--ATTTAATTAAATAAATAAAATTT
7551 AA
1 AA
7553 TCCATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 9 0.28
34 12 0.38
35 11 0.34
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATAAATTATTTAATTAAATAAATAAAATTT
Found at i:8223 original size:19 final size:19
Alignment explanation
Indices: 8196--8239 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8186 AAGTGTATGT
**
8196 AATTAATTTTTTATAAATA
1 AATTAATTTAATATAAATA
* *
8215 AATTTATTTAATATAAATT
1 AATTAATTTAATATAAATA
8234 AATTAA
1 AATTAA
8240 ATTTTATTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAATTTAATATAAATA
Found at i:8266 original size:16 final size:18
Alignment explanation
Indices: 8236--8273 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
8226 TATAAATTAA
*
8236 TTAAATTTTATTTAAT-T
1 TTAAATTTTAATTAATCT
8253 TTAAA-TTTAATTAATCT
1 TTAAATTTTAATTAATCT
8270 TTAA
1 TTAA
8274 TCGAATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAATTTTAATTAATCT
Found at i:12676 original size:6 final size:6
Alignment explanation
Indices: 12665--12703 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
12655 TATTACTCTC
*
12665 TCTTTT TCTTTT CTCTTTT TTTTTT TCTTTT TCTTTT TC
1 TCTTTT TCTTTT -TCTTTT TCTTTT TCTTTT TCTTTT TC
12704 CGGGGTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:12681 original size:13 final size:13
Alignment explanation
Indices: 12663--12701 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
12653 TGTATTACTC
12663 TCTCTTTTTCTTT
1 TCTCTTTTTCTTT
12676 TCTCTTTTT-TTT
1 TCTCTTTTTCTTT
*
12688 TTTCTTTTTCTTT
1 TCTCTTTTTCTTT
12701 T
1 T
12702 TCCGGGGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TCTCTTTTTCTTT
Found at i:12970 original size:14 final size:14
Alignment explanation
Indices: 12951--13004 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
12941 CGAATAAGTC
12951 TTTATTTATATTTA
1 TTTATTTATATTTA
*
12965 TTTATTTATTTTTGA
1 TTTATTTATATTT-A
*
12980 GTT-TTTATATTTA
1 TTTATTTATATTTA
12993 GTTTATTT-TATT
1 -TTTATTTATATT
13005 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 1 0.03
14 26 0.79
15 6 0.18
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (14 bp):
TTTATTTATATTTA
Found at i:13012 original size:28 final size:28
Alignment explanation
Indices: 12955--13013 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
12945 TAAGTCTTTA
* **
12955 TTTATATTTATTTATTTATTTTTGAGTT
1 TTTATATTTATTTATTTATATTAAAGTT
*
12983 TTTATATTTAGTTTATTT-TATTAAATTT
1 TTTATATTTA-TTTATTTATATTAAAGTT
13011 TTT
1 TTT
13014 TGAAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (28 bp):
TTTATATTTATTTATTTATATTAAAGTT
Found at i:13023 original size:37 final size:35
Alignment explanation
Indices: 12951--13050 Score: 83
Period size: 38 Copynumber: 2.7 Consensus size: 35
12941 CGAATAAGTC
* * **
12951 TTTATTTATATTTATTTATTTATTTTTGAGTTTTTAT
1 TTTATTTAT-TTTATTAAATT-TTTTTGAAATTTTAT
12988 ATTTAGTTTATTTTATTAAATTTTTTTGAAATTTTAT
1 -TTTA-TTTATTTTATTAAATTTTTTTGAAATTTTAT
* *
13025 TTAAAATTTGATTTTATTATATTTTT
1 TT--TATTT-ATTTTATTAAATTTTT
13051 AAGTTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
36 2 0.04
37 16 0.31
38 29 0.56
39 5 0.10
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (35 bp):
TTTATTTATTTTATTAAATTTTTTTGAAATTTTAT
Found at i:13672 original size:19 final size:20
Alignment explanation
Indices: 13648--13692 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
13638 CCGCTTGAGT
13648 TTTATTTTTTATAA-TTAAA
1 TTTATTTTTTATAATTTAAA
13667 TTTA-TTTTTATAATTTAAA
1 TTTATTTTTTATAATTTAAA
*
13686 TTGATTT
1 TTTATTT
13693 AATTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 12 0.52
20 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTATTTTTTATAATTTAAA
Found at i:13769 original size:38 final size:38
Alignment explanation
Indices: 13690--13771 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
13680 TTTAAATTGA
*
13690 TTTAATTTAAAATATAATTATAAATTAAAATTTATTAT
1 TTTAATTTAAAATATAATTATAAATTAAAATATATTAT
*
13728 TTTAATTT-AAAT-TAATTATAAAAGTATTAAATATATT-T
1 TTTAATTTAAAATATAATTAT-AAA-T-TAAAATATATTAT
13766 TTTAAT
1 TTTAAT
13772 ACAAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 7 0.18
37 7 0.18
38 16 0.41
39 9 0.23
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (38 bp):
TTTAATTTAAAATATAATTATAAATTAAAATATATTAT
Done.