Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 141 of 141
Found at i:42755871 original size:33 final size:33
Alignment explanation
Indices: 42755833--42755926 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 33
42755823 GATTACTCAC
*
42755833 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTTGATTTCTTTT-CAGACTCTCTTTCTTT
*
42755866 TTCACTTGATTTC-TTT-AGACTCTTTTTCTTT
1 TTCACTTGATTTCTTTTCAGACTCTCTTTCTTT
42755897 TTCACTTGATTTCTTTTCA-AGCTCTCTTTC
1 TTCACTTGATTTCTTTTCAGA-CTCTCTTTC
42755927 AATTTCTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
31 27 0.50
32 4 0.07
33 19 0.35
34 4 0.07
ACGTcount: A:0.13, C:0.24, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTTGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:42755915 original size:15 final size:16
Alignment explanation
Indices: 42755859--42755913 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
42755849 ACAGACTCTC
42755859 TTTCTTTTTCACTTGA
1 TTTCTTTTTCACTTGA
** *
42755875 TTTC-TTTAGACTCT-T
1 TTTCTTTTTCACT-TGA
42755890 TTTCTTTTTCACTTGA
1 TTTCTTTTTCACTTGA
42755906 TTTCTTTT
1 TTTCTTTT
42755914 CAAGCTCTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.11, C:0.18, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTCTTTTTCACTTGA
Found at i:42755953 original size:27 final size:27
Alignment explanation
Indices: 42755923--42756009 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
42755913 TCAAGCTCTC
*
42755923 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTC-CATTTTCTT
* *
42755950 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTC-CATTTTCTT
42755979 TTTCAATTTTCTTTTCTT-CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCCATTTTCTT
42756006 TTTC
1 TTTC
42756010 TCTCACTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 25 0.49
29 18 0.35
30 8 0.16
ACGTcount: A:0.11, C:0.18, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCCATTTTCTT
Found at i:42755964 original size:17 final size:18
Alignment explanation
Indices: 42755941--42755983 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
42755931 TCTTTTTTCG
* *
42755941 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
42755959 -TTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
42755976 CTTTTTCA
1 CTTTTTCA
42755984 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:42755985 original size:29 final size:27
Alignment explanation
Indices: 42755944--42756009 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
42755934 TTTTTCGCTT
42755944 TTTCTTTTTCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
42755973 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
42756000 TTTCTTTTTC
1 TTTCTTTTTC
42756010 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
29 16 0.46
30 5 0.14
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:42755993 original size:12 final size:12
Alignment explanation
Indices: 42755944--42756042 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
42755934 TTTTTCGCTT
42755944 TTTCTTTTTCAA
1 TTTCTTTTTCAA
42755956 TTT-TTTTTC-A
1 TTTCTTTTTCAA
42755966 -TTC----TCAA
1 TTTCTTTTTCAA
42755973 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
42755985 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
42756000 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
42756012 TCACTTTTTCGA
1 TTTCTTTTTCAA
42756024 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
42756036 TCTCTTT
1 TTTCTTT
42756043 CTCCTTTTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 3 0.05
9 2 0.03
10 1 0.02
11 6 0.09
12 33 0.50
13 7 0.11
14 7 0.11
15 4 0.06
ACGTcount: A:0.12, C:0.20, G:0.01, T:0.67
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:42756051 original size:24 final size:24
Alignment explanation
Indices: 42755966--42756052 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
42755956 TTTTTTTTCA
* *
42755966 TTCTCAATTTCTTTTTCAATTTTCTT
1 TTCTCATTTTCTTTTTCAA-TCTC-T
** *
42755992 TTCTTCATTTTCTTTTTCTCTCACT
1 TTC-TCATTTTCTTTTTCAATCTCT
*
42756017 TTTTCGA-TTTCTTTTTCAATCTCT
1 TTCTC-ATTTTCTTTTTCAATCTCT
*
42756041 TTCTCCTTTTCT
1 TTCTCATTTTCT
42756053 CGCTCAATGG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
24 25 0.53
25 4 0.09
26 5 0.11
27 13 0.28
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.64
Consensus pattern (24 bp):
TTCTCATTTTCTTTTTCAATCTCT
Found at i:42757755 original size:10 final size:10
Alignment explanation
Indices: 42757739--42757796 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
42757729 CAACTCCGAC
42757739 CAGCTCAATT
1 CAGCTCAATT
* *
42757749 GAGCTCATTT
1 CAGCTCAATT
42757759 CAGCTCAA-T
1 CAGCTCAATT
42757768 CGAGCTCAATT
1 C-AGCTCAATT
*
42757779 TAGCTACAATT
1 CAGCT-CAATT
42757790 CAGCTCA
1 CAGCTCA
42757797 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:42757762 original size:20 final size:20
Alignment explanation
Indices: 42757739--42757799 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
42757729 CAACTCCGAC
42757739 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
42757759 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
42757780 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
42757800 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:42759160 original size:14 final size:14
Alignment explanation
Indices: 42759141--42759189 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
42759131 CAAAAAAATC
42759141 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
* *
42759155 AAAAAAAATTTGATTG
1 AAAAAAAATTCGA--A
42759171 AAAAAAAATTC-AA
1 AAAAAAAATTCGAA
42759184 AAAAAA
1 AAAAAA
42759190 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 6 0.21
14 12 0.41
15 1 0.03
16 10 0.34
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:42762252 original size:10 final size:10
Alignment explanation
Indices: 42762236--42762293 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
42762226 CAACTCCGAC
42762236 CAGCTCAATT
1 CAGCTCAATT
* *
42762246 GAGCTCATTT
1 CAGCTCAATT
42762256 CAGCTCAA-T
1 CAGCTCAATT
42762265 CGAGCTCAATT
1 C-AGCTCAATT
*
42762276 TAGCTACAATT
1 CAGCT-CAATT
42762287 CAGCTCA
1 CAGCTCA
42762294 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:42762259 original size:20 final size:20
Alignment explanation
Indices: 42762236--42762296 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
42762226 CAACTCCGAC
42762236 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
42762256 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
42762277 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
42762297 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:42764439 original size:29 final size:29
Alignment explanation
Indices: 42764406--42764474 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
42764396 ATGTATTAGT
*
42764406 TTAGGACATATTTAAAACACTTGAA-TAAA
1 TTAGGACATATTTAAAACACTTAAACT-AA
42764435 TTAGGACATATTTAAAACACTTAAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
42764464 TTAGGACATAT
1 TTAGGACATAT
42764475 CTAATTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACTTAAACTAA
Found at i:42769500 original size:21 final size:21
Alignment explanation
Indices: 42769476--42769516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42769466 AAAAGAAAAA
42769476 GAGAAATGAAAG-AAAAAGAGG
1 GAGAAA-GAAAGCAAAAAGAGG
*
42769497 GAGAGAGAAAGCAAAAAGAG
1 GAGAAAGAAAGCAAAAAGAG
42769517 TTTGAGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.02
Consensus pattern (21 bp):
GAGAAAGAAAGCAAAAAGAGG
Found at i:42784286 original size:18 final size:17
Alignment explanation
Indices: 42784250--42784304 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
42784240 TCTCTTTTCA
*
42784250 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
*
42784267 TTCTTTTTTTTATGATTT
1 TTCTTTTTTTT-TGAATT
* *
42784285 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
42784302 TTC
1 TTC
42784305 GCTCTTTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:42786548 original size:11 final size:12
Alignment explanation
Indices: 42786520--42786553 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
42786510 ATGCAATTTT
42786520 TTTTTCTTTTCAA
1 TTTTT-TTTTCAA
42786533 TTTTTTTTTCAA
1 TTTTTTTTTCAA
42786545 TTTTTTTTT
1 TTTTTTTTT
42786554 TGGACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:42786549 original size:13 final size:13
Alignment explanation
Indices: 42786519--42786554 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
42786509 TATGCAATTT
42786519 TTTTTTCTTTTCAA
1 TTTTTT-TTTTCAA
42786533 -TTTTTTTTTCAA
1 TTTTTTTTTTCAA
42786545 TTTTTTTTTT
1 TTTTTTTTTT
42786555 GGACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:42791136 original size:18 final size:17
Alignment explanation
Indices: 42791100--42791154 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
42791090 TCTCTTTTCA
*
42791100 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
*
42791117 TTCTTTTTTTTATGATTT
1 TTCTTTTTTTT-TGAATT
* *
42791135 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
42791152 TTC
1 TTC
42791155 GCTCTTTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:42797704 original size:21 final size:21
Alignment explanation
Indices: 42797655--42797721 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
42797645 CCTCTTTGAA
* * *
42797655 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
42797678 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
42797699 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
42797720 CC
1 CC
42797722 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:42798057 original size:12 final size:13
Alignment explanation
Indices: 42798020--42798054 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
42798010 ATAGGTGCGT
*
42798020 AAAAAAAAGTTCGA
1 AAAAAAAAATT-GA
42798034 AAAAAAAAATTGA
1 AAAAAAAAATTGA
42798047 AAAAAAAA
1 AAAAAAAA
42798055 TTGCATACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTGA
Done.