Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3647
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: 50670
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:200 original size:30 final size:30
Alignment explanation
Indices: 166--262 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
156 AGCTCACTCC
166 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
196 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
226 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
256 TAGCTCA
1 TAGCTCA
263 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:1957 original size:11 final size:11
Alignment explanation
Indices: 1941--1982 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1931 AGGAAATTCG
1941 AAAAAAAATTT
1 AAAAAAAATTT
**
1952 AAAAAAAATCG
1 AAAAAAAATTT
*
1963 AAAAAAAAATT
1 AAAAAAAATTT
1974 AAAAAAAAT
1 AAAAAAAAT
1983 CGAAGTATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:1963 original size:22 final size:22
Alignment explanation
Indices: 1938--1986 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1928 AAGAGGAAAT
*
1938 TCGAAAAAAAATTTAAAAAAAA
1 TCGAAAAAAAAATTAAAAAAAA
1960 TCGAAAAAAAAATTAAAAAAAA
1 TCGAAAAAAAAATTAAAAAAAA
1982 TCGAA
1 TCGAA
1987 GTATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (22 bp):
TCGAAAAAAAAATTAAAAAAAA
Found at i:2938 original size:37 final size:37
Alignment explanation
Indices: 2887--2957 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
2877 CATTCTTGTA
2887 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
2924 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
2958 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:2957 original size:6 final size:6
Alignment explanation
Indices: 2897--2946 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
2887 AAGAGAAAAC
*
2897 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
2946 A
1 A
2947 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:3039 original size:11 final size:12
Alignment explanation
Indices: 3007--3037 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2997 TTGAGAGAAC
3007 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3019 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3031 TTGAAAA
1 TTGAAAA
3038 GCAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:5260 original size:30 final size:30
Alignment explanation
Indices: 5179--5261 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
5169 ATTTAGCTCA
*
5179 CTCACGAGCTAAACCTTAGCTCAACTTCAG
1 CTCACGAGCTAAAGCTTAGCTCAACTTCAG
* * ** * *
5209 CTTAGGAG-TTTAGCCTCAGCTCAACTTTAG
1 CTCACGAGCTAAAG-CTTAGCTCAACTTCAG
5239 CTCACGAGCTAAAGCTTAGCTCA
1 CTCACGAGCTAAAGCTTAGCTCA
5262 TTTTAGTTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (30 bp):
CTCACGAGCTAAAGCTTAGCTCAACTTCAG
Found at i:7143 original size:20 final size:20
Alignment explanation
Indices: 7097--7143 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
7087 AGCTTGTTTC
*
7097 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
7117 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
7137 CAGCTCA
1 CAGCTCA
7144 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:9749 original size:48 final size:47
Alignment explanation
Indices: 9670--9775 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
9660 GAGTGTCATG
*
9670 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
9718 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
9766 GAAAAAGAAA
1 GAAAAAGAAA
9776 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:11490 original size:20 final size:20
Alignment explanation
Indices: 11444--11490 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
11434 AGCTTGTTTA
*
11444 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
11464 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
11484 CAGCTCA
1 CAGCTCA
11491 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:18512 original size:12 final size:11
Alignment explanation
Indices: 18470--18512 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
18460 ACATTTTCTC
18470 TTCTTTCTTCAA
1 TTCTTT-TTCAA
18482 CTTCTTTTTCAA
1 -TTCTTTTTCAA
*
18494 TTTTTTTTCACA
1 TTCTTTTTCA-A
18506 TTCTTTT
1 TTCTTTT
18513 CACTCTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 9 0.33
12 12 0.44
13 6 0.22
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (11 bp):
TTCTTTTTCAA
Found at i:21561 original size:16 final size:19
Alignment explanation
Indices: 21526--21562 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
21516 TCTAATACTG
21526 TTTTACTACTAAAGTTCAC
1 TTTTACTACTAAAGTTCAC
21545 TTTTAC-AC-AAA-TTCAC
1 TTTTACTACTAAAGTTCAC
21561 TT
1 TT
21563 AATCCATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 2 0.11
19 6 0.33
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTACTACTAAAGTTCAC
Found at i:21888 original size:99 final size:100
Alignment explanation
Indices: 21772--21963 Score: 280
Period size: 101 Copynumber: 1.9 Consensus size: 100
21762 AGCTATCTGG
* *
21772 TACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG-TCT-GGTACACGTAGTAGCC
1 TACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-ACAGTTCTGGGTACACATAGTAGCC
*
21835 CGCACTTAGTACTACACACGTGACCTCACCATCTAA
65 CGCACTTAGTACTACACACGCGACCTCACCATCTAA
* * *
21871 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTTGGGTACACATAGTAGCC
1 TACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAG-TTCTGGGTACACATAGTAGCC
* *
21936 TGCACTTAGTACTACACATGCGACCTCA
65 CGCACTTAGTACTACACACGCGACCTCA
21964 GAATAGATCA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 4 0.05
99 36 0.44
100 2 0.02
101 40 0.49
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (100 bp):
TACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAGTTCTGGGTACACATAGTAGCCC
GCACTTAGTACTACACACGCGACCTCACCATCTAA
Found at i:23977 original size:30 final size:30
Alignment explanation
Indices: 23943--24039 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
23933 TAAACTAAAA
23943 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
23973 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
24003 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
24032 ATGAGCTA
1 -TGAGCTA
24040 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:25958 original size:30 final size:30
Alignment explanation
Indices: 25924--26022 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
25914 TAAACTAAAA
*
25924 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
* * * * *
25954 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTGAAGT
* * *
25984 TGACCTACGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
26013 ATGAGCTAAG
1 -TGAGCTAAG
26023 AGTGAGCTCA
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
Found at i:32485 original size:30 final size:30
Alignment explanation
Indices: 32400--32496 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
32390 TAAACTAAAA
* *
32400 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
32430 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
32460 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
32489 ATGAGCTA
1 -TGAGCTA
32497 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:33908 original size:20 final size:21
Alignment explanation
Indices: 33871--33918 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
33861 GAGCTGGATT
*
33871 GAGCTGAATTCTAGCTCAAAC
1 GAGCTGAATTCGAGCTCAAAC
**
33892 GAGCTGAA-TCGAGCTCAATT
1 GAGCTGAATTCGAGCTCAAAC
33912 GAGCTGA
1 GAGCTGA
33919 TGGGAGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (21 bp):
GAGCTGAATTCGAGCTCAAAC
Found at i:37977 original size:30 final size:31
Alignment explanation
Indices: 37942--38002 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
37932 GTTCAAACTC
*
37942 GTTTTCTTTTTCAATGTCTTTT-TTTATTTT
1 GTTTTCTTGTTCAATGTCTTTTCTTTATTTT
* * *
37972 GTTTTCTTGTTCACTTTCTTTTCTTTTTTTT
1 GTTTTCTTGTTCAATGTCTTTTCTTTATTTT
38003 CTTTCATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.07, C:0.13, G:0.07, T:0.74
Consensus pattern (31 bp):
GTTTTCTTGTTCAATGTCTTTTCTTTATTTT
Found at i:47889 original size:11 final size:10
Alignment explanation
Indices: 47864--47909 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
47854 AAAAAGGAAT
47864 GAGCTAAAAC
1 GAGCTAAAAC
*
47874 GAGCTAAATTC
1 GAGCTAAA-AC
*
47885 GAGCTCAAAC
1 GAGCTAAAAC
*
47895 AAGCTAAAAC
1 GAGCTAAAAC
47905 GAGCT
1 GAGCT
47910 CAAGTGAGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:47894 original size:21 final size:20
Alignment explanation
Indices: 47864--47912 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
47854 AAAAAGGAAT
* * *
47864 GAGCTAAAACGAGCTAAATTC
1 GAGCTCAAACAAGCTAAA-AC
47885 GAGCTCAAACAAGCTAAAAC
1 GAGCTCAAACAAGCTAAAAC
47905 GAGCTCAA
1 GAGCTCAA
47913 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.14
Consensus pattern (20 bp):
GAGCTCAAACAAGCTAAAAC
Found at i:48319 original size:8 final size:8
Alignment explanation
Indices: 48303--48347 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
48293 CTTCTTTTTC
*
48303 TTTTCTTT
1 TTTTATTT
48311 TTTTATTT
1 TTTTATTT
48319 TTTTATTT
1 TTTTATTT
* *
48327 TTTGAATTC
1 TTT-TATTT
48336 TTTTATTT
1 TTTTATTT
48344 TTTT
1 TTTT
48348 CAATATATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 25 0.81
9 6 0.19
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:48339 original size:17 final size:16
Alignment explanation
Indices: 48300--48346 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
48290 TCACTTCTTT
* *
48300 TTCTTTTCTTTTTTTA
1 TTCTTTTATTTTTTAA
*
48316 TTTTTTTATTTTTTGAA
1 TTCTTTTATTTTTT-AA
48333 TTCTTTTATTTTTT
1 TTCTTTTATTTTTT
48347 TCAATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (16 bp):
TTCTTTTATTTTTTAA
Done.