Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1677
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: 24214
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:7772 original size:41 final size:40
Alignment explanation
Indices: 7577--7795 Score: 295
Period size: 40 Copynumber: 5.5 Consensus size: 40
7567 AAACCAAGTA
* * *
7577 CCTTCGGGATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
7616 CCTTCGGGACTTAGCCC-GATTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-TATAGTAACTCGCACAAATG
*
7656 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
7696 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
7736 CCTTTCTGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CC-TTC-GGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
7777 CCTTCGGAACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
7796 TTATCATCCG
Statistics
Matches: 165, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
39 18 0.11
40 110 0.67
41 34 0.21
42 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:13473 original size:27 final size:27
Alignment explanation
Indices: 13443--13494 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13433 ACAAGTGAGG
13443 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
13470 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
13495 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:15969 original size:51 final size:48
Alignment explanation
Indices: 15789--15975 Score: 205
Period size: 50 Copynumber: 3.8 Consensus size: 48
15779 GCCGAAGCTA
** * *
15789 TCTGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-ACAG
* *
15838 TCTGGTACACGTAATAGCCTGCACTTAGTACTACACACGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CA-CAG
** * *
15888 TCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
*
15936 TTTTCGGGTACACATAGTAGCCTGCACTTAGTACTACACA
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
15976 TGCGACCTCA
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
47 2 0.02
48 2 0.02
49 36 0.31
50 41 0.35
51 36 0.31
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (48 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
Found at i:15973 original size:101 final size:99
Alignment explanation
Indices: 15800--15986 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 99
15790 CTGGTATGCA
* * *
15800 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAATAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAATAGCCTGCACTTA
*
15865 GTACTACACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* * *
15899 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACACATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAATAGCCTGCAC
*
15963 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
15987 AATAGATCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.39
101 43 0.56
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAATAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:17631 original size:13 final size:13
Alignment explanation
Indices: 17613--17639 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17603 TAAGTAATCA
17613 CACACGGGCGTGT
1 CACACGGGCGTGT
17626 CACACGGGCGTGT
1 CACACGGGCGTGT
17639 C
1 C
17640 CATGCCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:18000 original size:13 final size:13
Alignment explanation
Indices: 17969--18005 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17959 AAATATTTGA
17969 CTTGTTCTTAATT
1 CTTGTTCTTAATT
17982 -TGTGTTCTTAATT
1 CT-TGTTCTTAATT
17995 CTTGTT-TTAAT
1 CTTGTTCTTAAT
18006 ATTCCGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.27
13 15 0.68
14 1 0.05
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:20838 original size:79 final size:81
Alignment explanation
Indices: 20702--20886 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
20692 TTGAATGATG
*
20702 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
20766 TGTGTGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
20781 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20843 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
20861 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20887 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:20893 original size:40 final size:40
Alignment explanation
Indices: 20702--20886 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
20692 TTGAATGATG
* * * *
20702 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
20742 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
20782 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
20821 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
20862 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20887 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 34 0.27
40 82 0.66
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:20908 original size:79 final size:79
Alignment explanation
Indices: 20755--20919 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
20745 GGACTAAGAT
* * **
20755 CCGAAGGCATTTGTGTGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20820 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20834 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20897 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20913 CCGAAGG
1 CCGAAGG
20920 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.