Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3488
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: 57407
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:13257 original size:51 final size:51
Alignment explanation
Indices: 13192--13361 Score: 158
Period size: 50 Copynumber: 3.3 Consensus size: 51
13182 GATGAAAAAG
13192 GAAAAGAAAGAAAAAAAAAAGCTCTCAT-TTGTTCTTGGAACGAATAAAGAA
1 GAAAAGAAA-AAAAAAAAAAGCTCTCATGTTGTTCTTGGAACGAATAAAGAA
* *
13243 GAAAAG--AAGAAAAAAAAGCTTCTCAATGTTGTT-TTGGCA-GAATAGAAGAAAA
1 GAAAAGAAAAAAAAAAAAAGC-TCTC-ATGTTGTTCTTGGAACGAATA-AAG--AA
* *
13295 AAAAAGATGAAAAAAAAGATAAAGCTCTCATGTTGTTCTTGGACCGAAT--AGAA
1 GAAAAGA--AAAAAAAA-A-AAAGCTCTCATGTTGTTCTTGGAACGAATAAAGAA
13348 G-AAAGAAAAAAAAA
1 GAAAAGAAAAAAAAA
13362 GGAAAAAGGC
Statistics
Matches: 98, Mismatches: 7, Indels: 29
0.73 0.05 0.22
Matches are distributed among these distances:
48 11 0.11
49 10 0.10
50 18 0.18
51 11 0.11
52 12 0.12
53 2 0.02
55 2 0.02
56 14 0.14
57 9 0.09
58 9 0.09
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (51 bp):
GAAAAGAAAAAAAAAAAAAGCTCTCATGTTGTTCTTGGAACGAATAAAGAA
Found at i:13368 original size:58 final size:58
Alignment explanation
Indices: 13257--13368 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
13247 AGAAGAAAAA
* *
13257 AAAGCTTCTCAATGTTGTTTTGGCAGAATAGAAGAAAAAAAAAGATGAAAAAAAAGAT
1 AAAGCTTCTCAATGTTGTTTTGGCAGAATAGAAGAAAAAAAAAAAAGAAAAAAAAGAT
* *
13315 AAAGC-TCTC-ATGTTGTTCTTGGACCGAATAGAAGAAAGAAAAAAAAAGGAAAAA
1 AAAGCTTCTCAATGTTGTT-TTGG-CAGAATAGAAGAAA-AAAAAAAAAGAAAAAA
13369 GGCTTTGAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 8 0.17
57 8 0.17
58 18 0.38
59 13 0.28
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.21
Consensus pattern (58 bp):
AAAGCTTCTCAATGTTGTTTTGGCAGAATAGAAGAAAAAAAAAAAAGAAAAAAAAGAT
Found at i:14727 original size:39 final size:40
Alignment explanation
Indices: 14641--14866 Score: 271
Period size: 40 Copynumber: 5.6 Consensus size: 40
14631 AGTGGACTAG
* *
14641 TCCGGGCTTAAGTCCCGAA-GCATTTGTGCAATGTTATTACA
1 TCCGGGC-TAAGTCCCGAAGGCATTTGTGCGA-GTTATTATA
*
14682 TCCGGGCTAAGTCCCGAA-GCATTTGTGCGAGTTATTACA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
* *
14721 TCCGGGCTAAGTCCCAAAGGCATTTTGTAGCGAGCTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCA-TTTGT-GCGAG-TTATTATA
*
14764 TCCGGGCTAAGTCCCAAAGGCATTTGGTGCGAG-TATTATA
1 TCCGGGCTAAGTCCCGAAGGCATTT-GTGCGAGTTATTATA
* *
14804 TCCGGCCTAAGTCCCGAAGGCATTGGTGCGAGTTA-TATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
* *
14843 TCTGGGCCTATGTCCCGAAGGCAT
1 TCCGGG-CTAAGTCCCGAAGGCAT
14867 GAGCGAGTAG
Statistics
Matches: 167, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
39 41 0.25
40 71 0.43
41 12 0.07
42 13 0.08
43 30 0.18
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
Found at i:14807 original size:83 final size:79
Alignment explanation
Indices: 14649--14866 Score: 244
Period size: 83 Copynumber: 2.7 Consensus size: 79
14639 AGTCCGGGCT
* * * *
14649 TAAGTCCCGAA-GCATTTGTGCAATGTTATTACATCCGGGCTAAGTCCCGAA-GCATTTGTGCGA
1 TAAGTCCCAAAGGCATTGGTGCGA-GTTA-TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGA
*
14712 GTTATTACATCCGGGC
64 GTTATTACATCCGGCC
* *
14728 TAAGTCCCAAAGGCATTTTGTAGCGAGCTTACTATATCCGGGCTAAGTCCCAAAGGCATTTGGTG
1 TAAGTCCCAAAGGCA-TTGGT-GCGAG-TTA-TATATCCGGGCTAAGTCCCGAAGGCATTT-GTG
*
14793 CGAG-TATTATATCCGGCC
61 CGAGTTATTACATCCGGCC
* * *
14811 TAAGTCCCGAAGGCATTGGTGCGAGTTATATATCTGGGCCTATGTCCCGAAGGCAT
1 TAAGTCCCAAAGGCATTGGTGCGAGTTATATATCCGGG-CTAAGTCCCGAAGGCAT
14867 GAGCGAGTAG
Statistics
Matches: 120, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
79 19 0.16
80 21 0.17
81 11 0.09
82 30 0.25
83 32 0.27
84 7 0.06
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (79 bp):
TAAGTCCCAAAGGCATTGGTGCGAGTTATATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
TATTACATCCGGCC
Found at i:14864 original size:123 final size:123
Alignment explanation
Indices: 14641--14866 Score: 307
Period size: 123 Copynumber: 1.8 Consensus size: 123
14631 AGTGGACTAG
* * *
14641 TCCGGGCTTAAGTCCCGAAGCATTTGTGCAATGTTATTACATCCGGGCTAAGTCCCGAAGCATTT
1 TCCGGGCTTAAGTCCCAAAGCATTTGTGCAATGTTATTACATCCGGCCTAAGTCCCGAAGCATTG
14706 GTGCGAGTTATTACATCCGGGCTAAGTCCCAAAGGCATTTTGTAGCGAGCTTACTATA
66 GTGCGAGTTATTACATCCGGGCTAAGTCCCAAAGGCATTTTGTAGCGAGCTTACTATA
* *
14764 TCCGGGC-TAAGTCCCAAAGGCATTTGGTGCGA-G-TATTATATCCGGCCTAAGTCCCGAAGGCA
1 TCCGGGCTTAAGTCCCAAA-GCATTT-GTGCAATGTTATTACATCCGGCCTAAGTCCCGAA-GCA
* * * *
14826 TTGGTGCGAGTTA-TATATCTGGGCCTATGTCCCGAAGGCAT
63 TTGGTGCGAGTTATTACATCCGGG-CTAAGTCCCAAAGGCAT
14867 GAGCGAGTAG
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
122 41 0.46
123 44 0.49
124 5 0.06
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (123 bp):
TCCGGGCTTAAGTCCCAAAGCATTTGTGCAATGTTATTACATCCGGCCTAAGTCCCGAAGCATTG
GTGCGAGTTATTACATCCGGGCTAAGTCCCAAAGGCATTTTGTAGCGAGCTTACTATA
Found at i:41932 original size:46 final size:46
Alignment explanation
Indices: 41831--41918 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
41821 TGTAACCCGC
* * *
41831 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGACGCTCCCAT
* * *
41877 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGACGCTC
41919 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGACGCTCCCAT
Found at i:44472 original size:21 final size:20
Alignment explanation
Indices: 44443--44488 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
44433 CGAAATGCAA
44443 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
44464 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
44484 T-AACC
1 TCAACC
44489 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:48674 original size:39 final size:39
Alignment explanation
Indices: 48630--48710 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
48620 AGTTTAACTT
*
48630 ATGCCTTCATATGTTGCACGGAACAATCTCTCTCCACTA
1 ATGCCTTCATATGTTGCACGCAACAATCTCTCTCCACTA
48669 ATGCCTTCATATGTTGCACGCAACAATCTCTCTCCACTA
1 ATGCCTTCATATGTTGCACGCAACAATCTCTCTCCACTA
48708 ATG
1 ATG
48711 TAGGTAGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (39 bp):
ATGCCTTCATATGTTGCACGCAACAATCTCTCTCCACTA
Found at i:52051 original size:29 final size:30
Alignment explanation
Indices: 51992--52052 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
51982 GCCTTTTGAA
* * * *
51992 AATATTTACAAAAATAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAACAAAATTTT
52022 AATATTTACAAAAAGAG-CAACAAAATTTT
1 AATATTTACAAAAAGAGACAACAAAATTTT
52051 AA
1 AA
52053 AAATAGTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACAAAATTTT
Done.