Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2760
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: 33143
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7906 original size:40 final size:40
Alignment explanation
Indices: 7832--8036 Score: 272
Period size: 40 Copynumber: 5.2 Consensus size: 40
7822 TGGATGATAA
* * *
7832 CGAAGGCATTTGTGCTAGTGACTA-ATTCCAGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
*
7872 CGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
7912 CGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* *
7952 CGAAGGCATTGGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * * *
7992 CGAAGGCATTTGAGTGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
8031 CGAAGG
1 CGAAGG
8037 TACTTGGTTT
Statistics
Matches: 149, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 16 0.11
40 132 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:17858 original size:21 final size:19
Alignment explanation
Indices: 17811--17850 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17801 TAACCCTAGG
17811 TTAATTAATTAAAATCTCT
1 TTAATTAATTAAAATCTCT
17830 TTAATTAATTAAAATCTCT
1 TTAATTAATTAAAATCTCT
17849 TT
1 TT
17851 CTAATTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTAATTAAAATCTCT
Found at i:19005 original size:49 final size:49
Alignment explanation
Indices: 18936--19108 Score: 156
Period size: 49 Copynumber: 3.6 Consensus size: 49
18926 TGACATGTGT
* *
18936 CAGTGTAAGACCTCTCTGGGACATGGCATCGACGC-CAATAGAT-AAGGGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCAATAGATGAA-AGC
* * * * * **
18985 CAGTGTAAAACCTGTTTGGGACACGGCATCGACCTCGATATATGAAATT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
* ** **
19034 CAGTGTAAGACCTGTCTGGGACATGGCATCGACTTTGAT-G-TGCTAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
*
19081 GAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
19109 GTTGGCATCT
Statistics
Matches: 101, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
47 14 0.14
48 16 0.16
49 69 0.68
50 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
Found at i:21791 original size:28 final size:27
Alignment explanation
Indices: 21705--21794 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
21695 GTGACAGAGT
*
21705 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
21734 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
21761 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
21789 CACCAG
1 CACCAG
21795 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:21947 original size:28 final size:28
Alignment explanation
Indices: 21900--21963 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
21890 AAATTAACCC
*
21900 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
21928 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
21956 TAGGGGTA
1 TAGGGGTA
21964 CTCTAGTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:24323 original size:40 final size:40
Alignment explanation
Indices: 24246--24466 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
24236 ACCCAAGTAT
* *
24246 CTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
24285 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
24325 CTTCGGGACTTAGCCCGGATATAGTCACTGGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
24365 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
24405 CTTCGGATCTTAGTCCGGATATAGTCACTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
24445 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
24467 CATTCGAATA
Statistics
Matches: 162, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 147 0.91
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Done.