Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold893
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: 11144
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Found at i:1472 original size:47 final size:47
Alignment explanation
Indices: 1418--1610 Score: 287
Period size: 47 Copynumber: 4.1 Consensus size: 47
1408 TAGGATTTTC
** * *
1418 TGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCAA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
*
1465 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCCA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
* *
1512 TGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
* * * *
1559 TGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTAA
1 TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
1606 TGTGA
1 TGTGA
1611 AATATGTATG
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
TGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
Found at i:1925 original size:37 final size:37
Alignment explanation
Indices: 1817--1925 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
1807 GGAAATATAT
*
1817 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
1854 TCCGGGTAAGACTCGATGACTACATGAGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
1891 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
1926 CGTCTGAGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:3108 original size:39 final size:39
Alignment explanation
Indices: 3065--3270 Score: 290
Period size: 39 Copynumber: 5.3 Consensus size: 39
3055 GTGTGAGATA
*
3065 TATATCCGGGCTAATTCCCGAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * *
3104 TATATCTGAGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* *
3143 TATATCCGAGCTAAGTCCCAAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* *
3182 TATACCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * *
3221 TATAT-CGAGGCTAAGTCTCGACGGC-TTTGTGCTGGTAT
1 TATATCCG-GGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
3259 TATATCCGGGCT
1 TATATCCGGGCT
3271 TAAAGTCCTG
Statistics
Matches: 149, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
38 22 0.15
39 127 0.85
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
Found at i:9893 original size:39 final size:38
Alignment explanation
Indices: 9783--9976 Score: 258
Period size: 37 Copynumber: 5.2 Consensus size: 38
9773 GTGTGAGATA
*
9783 TATATCCGGGCTAATTCCCGAAGGCATT-GTGCTGGTGT
1 TATATCC-GGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
9821 TATATCTGGCTAAGT-CCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
9858 TATATCCGAGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
1 TATATCCG-GCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
9897 TATACCCGGCTAAGT-CCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * *
9934 T-TAT-CGGCTAAGTCTCG-AGGC-TTTGTGCTGGTAT
1 TATATCCGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
9968 TATATCCGG
1 TATATCCGG
9977 GCTTAAAGTC
Statistics
Matches: 140, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
34 12 0.09
35 16 0.11
36 18 0.13
37 46 0.33
38 20 0.14
39 28 0.20
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (38 bp):
TATATCCGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
Found at i:9910 original size:76 final size:74
Alignment explanation
Indices: 9783--9976 Score: 259
Period size: 76 Copynumber: 2.6 Consensus size: 74
9773 GTGTGAGATA
* * * *
9783 TATATCCGGGCTAATTCCCGAAGGCATTGTGCTGGTGTTATATCTGGCTAAGTCCGAAGGCATTC
1 TATATCC-GGCTAAGTCCCAAAGGCATTGTGCTGGTGTTATACCCGGCTAAGTCCGAAGGCATTC
9848 GTGCTGGTGT
65 GTGCTGGTGT
9858 TATATCCGAGCTAAGTCCCAAAGGCATTCGTGCTGGTGTTATACCCGGCTAAGTCCGAAGGCATT
1 TATATCCG-GCTAAGTCCCAAAGGCATT-GTGCTGGTGTTATACCCGGCTAAGTCCGAAGGCATT
9923 CGTGCTGGTGT
64 CGTGCTGGTGT
* * * * *
9934 T-TAT-CGGCTAAGTCTC-GAGGCTTTGTGCTGGTATTATATCCGG
1 TATATCCGGCTAAGTCCCAAAGGCATTGTGCTGGTGTTATACCCGG
9977 GCTTAAAGTC
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
71 17 0.16
72 6 0.06
73 9 0.08
74 3 0.03
75 27 0.25
76 46 0.43
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (74 bp):
TATATCCGGCTAAGTCCCAAAGGCATTGTGCTGGTGTTATACCCGGCTAAGTCCGAAGGCATTCG
TGCTGGTGT
Done.