Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2717
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: 40229
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1197 original size:42 final size:44
Alignment explanation
Indices: 1127--1244 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 44
1117 TGGTTGAGCA
*
1127 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCAAATG
1 TCCG-ACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCAAACG
* ** *
1172 TCCGACTCG-TGAGTT-AGTCTGAGTTCTTTATGGATGCGAACG
1 TCCGACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCAAACG
*
1214 CCCGAGCTCGTTGAGTTGAGTCCGAG-TCACT
1 TCCGA-CTCGTTGAGTTGAGTCCGAGTTCACT
1245 TAGGGGGGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
42 26 0.43
43 10 0.16
44 14 0.23
45 11 0.18
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (44 bp):
TCCGACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCAAACG
Found at i:6945 original size:46 final size:46
Alignment explanation
Indices: 6893--7017 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
6883 GGTTGAGCGT
* *
6893 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * *
6939 CTGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
*
6985 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
7018 GGGGCGGGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:14013 original size:40 final size:40
Alignment explanation
Indices: 13958--14102 Score: 272
Period size: 40 Copynumber: 3.6 Consensus size: 40
13948 CGGATAATAA
13958 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
13998 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
14038 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
14078 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
14103 AGTGAGTAGC
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:19499 original size:40 final size:40
Alignment explanation
Indices: 19444--19519 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
19434 TATTCGGATG
*
19444 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTCACT
19484 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
19520 AGCTATGTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTCACT
Found at i:37035 original size:26 final size:26
Alignment explanation
Indices: 37006--37109 Score: 172
Period size: 26 Copynumber: 4.0 Consensus size: 26
36996 ATGCCCATCG
*
37006 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
37032 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* *
37058 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
*
37084 TGGAACATTTATCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
37110 ATTTGTACCA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
TGGAACATTTACCTAACCCATTATCA
Done.