Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5279.1
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: 27345
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:319 original size:28 final size:28
Alignment explanation
Indices: 279--349 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
269 TTCCATTATA
* * *
279 CAATGTATTAGACTTTTTTTTATGGCTG
1 CAATGCATTAGACATTTTTTTATGACTG
307 CAATGCATTAGACATTTTTTTATGACTG
1 CAATGCATTAGACATTTTTTTATGACTG
*
335 CATTGCATTAGACAT
1 CAATGCATTAGACAT
350 AAACTTCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (28 bp):
CAATGCATTAGACATTTTTTTATGACTG
Found at i:4928 original size:40 final size:40
Alignment explanation
Indices: 4873--4984 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
4863 TATTCGGATG
4873 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
1 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* *
4913 ATATCCGGACTAAGATCCGAAGGCAATTGTGCTAGTTATT
1 ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
* ** *
4953 ATAACCGGGTTAAG-TCCCGAAGGCATTCGTGC
1 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGC
4985 GGGTTATTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 63 0.98
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (40 bp):
ATATCCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACT
Found at i:4991 original size:40 final size:40
Alignment explanation
Indices: 4889--5059 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
4879 GGACTAAGAT
* * * * **
4889 CCGAAGGCATTTGTGCTAGTTACTATATCCGGACTAAGAT-
1 CCGAAGGCATTCGTGCGAGTTATTATAACCGGGTTAAG-TC
*
4929 CCGAAGGCAATT-GTGCTAGTTATTATAACCGGGTTAAGTC
1 CCGAAGGC-ATTCGTGCGAGTTATTATAACCGGGTTAAGTC
*
4969 CCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTATAACCGGGTTAAGTC
* *
5009 CCGAAGGTATTCGTGCGGGTTATTAT-ACCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTATAACCGGGTTAAGTC
*
5048 CCAAAGGCATTC
1 CCGAAGGCATTC
5060 ATTCTAGTTG
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 27 0.23
40 89 0.75
41 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTATAACCGGGTTAAGTC
Found at i:8225 original size:38 final size:38
Alignment explanation
Indices: 8182--8257 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
8172 TCCATCCTTT
8182 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
8220 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
8258 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:9538 original size:40 final size:40
Alignment explanation
Indices: 9444--9588 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
9434 TACTCGAATG
*
9444 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* **
9485 ACATCCGAACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
9525 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
9565 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
9589 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.68
41 27 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:24051 original size:46 final size:46
Alignment explanation
Indices: 23956--24078 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 46
23946 TATCTGTGCT
*
23956 GATGCCATGTCCCAAACATGGTCTTACACTGACACATCTCATAGTC
1 GATGCCATGTCCCAAACATGGTCTTACACTGACACATCTCATAGCC
* *
24002 GATG-CATGTCCCAAACAT-GTCTTACACTAGCACTCGTCTCA-ATGCC
1 GATGCCATGTCCCAAACATGGTCTTACACT-G-ACACATCTCATA-GCC
*
24048 GATGCCATGTCCCAGACATGGTCTTACACTG
1 GATGCCATGTCCCAAACATGGTCTTACACTG
24079 GCTCTCATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
44 10 0.15
45 16 0.24
46 18 0.26
47 14 0.21
48 10 0.15
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (46 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGACACATCTCATAGCC
Done.