Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2832
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: 31646
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1125 original size:39 final size:40
Alignment explanation
Indices: 1067--1210 Score: 184
Period size: 39 Copynumber: 3.6 Consensus size: 40
1057 CTCGCACAAG
* * * * *
1067 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1107 GCCTTC-GGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
1146 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
1187 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
1211 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 37 0.41
40 24 0.26
41 27 0.30
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:9116 original size:39 final size:40
Alignment explanation
Indices: 9071--9238 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
9061 CGGGGTTTAG
* * *
9071 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
9110 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
9150 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
9190 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
9231 CCGGATAT
1 CCGGATAT
9239 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:9221 original size:41 final size:40
Alignment explanation
Indices: 9094--9238 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
9084 CTCGCACAAG
* * * * *
9094 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
9134 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
9174 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
9215 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
9239 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:20878 original size:46 final size:45
Alignment explanation
Indices: 20719--20892 Score: 206
Period size: 46 Copynumber: 3.8 Consensus size: 45
20709 GGTTGAGCAT
* *
20719 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
*** * * * *
20764 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCAACGC
*
20809 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
*
20857 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20893 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
45 31 0.29
46 46 0.43
47 28 0.26
48 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:23837 original size:15 final size:15
Alignment explanation
Indices: 23798--23876 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
23788 GTATCTTGGG
*
23798 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
23813 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
23828 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
23842 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
23857 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
23871 TTTCTT
1 TTTCTT
23877 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:23861 original size:29 final size:29
Alignment explanation
Indices: 23789--23875 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
23779 CATAGTATCG
* * * *
23789 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
23819 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
23848 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
23876 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Done.