Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1826
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: 19016
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5923 original size:19 final size:20
Alignment explanation
Indices: 5899--5936 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5889 GGTACCACCA
5899 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
5918 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
5937 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:6323 original size:93 final size:92
Alignment explanation
Indices: 6165--6334 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 92
6155 GCCCCTAAGT
* *
6165 GAACTCGGACTCAACTCAACGAGCTGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
6230 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* *
6257 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCT-GGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
6322 CGAGTTCGGATGC
65 CGAGTTCGGATGC
6335 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 24 0.33
93 49 0.67
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:6324 original size:46 final size:46
Alignment explanation
Indices: 6160--6331 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
6150 AACCCGCCCC
* * *
6160 TAAGTGAACTCGGACTCAACTCAACGAGCT-GGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
6205 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
6253 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
6298 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
6332 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 30 0.28
46 31 0.29
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:6350 original size:46 final size:46
Alignment explanation
Indices: 6159--6343 Score: 150
Period size: 45 Copynumber: 4.0 Consensus size: 46
6149 TAACCCGCCC
* * * * * *
6159 CTAAGTGAACTCGGACTCAACTCAACGAGCTGGGCGTTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
*
6205 -TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCAT
* * * * *
6252 CTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCAT
6298 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
6343 C
1 C
6344 CTAGTGACAT
Statistics
Matches: 111, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
43 1 0.01
44 11 0.10
45 32 0.29
46 30 0.27
47 30 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
Found at i:6782 original size:29 final size:29
Alignment explanation
Indices: 6750--6805 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
6740 ATTTAATACG
6750 AACTTTAAAAAAATTACACTTTTGCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCTA
*** *
6779 AACTTTTGCATAATTACACTTTTGCCC
1 AACTTTAAAAAAATTACACTTTTGCCC
6806 CTAGGCTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
AACTTTAAAAAAATTACACTTTTGCCCTA
Found at i:7920 original size:39 final size:39
Alignment explanation
Indices: 7872--7950 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
7862 CTTAACATTA
**
7872 ATTCAAGCTATATTGGGCATATAATTTATTTCATAATTT
1 ATTCAAGCTATATCAGGCATATAATTTATTTCATAATTT
*
7911 ATTCAAGCTATATCAGGCATATAATTTATTTCATACTTT
1 ATTCAAGCTATATCAGGCATATAATTTATTTCATAATTT
7950 A
1 A
7951 AACATTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (39 bp):
ATTCAAGCTATATCAGGCATATAATTTATTTCATAATTT
Found at i:12372 original size:47 final size:47
Alignment explanation
Indices: 12254--12426 Score: 189
Period size: 47 Copynumber: 3.7 Consensus size: 47
12244 TAGGGGTTGA
* *
12254 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* *
12302 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--AG
* * *
12347 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAAC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
*
12394 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
12427 TAGGGGCGGG
Statistics
Matches: 108, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
43 6 0.06
45 32 0.30
46 30 0.28
47 34 0.31
48 1 0.01
49 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAAG
Found at i:12423 original size:92 final size:93
Alignment explanation
Indices: 12254--12423 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 93
12244 TAGGGGTTGA
* *
12254 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
12319 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
12347 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
12411 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12424 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 40 0.55
93 33 0.45
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.