Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1057
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: 33732
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:897 original size:47 final size:47
Alignment explanation
Indices: 825--994 Score: 154
Period size: 46 Copynumber: 3.6 Consensus size: 47
815 GTTATTGTGG
** * * **
825 GCTAGTGTAAGATGTGTCTGGGACATGCATCGGCCA-C-ATTATGAGA
1 GCTAGTGTAAGACATGTCCGGGACATGCATCGGCCATCGA-GACAAGA
*
871 GCCTA-TGTAAGACCATGTCCGGGACATGGCATCGG-CATCGAGACAAGT
1 G-CTAGTGTAAGA-CATGTCCGGGACAT-GCATCGGCCATCGAGACAAGA
* *
919 GCTAGTGTAAGACATGTCCGGGACATGCATCGGCC-TTGAGACGTA-A
1 GCTAGTGTAAGACATGTCCGGGACATGCATCGGCCATCGAGAC-AAGA
* *
965 GCCAGTGTAAGACATGTCTGGGACATGCAT
1 GCTAGTGTAAGACATGTCCGGGACATGCAT
995 AAGTTAAGAC
Statistics
Matches: 104, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
46 49 0.47
47 35 0.34
48 19 0.18
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCCGGGACATGCATCGGCCATCGAGACAAGA
Found at i:10844 original size:93 final size:93
Alignment explanation
Indices: 10731--10902 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
10721 CGCCCATAAG
* *
10731 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10796 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
10824 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10889 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
10903 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:10899 original size:46 final size:46
Alignment explanation
Indices: 10724--10899 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
10714 TGTAACCCGC
* * *
10724 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
10770 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
10820 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10863 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
10900 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:17225 original size:46 final size:46
Alignment explanation
Indices: 17167--17340 Score: 276
Period size: 46 Copynumber: 3.8 Consensus size: 46
17157 TGTAACCCGC
* * *
17167 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
17213 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
17259 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
*
17305 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
17341 ATGCTCAACC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:19821 original size:46 final size:46
Alignment explanation
Indices: 19771--19991 Score: 290
Period size: 46 Copynumber: 4.8 Consensus size: 46
19761 TGGTTGAGCA
*
19771 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
19817 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
19862 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
19910 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
19955 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19992 GCGGGTTACA
Statistics
Matches: 156, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
45 47 0.30
46 64 0.41
47 29 0.19
48 3 0.02
50 4 0.03
51 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:27128 original size:46 final size:46
Alignment explanation
Indices: 27027--27153 Score: 211
Period size: 46 Copynumber: 2.8 Consensus size: 46
27017 GGTTGAGCAT
* *
27027 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
27072 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
27118 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27154 GCGGGTTACA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 34 0.44
46 43 0.56
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Done.