Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1908
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: 32654
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Found at i:741 original size:1 final size:1
Alignment explanation
Indices: 735--812 Score: 102
Period size: 1 Copynumber: 78.0 Consensus size: 1
725 AGGTTCAACA
* * * ** *
735 GGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGTGGGGGAGATGGGGGGTGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
800 GGGGGGGGGGGGG
1 GGGGGGGGGGGGG
813 AACCTTTTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.04, C:0.00, G:0.92, T:0.04
Consensus pattern (1 bp):
G
Found at i:19856 original size:93 final size:93
Alignment explanation
Indices: 19749--19919 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
19739 CGCCCTAAGT
* *
19749 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19814 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
19842 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
19907 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19920 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:19916 original size:46 final size:46
Alignment explanation
Indices: 19744--19916 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
19734 TAACCCGCCC
* * *
19744 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
19790 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
19838 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
19883 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
19917 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:20360 original size:30 final size:30
Alignment explanation
Indices: 20326--20385 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20316 ATTTAATACG
20326 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
20356 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
20386 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:27241 original size:27 final size:28
Alignment explanation
Indices: 27157--27254 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
27147 CATGAGATTG
* * * *
27157 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
27186 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27214 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27241 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
27255 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27265 original size:27 final size:27
Alignment explanation
Indices: 27185--27267 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
27175 TAAATTGTAC
* *
27185 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
27213 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
27240 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
27267 A
1 A
27268 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:30953 original size:46 final size:46
Alignment explanation
Indices: 30886--31061 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
30876 TGTAACCCGC
*
30886 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
30932 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * * * *
30982 --TTCA-CGAACTC-GACTCAACTCTCAATGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAA--CTCAACGAGTTCGGGCGTTCGCAT
31026 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG
31062 ATGCTCAACC
Statistics
Matches: 104, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 1 0.01
46 56 0.54
47 12 0.12
48 23 0.22
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:31023 original size:94 final size:93
Alignment explanation
Indices: 30894--31065 Score: 274
Period size: 94 Copynumber: 1.8 Consensus size: 93
30884 GCCCATAAGT
* * *
30894 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
30959 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
30987 GAACTC-GACTCAACTCTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTC
1 GAACTCAGACTCAA--CTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTC
31051 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
31066 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 7 0.10
93 6 0.08
94 59 0.82
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:31521 original size:30 final size:30
Alignment explanation
Indices: 31487--31546 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
31477 ATTTAATACG
31487 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
31517 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
31547 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.