Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1951
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: 18509
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Found at i:4742 original size:19 final size:19
Alignment explanation
Indices: 4718--4757 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4708 AGCTCCCATG
4718 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
4737 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
4756 TA
1 TA
4758 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:8011 original size:27 final size:27
Alignment explanation
Indices: 7844--8021 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
7834 TAAATTGTAC
*
7844 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
7871 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
7897 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
7925 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
7953 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
7980 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
8007 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8022 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:8012 original size:82 final size:81
Alignment explanation
Indices: 7841--8021 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
7831 GATTAAATTG
* * * *
7841 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
7906 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
7922 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
7986 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
8004 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
8022 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:15938 original size:27 final size:27
Alignment explanation
Indices: 15771--15948 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
15761 TAAATTGTAC
*
15771 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
15798 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
15824 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
15852 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
15880 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
15907 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
15934 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15949 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:15939 original size:82 final size:81
Alignment explanation
Indices: 15768--15948 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
15758 GATTAAATTG
* * * *
15768 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
15833 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
15849 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
15913 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
15931 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
15949 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:18273 original size:42 final size:41
Alignment explanation
Indices: 18175--18275 Score: 100
Period size: 41 Copynumber: 2.4 Consensus size: 41
18165 AATTTACGTG
* ** *
18175 TAAGACCATGTCTGGGACATCGGCATCATATCTGTTTTGTA
1 TAAGACCACGTCTGGGACAGAGGCATCATATCTGTTCTGTA
*
18216 TAAGACC-CTATCTGGGACAGAGGCATCGATA-CTGATTACT-TA
1 TAAGACCAC-GTCTGGGACAGAGGCATC-ATATCTG-TT-CTGTA
18258 TAAGACCACGTCTGGGAC
1 TAAGACCACGTCTGGGAC
18276 GTTGGCATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
41 25 0.51
42 22 0.45
43 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (41 bp):
TAAGACCACGTCTGGGACAGAGGCATCATATCTGTTCTGTA
Done.