Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1379
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: 17041
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Found at i:3643 original size:20 final size:20
Alignment explanation
Indices: 3581--3644 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
3571 TAAACATGGT
3581 ATGTATGATATGC-CATGAC
1 ATGTATGATATGCACATGAC
*
3600 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
3620 ATGTATAGATATGCACGTG-C
1 ATGTAT-GATATGCACATGAC
3640 ATGTA
1 ATGTA
3645 ATCATAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.32
20 16 0.40
21 11 0.28
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:3758 original size:23 final size:23
Alignment explanation
Indices: 3694--3814 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
3684 GGAAGTGGAA
3694 AAAGGGCTTATGCCCCAGATTA-T
1 AAAGGGCTTATGCCCCAG-TTATT
* *
3717 AAAGGG-TTGTGCCCAAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
3739 AAAGGGCTTATGCCCCAGTTAATT
1 AAAGGGCTTATGCCCCAGTT-ATT
*
3763 AAAGGGCTTGTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
3786 GAAA-GGCTAATG-CCCAGGTTATT
1 -AAAGGGCTTATGCCCCA-GTTATT
*
3809 TAAGGG
1 AAAGGG
3815 GCCTTTGCCC
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
21 3 0.04
22 22 0.26
23 34 0.40
24 25 0.30
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:3799 original size:47 final size:45
Alignment explanation
Indices: 3694--3800 Score: 146
Period size: 47 Copynumber: 2.3 Consensus size: 45
3684 GGAAGTGGAA
3694 AAAGGGCTTATGCCCCAGATTATAAAGGGTTGTGCCCAAGTTATT
1 AAAGGGCTTATGCCCCAGATTATAAAGGGTTGTGCCCAAGTTATT
*
3739 AAAGGGCTTATGCCCCAG-TTAATTAAAGGGCTTGTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGATT-A-TAAAGGG-TTGTGCCCAAGTTATT
*
3786 GAAA-GGCTAATGCCC
1 -AAAGGGCTTATGCCC
3801 AGGTTATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
44 2 0.04
45 19 0.34
46 7 0.12
47 25 0.45
48 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (45 bp):
AAAGGGCTTATGCCCCAGATTATAAAGGGTTGTGCCCAAGTTATT
Found at i:3824 original size:47 final size:47
Alignment explanation
Indices: 3694--3838 Score: 142
Period size: 47 Copynumber: 3.1 Consensus size: 47
3684 GGAAGTGGAA
*
3694 AAAGGGCTTATGCCCCAGATT-A-TAAAGGG-TTGTGCCCAAGTTATT
1 AAAGGGCTAATGCCCCAG-TTAATTAAAGGGCTTGTGCCCAAGTTATT
* *
3739 AAAGGGCTTATGCCCCAGTTAATTAAAGGGCTTGTGCCCCAGTTATT
1 AAAGGGCTAATGCCCCAGTTAATTAAAGGGCTTGTGCCCAAGTTATT
* * **
3786 GAAA-GGCTAATG-CCCAGGTTATTTAAGGGGCCTT-TGCCCTTG-TATT
1 -AAAGGGCTAATGCCCCA-GTTAATTAAAGGG-CTTGTGCCCAAGTTATT
3832 AAAGGGC
1 AAAGGGC
3839 CCTTTATGGC
Statistics
Matches: 87, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
44 2 0.02
45 22 0.25
46 18 0.21
47 39 0.45
48 6 0.07
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (47 bp):
AAAGGGCTAATGCCCCAGTTAATTAAAGGGCTTGTGCCCAAGTTATT
Found at i:3935 original size:45 final size:42
Alignment explanation
Indices: 3871--4027 Score: 151
Period size: 41 Copynumber: 3.6 Consensus size: 42
3861 TAAAGGGCAT
3871 AGCCCTTTAAT-ACTGGGGCATAAGCCTTTAATAACAAGGGACTA
1 AGCCCTTTAATAACT-GGGCATAAGCCTTTAATAAC-AGGGAC-A
* * * *
3915 GAGCCCCTTAATAACTGGGCAATACGCCTTTCAAATATCGGGGCACA
1 -AGCCCTTTAATAACTGGGC-ATAAGCCTTT--AATAACAGGG-ACA
* *
3962 AGCCCTTTAATAA-TGGGCA-AAGCCTTTAATAACTGGGGCA
1 AGCCCTTTAATAACTGGGCATAAGCCTTTAATAACAGGGACA
4002 CAGCCCTTTAA-AACTGGGCATAAGCC
1 -AGCCCTTTAATAACTGGGCATAAGCC
4028 CCTTTTCACT
Statistics
Matches: 95, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
40 4 0.04
41 24 0.25
42 5 0.05
43 7 0.07
44 1 0.01
45 19 0.20
46 24 0.25
47 4 0.04
48 7 0.07
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (42 bp):
AGCCCTTTAATAACTGGGCATAAGCCTTTAATAACAGGGACA
Found at i:4032 original size:22 final size:21
Alignment explanation
Indices: 3865--4028 Score: 115
Period size: 21 Copynumber: 7.5 Consensus size: 21
3855 AGTTATTAAA
*
3865 GGGCATAGCCCTTTAAT-ACT
1 GGGCAAAGCCCTTTAATAACT
*
3885 GGGGCATAAG-CCTTTAATAACAA
1 -GGGCA-AAGCCCTTTAATAAC-T
* *
3908 GGGACTAGAGCCCCTTAATAACT
1 GGG-C-AAAGCCCTTTAATAACT
* *
3931 GGGCAATA-CGCCTTTCAAATATCG
1 GGGCAA-AGC-CCTTT--AATAACT
3955 GGGCACAAGCCCTTTAATAA-T
1 GGGCA-AAGCCCTTTAATAACT
3976 GGGCAAAG-CCTTTAATAACT
1 GGGCAAAGCCCTTTAATAACT
*
3996 GGGGCACAGCCCTTTAA-AACT
1 -GGGCAAAGCCCTTTAATAACT
4017 GGGCATAAGCCC
1 GGGCA-AAGCCC
4029 CTTTTCACTT
Statistics
Matches: 114, Mismatches: 13, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
19 10 0.09
20 9 0.08
21 36 0.32
22 24 0.21
23 6 0.05
24 27 0.24
25 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
GGGCAAAGCCCTTTAATAACT
Found at i:4147 original size:20 final size:20
Alignment explanation
Indices: 4105--4148 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4095 CAGTACCTAT
**
4105 ATGTGCATCATCATACTGTC
1 ATGTGCATCATCATACTACC
4125 ATGTGCAT-ATCATACATACC
1 ATGTGCATCATCATAC-TACC
4145 ATGT
1 ATGT
4149 TTATCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTGCATCATCATACTACC
Done.