Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2634
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: 28481
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:3758 original size:9 final size:9
Alignment explanation
Indices: 3734--3780 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
3724 TGGCTGAAGC
3734 TCTTCCTCT
1 TCTTCCTCT
* *
3743 TCATCCTCG
1 TCTTCCTCT
3752 TCTTCCTCT
1 TCTTCCTCT
*
3761 TCTTCTTCT
1 TCTTCCTCT
*
3770 TCCTCCTCT
1 TCTTCCTCT
3779 TC
1 TC
3781 CTCACCATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.51
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:3767 original size:24 final size:24
Alignment explanation
Indices: 3733--3783 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3723 GTGGCTGAAG
*
3733 CTCTTCCTCTTCATCCTCGTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
* *
3757 CTCTTCTTCTTCTTCCTCCTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
3781 CTC
1 CTC
3784 ACCATCATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (24 bp):
CTCTTCCTCTTCATCCTCCTCTTC
Found at i:3806 original size:12 final size:12
Alignment explanation
Indices: 3786--3828 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
3776 TCTTCCTCAC
*
3786 CATCATCGTCGT
1 CATCATCGTCAT
*
3798 CATCGTCGTCAT
1 CATCATCGTCAT
*
3810 CATCCTCGTCAT
1 CATCATCGTCAT
3822 CATCATC
1 CATCATC
3829 CTCGTCTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.33
Consensus pattern (12 bp):
CATCATCGTCAT
Found at i:3824 original size:15 final size:15
Alignment explanation
Indices: 3800--3834 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3790 ATCGTCGTCA
*
3800 TCGTCGTCATCATCC
1 TCGTCATCATCATCC
3815 TCGTCATCATCATCC
1 TCGTCATCATCATCC
3830 TCGTC
1 TCGTC
3835 TCCACTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.40, G:0.11, T:0.34
Consensus pattern (15 bp):
TCGTCATCATCATCC
Found at i:3932 original size:21 final size:21
Alignment explanation
Indices: 3908--3947 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3898 TGCATCCTCC
3908 TCATCTGCAT-CTTCATCTTGA
1 TCATCT-CATGCTTCATCTTGA
*
3929 TCATCTCCTGCTTCATCTT
1 TCATCTCATGCTTCATCTT
3948 CTCATCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.45
Consensus pattern (21 bp):
TCATCTCATGCTTCATCTTGA
Found at i:9158 original size:93 final size:93
Alignment explanation
Indices: 8999--9184 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
8989 AGCTACGTCC
* *
8999 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATGACGAAATAACT
1 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
9064 ATTCAATCATAACTAACCTTGATGGTCT
66 ATTCAATCATAACTAACCTTGATGGTCT
9092 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
1 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
9157 ATTCAATCATAACTAACCTTGATGGTCT
66 ATTCAATCATAACTAACCTTGATGGTCT
9185 TGTCATCACC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (93 bp):
CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
ATTCAATCATAACTAACCTTGATGGTCT
Done.