Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.A12G026000.1.v1.1
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, 756
Length: 1261
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Found at i:734 original size:21 final size:21
Alignment explanation
Indices: 708--978 Score: 142
Period size: 21 Copynumber: 13.0 Consensus size: 21
698 TGTTCGCTCC
708 CTCCACCTCCACCAGTTCAAT
1 CTCCACCTCCACCAGTTCAAT
* **
729 CTCCACCACCACCAGTTCGCT
1 CTCCACCTCCACCAGTTCAAT
750 CCCCTCCACCTCCACCAGTTCAAT
1 ---CTCCACCTCCACCAGTTCAAT
* * **
774 CACCACCACCACCAGTTCGCT
1 CTCCACCTCCACCAGTTCAAT
* * * *
795 CCCCTCCACCACCCG-TCTACA-
1 CTCCACCTCCACCAGTTC-A-AT
816 CTCCACCTCCACCAGTTC--T
1 CTCCACCTCCACCAGTTCAAT
*
835 CTCC-CCTCCACCACCCGTCTC-CT
1 CTCCACCTCCACCA---GT-TCAAT
*
858 TTCCACCTCCACCAGTTCAAT
1 CTCCACCTCCACCAGTTCAAT
*
879 CTCCACCACCACCAGTTC--T
1 CTCCACCTCCACCAGTTCAAT
*
898 CTCC-CCTCCACCACCGTCTC-CT
1 CTCCACCTCCACCA--GT-TCAAT
920 -TCCACCT-CACCAGTTCAA-
1 CTCCACCTCCACCAGTTCAAT
* * *
938 -T-CACCACCACCCG-TCTATT
1 CTCCACCTCCACCAGTTC-AAT
*
957 CTCCACATCCACCAGTTCAAT
1 CTCCACCTCCACCAGTTCAAT
978 C
1 C
979 ACAACCACCA
Statistics
Matches: 192, Mismatches: 32, Indels: 52
0.70 0.12 0.19
Matches are distributed among these distances:
17 6 0.03
18 26 0.14
19 11 0.06
20 7 0.04
21 101 0.53
22 10 0.05
23 4 0.02
24 27 0.14
ACGTcount: A:0.20, C:0.53, G:0.06, T:0.22
Consensus pattern (21 bp):
CTCCACCTCCACCAGTTCAAT
Found at i:767 original size:45 final size:45
Alignment explanation
Indices: 687--846 Score: 206
Period size: 45 Copynumber: 3.6 Consensus size: 45
677 CTACTCACCA
* *
687 CCACCACAACCTGTTCGCT-CCCTCCACCTCCACCAGTTCAATCT
1 CCACCACCACCAGTTCGCTCCCCTCCACCTCCACCAGTTCAATCT
*
731 CCACCACCACCAGTTCGCTCCCCTCCACCTCCACCAGTTCAATCA
1 CCACCACCACCAGTTCGCTCCCCTCCACCTCCACCAGTTCAATCT
*
776 CCACCACCACCAGTTCGCTCCCCTCCA---CCACCCG-TCTACA-CT
1 CCACCACCACCAGTTCGCTCCCCTCCACCTCCACCAGTTC-A-ATCT
* *
818 CCACCTCCACCAGTTCTCTCCCCTCCACC
1 CCACCACCACCAGTTCGCTCCCCTCCACC
847 ACCCGTCTCC
Statistics
Matches: 104, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
41 2 0.02
42 33 0.32
43 1 0.01
44 17 0.16
45 51 0.49
ACGTcount: A:0.19, C:0.55, G:0.06, T:0.19
Consensus pattern (45 bp):
CCACCACCACCAGTTCGCTCCCCTCCACCTCCACCAGTTCAATCT
Found at i:846 original size:63 final size:63
Alignment explanation
Indices: 753--945 Score: 191
Period size: 63 Copynumber: 3.1 Consensus size: 63
743 GTTCGCTCCC
** * * * *
753 CTCCACCTCCACCAGTTCAATCACCACCACCACCAGT-TCGCTCCCCTCCACCACCCG-TCTACA
1 CTCCACCTCCACCAGTTCTCTCCCCTCCACCACCAGTCTC-CTCCCCACCACCACCAGTTC-A-A
816 -
63 T
* ** *
816 CTCCACCTCCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTTCCACCTCCACCAGTTCAAT
1 CTCCACCTCCACCAGTTCTCTCCCCTCCACCACCAGTCTCCTCCCCACCACCACCAGTTCAAT
* * *
879 CTCCACCACCACCAGTTCTCTCCCCTCCACCACC-GTCTCCT-TCCACC-TCACCAGTTCAAT
1 CTCCACCTCCACCAGTTCTCTCCCCTCCACCACCAGTCTCCTCCCCACCACCACCAGTTCAAT
*
939 CACCACC
1 CTCCACC
946 ACCCGTCTAT
Statistics
Matches: 114, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
60 18 0.16
61 6 0.05
62 8 0.07
63 78 0.68
64 4 0.04
ACGTcount: A:0.19, C:0.54, G:0.05, T:0.21
Consensus pattern (63 bp):
CTCCACCTCCACCAGTTCTCTCCCCTCCACCACCAGTCTCCTCCCCACCACCACCAGTTCAAT
Found at i:863 original size:42 final size:42
Alignment explanation
Indices: 729--875 Score: 163
Period size: 42 Copynumber: 3.4 Consensus size: 42
719 CCAGTTCAAT
* *
729 CTCCACCACCACCAGTTCGCTCCCCTCCACCTCCACCAGT-T-CAA
1 CTCCACCTCCACCAGTTCGCTCCCCTCCA---CCACCCGTCTAC-A
* *
773 TCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTACA
1 -CTCCACCTCCACCAGTTCGCTCCCCTCCACCACCCGTCTACA
* * *
816 CTCCACCTCCACCAGTTCTCTCCCCTCCACCACCCGTCTCCT
1 CTCCACCTCCACCAGTTCGCTCCCCTCCACCACCCGTCTACA
*
858 TTCCACCTCCACCAGTTC
1 CTCCACCTCCACCAGTTC
876 AATCTCCACC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
42 61 0.66
43 2 0.02
44 1 0.01
45 28 0.30
ACGTcount: A:0.18, C:0.56, G:0.06, T:0.20
Consensus pattern (42 bp):
CTCCACCTCCACCAGTTCGCTCCCCTCCACCACCCGTCTACA
Found at i:948 original size:39 final size:41
Alignment explanation
Indices: 905--990 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 41
895 TCTCTCCCCT
* * *
905 CCACCACCGTCTCCT-TCCACCT-CACCAGTTCAATCACCA
1 CCACCACCGTCTACTCTCCACATCCACCAGTTCAATCACAA
*
944 CCA-C-CCGTCTATTCTCCACATCCACCAGTTCAATCACAA
1 CCACCACCGTCTACTCTCCACATCCACCAGTTCAATCACAA
983 CCACCACC
1 CCACCACC
991 AACTTCACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 7 0.18
38 7 0.18
39 22 0.56
40 1 0.03
41 2 0.05
ACGTcount: A:0.26, C:0.50, G:0.05, T:0.20
Consensus pattern (41 bp):
CCACCACCGTCTACTCTCCACATCCACCAGTTCAATCACAA
Found at i:948 original size:63 final size:63
Alignment explanation
Indices: 818--948 Score: 223
Period size: 63 Copynumber: 2.1 Consensus size: 63
808 CGTCTACACT
* *
818 CCACCTCCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTTCCACCTCCACCAGTTCAATCT
1 CCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTTCCACCTCCACCAGTTCAATCA
881 CCACCACCACCAGTTCTCTCCCCTCCACCA-CCGTCTCC-TTCCACCT-CACCAGTTCAATCA
1 CCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTTCCACCTCCACCAGTTCAATCA
941 CCACCACC
1 CCACCACC
949 CGTCTATTCT
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
60 21 0.32
61 8 0.12
62 8 0.12
63 29 0.44
ACGTcount: A:0.18, C:0.55, G:0.05, T:0.22
Consensus pattern (63 bp):
CCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTTCCACCTCCACCAGTTCAATCA
Done.