Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00716.F1
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, 814
Length: 1357
ACGTcount: A:0.30, C:0.40, G:0.10, T:0.20
Found at i:324 original size:51 final size:50
Alignment explanation
Indices: 283--1023 Score: 697
Period size: 51 Copynumber: 15.5 Consensus size: 50
273 CAACTCCTGT
*
283 TTACAAGTATAAGTCTCCACCACCTCCACCACCATCACCACCCAAGCATCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
334 TTACAAGTACAAGTCTCCTCCACCTCCACCACCATCACCACCCAAGCATCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
* * * *
385 TTACAAGTACAAG--TCCCCACCACCACCACCATCACCACCTAAACACCC
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
* *
433 CTACAAGTACAAG--TCCCCA-C-CC-CCACCATCACCACCCAAGCACCC
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
*
478 TTACAAGTACAAGTCT--CCA-C-CC-CCA-C--CACC-TCC-AG--T--
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
* * *
514 TTACAAGTATAAGTCTCCACCACCTCCACCTCCATCACCACCCAAGCACCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
* *
565 CTACAAGTACAAGTCT--CCA-C-CC-CCA-C--CACC-TCC-AG--T--
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
* * *
601 TTACAAGTATAAGTCTCCACCACCTCCACCTCCATCACCACCCAAGCACCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
* *
652 TTACAAGTACAAGTCCCCACCACCTCCACCACCATCACCACCAAAGCATCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
* * * *
703 TTACAAATACAAGTCT--CCACCACCACCACCATCCCCACCTAAGCATCC
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
* * * * *
751 CTACAAGTACAAGTCCCCACCACCACCACCACCATCCCCACCAAAGCATCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
* * * * *
802 CTACAAGTACAAGTCCCCCCACCACCACCACCGTCACCACCCAAGCACCC
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
* * * *
852 CTACAAGTACAAGTCACCTCCACCACCACCACCATCACC-CCCAAGCACCC
1 TTACAAGTACAAGTCTCC-CCACCTCCACCACCATCACCACCCAAGCATCC
* * *
902 TTACAAGTACAAG--TCCCCA-C-CC-CCACCGTCACCACCTAAGCACCC
1 TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
* * * * *
947 CTACAAGTACAAGTCACCCCCACCACCCCCACCATCACC-CCCAAGCACCC
1 TTACAAGTACAAGTC-TCCCCACCTCCACCACCATCACCACCCAAGCATCC
997 TTACAAGTACAAGTCTCCACCACCTCC
1 TTACAAGTACAAGTCTCC-CCACCTCC
1024 TCCTCCAGTT
Statistics
Matches: 589, Mismatches: 57, Indels: 89
0.80 0.08 0.12
Matches are distributed among these distances:
36 29 0.05
39 6 0.01
40 6 0.01
41 8 0.01
42 12 0.02
43 2 0.00
44 12 0.02
45 76 0.13
46 9 0.02
47 10 0.02
48 98 0.17
49 6 0.01
50 101 0.17
51 214 0.36
ACGTcount: A:0.31, C:0.49, G:0.06, T:0.14
Consensus pattern (50 bp):
TTACAAGTACAAGTCTCCCCACCTCCACCACCATCACCACCCAAGCATCC
Found at i:498 original size:39 final size:40
Alignment explanation
Indices: 410--492 Score: 94
Period size: 45 Copynumber: 1.9 Consensus size: 40
400 CCCACCACCA
*
410 CCACCATCACCACCTAAACACCCCTACAAGTACAAGTCCCCACCC
1 CCACCATCACCACCCAAACACCCCTACAAGTACAAGT-----CCC
* *
455 CCACCATCACCACCCAAGCACCCTTACAAGTACAAGTC
1 CCACCATCACCACCCAAACACCCCTACAAGTACAAGTC
493 TCCACCCCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.48, G:0.06, T:0.12
Consensus pattern (40 bp):
CCACCATCACCACCCAAACACCCCTACAAGTACAAGTCCC
Found at i:518 original size:36 final size:36
Alignment explanation
Indices: 478--547 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
468 CCAAGCACCC
*
478 TTACAAGTACAAGTCTCCACCCCCACCACCTCCAGT
1 TTACAAGTACAAGTCTCCACCACCACCACCTCCAGT
* *
514 TTACAAGTATAAGTCTCCACCACCTCCACCTCCA
1 TTACAAGTACAAGTCTCCACCACCACCACCTCCA
548 TCACCACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.43, G:0.07, T:0.21
Consensus pattern (36 bp):
TTACAAGTACAAGTCTCCACCACCACCACCTCCAGT
Found at i:564 original size:87 final size:87
Alignment explanation
Indices: 458--681 Score: 412
Period size: 87 Copynumber: 2.6 Consensus size: 87
448 CCCACCCCCA
458 CCATCACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTA
1 CCATCACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTA
523 TAAGTCTCCACCACCTCCACCT
66 TAAGTCTCCACCACCTCCACCT
*
545 CCATCACCACCCAAGCACCCCTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTA
1 CCATCACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTA
610 TAAGTCTCCACCACCTCCACCT
66 TAAGTCTCCACCACCTCCACCT
* * *
632 CCATCACCACCCAAGCACCCTTACAAGTACAAGTCCCCACCACCTCCACC
1 CCATCACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCCCCACCACC
682 ACCATCACCA
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 132 1.00
ACGTcount: A:0.29, C:0.48, G:0.07, T:0.17
Consensus pattern (87 bp):
CCATCACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCCCCACCACCTCCAGTTTACAAGTA
TAAGTCTCCACCACCTCCACCT
Found at i:606 original size:36 final size:36
Alignment explanation
Indices: 566--634 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
556 CAAGCACCCC
*
566 TACAAGTACAAGTCTCCACCCCCACCACCTCCAGTT
1 TACAAGTACAAGTCTCCACCACCACCACCTCCAGTT
* *
602 TACAAGTATAAGTCTCCACCACCTCCACCTCCA
1 TACAAGTACAAGTCTCCACCACCACCACCTCCA
635 TCACCACCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.43, G:0.07, T:0.20
Consensus pattern (36 bp):
TACAAGTACAAGTCTCCACCACCACCACCTCCAGTT
Found at i:943 original size:95 final size:95
Alignment explanation
Indices: 635--1017 Score: 491
Period size: 95 Copynumber: 3.9 Consensus size: 95
625 TCCACCTCCA
* * * *
635 TCACCACCCAAGCACCCTTACAAGTACAAGTCCCCACCACCTCCACCACCATCACCACCAAAGCA
1 TCACCACCCAAGCACCCCTACAAGTACAAGTCACCACCACCACCACCACCATCACC-CCCAAGCA
* * * *
700 TCCTTACAAATACAAGTCTCCACCACCACCACCA
65 CCCTTACAAGTACAAG--TCC-CCACCCCCACCG
* * * *
734 TCCCCACCTAAGCATCCCTACAAGTACAAGTCCCCACCACCACCACCACCATC-CCCACCAAAGC
1 TCACCACCCAAGCACCCCTACAAGTACAAGTCACCACCACCACCACCACCATCACCC-CC-AAGC
798 ATCCC-TACAAGTACAAGTCCCCCCACCACCACCACCG
64 A-CCCTTACAAGTACAAGT--CCCCA-C-CC-CCACCG
*
835 TCACCACCCAAGCACCCCTACAAGTACAAGTCACCTCCACCACCACCACCATCACCCCCAAGCAC
1 TCACCACCCAAGCACCCCTACAAGTACAAGTCACCACCACCACCACCACCATCACCCCCAAGCAC
900 CCTTACAAGTACAAGTCCCCACCCCCACCG
66 CCTTACAAGTACAAGTCCCCACCCCCACCG
* * *
930 TCACCACCTAAGCACCCCTACAAGTACAAGTCACCCCCACCACCCCCACCATCACCCCCAAGCAC
1 TCACCACCCAAGCACCCCTACAAGTACAAGTCACCACCACCACCACCACCATCACCCCCAAGCAC
*
995 CCTTACAAGTACAAGTCTCCACC
66 CCTTACAAGTACAAGTCCCCACC
1018 ACCTCCTCCT
Statistics
Matches: 255, Mismatches: 19, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
95 90 0.35
96 2 0.01
97 3 0.01
98 11 0.04
99 70 0.27
100 21 0.08
101 55 0.22
102 3 0.01
ACGTcount: A:0.32, C:0.50, G:0.07, T:0.12
Consensus pattern (95 bp):
TCACCACCCAAGCACCCCTACAAGTACAAGTCACCACCACCACCACCACCATCACCCCCAAGCAC
CCTTACAAGTACAAGTCCCCACCCCCACCG
Done.