Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g00709.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, 798
Length: 1330
ACGTcount: A:0.26, C:0.40, G:0.08, T:0.27
Found at i:231 original size:15 final size:15
Alignment explanation
Indices: 213--242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
203 CTCCTTACTA
*
213 TTACAATTCACCACC
1 TTACAAGTCACCACC
228 TTACAAGTCACCACC
1 TTACAAGTCACCACC
243 GCCGCCTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.40, G:0.03, T:0.23
Consensus pattern (15 bp):
TTACAAGTCACCACC
Found at i:359 original size:48 final size:48
Alignment explanation
Indices: 307--882 Score: 319
Period size: 48 Copynumber: 11.9 Consensus size: 48
297 ACCTCCTCCT
* * *
307 TACTATTACAAATCACCACCACCCCCTTCACCTAGTCCCCCACCATCA
1 TACTACTACAAGTCACCACCTCCCCCTTCACCTAGTCCCCCACCATCA
* * * * * *
355 TACTACTACAACTCACCACCTCCACCATCTCCT--TCACCACCTCC-TCCT
1 TACTACTACAAGTCACCACCTCCCCCTTCACCTAGTC-CC-CCACCAT-CA
* * *
403 TACTACTACAAATCACCACCACCACCC-TCACCTAGTCCCCCACCACCA
1 TACTACTACAAGTCACCACCTCC-CCCTTCACCTAGTCCCCCACCATCA
* * * * *
451 TACTACTACAAGTCACCACCTCCACCATCTCCT--TCACCACC-CCCTCCT
1 TACTACTACAAGTCACCACCTCCCCCTTCACCTAGTC-CC-CCACCAT-CA
* * * *
499 TACTATTACAAGTCTCCACC-CCCACCCTCACCTAGTCCCCCACCACCA
1 TACTACTACAAGTCACCACCTCCC-CCTTCACCTAGTCCCCCACCATCA
* * * * * *
547 TACTACTACAAGTCACCACCTGCACCATCTCCT--TCACCACCTCC-TCCT
1 TACTACTACAAGTCACCACCTCCCCCTTCACCTAGTC-CC-CCACCAT-CA
* * * *
595 TACTATTACAAGTCTCCACC-CCCGCCCTCACCTAGTCCCCCACCACCA
1 TACTACTACAAGTCACCACCTCCC-CCTTCACCTAGTCCCCCACCATCA
* * * *
643 TACTACTACAAGTCACCACCTCCACCGTCTC-CCTCA--CCACCTCC-TCCT
1 TACTACTACAAGTCACCACCTCC-CCCT-TCACCT-AGTCCCCCACCAT-CA
* * *
691 TACTACTACAAATCACCACCACCACCC-TCACCTAGTCCCCCACCACCA
1 TACTACTACAAGTCACCACCTCC-CCCTTCACCTAGTCCCCCACCATCA
* * * * * *
739 TACTACTACAAGTCACCACCTCCACCATCCCCCTCA--CCACCTCC-TCCT
1 TACTACTACAAGTCACCACCTCC-CCCTTCACCT-AGTCCCCCACCAT-CA
* * * * * *
787 TACTACTACAAATCACCATCACCACCTTCACCTAGTCCTCCACCACCA
1 TACTACTACAAGTCACCACCTCCCCCTTCACCTAGTCCCCCACCATCA
* * * *
835 TACTACTACAAGTCTCCAGTACCTCCACCATCTCCTAGTCCCCCACCA
1 TACTACTACAAGTCACC---ACCTCCCCCTTCACCTAGTCCCCCACCA
883 CCATCTCCCT
Statistics
Matches: 397, Mismatches: 90, Indels: 79
0.70 0.16 0.14
Matches are distributed among these distances:
46 10 0.03
47 23 0.06
48 309 0.78
49 21 0.05
50 11 0.03
51 23 0.06
ACGTcount: A:0.26, C:0.51, G:0.03, T:0.21
Consensus pattern (48 bp):
TACTACTACAAGTCACCACCTCCCCCTTCACCTAGTCCCCCACCATCA
Found at i:423 original size:96 final size:95
Alignment explanation
Indices: 293--870 Score: 886
Period size: 96 Copynumber: 6.0 Consensus size: 95
283 TCTCCACCTC
* *
293 CACCACCTCCTCCTTACTATTACAAATCACCACCACCCCCTTCACCTAGTCCCCCACCATCATAC
1 CACCACCTCCTCCTTACTACTACAAATCACCACCACCCCC-TCACCTAGTCCCCCACCACCATAC
*
358 TACTACAACTCACCACCTCCACCATCTCCTT
65 TACTACAAGTCACCACCTCCACCATCTCCTT
389 CACCACCTCCTCCTTACTACTACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATAC
1 CACCACCTCCTCCTTACTACTACAAATCACCACCACC-CCCTCACCTAGTCCCCCACCACCATAC
454 TACTACAAGTCACCACCTCCACCATCTCCTT
65 TACTACAAGTCACCACCTCCACCATCTCCTT
* * * * *
485 CACCACCCCCTCCTTACTATTACAAGTCTCCACCCCCACCCTCACCTAGTCCCCCACCACCATAC
1 CACCACCTCCTCCTTACTACTACAAATCACCACCACC-CCCTCACCTAGTCCCCCACCACCATAC
*
550 TACTACAAGTCACCACCTGCACCATCTCCTT
65 TACTACAAGTCACCACCTCCACCATCTCCTT
* * * *
581 CACCACCTCCTCCTTACTATTACAAGTCTCCACCCCCGCCCTCACCTAGTCCCCCACCACCATAC
1 CACCACCTCCTCCTTACTACTACAAATCACCACCACC-CCCTCACCTAGTCCCCCACCACCATAC
* *
646 TACTACAAGTCACCACCTCCACCGTCTCCCT
65 TACTACAAGTCACCACCTCCACCATCTCCTT
677 CACCACCTCCTCCTTACTACTACAAATCACCACCACCACCCTCACCTAGTCCCCCACCACCATAC
1 CACCACCTCCTCCTTACTACTACAAATCACCACCACC-CCCTCACCTAGTCCCCCACCACCATAC
* *
742 TACTACAAGTCACCACCTCCACCATCCCCCT
65 TACTACAAGTCACCACCTCCACCATCTCCTT
* * *
773 CACCACCTCCTCCTTACTACTACAAATCACCATCACCACCTTCACCTAGTCCTCCACCACCATAC
1 CACCACCTCCTCCTTACTACTACAAATCACCACCACC-CCCTCACCTAGTCCCCCACCACCATAC
*
838 TACTACAAGTCTCCAGTACCTCCACCATCTCCT
65 TACTACAAGTCACC---ACCTCCACCATCTCCT
871 AGTCCCCCAC
Statistics
Matches: 451, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
96 434 0.96
97 3 0.01
99 14 0.03
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.21
Consensus pattern (95 bp):
CACCACCTCCTCCTTACTACTACAAATCACCACCACCCCCTCACCTAGTCCCCCACCACCATACT
ACTACAAGTCACCACCTCCACCATCTCCTT
Found at i:986 original size:48 final size:48
Alignment explanation
Indices: 877--1007 Score: 138
Period size: 48 Copynumber: 2.7 Consensus size: 48
867 TCCTAGTCCC
* * * * * *
877 CCACCACCATCTCCCTCACCACCACCTCCATACTACTACAAATCTCCT
1 CCACCTCCATCTCCATCACCCCCACCTCCTTACTACTACAAATCACCA
* * *
925 CC-TCTACCGTCTCCATCACCCCCTCCTCCTTACTACTACAAATCACCA
1 CCACCT-CCATCTCCATCACCCCCACCTCCTTACTACTACAAATCACCA
* * *
973 CCACCTCCTTCTCCATCACCCCCGCCACCTTACTA
1 CCACCTCCATCTCCATCACCCCCACCTCCTTACTA
1008 TTATAAGTCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 1 0.01
48 65 0.96
49 2 0.03
ACGTcount: A:0.23, C:0.53, G:0.02, T:0.23
Consensus pattern (48 bp):
CCACCTCCATCTCCATCACCCCCACCTCCTTACTACTACAAATCACCA
Done.