Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01610.P20
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: 9767
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Found at i:529 original size:34 final size:35
Alignment explanation
Indices: 486--556 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
476 CATTCTTTAC
486 CTAGAGTTTCT-CCTCTTTTTTGGTACATAATTAG
1 CTAGAGTTTCTCCCTCTTTTTTGGTACATAATTAG
520 CTAGAGTTTCTCCCTCTTTTTTGGTACATAATTAG
1 CTAGAGTTTCTCCCTCTTTTTTGGTACATAATTAG
555 CT
1 CT
557 TTCTTCTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 11 0.31
35 25 0.69
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (35 bp):
CTAGAGTTTCTCCCTCTTTTTTGGTACATAATTAG
Found at i:1820 original size:39 final size:39
Alignment explanation
Indices: 1766--1848 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
1756 CCACTGGCCA
*
1766 CCACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT
* **
1805 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATTGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT
1844 CCACC
1 CCACC
1849 CGTCACCACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (39 bp):
CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT
Found at i:4169 original size:31 final size:31
Alignment explanation
Indices: 4133--4195 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4123 TTCCTTATTT
4133 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
4164 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
4195 C
1 C
4196 TTCTCGTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57
Consensus pattern (31 bp):
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
Found at i:5926 original size:42 final size:42
Alignment explanation
Indices: 5860--5974 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
5850 CATTCTCTTT
* * * * *
5860 TCTATTCCAGGTAAATACCGCTCATATCCCACCTTGGAATAA
1 TCTATTCCAGGGATATCCCTCTCATATCCCACCTTAGAATAA
* *
5902 TCTATTCCAGGGATATCCCTCTCATTTGCCC-TCTTAGAATAA
1 TCTATTCCAGGGATATCCCTCTCATAT-CCCACCTTAGAATAA
* * * *
5944 TCAATTCCGGGGATACCCCTCTGATATCCCA
1 TCTATTCCAGGGATATCCCTCTCATATCCCA
5975 TCCCGGTCCG
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 3 0.05
42 53 0.90
43 3 0.05
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (42 bp):
TCTATTCCAGGGATATCCCTCTCATATCCCACCTTAGAATAA
Found at i:6114 original size:16 final size:16
Alignment explanation
Indices: 6095--6148 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
6085 CATTCCGAGG
6095 ATATCCCGGCTTAGGT
1 ATATCCCGGCTTAGGT
*
6111 ATATCCCGACTTAGG-
1 ATATCCCGGCTTAGGT
* *
6126 ATAGCCCGGCTGAGGT
1 ATATCCCGGCTTAGGT
6142 ATATCCC
1 ATATCCC
6149 ACCTGCGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (16 bp):
ATATCCCGGCTTAGGT
Found at i:9080 original size:39 final size:39
Alignment explanation
Indices: 9030--9110 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
9020 ACCGGCCACA
*
9030 ACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGTAC
1 ACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTAC
* * *
9069 ACCATCATCGTTCACCAGTCAGGTAGTCACCATCGGTCC
1 ACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTAC
9108 ACC
1 ACC
9111 CGTCACCACC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.20
Consensus pattern (39 bp):
ACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTAC
Done.