Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01882.P1
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, 928
Length: 1548
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Found at i:728 original size:6 final size:6
Alignment explanation
Indices: 717--798 Score: 69
Period size: 6 Copynumber: 13.2 Consensus size: 6
707 AAGGGAGACG
* *
717 AAGAGA AAGAGA AAGAGA AAGA-A AAGAAA AAGA-A GAAGAAGA AAGACA
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA -AAG-AGA AAGAGA
* *
765 AAGATGGGA AAGAGA AAGAGA AAAAGA AAAAGA A
1 AAGA---GA AAGAGA AAGAGA AAGAGA AAGAGA A
799 GAAAAAGGAT
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
5 6 0.09
6 50 0.76
7 4 0.06
8 1 0.02
9 5 0.08
ACGTcount: A:0.70, C:0.01, G:0.28, T:0.01
Consensus pattern (6 bp):
AAGAGA
Found at i:742 original size:48 final size:48
Alignment explanation
Indices: 629--742 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
619 CAAAGAAGAG
* * *
629 GAGAAGGAGAAGGAGAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAG
1 GAGAAGGAGAAAGAAAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAA
* * *
677 GAGAAGGA-AAAGAAAAAGGATAAAGAGGTTAAGGGAGACGAAGAGAAA
1 GAGAAGGAGAAAG-AAAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAA
*
725 GAGAAAGAGAAAGAAAAG
1 GAGAAGGAGAAAGAAAAG
743 AAAAAGAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 3 0.05
48 50 0.88
49 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.37, T:0.05
Consensus pattern (48 bp):
GAGAAGGAGAAAGAAAAGGATAAAGAGGTTAAGGAAAAAGAAGAGAAA
Found at i:913 original size:9 final size:9
Alignment explanation
Indices: 899--924 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
889 TTCTTCTTCC
899 TCATCGTCG
1 TCATCGTCG
908 TCATCGTCG
1 TCATCGTCG
917 TCATCGTC
1 TCATCGTC
925 ATCTTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.35
Consensus pattern (9 bp):
TCATCGTCG
Found at i:941 original size:24 final size:24
Alignment explanation
Indices: 914--966 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
904 GTCGTCATCG
* *
914 TCGTCATCGTCATCTTCTTCTTCC
1 TCGTCATCATCATCATCTTCTTCC
* *
938 TCGTCATCATCTTCATCTTCTTCG
1 TCGTCATCATCATCATCTTCTTCC
962 TCGTC
1 TCGTC
967 TTCTGACTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.09, C:0.36, G:0.09, T:0.45
Consensus pattern (24 bp):
TCGTCATCATCATCATCTTCTTCC
Found at i:949 original size:21 final size:21
Alignment explanation
Indices: 923--963 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
913 GTCGTCATCG
*
923 TCATCTTCTTCTTCCTCGTCA
1 TCATCTTCATCTTCCTCGTCA
*
944 TCATCTTCATCTTCTTCGTC
1 TCATCTTCATCTTCCTCGTC
964 GTCTTCTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.05, T:0.49
Consensus pattern (21 bp):
TCATCTTCATCTTCCTCGTCA
Found at i:997 original size:6 final size:6
Alignment explanation
Indices: 986--1020 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
976 GGATTCAGAT
986 AAGAAA AAG-AA AAGAAA AGAGAAA AAGAAA AAGAA
1 AAGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAA
1021 GCAAGAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:1075 original size:24 final size:24
Alignment explanation
Indices: 1048--1103 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1038 ATAAAGAGCT
*
1048 GAAAGAAGATGA-ACACAAAGAGAA
1 GAAAGAAGACGAGACA-AAAGAGAA
*
1072 GAAAGATGACGAGACAAAAGAGAA
1 GAAAGAAGACGAGACAAAAGAGAA
1096 -AAAGAAGA
1 GAAAGAAGA
1104 AAAAGAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.62, C:0.07, G:0.27, T:0.04
Consensus pattern (24 bp):
GAAAGAAGACGAGACAAAAGAGAA
Done.