Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g03154.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, 1000
Length: 3351
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Found at i:766 original size:27 final size:27
Alignment explanation
Indices: 694--768 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
684 TGGACAAGGG
694 TCTGAAAATGCTGAAAAGAAATCTGAT
1 TCTGAAAATGCTGAAAAGAAATCTGAT
* * * *
721 TCT-AATAAGGATGACAAGAAATCTGGT
1 TCTGAA-AATGCTGAAAAGAAATCTGAT
*
748 TCTGAGAATGCTGAAAAGAAA
1 TCTGAAAATGCTGAAAAGAAA
769 GGAGATGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 2 0.05
27 35 0.92
28 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (27 bp):
TCTGAAAATGCTGAAAAGAAATCTGAT
Found at i:1088 original size:159 final size:159
Alignment explanation
Indices: 796--1354 Score: 890
Period size: 159 Copynumber: 3.5 Consensus size: 159
786 CAGGACTTAT
* * * * * *
796 GGGGATAAGGTTGATAAAAATGATGACAA--GGTGTCGGATAAACGCTCAGCT-GATCAGGTGAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGT-TC-GATAAAAGCTCTGATAG-TCAAGTG--
*
858 AAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATC
61 AAA-AAGAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATC
923 AGGTGAAAAAGAGCTCAAATGAAGTTTTCCCTAAA
125 AGGTGAAAAAGAGCTCAAATGAAGTTTTCCCTAAA
958 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
1023 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAATAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
1088 AAAAGAGCTCAAATGAAGTTTTCCCTAAA
131 AAAAGAGCTCAAATGAAGTTTTCCCTAAA
* *
1117 GTGGATAAGGTTGACAAAAATAATGACAATGTGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
* *
1182 GAGTTCAAATGAAGATGCCCCAAAAGGCGATAAGGTGTTTGATAAAAGCTCTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
*
1247 AAAAGAGCTCAAAAGAAGTTTTCCCTAAA
131 AAAAGAGCTCAAATGAAGTTTTCCCTAAA
* * *
1276 GGGGATAAGGTTGACAAAAGTAATGACAATGTGTTCGATAAAAGCTCTGGTAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
1341 GAGCTCAAATGAAG
66 GAGTTCAAATGAAG
1355 TTTTCCCATC
Statistics
Matches: 376, Mismatches: 18, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
159 322 0.86
160 3 0.01
162 45 0.12
163 3 0.01
164 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (159 bp):
GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
AAAAGAGCTCAAATGAAGTTTTCCCTAAA
Found at i:3217 original size:3 final size:3
Alignment explanation
Indices: 3209--3248 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3199 GGCCTTTAGT
3209 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3249 CCTTTAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Done.