Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00871.N2
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: 2583
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Found at i:2314 original size:20 final size:21
Alignment explanation
Indices: 2276--2315 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2266 ATGTCATATC
2276 AGTATTCTTATTCTGAATTTT
1 AGTATTCTTATTCTGAATTTT
2297 AGTATT-TTAATT-TGAATTT
1 AGTATTCTT-ATTCTGAATTT
2316 AATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (21 bp):
AGTATTCTTATTCTGAATTTT
Found at i:2419 original size:269 final size:269
Alignment explanation
Indices: 1940--2425 Score: 753
Period size: 269 Copynumber: 1.8 Consensus size: 269
1930 ATTAAGAGGG
*
1940 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTTCAATAGTTTTATGTCATA
1 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
2005 TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
66 TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
*
2070 GAAATTCAGGATAAGAATACTGATGTGGTATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
131 GAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
2135 TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
196 TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
2200 ATCAGGGGA
261 ATCAGGGGA
* *
2209 GAAAGGATTGTGTGAAATAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
1 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
* * * * * *** **** *
2274 TCAGTATTCTTATTCTGAATTT-TAGTATTTTAAT-TTGAATTTAATTTTTTTCAGGA-TAAAAT
66 TCAATATTCTTATCCAGAATTTCAAG-ATTTT-ATCCTGAAAAAAATCAAATTCA-AATTAAAAT
*
2336 TCTGAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTG
128 CCTGAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTG
*
2401 GTGTCACTGTTTCATACAATCCTTT
193 GCGTCACTGTTTCATACAATCCTTT
2426 CCTTATATCA
Statistics
Matches: 195, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
268 2 0.01
269 190 0.97
270 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (269 bp):
GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
GAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
ATCAGGGGA
Done.