Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00871.N5
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, 517
Length: 863
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Found at i:594 original size:20 final size:21
Alignment explanation
Indices: 556--595 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
546 ATGTCATATC
556 AGTATTCTTATTCTGAATTTT
1 AGTATTCTTATTCTGAATTTT
577 AGTATT-TTAATT-TGAATTT
1 AGTATTCTT-ATTCTGAATTT
596 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:699 original size:269 final size:269
Alignment explanation
Indices: 220--705 Score: 753
Period size: 269 Copynumber: 1.8 Consensus size: 269
210 ATTAAGAGGG
*
220 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTTCAATAGTTTTATGTCATA
1 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
285 TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
66 TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
*
350 GAAATTCAGGATAAGAATACTGATGTGGTATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
131 GAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
415 TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
196 TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
480 ATCAGGGGA
261 ATCAGGGGA
* *
489 GAAAGGATTGTGTGAAATAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
1 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
* * * * * *** **** *
554 TCAGTATTCTTATTCTGAATTT-TAGTATTTTAAT-TTGAATTTAATTTTTTTCAGGA-TAAAAT
66 TCAATATTCTTATCCAGAATTTCAAG-ATTTT-ATCCTGAAAAAAATCAAATTCA-AATTAAAAT
*
616 TCTGAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTG
128 CCTGAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTG
*
681 GTGTCACTGTTTCATACAATCCTTT
193 GCGTCACTGTTTCATACAATCCTTT
706 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.