Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g02127.F2
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: 3798
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:2233 original size:375 final size:375
Alignment explanation
Indices: 1543--2294 Score: 1504
Period size: 375 Copynumber: 2.0 Consensus size: 375
1533 ATCGTATGAT
1543 TGAGGGACACCTAAAGTTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGGAACTG
1 TGAGGGACACCTAAAGTTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGGAACTG
1608 AACTATTTGATAACAAGCATTACCGAGAGATTGAAGCAGATGATGCAGTAGACGAAGATGATGGT
66 AACTATTTGATAACAAGCATTACCGAGAGATTGAAGCAGATGATGCAGTAGACGAAGATGATGGT
1673 GAACAAGACGATCAAGAGAACGAAGCTTTTGAAACCACGGAACTAGTTTCAGAAGGACCTGATGA
131 GAACAAGACGATCAAGAGAACGAAGCTTTTGAAACCACGGAACTAGTTTCAGAAGGACCTGATGA
1738 AGTACAGCAAGGAATTGAGGTTGAGATGATTGAACTAGATCATTTAGAGACAGAGGAGAGCAAAG
196 AGTACAGCAAGGAATTGAGGTTGAGATGATTGAACTAGATCATTTAGAGACAGAGGAGAGCAAAG
1803 GTGTTGAATTTGCTGTTGAGATGCAAGCTGAACTTCAGAGCAATGTGGACACTGAAAACCAGCAA
261 GTGTTGAATTTGCTGTTGAGATGCAAGCTGAACTTCAGAGCAATGTGGACACTGAAAACCAGCAA
1868 AGTGTGATCTCACCGCAGGCTAGTGTAATTCAACATGATGGCTTGAACAA
326 AGTGTGATCTCACCGCAGGCTAGTGTAATTCAACATGATGGCTTGAACAA
1918 TGAGGGACACCTAAAGTTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGGAACTG
1 TGAGGGACACCTAAAGTTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGGAACTG
1983 AACTATTTGATAACAAGCATTACCGAGAGATTGAAGCAGATGATGCAGTAGACGAAGATGATGGT
66 AACTATTTGATAACAAGCATTACCGAGAGATTGAAGCAGATGATGCAGTAGACGAAGATGATGGT
2048 GAACAAGACGATCAAGAGAACGAAGCTTTTGAAACCACGGAACTAGTTTCAGAAGGACCTGATGA
131 GAACAAGACGATCAAGAGAACGAAGCTTTTGAAACCACGGAACTAGTTTCAGAAGGACCTGATGA
2113 AGTACAGCAAGGAATTGAGGTTGAGATGATTGAACTAGATCATTTAGAGACAGAGGAGAGCAAAG
196 AGTACAGCAAGGAATTGAGGTTGAGATGATTGAACTAGATCATTTAGAGACAGAGGAGAGCAAAG
2178 GTGTTGAATTTGCTGTTGAGATGCAAGCTGAACTTCAGAGCAATGTGGACACTGAAAACCAGCAA
261 GTGTTGAATTTGCTGTTGAGATGCAAGCTGAACTTCAGAGCAATGTGGACACTGAAAACCAGCAA
2243 AGTGTGATCTCACCGCAGGCTAGTGTAATTCAACATGATGGCTTGAACAA
326 AGTGTGATCTCACCGCAGGCTAGTGTAATTCAACATGATGGCTTGAACAA
2293 TG
1 TG
2295 TGGACACTGA
Statistics
Matches: 377, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
375 377 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (375 bp):
TGAGGGACACCTAAAGTTTGATCCCAGTGTAATGGAGCCTGTAAGTGAGAGAGATGCTGGAACTG
AACTATTTGATAACAAGCATTACCGAGAGATTGAAGCAGATGATGCAGTAGACGAAGATGATGGT
GAACAAGACGATCAAGAGAACGAAGCTTTTGAAACCACGGAACTAGTTTCAGAAGGACCTGATGA
AGTACAGCAAGGAATTGAGGTTGAGATGATTGAACTAGATCATTTAGAGACAGAGGAGAGCAAAG
GTGTTGAATTTGCTGTTGAGATGCAAGCTGAACTTCAGAGCAATGTGGACACTGAAAACCAGCAA
AGTGTGATCTCACCGCAGGCTAGTGTAATTCAACATGATGGCTTGAACAA
Found at i:3522 original size:334 final size:334
Alignment explanation
Indices: 2913--3798 Score: 1754
Period size: 334 Copynumber: 2.7 Consensus size: 334
2903 GGAGTAGAAG
2913 AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
1 AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
2978 TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
66 TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
3043 CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTTTCATAA
131 CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTTTCATAA
*
3108 CTTTGAATAGCACTCTTAGCTTTCAATTCCTTTTTTTCTTCACAGTTCCTTAGGTTCTGGTTGCT
196 CTTTGAATAGCACTCTTAGCTTTCAATCCCTTTTTTTCTTCACAGTTCCTTAGGTTCTGGTTGCT
3173 TGGTTGAGAAGTATGAGATCAAATGAAAGTTAATTCCAGTATTTGTGGATATGCATCTTAACTGC
261 TGGTTGAGAAGTATGAGATCAAATGAAAGTTAATTCCAGTATTTGTGGATATGCATCTTAACTGC
3238 GTGTAGTTT
326 GTGTAGTTT
3247 AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
1 AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
3312 TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
66 TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
3377 CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTTTCATAA
131 CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTTTCATAA
3442 CTTTGAATAGCACTCTTAGCTTTCAATCCCTTTTTTTCTTCACAGTTCCTTAGGTTCTGGTTGCT
196 CTTTGAATAGCACTCTTAGCTTTCAATCCCTTTTTTTCTTCACAGTTCCTTAGGTTCTGGTTGCT
3507 TGGTTGAGAAGTATGAGATCAAATGAAAGTTAATTCCAGTATTTGTGGATATGCATCTTAACTGC
261 TGGTTGAGAAGTATGAGATCAAATGAAAGTTAATTCCAGTATTTGTGGATATGCATCTTAACTGC
3572 GTGTAGTTT
326 GTGTAGTTT
3581 AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
1 AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
3646 TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
66 TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
*
3711 CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTCTCATAA
131 CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTTTCATAA
3776 CTTTGAATAGCACTCTTAGCTTT
196 CTTTGAATAGCACTCTTAGCTTT
Statistics
Matches: 550, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 550 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (334 bp):
AAGAGATAGTTACTCCAGTTAGGCGTTCCAGCAGAATCAGAAACCAAGTTACATCTCCGTGACGA
TTGACAAGTTACATCTTATGTGTGTAACAGTAGCACTACTGTGCAATTCTAATGTGAATGAACCA
CTGTTGTTGGATGCAGACATTAGATTAGGACTTAATTGTACTATTATTCATTGTTCTTTTCATAA
CTTTGAATAGCACTCTTAGCTTTCAATCCCTTTTTTTCTTCACAGTTCCTTAGGTTCTGGTTGCT
TGGTTGAGAAGTATGAGATCAAATGAAAGTTAATTCCAGTATTTGTGGATATGCATCTTAACTGC
GTGTAGTTT
Done.