Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1078 ID=scaffold_1078-JGI_221_v2.0
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: 3564
ACGTcount: A:0.08, C:0.06, G:0.07, T:0.10
Warning! 2477 characters in sequence are not A, C, G, or T
Found at i:3381 original size:303 final size:302
Alignment explanation
Indices: 2824--3564 Score: 1151
Period size: 303 Copynumber: 2.4 Consensus size: 302
2814 NNNNNNNNNN
* * * * * *
2824 GAGTTGACGGGTGCGATCATCCCAGCACTAATGCGCTGTATCTCATAAGAACTCTCGCAGTT-AG
1 GAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC-CGCAGTTAAG
* * * * *
2888 CGTGCTCGGGGCGAGAGTAGTACTAGGATGGGTGTCCTCCTGGGAAGTGCTCGCGTTGTACCCCT
65 CGTGCT-TGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCT
* *
2953 CCCCATTTTATTTCATATAATTTTTTTTAAGTTGCATTTTCTCGGCGTGGCGTAACTCATTCGTT
129 -CCCATTTTATTTCATAGAATTTTTTTTAAGTTGCATTTTCTCGACGTGGCGTAACTCATTCGTT
* *
3018 ATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCAAATTTGCATTTAAATTCGAGG
193 ATTTGCGTTTTGTGAAATAAACAATCTGAAACGATATTCGGTCAAATTTGCATTTAAATTCGAGG
*
3083 CGCAAGTGCAATCAGGGGCAACCTTTATATGAATAGATTGCGCAA
258 CGCAAGTGCAATAAGGGGCAACCTTTATATGAATAGATTGCGCAA
* * *
3128 GAGTTAACAGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAATC
1 GAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGC
3193 GTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCC
66 GTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCC
* * *
3258 CATTTTATTTCATAGAATGTTTTTTTTAGTTGCATTTTCTTGACGTGGTGTAACTCATTCGTTAT
131 CATTTTATTTCATAGAAT-TTTTTTTAAGTTGCATTTTCTCGACGTGGCGTAACTCATTCGTTAT
* * * *
3323 TTTCGTTTTGTGAAATAAATAATCTGGAACGATATTCGGTCGAATTTGCATTTAAATTCGAGGCG
195 TTGCGTTTTGTGAAATAAACAATCTGAAACGATATTCGGTCAAATTTGCATTTAAATTCGAGGCG
* *
3388 CAAGTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAA
260 CAAGTGCAATAAGGGGCAACCTTTATATGAATAGATTGCGCAA
* *
3431 GAGTTGATGGGTGCGATCATACCAGCACTAATGCACCGGATCCAATCAGAACTCCGCAGTTAAGC
1 GAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGC
* *
3496 GTGCTTTGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCGTCGTGTTGCACCCCTCC
66 GTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCC
3561 CATT
131 CATT
Statistics
Matches: 400, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
302 19 0.05
303 328 0.82
304 53 0.13
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (302 bp):
GAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGC
GTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCC
CATTTTATTTCATAGAATTTTTTTTAAGTTGCATTTTCTCGACGTGGCGTAACTCATTCGTTATT
TGCGTTTTGTGAAATAAACAATCTGAAACGATATTCGGTCAAATTTGCATTTAAATTCGAGGCGC
AAGTGCAATAAGGGGCAACCTTTATATGAATAGATTGCGCAA
Done.