Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1087 ID=scaffold_1087-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: 2722
ACGTcount: A:0.10, C:0.07, G:0.09, T:0.12
Warning! 1677 characters in sequence are not A, C, G, or T
Found at i:2587 original size:303 final size:301
Alignment explanation
Indices: 2040--2722 Score: 1177
Period size: 303 Copynumber: 2.3 Consensus size: 301
2030 NNNNNNNNNN
* *
2040 TAGTTGCATTTTCTCGACGTGGTGTAACTCAATCGTTATTTGTGTTTTGTGAAATAAACAATTTG
1 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAACAA-TTG
*
2105 AAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTAT
65 AAACGATATTTGGTCGAAGTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTAT
* *
2170 ATGAATAGATTGCGCAAGAGTTTACGGGTGCGATCATACCAGCAATAATGCACCGGATCCCATCA
130 ATGAATAGATTGCGCAAGAGCTGACGGGTGCGATCATACCAGCAATAATGCACCGGATCCCATCA
* * *
2235 GAACTTCATAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
195 GAACTCCACAGTTAAGCGTGCTTGGGCCAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
2300 TCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTTTT
260 TCGTGTTGCACCCCTCCCATTTTATTTCATATAAT-GTTTTTT
* * * * *
2343 TAGTTGCATTTTCTTGACGTGGTGTAACTCTTTTGTTATTTGCGTTTTCTGAAATAAATAACTTG
1 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAACAA-TTG
2408 AAACGATATTTGGTCGAAGTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTAT
65 AAACGATATTTGGTCGAAGTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTAT
* *
2473 ATGAATAGATTGCGCCAGAGCTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
130 ATGAATAGATTGCGCAAGAGCTGACGGGTGCGATCATACCAGCAATAATGCACCGGATCCCATCA
* * *
2538 GAACTCCGCAGTTTAGCGTGCTTGGGCCAGAGTAGTACTAGGATGGGTGACCTCCTTGGAAGTCC
195 GAACTCCACAGTTAAGCGTGCTTGGGCCAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
2603 TCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTT
260 TCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTT
2645 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAACAATTGA
1 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAACAATTGA
2710 AACGATATTTGGT
66 AACGATATTTGGT
Statistics
Matches: 356, Mismatches: 24, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
301 17 0.05
302 63 0.18
303 276 0.78
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (301 bp):
TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAACAATTGA
AACGATATTTGGTCGAAGTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTATA
TGAATAGATTGCGCAAGAGCTGACGGGTGCGATCATACCAGCAATAATGCACCGGATCCCATCAG
AACTCCACAGTTAAGCGTGCTTGGGCCAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCT
CGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTT
Done.