Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1059 ID=scaffold_1059-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: 3393
ACGTcount: A:0.10, C:0.06, G:0.09, T:0.10
Warning! 2196 characters in sequence are not A, C, G, or T
Found at i:283 original size:169 final size:169
Alignment explanation
Indices: 1--458 Score: 754
Period size: 169 Copynumber: 2.7 Consensus size: 169
1 GGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGA
1 GGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGA
66 GCAGATTAAAGCTTAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCTAAAGTG
66 GCAGATTAAAGCTTAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCTAAAGTG
* *
131 GAGTGGATTGAAGCTGTGGGTAGAGAATACTATCTCTTT
131 GAGTGGATTAAAGCTGTGGGCAGAGAATACTATCTCTTT
* * * * *
170 GGTATTATAGTGGAACACATTAAAGTTAAAGGTAGCAAATCCTGTTTCCCTAGCATCGCAGCAGA
1 GGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGA
* * *
235 GCAGATTACAGCTTAGGACAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCTGAAGTG
66 GCAGATTAAAGCTTAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCTAAAGTG
* * * *
300 GAGTTGATTAAAGCTGTGGGCAGTGAATCCTATCTGTTT
131 GAGTGGATTAAAGCTGTGGGCAGAGAATACTATCTCTTT
** *
339 GGCATTATAGTGGAACACATTAAAGGAAAAGGTAGCGAATTTTGTTTCCCTAGCATCGCAGCGGA
1 GGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGA
*
404 GCAGATTAAAGCGTAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAAT
66 GCAGATTAAAGCTTAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAAT
459 NNNNNNNNNN
Statistics
Matches: 265, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
169 265 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (169 bp):
GGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGA
GCAGATTAAAGCTTAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCTAAAGTG
GAGTGGATTAAAGCTGTGGGCAGAGAATACTATCTCTTT
Found at i:2868 original size:169 final size:170
Alignment explanation
Indices: 2555--2875 Score: 556
Period size: 169 Copynumber: 1.9 Consensus size: 170
2545 NNNNNNNNNN
*
2555 ATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGG
1 ATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGA
2620 CAGTGAACTCTTATCTCCCTAGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAAGCTGT
66 CAGTGAACTCTTATCTCCCTAGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAAGCTGT
2685 GGGCAGTCAATCCTATCTCTTTGGCATTATAGTGGAACAC
131 GGGCAGTCAATCCTATCTCTTTGGCATTATAGTGGAACAC
* * *
2725 ATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGTAGCAGTTTACAGCTTAGGA
1 ATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGA
* * *
2790 CAGTGAA-TCTTATCTCCCTGGTGTTAAGACTTGAAATAGCTGTAGTGGAGTGGATTAAAGCTGT
66 CAGTGAACTCTTATCTCCCTAGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAAGCTGT
2854 GGGCAG-CGAATCCTATCTCTTT
131 GGGCAGTC-AATCCTATCTCTTT
2876 CGCAGTNNNN
Statistics
Matches: 143, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
168 1 0.01
169 74 0.52
170 68 0.48
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (170 bp):
ATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGA
CAGTGAACTCTTATCTCCCTAGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAAGCTGT
GGGCAGTCAATCCTATCTCTTTGGCATTATAGTGGAACAC
Found at i:3270 original size:169 final size:169
Alignment explanation
Indices: 2985--3393 Score: 667
Period size: 169 Copynumber: 2.4 Consensus size: 169
2975 NNNNNNNGCC
*
2985 AATCTTGTTTCCCTAGCATCGCAGCCGGAGTAGATTAAAGCTTAGGGA-AGCGAATCTTATCTCC
1 AATCTTGTTTCCCTAGCATCGCAG-CGGAGCAGATTAAAGCTTA-GGACAGCGAATCTTATCTCC
**
3049 CTGGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATGAAAGCTATGGGCAGTGAATCCTATCT
64 CTGGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATGAAAGCTATGGGCAGCAAATCCTATCT
3114 CTTTGGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCG
129 CTTTGGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCG
* *
3155 AATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTACAGCTTAGGACAGCGAATCTTATCTCCTT
1 AATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGACAGCGAATCTTATCTCCCT
* * *
3220 GGTGTTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAAGCTGTGGGCAGCAAATCCTATCTCT
66 GGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATGAAAGCTATGGGCAGCAAATCCTATCTCT
* * *
3285 TTGGTATTATAGTGGAACAGATTAAAGCTACAGGTAGCG
131 TTGGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCG
* *
3324 AATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGGCAGTGAATCTTATCTCCCT
1 AATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGACAGCGAATCTTATCTCCCT
*
3389 AGTCT
66 GGTCT
Statistics
Matches: 221, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
168 3 0.01
169 194 0.88
170 24 0.11
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (169 bp):
AATCTTGTTTCCCTAGCATCGCAGCGGAGCAGATTAAAGCTTAGGACAGCGAATCTTATCTCCCT
GGTCTTAAGACTTGAAATAGCTGAAGTGGAGTGGATGAAAGCTATGGGCAGCAAATCCTATCTCT
TTGGCATTATAGTGGAACACATTAAAGCTAAAGGTAGCG
Done.