Locus 6086

Sequence ID	2L_DroMel_CAF1
Location	17,083,998 – 17,084,143
Length	145
Max. P	0.632916

overview

Window 2

Location	17,083,998 – 17,084,103
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	83.62
Mean single sequence MFE	-36.74
Consensus MFE	-24.52
Energy contribution	-25.48
Covariance contribution	0.96
Combinations/Pair	1.31
Mean z-score	-1.76
Structure conservation index	0.67
SVM decision value	0.12
SVM RNA-class probability	0.591461
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17083998 105 - 22407834
AAGUAAGUCGUCGGAGUCUGUGCCGCAGGGCGGACACUCCUCUUCGGCGAUCUCGGAGAUAUGUUCAUCAUCCACGCUUAGUUGACUCUCCGAUGACUCUGUGAA
.....(((((((((((...((((((.((((.((.....))))))))))......((((((......))).)))...........)).)))))))))))....... ( -35.00)
>DroSec_CAF1 47876 105 - 1
AAGUAAGUCGUCGGUGUCCGAGUCACACGGAGGACACUCCUCUUCGCCGAUCUCGGAGAUAUGUUCAUCAUCCACGCUUAGUAGACUCUCCGAGGACUCUGUGAA
.....(((((((((((((((.......))))((.....))....)))))))((((((((..((.....))((.((.....)).)).))))))))))))....... ( -31.00)
>DroSim_CAF1 43422 105 - 1
AAGUAAGUCGUCGGUGUCGGUGUCGCAUGGAGGACACUCCUCUUCGCCGAUCUCGGAGAUAUGUUCAUCAUCUACGCUUAGUAGACUCUCCGAGGACUCUGUGAA
.......(((.(((.(((((((......((((....))))....))))...((((((((..((.....))(((((.....))))).))))))))))).)))))). ( -37.60)
>DroEre_CAF1 49097 105 - 1
AAUGAAGUCAAACGAGUUGUCGUCGCAGGGAGCACACUCCUCUUCGGCGAUCUCGGAGACAUAGUCGUUAUCCACGCUAAGUAGGCUGUCCGAUGACUGGGUGAA
......(((...((((..(((((((.((((((....)))).)).)))))))))))..))).((((((((...((.(((.....)))))...))))))))...... ( -35.80)
>DroYak_CAF1 48201 105 - 1
AAUCAAGUCAUCGGAGUCGUCGUCGCAGGGAGCACACUCCUCUUCGGCGAUUUCGGAGAUAUAGUCGUUAUCCACGCUGGGUAGACUGUCCGAUGACUGGGUGAA
.(((.(((((((((((..(((((((.((((((....)))).)).)))))))..).......(((((..(((((.....)))))))))))))))))))).)))... ( -44.30)
>consensus
AAGUAAGUCGUCGGAGUCGGCGUCGCAGGGAGGACACUCCUCUUCGGCGAUCUCGGAGAUAUGUUCAUCAUCCACGCUUAGUAGACUCUCCGAUGACUCUGUGAA
.....(((((((((.(((..(((((.((((((....)))).)).))))).....((((((......))).)))..........)))...)))))))))....... (-24.52 = -25.48 +   0.96)

alignment

secondary structure

dotplot

Window 3

Location	17,084,038 – 17,084,143
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	85.62
Mean single sequence MFE	-38.38
Consensus MFE	-25.28
Energy contribution	-26.08
Covariance contribution	0.80
Combinations/Pair	1.20
Mean z-score	-2.01
Structure conservation index	0.66
SVM decision value	0.20
SVM RNA-class probability	0.632916
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17084038 105 - 22407834
UCAUCGAUUGGUCUGUAGCCCGAUCGUAUUGGAAGUACGGAAGUAAGUCGUCGGAGUCUGUGCCGCAGGGCGGACACUCCUCUUCGGCGAUCUCGGAGAUAUGUU
..(((((((((.(....).))))))...((.((..(((....))).((((((((((...(((((((...)))).)))....)))))))))).)).)))))..... ( -36.60)
>DroSec_CAF1 47916 105 - 1
UCAUCGAUUGGUCUGUAGGCCGAUCGUAUUGGAAAUACGGAAGUAAGUCGUCGGUGUCCGAGUCACACGGAGGACACUCCUCUUCGCCGAUCUCGGAGAUAUGUU
.((.(((((((((....)))))))))...))((..(((....)))..))....((.((((((((....(((((.....))))).....)).)))))).))..... ( -37.80)
>DroSim_CAF1 43462 105 - 1
UCAUCGAUUGGUCUGUAGGCCGAUCGUAUUGGAAAUACGGAAGUAAGUCGUCGGUGUCGGUGUCGCAUGGAGGACACUCCUCUUCGCCGAUCUCGGAGAUAUGUU
(((.(((((((((....)))))))))...)))...(((....))).(((..((..(((((((......((((....))))....)))))))..))..)))..... ( -41.40)
>DroEre_CAF1 49137 105 - 1
ACUGCGAUUGGUCUGUAGGUCGAUCGUACUGGAGAUACGGAAUGAAGUCAAACGAGUUGUCGUCGCAGGGAGCACACUCCUCUUCGGCGAUCUCGGAGACAUAGU
..((((((((..(....)..))))))))(((......)))......(((...((((..(((((((.((((((....)))).)).)))))))))))..)))..... ( -39.80)
>DroYak_CAF1 48241 105 - 1
ACAUCGAUUGGUCUGUAGGUCGAUCGUAUUGGAGAUACGGAAUCAAGUCAUCGGAGUCGUCGUCGCAGGGAGCACACUCCUCUUCGGCGAUUUCGGAGAUAUAGU
.((.((((((..(....)..))))))...))..(((.....)))..(((..(((((((((((.....(((((....)))))...)))))))))))..)))..... ( -36.30)
>consensus
UCAUCGAUUGGUCUGUAGGCCGAUCGUAUUGGAAAUACGGAAGUAAGUCGUCGGAGUCGGCGUCGCAGGGAGGACACUCCUCUUCGGCGAUCUCGGAGAUAUGUU
....(((((((((....)))))))))..(((......)))......(((..(((.(((((((.....(((((....)))))...))))))).)))..)))..... (-25.28 = -26.08 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:01 2006