Locus 3309

Sequence ID	2R_DroMel_CAF1
Location	11,280,221 – 11,280,317
Length	96
Max. P	0.993296

overview

Window 4

Location	11,280,221 – 11,280,317
Length	96
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	72.35
Mean single sequence MFE	-31.56
Consensus MFE	-21.07
Energy contribution	-21.74
Covariance contribution	0.67
Combinations/Pair	1.12
Mean z-score	-1.99
Structure conservation index	0.67
SVM decision value	2.03
SVM RNA-class probability	0.986202
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11280221 96 + 20766785
UUUUGGAACAAUCGGAGCUUUGAAUGGAGCAGUAGCUUUGGUUGGAGCUGCCGAUGGAA------------CAGGAGCGGGAGCACUUGCUGAUCCUGGAGCUGUGAU
..........((((((((((..(..(((((....)))))..)..))))).)))))((..------------((((((((((....)))))...)))))...))..... ( -33.00)
>DroSec_CAF1 67429 90 + 1
UUUUGGAACAAUCGGAGCUUUGAAUGGAGCAGUAGCUUUGGUUGAAGCUGCCGAUGGAG------------------CGGGAGCAUUUGCUGAUCCUGGAGCUGUGAU
((..(((.((((((((((((..(..(((((....)))))..)..))))).)))))...(------------------(....))......)).)))..))........ ( -28.40)
>DroSim_CAF1 69851 90 + 1
UUUUGGAACAAUCGGAGCUUUGAAUGGAGCAGUAGCUUUGGUUGGAGCUGCCGANNNNN------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...........(((((((((..(..(((((....)))))..)..))))).)))).....------------------............................... ( -19.70)
>DroEre_CAF1 68836 108 + 1
UUUGGGAACAAUCGGAGCUUUGAAUGGAGCAGUAGCUCUGGUCGGAGCUGCCAAUGGAGCUGGAGCUGCAGCAGGAGCGGGAGCAUUUGCUGAUCCUGGAGCUGUGAU
.(((....)))..((((((((((..(((((....)))))..)))))))).))...(.(((((((....(((((((.((....)).))))))).)))...)))).)... ( -42.60)
>DroYak_CAF1 69143 102 + 1
UUUUGGAACAAUCGGUGCCUUGAAUGGAGCAGUAGCUUUGAUUGGAGCUGCCGAUGGUGCAGGA------GCAGGAGCGGGAGCAUUUGCUGAUCCUGGAGCUGUGAU
.......(((((((((..(((.((((((((....))))).))).)))..))))))(.(.(((((------(((((.((....)).)))))...))))).).))))... ( -34.10)
>consensus
UUUUGGAACAAUCGGAGCUUUGAAUGGAGCAGUAGCUUUGGUUGGAGCUGCCGAUGGAG____________CAGGAGCGGGAGCAUUUGCUGAUCCUGGAGCUGUGAU
..........(((((((((((((..(((((....)))))..)))))))).)))))......................(((((.((.....)).))))).......... (-21.07 = -21.74 +   0.67)

alignment

secondary structure

dotplot

Window 5

Location	11,280,221 – 11,280,317
Length	96
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	72.35
Mean single sequence MFE	-20.62
Consensus MFE	-11.74
Energy contribution	-12.57
Covariance contribution	0.83
Combinations/Pair	1.11
Mean z-score	-2.30
Structure conservation index	0.57
SVM decision value	2.39
SVM RNA-class probability	0.993296
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11280221 96 - 20766785
AUCACAGCUCCAGGAUCAGCAAGUGCUCCCGCUCCUG------------UUCCAUCGGCAGCUCCAACCAAAGCUACUGCUCCAUUCAAAGCUCCGAUUGUUCCAAAA
...(((......(((.(((..((((....)))).)))------------.)))(((((.((((........(((....)))........))))))))))))....... ( -21.79)
>DroSec_CAF1 67429 90 - 1
AUCACAGCUCCAGGAUCAGCAAAUGCUCCCG------------------CUCCAUCGGCAGCUUCAACCAAAGCUACUGCUCCAUUCAAAGCUCCGAUUGUUCCAAAA
............(((.((((....)).....------------------....(((((.(((((.......(((....))).......)))))))))))).))).... ( -19.44)
>DroSim_CAF1 69851 90 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------------------NNNNNUCGGCAGCUCCAACCAAAGCUACUGCUCCAUUCAAAGCUCCGAUUGUUCCAAAA
...............................------------------.....((((.((((........(((....)))........))))))))........... ( -11.89)
>DroEre_CAF1 68836 108 - 1
AUCACAGCUCCAGGAUCAGCAAAUGCUCCCGCUCCUGCUGCAGCUCCAGCUCCAUUGGCAGCUCCGACCAGAGCUACUGCUCCAUUCAAAGCUCCGAUUGUUCCCAAA
......((..(((((.((((....)))...).)))))..))(((....)))..(((((.((((..((...((((....))))...))..))))))))).......... ( -28.60)
>DroYak_CAF1 69143 102 - 1
AUCACAGCUCCAGGAUCAGCAAAUGCUCCCGCUCCUGC------UCCUGCACCAUCGGCAGCUCCAAUCAAAGCUACUGCUCCAUUCAAGGCACCGAUUGUUCCAAAA
..........(((((.(((.....((....))..))).------))))).((.(((((.((((........))))..((((........))))))))).))....... ( -21.40)
>consensus
AUCACAGCUCCAGGAUCAGCAAAUGCUCCCGCUCCUG____________CUCCAUCGGCAGCUCCAACCAAAGCUACUGCUCCAUUCAAAGCUCCGAUUGUUCCAAAA
............(((..(((....)))..........................(((((.((((........(((....)))........)))))))))...))).... (-11.74 = -12.57 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:21 2006