Locus 6542

Sequence ID	3R_DroMel_CAF1
Location	17,247,784 – 17,247,876
Length	92
Max. P	0.981133

overview

Window 7

Location	17,247,784 – 17,247,876
Length	92
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	76.99
Mean single sequence MFE	-20.26
Consensus MFE	-11.64
Energy contribution	-13.36
Covariance contribution	1.72
Combinations/Pair	1.24
Mean z-score	-2.36
Structure conservation index	0.57
SVM decision value	1.88
SVM RNA-class probability	0.981133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17247784 92 + 27905053
AAAUCCACUUUUUGUACACAUCAUUGUGUGCACUGAAAGAAAAUGAU-GUUUUUAUAGAAA--AUCGAAAGUGUACUCAUUCAAUUUUAAAGUAC---
.....(((((((((((((((....))))))))(((.(((((......-.))))).)))...--...)))))))......................--- ( -16.70)
>DroSec_CAF1 44210 92 + 1
AAAUGCACUUUUUGUACACAUUAUCGUGUACACUGAAAGAAACUGAU-GUUUUUAUAGAAA--AUCGAAAGUGUACUCAUACAAUUUUAAAGUAC---
...((((((((((((((((......)))))))(((..((((((....-)))))).)))...--...)))))))))....................--- ( -20.10)
>DroSim_CAF1 44881 92 + 1
AAAUGCACUUUUUGUACACAUCAGUGUGUACACUGCAAGAAAAUGAU-GUUUUUAUUGAAA--AUCGAAAGUGUACUCAUACAAUUUUAAAGUAA---
...(((((((((((((((((....))))))))...(((.((((....-..)))).)))...--...)))))))))....................--- ( -19.00)
>DroEre_CAF1 44958 94 + 1
AAAUGCACUUUUUGCACACAUCAUUGGGUGCACUGCAAGAUAAGUAUUGUACUUACAGCAA----AUAAAUAAUGCCUAUACAAUUUGUAAGUAUUUU
.(((((...(((((((..((((....))))...)))))))...)))))((((((((((((.----........)))..........)))))))))... ( -19.50)
>DroYak_CAF1 66982 98 + 1
AAAUGCACUUUUUGCACACAUCAUUGUGUGCACUGCAAAAUAAGUAUAUUUGUUUUAGAGACACGCGAAGGAAUACUUAUACAAGCUGUAAGUAUUUU
...(((......((((((((....))))))))((..((((((((....))))))))..))....)))..((((((((((((.....)))))))))))) ( -26.00)
>consensus
AAAUGCACUUUUUGUACACAUCAUUGUGUGCACUGCAAGAAAAUGAU_GUUUUUAUAGAAA__AUCGAAAGUGUACUCAUACAAUUUUAAAGUAC___
...(((((((((((((((((....))))))))(((.(((((........))))).)))........)))))))))....................... (-11.64 = -13.36 +   1.72)

alignment

secondary structure

dotplot

Window 8

Location	17,247,784 – 17,247,876
Length	92
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	76.99
Mean single sequence MFE	-18.62
Consensus MFE	-12.18
Energy contribution	-11.74
Covariance contribution	-0.44
Combinations/Pair	1.33
Mean z-score	-1.81
Structure conservation index	0.65
SVM decision value	0.85
SVM RNA-class probability	0.865378
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17247784 92 - 27905053
---GUACUUUAAAAUUGAAUGAGUACACUUUCGAU--UUUCUAUAAAAAC-AUCAUUUUCUUUCAGUGCACACAAUGAUGUGUACAAAAAGUGGAUUU
---.((((((((((((((..(((....))))))))--)))..........-..............(((((((......)))))))..))))))..... ( -16.80)
>DroSec_CAF1 44210 92 - 1
---GUACUUUAAAAUUGUAUGAGUACACUUUCGAU--UUUCUAUAAAAAC-AUCAGUUUCUUUCAGUGUACACGAUAAUGUGUACAAAAAGUGCAUUU
---((((((((((((((...(((....))).))))--)))..........-...............(((((((......))))))).))))))).... ( -19.50)
>DroSim_CAF1 44881 92 - 1
---UUACUUUAAAAUUGUAUGAGUACACUUUCGAU--UUUCAAUAAAAAC-AUCAUUUUCUUGCAGUGUACACACUGAUGUGUACAAAAAGUGCAUUU
---.(((((((((((((...(((....))).))))--)))..........-...............((((((((....)))))))).))))))..... ( -16.40)
>DroEre_CAF1 44958 94 - 1
AAAAUACUUACAAAUUGUAUAGGCAUUAUUUAU----UUGCUGUAAGUACAAUACUUAUCUUGCAGUGCACCCAAUGAUGUGUGCAAAAAGUGCAUUU
...((((.........))))..(((((.(((..----..((((((((............))))))))((((.((....)).))))))).))))).... ( -20.00)
>DroYak_CAF1 66982 98 - 1
AAAAUACUUACAGCUUGUAUAAGUAUUCCUUCGCGUGUCUCUAAAACAAAUAUACUUAUUUUGCAGUGCACACAAUGAUGUGUGCAAAAAGUGCAUUU
....(((((...((....((((((((.........................))))))))...))..((((((((....))))))))..)))))..... ( -20.41)
>consensus
___AUACUUUAAAAUUGUAUGAGUACACUUUCGAU__UUUCUAUAAAAAC_AUCAUUUUCUUGCAGUGCACACAAUGAUGUGUACAAAAAGUGCAUUU
...((((((...........))))))...................................((((.((((((((....)))))))).....))))... (-12.18 = -11.74 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:01 2006