Locus 4611

Sequence ID	X_DroMel_CAF1
Location	12,070,494 – 12,070,624
Length	130
Max. P	0.859043

overview

Window 0

Location	12,070,494 – 12,070,591
Length	97
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	84.97
Mean single sequence MFE	-35.97
Consensus MFE	-23.89
Energy contribution	-23.77
Covariance contribution	-0.12
Combinations/Pair	1.15
Mean z-score	-2.41
Structure conservation index	0.66
SVM decision value	0.82
SVM RNA-class probability	0.859043
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12070494 97 + 22224390
GCCCGUUUUGCUGUAACAAAAGCACACGAAGAUGAAGUUGGAGCUGGAGC------AGGAACAGUAGGAUUCCGGA--------------CUCAGGAUCCUGGGAUCCUGGAUCCAC
(((((....(((.((((...................)))).)))))).))------.((((........))))(((--------------..(((((((....)))))))..))).. ( -31.81)
>DroSec_CAF1 6377 96 + 1
GCCCGUUUUGCUGUAACAAAAGCACACGAAGAUGAAGUUGGAGCUGGAGC------AGGAACAGUAGGAUUCAGGA--------------CUCAGGAUCCUGGGAUCC-GGAUCCAC
.((.((((((((.((((...................)))).))).)))))------.)).......((((((.(((--------------(((((....))))).)))-)))))).. ( -30.31)
>DroSim_CAF1 6359 97 + 1
GCCCGUUUUGCUGUAACAAAAGCACACGAAGAUGAAGUUGGAGCUGGAGC------AGGAACAGUAGGAUUCAGGA--------------CUCAGGAUCCUGGGAUCCUGGAUCCAC
.((.((((((((.((((...................)))).))).)))))------.)).......((((((((((--------------(((((....))))).)))))))))).. ( -35.91)
>DroEre_CAF1 5953 117 + 1
GCCCGUUUUGCUGUAACAAAGGCACACGAAGAUGAAGUUGGAGUGGGAGUGGGAGCAGGAGCAGUAGGAUUCAGGAUUCAGGACGCAGGACUCGGGAUCCUGGAAUCCUGGAUCCAC
.(((((((..((.((((...................)))).))..))).)))).((....))....((((((((((((((((((.(.......).).)))).))))))))))))).. ( -42.31)
>DroYak_CAF1 5987 104 + 1
GCCCCUUUUGCUGUAACAAAAGUACACGAAGAUUAAGUUGGGGCAGGAGU------AGGAGCAGUAGGAUUCAGGAUUCAGGA-------CUCAGUAUUCUGGGAUCCUGGAUCCAC
((((((((((((.((((...................)))).)))))))).------.)).))...........((((((((((-------(((((....))))).)))))))))).. ( -39.51)
>consensus
GCCCGUUUUGCUGUAACAAAAGCACACGAAGAUGAAGUUGGAGCUGGAGC______AGGAACAGUAGGAUUCAGGA______________CUCAGGAUCCUGGGAUCCUGGAUCCAC
((((.....(((.((((...................)))).))).)).))................((((((((((..............(((((....))))).)))))))))).. (-23.89 = -23.77 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	12,070,532 – 12,070,624
Length	92
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	85.01
Mean single sequence MFE	-36.86
Consensus MFE	-25.40
Energy contribution	-26.28
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.10
Structure conservation index	0.69
SVM decision value	0.57
SVM RNA-class probability	0.787028
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12070532 92 + 22224390
UGGAGCUGGAGC------AGGAACAGUAGGAUUCCGGA--------------CUCAGGAUCCUGGGAUCCUGGAUCCACGACUUUGGCAGUGGGUUGAAUGAGCUGGCGGGC
....((..((((------.((((........))))(((--------------..(((((((....)))))))..)))..).)))..)).((.((((.....)))).)).... ( -36.60)
>DroSec_CAF1 6415 91 + 1
UGGAGCUGGAGC------AGGAACAGUAGGAUUCAGGA--------------CUCAGGAUCCUGGGAUCC-GGAUCCACGACUUUGGCAGUGGGUUGAAUGAGCUGGCGGGC
....((..(..(------(.........((((((.(((--------------(((((....))))).)))-)))))).((((((.......))))))..))..)..)).... ( -32.20)
>DroSim_CAF1 6397 92 + 1
UGGAGCUGGAGC------AGGAACAGUAGGAUUCAGGA--------------CUCAGGAUCCUGGGAUCCUGGAUCCACGACUUUGGCAGUGGGUUGAAUGAGCUGGCGGGC
....((..(..(------(.........((((((((((--------------(((((....))))).)))))))))).((((((.......))))))..))..)..)).... ( -37.80)
>DroEre_CAF1 5991 111 + 1
UGGAGUGGGAGUGGGAGCAGGAGCAGUAGGAUUCAGGAUUCAGGACGCAGGACUCGGGAUCCUGGAAUCCUGGAUCCACGACU-UGCCAGUGGGUUGAAUGAGCUGGCGGGC
........((((.(..((....))....((((((((((((((((((.(.......).).)))).))))))))))))).).)))-)(((.((.((((.....)))).)).))) ( -42.70)
>DroYak_CAF1 6025 99 + 1
UGGGGCAGGAGU------AGGAGCAGUAGGAUUCAGGAUUCAGGA-------CUCAGUAUUCUGGGAUCCUGGAUCCACGACUUUGGCAGUGGGUUGAAUGAGCUGGCGGGC
....((....((------..(((..((.(((((((((((((.(((-------........))).)))))))))))))))..)))..)).((.((((.....)))).))..)) ( -35.00)
>consensus
UGGAGCUGGAGC______AGGAACAGUAGGAUUCAGGA______________CUCAGGAUCCUGGGAUCCUGGAUCCACGACUUUGGCAGUGGGUUGAAUGAGCUGGCGGGC
....(((((...................((((((((((..............(((((....))))).)))))))))).((((((.......))))))......))))).... (-25.40 = -26.28 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:23 2006