Locus 7902

Sequence ID	X_DroMel_CAF1
Location	19,680,846 – 19,680,977
Length	131
Max. P	0.947754

overview

Window 1

Location	19,680,846 – 19,680,938
Length	92
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.26
Mean single sequence MFE	-24.72
Consensus MFE	-16.67
Energy contribution	-17.12
Covariance contribution	0.45
Combinations/Pair	1.17
Mean z-score	-2.35
Structure conservation index	0.67
SVM decision value	1.37
SVM RNA-class probability	0.947754
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19680846 92 + 22224390
AGUCACUCUUUUCCAAAUGCAG----------------------CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUC--GACGAGAGAUCUGCAAUUACAAACCGUUUGUUGU----GUGC
...(((...........(((((----------------------.........((....)).(((((((((.....--))))))))).)))))...((((........))))----))). ( -22.20)
>DroSec_CAF1 54679 92 + 1
AGUCACUCUUUUCCAAAUGCAG----------------------CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUC--GACGAGAGAUCUGCAUUUACAAUCCGUUUGUUGU----GUGC
...(((........((((((((----------------------.........((....)).(((((((((.....--))))))))).))))))))(((((......)))))----))). ( -26.30)
>DroSim_CAF1 41594 92 + 1
AGUCACUCUUUUCCAAAUGCAG----------------------CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUC--GACGAGAGAUCUGCAAUUACAAUCCGUUUGUUGU----GUGC
...(((...........(((((----------------------.........((....)).(((((((((.....--))))))))).)))))...(((((......)))))----))). ( -23.50)
>DroEre_CAF1 65894 94 + 1
AGUCACUCUUUUCCAAAUGCAG----------------------CUCUCUUUUUGGUUCCAUUCUCCCGACAAAUC--GGCGAGAGAUCUGCAAUUACAAUCUGU--GUUGUGUGCGUGC
...(((...........(((((----------------------.((((((..((....)).....((((....))--)).)))))).)))))..((((((....--))))))...))). ( -21.80)
>DroYak_CAF1 68149 91 + 1
AGUCACUCUUUUCCAAAUGCAG----------------------CUCUCUUUUUGGU-CCAGUCUCCCGUCAAAUC--GGCGAGAGAUCUGCAAUUACAAGCUGUUUGUUGU----GUGC
.............(((..((((----------------------((......(((..-.(((((((.((((.....--)))).)))).)))))).....))))))...))).----.... ( -21.70)
>DroAna_CAF1 79666 115 + 1
AGUCACACUGUUCCAGAUGCACUCUCCACUCUCCACACUCCACUCUCUCUCUCUGAC-UGUCUCUCCCGCUCAAUGAGAGCGGGAGAUCUGCAAUUACAAUCUGUUUUUGGU----GUGG
...(((((((...((((((((....................((..((.......)).-.)).((((((((((.....))))))))))..)))).......))))....))))----))). ( -32.81)
>consensus
AGUCACUCUUUUCCAAAUGCAG______________________CUCUCUUUUUGGUCCCAUUCUCCCGUCAAAUC__GACGAGAGAUCUGCAAUUACAAUCCGUUUGUUGU____GUGC
...(((...........(((((...............................((....)).(((((((((.......))))))))).)))))...((((........))))....))). (-16.67 = -17.12 +   0.45)

alignment

secondary structure

dotplot

Window 2

Location	19,680,846 – 19,680,938
Length	92
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.26
Mean single sequence MFE	-26.84
Consensus MFE	-18.47
Energy contribution	-18.63
Covariance contribution	0.17
Combinations/Pair	1.19
Mean z-score	-2.09
Structure conservation index	0.69
SVM decision value	1.18
SVM RNA-class probability	0.926408
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19680846 92 - 22224390
GCAC----ACAACAAACGGUUUGUAAUUGCAGAUCUCUCGUC--GAUUUGACGAGAGAAUGGGACCAAAAAGAGAG----------------------CUGCAUUUGGAAAAGAGUGACU
....----.......((..(((.(((.(((((.(((((((((--.....))))))))).((....)).........----------------------))))).))).)))...)).... ( -25.70)
>DroSec_CAF1 54679 92 - 1
GCAC----ACAACAAACGGAUUGUAAAUGCAGAUCUCUCGUC--GAUUUGACGAGAGAAUGGGACCAAAAAGAGAG----------------------CUGCAUUUGGAAAAGAGUGACU
...(----((.((((.....))))((((((((.(((((((((--.....))))))))).((....)).........----------------------))))))))........)))... ( -27.80)
>DroSim_CAF1 41594 92 - 1
GCAC----ACAACAAACGGAUUGUAAUUGCAGAUCUCUCGUC--GAUUUGACGAGAGAAUGGGACCAAAAAGAGAG----------------------CUGCAUUUGGAAAAGAGUGACU
...(----((.((((.....))))...(((((.(((((((((--.....))))))))).((....)).........----------------------)))))...........)))... ( -24.80)
>DroEre_CAF1 65894 94 - 1
GCACGCACACAAC--ACAGAUUGUAAUUGCAGAUCUCUCGCC--GAUUUGUCGGGAGAAUGGAACCAAAAAGAGAG----------------------CUGCAUUUGGAAAAGAGUGACU
............(--((...((.(((.(((((..(((((.((--((....)))).....((....))....)))))----------------------))))).))).))....)))... ( -22.30)
>DroYak_CAF1 68149 91 - 1
GCAC----ACAACAAACAGCUUGUAAUUGCAGAUCUCUCGCC--GAUUUGACGGGAGACUGG-ACCAAAAAGAGAG----------------------CUGCAUUUGGAAAAGAGUGACU
...(----((.((((.....))))...(((((..(((((...--..((((.(((....))).-..))))..)))))----------------------)))))...........)))... ( -22.30)
>DroAna_CAF1 79666 115 - 1
CCAC----ACCAAAAACAGAUUGUAAUUGCAGAUCUCCCGCUCUCAUUGAGCGGGAGAGACA-GUCAGAGAGAGAGAGUGGAGUGUGGAGAGUGGAGAGUGCAUCUGGAACAGUGUGACU
.(((----((......(((((.(((.(..(...((((((((((.....)))))))))).(((-.((..............)).))).....)..)....)))))))).....)))))... ( -38.14)
>consensus
GCAC____ACAACAAACAGAUUGUAAUUGCAGAUCUCUCGCC__GAUUUGACGAGAGAAUGGGACCAAAAAGAGAG______________________CUGCAUUUGGAAAAGAGUGACU
....................((.(((.(((((.(((((((((.......))))))))).((....))...............................))))).))).)).......... (-18.47 = -18.63 +   0.17)

alignment

secondary structure

dotplot

Window 3

Location	19,680,868 – 19,680,977
Length	109
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	87.62
Mean single sequence MFE	-36.80
Consensus MFE	-25.36
Energy contribution	-25.52
Covariance contribution	0.16
Combinations/Pair	1.24
Mean z-score	-1.99
Structure conservation index	0.69
SVM decision value	0.20
SVM RNA-class probability	0.628744
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19680868 109 + 22224390
CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUCGACGAGAGAUCUGCAAUUACAAACCGUUUGUUGU----GUGCGUGCCAGUGGCGUAUGCAGUGAAUGGUAAAGGGGGGCUG
..........((((((..(((((((((.....))))))))).............((((((..((((----((((((.......))))))))))..)))))).....)))))). ( -46.10)
>DroSec_CAF1 54701 104 + 1
CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUCGACGAGAGAUCUGCAUUUACAAUCCGUUUGUUGU----GUGCGUGCCAGUGGCGUAUGCAGUGAAUUGUAAGG-GG----G
............((((..(((((((((.....))))))))).......(((((....(((..((((----((((((.......))))))))))..))))))))))-))----. ( -36.80)
>DroSim_CAF1 41616 105 + 1
CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUCGACGAGAGAUCUGCAAUUACAAUCCGUUUGUUGU----GUGCGUGCCAGUGGCGUAUGCAGUGAAUUGUGAGGGGG----G
............((((..(((((((((.....))))))))).......(((((....(((..((((----((((((.......))))))))))..)))))))))))).----. ( -37.00)
>DroEre_CAF1 65916 106 + 1
CUCUCUUUUUGGUUCCAUUCUCCCGACAAAUCGGCGAGAGAUCUGCAAUUACAAUCUGU--GUUGUGUGCGUGCGUGCCAGUGGCGUAUGCAGAAAAUCGUAGGGGGG-----
((((((...(((((...(((((((((....)))).))))).((((((..((((((....--))))))(((((((......)).))))))))))).))))).)))))).----- ( -33.50)
>DroYak_CAF1 68171 104 + 1
CUCUCUUUUUGGU-CCAGUCUCCCGUCAAAUCGGCGAGAGAUCUGCAAUUACAAGCUGUUUGUUGU----GUGCGUGCCAGUGGUGUACGUAGUAAAUCGUAAGGGGG----G
((((((((.((((-.(((((((.((((.....)))).)))).)))...((((.(((.....)))..----.((((((((....).))))))))))))))).)))))))----) ( -30.60)
>consensus
CUCUCUUUUUGGUCCCAUUCUCUCGUCAAAUCGACGAGAGAUCUGCAAUUACAAUCCGUUUGUUGU____GUGCGUGCCAGUGGCGUAUGCAGUGAAUCGUAAGGGGG____G
..((((((.((((.....(((((((((.....))))))))).((((....(((((......)))))....((((((.......))))))))))...)))).))))))...... (-25.36 = -25.52 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:22 2006