Locus 5736

Sequence ID 2L_DroMel_CAF1
Location 16,336,319 – 16,336,477
Length 158
Max. P 0.629542
window9087 window9088

overview

Window 7

Location 16,336,319 – 16,336,439
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.76
Mean single sequence MFE -17.02
Consensus MFE -3.41
Energy contribution -5.29
Covariance contribution 1.88
Combinations/Pair 1.16
Mean z-score -1.57
Structure conservation index 0.20
SVM decision value 0.08
SVM RNA-class probability 0.571303
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16336319 120 - 22407834
GGUCAAUCAAAAACGCUCCAAUAGUCCAGUAUAUAAACUUUAAAAGGCGCCACCUAAAGGAAUCAAUAAUGUUGGAGCAAAAUGAUCUUAAAGCAAUCUUUUACAGUCCCAUCAAAUUUA
((............(((((((((.((((((......))).....(((.....)))...)))........))))))))).....(((..(((((.....)))))..))))).......... ( -19.90)
>DroSec_CAF1 10251 99 - 1
GAUCAAUCAGAAACGCUCCAAU--------AUAUAAACUUUAAAA-------------GGAGUCAAUAAUAUUGGAGCAAAAUGACCUUAAAGCAAUCUUUUACAGUCCCAUCAAAUUUA
(((...........((((((((--------((((..(((((....-------------)))))..)).)))))))))).....(((..(((((.....)))))..)))..)))....... ( -19.60)
>DroSim_CAF1 10878 99 - 1
GAUCAAUCAGAAACGCUCCAAU--------AUAUAAACUUUAAAA-------------GGAGUCAAUAAUAUUGGAGCAAAAUGACCUUAAAGCAAUCUUUUACAGUCCCAUCAAAUUUA
(((...........((((((((--------((((..(((((....-------------)))))..)).)))))))))).....(((..(((((.....)))))..)))..)))....... ( -19.60)
>DroEre_CAF1 10749 120 - 1
GAUCAGUCAAAAGCGCUCCGAUAGUCCAAUAUAUAAACAUUAAAAGGCGCCACCUGCAGGAAUAAAUAAUAUGGGUCCAUAAUGAUCUUAAAGCAAUCUCUUACAGUCCUAUCAAACUUA
(((.((......(((((............................)))))...(((.((((...........(((((......)))))..........)))).)))..)))))....... ( -13.39)
>DroYak_CAF1 11855 101 - 1
GAUCUAUC-------------------GAUCUAUAAACAUAAAAAGGCGCCACCUAGAGGAAUAAAUAAUAUAGAAACAUAAGGACCUUAAAGCAAUCUUUUACAGUCCUAUCAAAUUUA
(((.....-------------------..((((((..........(....).((....)).........))))))......(((((..(((((.....)))))..))))))))....... ( -12.60)
>consensus
GAUCAAUCAAAAACGCUCCAAU_______UAUAUAAACUUUAAAAGGCGCCACCU__AGGAAUCAAUAAUAUUGGAGCAAAAUGACCUUAAAGCAAUCUUUUACAGUCCCAUCAAAUUUA
(((...........((((((((................................................)))))))).....(((..(((((.....)))))..)))..)))....... ( -3.41 =  -5.29 +   1.88)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,336,359 – 16,336,477
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 71.71
Mean single sequence MFE -18.30
Consensus MFE -1.85
Energy contribution -3.93
Covariance contribution 2.08
Combinations/Pair 1.10
Mean z-score -1.59
Structure conservation index 0.10
SVM decision value 0.20
SVM RNA-class probability 0.629542
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16336359 118 - 22407834
AAAAGGAAUUCUAAGCAUUUAAUAAGGUCCAAAGACAGGGUCAAUCAAAAACGCUCCAAUAGUCCAGUAUAUAAACUUUAAAAGGCGCCACCUAAAGGAAUCAAUAAUGUUGGAGCAA
.........................(..((.......))..)..........(((((((((.((((((......))).....(((.....)))...)))........))))))))).. ( -22.60)
>DroSec_CAF1 10291 97 - 1
AAGAGGAAUUCAAAGCAUUUAAUAAGGCCCAAAGACAGGAUCAAUCAGAAACGCUCCAAU--------AUAUAAACUUUAAAA-------------GGAGUCAAUAAUAUUGGAGCAA
.........................(..((.......))..)..........((((((((--------((((..(((((....-------------)))))..)).)))))))))).. ( -19.40)
>DroSim_CAF1 10918 97 - 1
AAGAGGAAUUCAAAGCAUUUAAUAAGGCCCAAAGACAGGAUCAAUCAGAAACGCUCCAAU--------AUAUAAACUUUAAAA-------------GGAGUCAAUAAUAUUGGAGCAA
.........................(..((.......))..)..........((((((((--------((((..(((((....-------------)))))..)).)))))))))).. ( -19.40)
>DroEre_CAF1 10789 118 - 1
AAGGGAAGUUCAAAGCAUCGAAUAAAGCCCAAGGACAGGAUCAGUCAAAAGCGCUCCGAUAGUCCAAUAUAUAAACAUUAAAAGGCGCCACCUGCAGGAAUAAAUAAUAUGGGUCCAU
..((...((((........))))...(((((.((((.(((...((.....))..)))....)))).................(((.....)))................))))))).. ( -20.10)
>DroYak_CAF1 11895 99 - 1
AAGGAGAAUUCAAAGCACCUAAUAAAGCCCAAAGACAGGAUCUAUC-------------------GAUCUAUAAACAUAAAAAGGCGCCACCUAGAGGAAUAAAUAAUAUAGAAACAU
........(((...((.(((......(........).(((((....-------------------)))))............))).))..((....)).............))).... ( -10.00)
>consensus
AAGAGGAAUUCAAAGCAUUUAAUAAGGCCCAAAGACAGGAUCAAUCAAAAACGCUCCAAU_______UAUAUAAACUUUAAAAGGCGCCACCU__AGGAAUCAAUAAUAUUGGAGCAA
............................((.......)).............((((((((................................................)))))))).. ( -1.85 =  -3.93 +   2.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:26 2006