Locus 367

Sequence ID 2R_DroMel_CAF1
Location 2,352,443 – 2,352,786
Length 343
Max. P 0.955623
window724 window725 window726

overview

Window 4

Location 2,352,443 – 2,352,550
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.98
Mean single sequence MFE -32.32
Consensus MFE -27.12
Energy contribution -27.32
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -1.38
Structure conservation index 0.84
SVM decision value 0.32
SVM RNA-class probability 0.688228
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2352443 107 - 20766785
AUCCGCAAAAGCCGCAAAACUUUGGCUAGCCGCCAUCAUUAGCCGUUGUCAGGCGUC-------------AGGCUGUCAUUAAAAAUGGCUUAAACAUCAGCCCAGUAGGCGGUUGAAAA
.........(((((........)))))(((((((.......(((.......)))...-------------.(((((...((((.......))))....))))).....)))))))..... ( -30.30)
>DroSec_CAF1 2050 107 - 1
AUCCGCAAAAGCCGCAAAACUUUGGCUAGCCGCCAUCAUUAGCCGUUGUCAGGCGUC-------------AGGCUGUCAUUAAAAAUGGCUUAAACAUCAGCCCAGUAGGCGGUCGAAAA
.........(((((........))))).((((((.......(((.......)))...-------------.(((((...((((.......))))....))))).....))))))...... ( -29.20)
>DroSim_CAF1 2074 107 - 1
AUCCGCAAAAGCCGCAAAACUUUGGCUAGCCGCCAUCAUUAGCCGUUGUCAGGCGUC-------------AGGCUGUCAUUAAAAAUGGCUUAAACAUCAGCCCAGUAGGCGGUCGAAAA
.........(((((........))))).((((((.......(((.......)))...-------------.(((((...((((.......))))....))))).....))))))...... ( -29.20)
>DroEre_CAF1 1912 120 - 1
AUCCGCAAAAGCCGCAAAACUUUGGCUAGCCGCCAUCAUUAGCCGUUGUCAGGCGCCAGGCGCCAGCGCCAGGCUGUCAUUAAAAAUGGCUUAAACAUCAGGCCAGCAGGCGGUUGAAAA
.........(((((........)))))(((((((.......(((.......)))(((.((((....)))).)))............((((((.......))))))...)))))))..... ( -42.50)
>DroYak_CAF1 2048 107 - 1
AUCCGCAAAAGCCGCAAAACUUUGGCUAGCCGCCAUCAUUAGCCGUUGUCAGGCGUC-------------AGUUUGUCAUUAAAAAUGGCUUAAACAUCAGGCCAGCAGGCGGUUGAUAC
.........(((((........)))))(((((((............((.(((((...-------------.))))).)).......((((((.......))))))...)))))))..... ( -30.40)
>consensus
AUCCGCAAAAGCCGCAAAACUUUGGCUAGCCGCCAUCAUUAGCCGUUGUCAGGCGUC_____________AGGCUGUCAUUAAAAAUGGCUUAAACAUCAGCCCAGUAGGCGGUUGAAAA
.........(((((........)))))(((((((.......(((.......))).................(((((...((((.......))))....))))).....)))))))..... (-27.12 = -27.32 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,352,550 – 2,352,666
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.47
Mean single sequence MFE -24.86
Consensus MFE -23.04
Energy contribution -23.40
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.93
SVM decision value 1.46
SVM RNA-class probability 0.955623
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2352550 116 + 20766785
UAAAAUUGAAAACGCUUGCAUUCAUUAAUCCUGCCAACGGAAA----AACCCAACUAGAACGUGACAUGAGGCAGGUGUCGCAUUAAUUAGUGUAAGCAUUCACACGGCUCCCACUCCAC
......((((...(((((((((.((((((((((((...((...----...)).((......)).......))))))......)))))).))))))))).))))...((........)).. ( -26.70)
>DroSec_CAF1 2157 116 + 1
UAAAAUUGAAAACGCUUGCAUUCAUUAAUCCCGCCAACUGAAA----AACCCAACUAGAACGUGACAUGAGGCAGGUGUCGCAUUAAUUAGUGUAAGCAUUCACACGGCUCCCACUCCAC
......((((...(((((((((.((((((........(((...----........)))...(((((((.......))))))))))))).))))))))).))))...((........)).. ( -22.30)
>DroSim_CAF1 2181 116 + 1
UAAAAUUGAAAACGCUUGCAUUCAUUAAUCCCGCCAACGGAAA----AACCCAACUAGAACGUGACAUGAGGCAGGUGUCGCAUUAAUUAGUGUAAGCAUUCACACGGCUCCCACUCCAC
......((((...(((((((((.((((((.(((....)))...----..............(((((((.......))))))))))))).))))))))).))))...((........)).. ( -26.30)
>DroEre_CAF1 2032 115 + 1
UAAAAUUGAAAACGC-UGCAUUAAUUAAUCCCGCCAACGGAAG----AAUCCAACUAAAACGUGACAUGAGACAGGUGUCGCAUUAAUUAGUGCAAGCAUUCACACGGCUCCCUCUCCAC
......((((...((-(((((((((((((.(((....)))...----..............(((((((.......))))))))))))))))))).))).))))...((........)).. ( -27.50)
>DroYak_CAF1 2155 120 + 1
UAAAAUUGAAAACGCUUGCAUUCAUUAAUCCCGCCAACAGAAAAAAAAACCCAACUAGAACGUGACAUGAGACAGGUGUCGCAUUAAUUAGUGUAAGCAUUCAUACGGCUCCCACUCCAC
......((((...(((((((((.((((((..(.......).....................(((((((.......))))))))))))).))))))))).))))...((........)).. ( -21.50)
>consensus
UAAAAUUGAAAACGCUUGCAUUCAUUAAUCCCGCCAACGGAAA____AACCCAACUAGAACGUGACAUGAGGCAGGUGUCGCAUUAAUUAGUGUAAGCAUUCACACGGCUCCCACUCCAC
......((((...(((((((((.((((((.(((....))).....................(((((((.......))))))))))))).))))))))).))))...((........)).. (-23.04 = -23.40 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,352,666 – 2,352,786
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -32.68
Consensus MFE -29.44
Energy contribution -29.56
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.19
Structure conservation index 0.90
SVM decision value 0.16
SVM RNA-class probability 0.611350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2352666 120 - 20766785
AAGACGGUGCGGAAUGCCGUUUGCAAUAAUUUAACUCAAGCCAUCUUGACCCAAAUUGCGGAGUGACACAUCUCGGCGAAAUGAAACCGCCCGCCCGAGGAAACUUUCAUUUCGCAAGCU
.(((((((.......)))))))((...........(((((....)))))......(((((((((((........((((.........)))).....(((....)))))))))))))))). ( -34.70)
>DroSec_CAF1 2273 120 - 1
AAGACGGUGCGGAAUGCCGUUUGCAAUAAUUUAACUCAAGCCAUCUUGACCCAAAUUGCGGAGUGACACAUCUCGGCGAAAUGAAACCGCCCGCCCGAGGAAACUUUCAUUUCGCAAGCU
.(((((((.......)))))))((...........(((((....)))))......(((((((((((........((((.........)))).....(((....)))))))))))))))). ( -34.70)
>DroSim_CAF1 2297 120 - 1
AAGACGGUGCGGAAUGCCGUUUGCAAUAAUUUAACUCAAGCCAUCUUGACCCAAAUUGCGGAGUGACACAUCUCGGCGAAAUGAAACCGCCCGCCCGAGGAAACUUUCAUUUCGCAAGCU
.(((((((.......)))))))((...........(((((....)))))......(((((((((((........((((.........)))).....(((....)))))))))))))))). ( -34.70)
>DroEre_CAF1 2147 120 - 1
AAGUCGGUGCUGAACGGCGCUUGCAAUAAUUUAACUCAAGCCAUCUUGACCCAAAUUGCGGAGUGACACAUCUCGGUGAAAUUAAAACGCCCGCCCGAGGAAACUUUCUUUUCGCAAGAU
..((.((((((....)))))).))...........(((((....)))))......((((((((.((........((((.............)))).(((....))))).))))))))... ( -28.12)
>DroYak_CAF1 2275 120 - 1
AAGACGGUGCGGAAUGCCGUUUGCAAUAAUUUAACUCAAGCCAUCUUGACCCAAAUUGCGAAGUGACACAUCUCGGCGAAAUUAAACCGCCCGCCCGAGGAAACUUUCAUUUUGCAAGAC
.(((((((.......))))))).............(((((....)))))......(((((((((((........((((.........)))).....(((....))))))))))))))... ( -31.20)
>consensus
AAGACGGUGCGGAAUGCCGUUUGCAAUAAUUUAACUCAAGCCAUCUUGACCCAAAUUGCGGAGUGACACAUCUCGGCGAAAUGAAACCGCCCGCCCGAGGAAACUUUCAUUUCGCAAGCU
.(((((((.......))))))).............(((((....)))))......(((((((((((........((((.........)))).....(((....))))))))))))))... (-29.44 = -29.56 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:37 2006