Locus 5187

Sequence ID 2R_DroMel_CAF1
Location 16,857,879 – 16,858,011
Length 132
Max. P 0.988012
window8291 window8292 window8293

overview

Window 1

Location 16,857,879 – 16,857,990
Length 111
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.30
Mean single sequence MFE -36.48
Consensus MFE -25.61
Energy contribution -26.42
Covariance contribution 0.81
Combinations/Pair 1.27
Mean z-score -1.69
Structure conservation index 0.70
SVM decision value 0.01
SVM RNA-class probability 0.539923
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16857879 111 - 20766785
AUAUUCCAGCUGAUUUUCCAGUUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAAUGGCGUCAGACAUAUCGCGUGCCGAACAACUGGAGUAAGU
.((((((((((((((..((((.(((((((.....)))))))...))))...))).))).......(((((...(((..........))).))))).....))))))))... ( -37.80)
>DroSec_CAF1 8306 111 - 1
GUAUUCCAGCUGACUUUCCAGCUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAAUGGCGUCAGACAUAUCGCGUGCCGAACAACUGGAGUAAGU
.(((((((((((..((.((((.(((((((.....)))))))...))))...))..))).......(((((...(((..........))).))))).....))))))))... ( -35.40)
>DroSim_CAF1 8349 111 - 1
GUACUCCAGCUGAUUUUCCAGCUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAGUGGAGUCAGACAUAUCGCGUGCCGAACAACUGGAGUAAGU
.((((((((((((((..((((.(((((((.....)))))))...))))...))).))).......(((((((((.((.....)).)))).))))).....))))))))... ( -38.70)
>DroEre_CAF1 8482 111 - 1
GUAUUCCAGCUGAUUUUCCAGUUGGUCCUGGCAAACGAUUAUUCCUGGUGUAAUCCACAAUUAUGCGGCAACGGAGUGAAACAUAUCGCGUGCCGAAAUACUGGAGUAAGU
((((((((((((......)))))))...(((((..((((((((((..(((((((.....)))))))(....))))))))......)))..))))).))))).......... ( -32.30)
>DroYak_CAF1 8395 111 - 1
GUAUUCCAGCUGAUUUUCCAGUUGGUCCUGGCUACGGAUUAUUCCUGGUGUAAUCCAGAGUUAUGCGGCAAUGGUGUGAAACAUAUCGCGUGCCGAAAUACUGGAGUAAGU
.((((((((((((((..((((.((((((.......))))))...))))...))).))).......(((((.(((((((...)))))))..))))).....))))))))... ( -35.90)
>DroAna_CAF1 11762 111 - 1
AUUUUCCAGCUGAUGGUGCAGUUGGUCCUGGCCAAGGACUUCAGCUGGUGUGAUCCCAGUCUGUGUGAGCCCACCCAGAGGCACAUUGCCUGCCGGAAUACUGGUGUAAGU
.....((((((((.(((.(..(((((....)))))).)))))))))))....(..((((((((.(((....))).))))((((.......))))......))))..).... ( -38.80)
>consensus
GUAUUCCAGCUGAUUUUCCAGUUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAAUGGCGUCAGACAUAUCGCGUGCCGAAAAACUGGAGUAAGU
.((((((((..((((..((((.(((((((.....)))))))...))))...))))......(((((((..(((........))).)))))))........))))))))... (-25.61 = -26.42 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,857,919 – 16,858,011
Length 92
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 75.94
Mean single sequence MFE -30.88
Consensus MFE -18.94
Energy contribution -19.88
Covariance contribution 0.95
Combinations/Pair 1.19
Mean z-score -2.38
Structure conservation index 0.61
SVM decision value 1.97
SVM RNA-class probability 0.984349
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16857919 92 + 20766785
UUGCCGCAUAAAUCUGGAUCACACCAGGAAUAAUCCUUGGCCAGGAUCAACUGGAAAAUCAGCUGGAAUAUGGCCAAGCAGA-------------------UCAAAGGCGA
(((((.......(((((......))))).......((((((((...(((.(((......))).)))....))))))))....-------------------.....))))) ( -28.90)
>DroSec_CAF1 8346 91 + 1
UUGCCGCAUAAAUCUGGAUCACACCAGGAAUAAUCCUUGGCCAGGAUCAGCUGGAAAGUCAGCUGGAAUACGGCCAGGCAGA-------------------UCAAAGGCG-
..(((.......(((((......))))).......(((((((....((((((((....)))))))).....)))))))....-------------------.....))).- ( -32.40)
>DroSim_CAF1 8389 91 + 1
CUGCCGCAUAAAUCUGGAUCACACCAGGAAUAAUCCUUGGCCAGGAUCAGCUGGAAAAUCAGCUGGAGUACGGCCAGGCAGA-------------------UCAAAGGCG-
(((((.......(((((......))))).........(((((....(((((((......))))))).....)))))))))).-------------------.........- ( -32.70)
>DroEre_CAF1 8522 103 + 1
UUGCCGCAUAAUUGUGGAUUACACCAGGAAUAAUCGUUUGCCAGGACCAACUGGAAAAUCAGCUGGAAUACGGCCAGGCAGACACCUCCACGG-------AUCAAAGGCA-
.((((......(((((((.........((....))(((((((....((....)).......((((.....))))..)))))))...)))))))-------......))))- ( -30.50)
>DroYak_CAF1 8435 103 + 1
UUGCCGCAUAACUCUGGAUUACACCAGGAAUAAUCCGUAGCCAGGACCAACUGGAAAAUCAGCUGGAAUACAGCCAGGAAGACACUUCCACGA-------CUCAAAGGCG-
..(((.......(((((......))))).......(((..((((......)))).......((((.....))))..(((((...)))))))).-------......))).- ( -28.40)
>DroAna_CAF1 11802 109 + 1
GGCUCACACAGACUGGGAUCACACCAGCUGAAGUCCUUGGCCAGGACCAACUGCACCAUCAGCUGGAAAAUGGCCACGCAGGCAG-UCCAGGAAAUGACCAUCGAAGACA-
((.(((..(((.((((.......)))))))...((((((((((...(((.(((......))).)))....))))))....((...-.))))))..)))))..........- ( -32.40)
>consensus
UUGCCGCAUAAAUCUGGAUCACACCAGGAAUAAUCCUUGGCCAGGACCAACUGGAAAAUCAGCUGGAAUACGGCCAGGCAGA___________________UCAAAGGCG_
..(((.......(((((......))))).......(((((((....(((.(((......))).))).....)))))))............................))).. (-18.94 = -19.88 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,857,919 – 16,858,011
Length 92
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 75.94
Mean single sequence MFE -34.43
Consensus MFE -25.43
Energy contribution -24.93
Covariance contribution -0.49
Combinations/Pair 1.32
Mean z-score -2.45
Structure conservation index 0.74
SVM decision value 2.10
SVM RNA-class probability 0.988012
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16857919 92 - 20766785
UCGCCUUUGA-------------------UCUGCUUGGCCAUAUUCCAGCUGAUUUUCCAGUUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAA
..(((...((-------------------((((((((((((.....((((((......))))))....))))))))((((((.......)))))))))))).....))).. ( -34.00)
>DroSec_CAF1 8346 91 - 1
-CGCCUUUGA-------------------UCUGCCUGGCCGUAUUCCAGCUGACUUUCCAGCUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAA
-.(((...((-------------------(((...((((((.....((((((......))))))....)))))).(((((((.......)))))))))))).....))).. ( -33.70)
>DroSim_CAF1 8389 91 - 1
-CGCCUUUGA-------------------UCUGCCUGGCCGUACUCCAGCUGAUUUUCCAGCUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAG
-.(((...((-------------------(((...((((((.....((((((......))))))....)))))).(((((((.......)))))))))))).....))).. ( -33.70)
>DroEre_CAF1 8522 103 - 1
-UGCCUUUGAU-------CCGUGGAGGUGUCUGCCUGGCCGUAUUCCAGCUGAUUUUCCAGUUGGUCCUGGCAAACGAUUAUUCCUGGUGUAAUCCACAAUUAUGCGGCAA
-((((......-------.((.((((.(((.((((.((.......(((((((......))))))).)).)))).)))....))))))(((((((.....))))))))))). ( -32.10)
>DroYak_CAF1 8435 103 - 1
-CGCCUUUGAG-------UCGUGGAAGUGUCUUCCUGGCUGUAUUCCAGCUGAUUUUCCAGUUGGUCCUGGCUACGGAUUAUUCCUGGUGUAAUCCAGAGUUAUGCGGCAA
-.(((....((-------(((.(((((...))))))))))(((..(((((((......)))))))...(((((..(((((((.......)))))))..))))))))))).. ( -35.80)
>DroAna_CAF1 11802 109 - 1
-UGUCUUCGAUGGUCAUUUCCUGGA-CUGCCUGCGUGGCCAUUUUCCAGCUGAUGGUGCAGUUGGUCCUGGCCAAGGACUUCAGCUGGUGUGAUCCCAGUCUGUGUGAGCC
-.(((((...((((((......(((-((..((((...((((((........))))))))))..))))))))))))))))..(((((((.(....))))).)))........ ( -37.30)
>consensus
_CGCCUUUGA___________________UCUGCCUGGCCGUAUUCCAGCUGAUUUUCCAGUUGAUCCUGGCCAAGGAUUAUUCCUGGUGUGAUCCAGAUUUAUGCGGCAA
..(((..............................((((((.....((((((......))))))....)))))).(((((((.......)))))))..........))).. (-25.43 = -24.93 +  -0.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:43 2006