Locus 5347

Sequence ID 2R_DroMel_CAF1
Location 17,288,888 – 17,289,031
Length 143
Max. P 0.936231
window8541 window8542 window8543

overview

Window 1

Location 17,288,888 – 17,288,991
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -26.09
Consensus MFE -16.09
Energy contribution -17.96
Covariance contribution 1.86
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.62
SVM decision value 0.61
SVM RNA-class probability 0.799974
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17288888 103 - 20766785
CUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGA-AGCCC--------GGG-------UAAUAACAGCAUCCUCACA
.(((((((((..((....))..)))))))))...-((((((((((((......)))...(((.....))).......-)))).--------.))-------)))................ ( -26.40)
>DroPse_CAF1 15299 96 - 1
--------GUCCUCUCAUAACUGGGCCAACAAUUUUUACUGACUCAUUAAAAUGUGGCAGUCAAUUUGACAGAGAGA-UUCCCUUAGGGAUGGG-------UGGCACGAGUA--------
--------((((((((........((((...(((((............))))).)))).(((.....))).))))).-..(((........)))-------.))).......-------- ( -22.50)
>DroSec_CAF1 13258 103 - 1
CUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGA-ACCCC--------GGG-------UAAUAACAGCAUCAUCGCA
.(((((((((..((....))..)))))))))...-(((((.((.(((......))))).(((.....))).......-.....--------.))-------))).....((......)). ( -26.20)
>DroSim_CAF1 14966 103 - 1
CUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGA-ACCCC--------GGG-------UAAUAACAGCACCCUCGCA
.(((((((((..((....))..)))))))))...-......((.(((......))))).(((.....))).......-.....--------(((-------(.........))))..... ( -26.20)
>DroEre_CAF1 9009 103 - 1
CUCCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGA-ACCCC--------GGG-------UAAUAACAGCAUCCUCCCA
..(((((((........(((.((((((((.....-...)))))))))))......))).(((.....))).......-....)--------)))-------................... ( -23.34)
>DroAna_CAF1 739 112 - 1
UUGCUGGCCUCCUUUCAUAACUGGGCCGGCAAUUUUUACUGGCUCAUUAAAAUGUGGCAGUCAAUUUGACAAAAUGGAACCCU--------CUGUCCUGCCAAAAAGCCGCAUCCCCAUA
((((((((((..((....))..))))))))))........(((((((....)))((((((((.....))).....(((.....--------...))))))))...))))........... ( -31.90)
>consensus
CUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU_UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGA_ACCCC________GGG_______UAAUAACAGCAUCCUCACA
.((((((((........(((.((((((((.........)))))))))))......))).(((.....))).....................................)))))........ (-16.09 = -17.96 +   1.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 17,288,913 – 17,289,031
Length 118
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 84.79
Mean single sequence MFE -32.80
Consensus MFE -24.67
Energy contribution -25.45
Covariance contribution 0.78
Combinations/Pair 1.11
Mean z-score -3.32
Structure conservation index 0.75
SVM decision value 0.93
SVM RNA-class probability 0.884540
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17288913 118 + 20766785
CUUCUUUUUGUCAAAUUGACUGCCAUAUUUUAAUGAGCCAGUAA-AAUUGCUGGCCCAGUUAUGAAAGGAGGCCAGCAGAUAUAGCCAAAAUGGUAAAUGGCCCCAAAUUGACAAAGAA
....((((((((((..((((((.(((......))).(((((((.-...))))))).)))))).....((.(((((.........(((.....)))...)))))))...)))))))))). ( -37.50)
>DroPse_CAF1 15324 102 + 1
AAUCUCUCUGUCAAAUUGACUGCCACAUUUUAAUGAGUCAGUAAAAAUUGUUGGCCCAGUUAUGAGAGGAC-----------------AAUCGGGAAAUGGCCAGAAAUUGACAAAGAA
....(((.(((((((((((((..............)))))))........((((((...((.(((......-----------------..))).))...))))))...)))))).))). ( -24.54)
>DroSec_CAF1 13283 118 + 1
GUUCUUUUUGUCAAAUUGACUGCCAUAUUUUAAUGAGCCAGUAA-AAUUGCUGGCCCAGUUAUGAAAGGAGGCCAGCAGAUAUAGCCAAAAUGGUAAAUGGCCCCAAAUUGACAAAGAA
....((((((((((..((((((.(((......))).(((((((.-...))))))).)))))).....((.(((((.........(((.....)))...)))))))...)))))))))). ( -37.50)
>DroSim_CAF1 14991 118 + 1
GUUCUUUUUGUCAAAUUGACUGCCAUAUUUUAAUGAGCCAGUAA-AAUUGCUGGCCCAGUUAUGAAAGGAGGCCAGCAGAUAUAGCCAAAAUGGUAAAUGGCCCCAAAUUGACAAAGAA
....((((((((((..((((((.(((......))).(((((((.-...))))))).)))))).....((.(((((.........(((.....)))...)))))))...)))))))))). ( -37.50)
>DroEre_CAF1 9034 118 + 1
GUUCUUUUUGUCAAAUUGACUGCCAUAUUUUAAUGAGCCAGUAA-AAUUGCUGGCCCAGUUAUGAAAGGAGGCCAGGAGAUAUAGCCAAAAUGGGAAAUGGGCCCAAAUUGACAAAGAA
....(((((((((((((..(((((...(((((.((.(((((((.-...))))))).))....)))))...)).)))..)))..........((((.......))))..)))))))))). ( -35.20)
>DroPer_CAF1 15228 102 + 1
AAUCUCUCUGUCAAAUUGACUGCCACAUUUUAAUGAGUCAGUAAAAAUUGUUGGCCCAGUUAUGAGAGGAC-----------------AAUCGGGAAAUGGCCAGAAAUUGACAAAGAA
....(((.(((((((((((((..............)))))))........((((((...((.(((......-----------------..))).))...))))))...)))))).))). ( -24.54)
>consensus
GUUCUUUUUGUCAAAUUGACUGCCAUAUUUUAAUGAGCCAGUAA_AAUUGCUGGCCCAGUUAUGAAAGGAGGCCAGCAGAUAUAGCCAAAAUGGGAAAUGGCCCCAAAUUGACAAAGAA
....((((((((((.(((...(((((.(((((.((.(((((((.....))))))).))....)))))...(((...........)))..........)))))..))).)))))))))). (-24.67 = -25.45 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,288,913 – 17,289,031
Length 118
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 84.79
Mean single sequence MFE -33.30
Consensus MFE -24.34
Energy contribution -25.73
Covariance contribution 1.39
Combinations/Pair 1.07
Mean z-score -4.04
Structure conservation index 0.73
SVM decision value 1.25
SVM RNA-class probability 0.936231
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17288913 118 - 20766785
UUCUUUGUCAAUUUGGGGCCAUUUACCAUUUUGGCUAUAUCUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGAAG
(((((((((((.((((.(((((..........(((((((..(((((((((..((....))..)))))))))...-.)).))))).........)))))..)))).))))))..))))). ( -38.91)
>DroPse_CAF1 15324 102 - 1
UUCUUUGUCAAUUUCUGGCCAUUUCCCGAUU-----------------GUCCUCUCAUAACUGGGCCAACAAUUUUUACUGACUCAUUAAAAUGUGGCAGUCAAUUUGACAGAGAGAUU
(((((((((((....(((((.......((..-----------------......)).......)))))...........((((((((......)))..)))))..)))))))))))... ( -25.34)
>DroSec_CAF1 13283 118 - 1
UUCUUUGUCAAUUUGGGGCCAUUUACCAUUUUGGCUAUAUCUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGAAC
(((((((((((.((((.(((((..........(((((((..(((((((((..((....))..)))))))))...-.)).))))).........)))))..)))).))))))..))))). ( -38.61)
>DroSim_CAF1 14991 118 - 1
UUCUUUGUCAAUUUGGGGCCAUUUACCAUUUUGGCUAUAUCUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGAAC
(((((((((((.((((.(((((..........(((((((..(((((((((..((....))..)))))))))...-.)).))))).........)))))..)))).))))))..))))). ( -38.61)
>DroEre_CAF1 9034 118 - 1
UUCUUUGUCAAUUUGGGCCCAUUUCCCAUUUUGGCUAUAUCUCCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU-UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGAAC
(((((((((((.(((.(((.............(((((.......)))))............((((((((.....-...)))))))).........)))...))).))))))..))))). ( -33.00)
>DroPer_CAF1 15228 102 - 1
UUCUUUGUCAAUUUCUGGCCAUUUCCCGAUU-----------------GUCCUCUCAUAACUGGGCCAACAAUUUUUACUGACUCAUUAAAAUGUGGCAGUCAAUUUGACAGAGAGAUU
(((((((((((....(((((.......((..-----------------......)).......)))))...........((((((((......)))..)))))..)))))))))))... ( -25.34)
>consensus
UUCUUUGUCAAUUUGGGGCCAUUUACCAUUUUGGCUAUAUCUGCUGGCCUCCUUUCAUAACUGGGCCAGCAAUU_UUACUGGCUCAUUAAAAUAUGGCAGUCAAUUUGACAAAAAGAAC
...((((((((.(((..(((((..........(((((.......)))))............((((((((.........)))))))).......)))))...))).))))))))...... (-24.34 = -25.73 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:43 2006