Locus 5173

Sequence ID 3L_DroMel_CAF1
Location 14,242,813 – 14,243,048
Length 235
Max. P 0.996902
window8189 window8190 window8191

overview

Window 9

Location 14,242,813 – 14,242,931
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 93.04
Mean single sequence MFE -25.12
Consensus MFE -19.28
Energy contribution -20.08
Covariance contribution 0.80
Combinations/Pair 1.06
Mean z-score -1.89
Structure conservation index 0.77
SVM decision value 0.47
SVM RNA-class probability 0.750530
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14242813 118 - 23771897
UUGGCACGAAUUUCAACGAGAGUGACUGGUUAAUUUAGUCAAAAAGGUCUGACUGACAAGCAAAUCGGAAAAUUUCAAAGAGGAAAAUUGAAAAAUUAGCCCAGAUGAAUGGAAUUAA
........(((((((((....))((((((.....))))))......(((((.((((........)))).............((..((((....))))..)))))))...))))))).. ( -21.90)
>DroSec_CAF1 73454 117 - 1
UUGCCACGAAU-UCAACGAGAGUGACUGGUUAAUUUAGUCAAAAAGGUCUGGCUGACAAGCCAAUCGGGAAAUAUCAAAGAGGAAAAUUGAAAAAUUAGCCUAGAUGAAUGGAAUUAA
........(((-((..(((...(((((((.....)))))))........(((((....))))).))).......(((...(((..((((....))))..)))...)))...))))).. ( -26.70)
>DroSim_CAF1 73535 118 - 1
UUGGCACGAAUUUCAACGAGAGUGACUGGUUAAUUUAGUCAAAAAGGUCUGGCUGACAAGCCAAUCGGGAAAUAUCAAAGAGGAAAAUUGAAAAAUUAGCCUAGAUGAAUGGAAUUAA
........(((((((.(((...(((((((.....)))))))........(((((....))))).))).......(((...(((..((((....))))..)))...))).))))))).. ( -28.10)
>DroEre_CAF1 72509 117 - 1
UUUGCACGAAU-UCAACGAGAGUGACUGGUUAAUUUAGUCAAAAAGGUCUGACUGACAAGCCAAUCGGGAAAUUUCAAAGAGGAAAAUUGAAAAAUUAUACUUGAUGACUGAAAUUAA
......(((..-(((.(....)))).(((((...(((((((........)))))))..))))).)))...(((((((..(((...((((....))))...)))......))))))).. ( -21.70)
>DroYak_CAF1 75928 118 - 1
UUUGCACGAAUUUCAACAAGAGUGACUGGUUAAUUUAGUCAAAAAGGUCUGACUGACAAGCCAAUCGGGAAACUUCAGAGAUGAAAAUUGAAAAAUUAGCCUUGUUGAAUGGAAUUAA
...........(((((((((.((((.(((((...(((((((........)))))))..))))).)).(....)((((....))))((((....)))).)))))))))))......... ( -27.20)
>consensus
UUGGCACGAAUUUCAACGAGAGUGACUGGUUAAUUUAGUCAAAAAGGUCUGACUGACAAGCCAAUCGGGAAAUUUCAAAGAGGAAAAUUGAAAAAUUAGCCUAGAUGAAUGGAAUUAA
........(((((((((....))((.(((((...(((((((........)))))))..))))).))........(((...(((..((((....))))..)))...))).))))))).. (-19.28 = -20.08 +   0.80)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,242,892 – 14,243,009
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 96.75
Mean single sequence MFE -21.52
Consensus MFE -19.50
Energy contribution -19.74
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.14
Structure conservation index 0.91
SVM decision value 2.77
SVM RNA-class probability 0.996902
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14242892 117 + 23771897
ACUAAAUUAACCAGUCACUCUCGUUGAAAUUCGUGCCAACAAAAAUCUGGCAUACAAAAUAUGUAAUUUCGCAAAUCAAUUACCCAAACCAAAGGGCAAAACACGGCCGGAUGAAUU
......(((((.((.....)).)))))(((((((....))....(((((((.((((.....)))).................(((........))).........)))))))))))) ( -20.70)
>DroSec_CAF1 73533 116 + 1
ACUAAAUUAACCAGUCACUCUCGUUGA-AUUCGUGGCAACAAAAAUCUGGCAUACAAAAUAUGUAAUUUUGCAAAUCAAUUACCCAAACCAAAGGGCAAAACACAGCCGGAUGAAUU
......(((((.((.....)).)))))-((((.((....))...(((((((...((((((.....))))))...........(((........))).........))))))))))). ( -22.80)
>DroSim_CAF1 73614 117 + 1
ACUAAAUUAACCAGUCACUCUCGUUGAAAUUCGUGCCAACAAAAAUCUGGCAUACAAAAUAUGUAAUUUCGCAAAUCAAUUACCCAAACCAACGGGCAAAACACAGCCGGAUGAAUU
......(((((.((.....)).)))))(((((((....))....(((((((.((((.....)))).................(((........))).........)))))))))))) ( -20.90)
>DroEre_CAF1 72588 116 + 1
ACUAAAUUAACCAGUCACUCUCGUUGA-AUUCGUGCAAACAAAAAUCUGGCAUACAAAAUAUGUAAUUUCGCAAAUCAAUUACCCAAACCAAAGGGCAAAACACGGCCGGAUGAAUU
......(((((.((.....)).)))))-((((((....))....(((((((.((((.....)))).................(((........))).........))))))))))). ( -19.90)
>DroYak_CAF1 76007 117 + 1
ACUAAAUUAACCAGUCACUCUUGUUGAAAUUCGUGCAAACAAAAAUCUGGCAUACGAAAUAUGUAAUUUCGCAAAUCAAUUACCCAAACCAAAGGGCAAAACACGGCCGGAUGAAUU
......(((((.((.....)).)))))(((((((....))....(((((((...((((((.....))))))...........(((........))).........)))))))))))) ( -23.30)
>consensus
ACUAAAUUAACCAGUCACUCUCGUUGAAAUUCGUGCCAACAAAAAUCUGGCAUACAAAAUAUGUAAUUUCGCAAAUCAAUUACCCAAACCAAAGGGCAAAACACGGCCGGAUGAAUU
......(((((.((.....)).)))))(((((((....))....(((((((.((((.....)))).................(((........))).........)))))))))))) (-19.50 = -19.74 +   0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,242,931 – 14,243,048
Length 117
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 96.76
Mean single sequence MFE -26.58
Consensus MFE -24.64
Energy contribution -24.52
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.50
Structure conservation index 0.93
SVM decision value 1.29
SVM RNA-class probability 0.938141
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14242931 117 - 23771897
GGGAAUUUUCAACUAAUUCCAUUCGGCAUUU-CGCACUCUAAUUCAUCCGGCCGUGUUUUGCCCUUUGGUUUGGGUAAUUGAUUUGCGAAAUUACAUAUUUUGUAUGCCAGAUUUUUG
.((((((.......))))))....(((((((-((((...(((((.(((((((((............))).)))))))))))...))))))).((((.....))))))))......... ( -29.60)
>DroSec_CAF1 73571 117 - 1
GGGAAUUUUCAACUAAUUCCAUUCGGCAUUU-CUCACUGUAAUUCAUCCGGCUGUGUUUUGCCCUUUGGUUUGGGUAAUUGAUUUGCAAAAUUACAUAUUUUGUAUGCCAGAUUUUUG
.((((((.......))))))....(((((..-.....(((((((......((......((((((........)))))).......))..)))))))........)))))......... ( -25.78)
>DroSim_CAF1 73653 117 - 1
GGGAAUUUUCAACUAAUUCCAUUCGGCAUUU-CUCACUCUAAUUCAUCCGGCUGUGUUUUGCCCGUUGGUUUGGGUAAUUGAUUUGCGAAAUUACAUAUUUUGUAUGCCAGAUUUUUG
.((((((.......))))))....((((...-...((.((((..((.(.(((........))).).))..))))))........((((((((.....))))))))))))......... ( -26.30)
>DroEre_CAF1 72626 117 - 1
GGGAAUUUUCAACUAAUUCCAUUCGGCAUUU-CUCACUCUAAUUCAUCCGGCCGUGUUUUGCCCUUUGGUUUGGGUAAUUGAUUUGCGAAAUUACAUAUUUUGUAUGCCAGAUUUUUG
.((((((.......))))))....((((...-...((.((((..((...(((........)))...))..))))))........((((((((.....))))))))))))......... ( -24.50)
>DroYak_CAF1 76046 118 - 1
GGGAAUUCUCAACUAAUUCCAUUCGGCAUUCACUCACUCUAAUUCAUCCGGCCGUGUUUUGCCCUUUGGUUUGGGUAAUUGAUUUGCGAAAUUACAUAUUUCGUAUGCCAGAUUUUUG
.((((((.......))))))....((((.(((.(.((.((((..((...(((........)))...))..)))))).).)))..((((((((.....))))))))))))......... ( -26.70)
>consensus
GGGAAUUUUCAACUAAUUCCAUUCGGCAUUU_CUCACUCUAAUUCAUCCGGCCGUGUUUUGCCCUUUGGUUUGGGUAAUUGAUUUGCGAAAUUACAUAUUUUGUAUGCCAGAUUUUUG
.((((((.......))))))....((((.......((((....(((...(((........)))...)))...))))........((((((((.....))))))))))))......... (-24.64 = -24.52 +  -0.12)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:45 2006