Locus 710

Sequence ID 2L_DroMel_CAF1
Location 2,055,145 – 2,055,280
Length 135
Max. P 0.960540
window1162 window1163 window1164

overview

Window 2

Location 2,055,145 – 2,055,241
Length 96
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -27.70
Consensus MFE -18.08
Energy contribution -18.84
Covariance contribution 0.76
Combinations/Pair 1.12
Mean z-score -2.59
Structure conservation index 0.65
SVM decision value 1.52
SVM RNA-class probability 0.960540
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2055145 96 - 22407834
AUUACUUAUGUAUCACCUGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUUAACGGAUACGCGAUGCUUACGUAAGUAA-UA------------------AAGUUGCACGAA
((((((((((((.......((.((((((.....)))))))).......((((....((....)).))))..)))))))))))-).------------------............ ( -24.00)
>DroSec_CAF1 72692 114 - 1
AUUACUUAUGUAUCUCCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUUUUAACGGAUACGCGAUGCUUACGUAAGUAA-UAAAUAAGUACGAGCCCAUAAAGUAGCACGAA
..((((((((((((.....((.((((((.....))))))))...............((....)).)))))((((....))))-...)))))))((.((..........)).)).. ( -24.90)
>DroSim_CAF1 71357 114 - 1
AUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUUAACGGAUACGCGAUGCUUACGUAAGUAA-UAAAUAAGUACGAGCCCAUAAAGUAGCACGAA
((((((((((((.((..(((..((((((.....))))))..........((((....))))..))).))..)))))))))))-).........((.((..........)).)).. ( -25.90)
>DroEre_CAF1 71898 103 - 1
AUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUGCAUCUUAACGGAUGCGCGGUGCAUGCGUAAG------------UAGGAGCUUCAAAAGUAGCACAAA
.(((((((((((((((((.((.((((((.....))))))))......((((((....))))))).)))).)))))))))------------)))..(((........)))..... ( -39.40)
>DroYak_CAF1 75192 115 - 1
AUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUCAACGGCUGCGCUUCGCAUACGUAAGCAACUAUAUUAUUACGAGCUCAUAAAGUAGCCCAAA
.(((((((((..((....(((.((((((.....))))))(((....)))........)))...((((((....)).))))..............))...))).))))))...... ( -24.30)
>consensus
AUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUUAACGGAUACGCGAUGCUUACGUAAGUAA_UA_AU_A_UACGAGCCCAUAAAGUAGCACGAA
.(((((((((((.....(((..((((((.....))))))..........((((....))))..))).....)))))))))))................................. (-18.08 = -18.84 +   0.76) 

alignment

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secondary structure

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dotplot

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Window 3

Location 2,055,161 – 2,055,280
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.47
Mean single sequence MFE -32.29
Consensus MFE -26.05
Energy contribution -26.89
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.58
Structure conservation index 0.81
SVM decision value 0.31
SVM RNA-class probability 0.680942
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2055161 119 + 22407834
ACUUACGUAAGCAUCGCGUAUCCGUUAAGAUGAAAAGUUCCUCAACCAAUUUGGUUGAUGGCAGGUGAUACAUAAGUAAUGAUUCCAAUUGCCCCC-GCCAGAAGCACUUAAGAUACGCC
...............(((((((..(((((.((.........((((((.....))))))((((.((..((..................))..))...-))))....)))))))))))))). ( -28.67)
>DroSec_CAF1 72726 119 + 1
ACUUACGUAAGCAUCGCGUAUCCGUUAAAAUGAAAAGUUCCUCAACCAAUUUGGUUGAUGGCGGGAGAUACAUAAGUAAUGAUUCCAAUUGCCCCC-GCCAGAAGCACUUAAGAUACGCC
...............(((((((...................((((((.....))))))(((((((.(........(((((.......)))))))))-))))...........))))))). ( -31.80)
>DroSim_CAF1 71391 119 + 1
ACUUACGUAAGCAUCGCGUAUCCGUUAAGAUGAAAAGUUCCUCAACCAAUUUGGUUGAUGGCGGGUGAUACAUAAGUAAUGAUUCCAAUUGCCCCC-GCCAGAAGCACUUAAGAUACGCC
...............(((((((..(((((.((.........((((((.....))))))(((((((.(........(((((.......)))))))))-))))....)))))))))))))). ( -34.50)
>DroEre_CAF1 71922 118 + 1
-CUUACGCAUGCACCGCGCAUCCGUUAAGAUGCAAAGUUCCUCAACCAAUUUGGUUGAUGGCGGGUGAUACAUAAGUAAUGAUUCCAAUUGCCCCC-GCCAGAAGCACUUAAGAUACGCC
-..............(((.(((..(((((.(((........((((((.....))))))(((((((.(........(((((.......)))))))))-))))...))))))))))).))). ( -33.90)
>DroYak_CAF1 75227 120 + 1
GCUUACGUAUGCGAAGCGCAGCCGUUGAGAUGAAAAGUUCCUCAACCAAUUUGGUUGAUGGCGGGUGAUACAUAAGUAAUGAUUCCAAUUGCCCCCAGCCAGAAGCACUUAAGAUACGCC
.....(((((...(((.((....((((((...........))))))...((((((((..(((((..((..(((.....)))..))...)))))..)))))))).)).)))...))))).. ( -32.60)
>consensus
ACUUACGUAAGCAUCGCGUAUCCGUUAAGAUGAAAAGUUCCUCAACCAAUUUGGUUGAUGGCGGGUGAUACAUAAGUAAUGAUUCCAAUUGCCCCC_GCCAGAAGCACUUAAGAUACGCC
...............(((((((..(((((.((.........((((((.....))))))(((((((..((..................))..)))...))))....)))))))))))))). (-26.05 = -26.89 +   0.84) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,055,161 – 2,055,280
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.47
Mean single sequence MFE -37.12
Consensus MFE -30.70
Energy contribution -30.54
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.94
Structure conservation index 0.83
SVM decision value 1.39
SVM RNA-class probability 0.949583
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2055161 119 - 22407834
GGCGUAUCUUAAGUGCUUCUGGC-GGGGGCAAUUGGAAUCAUUACUUAUGUAUCACCUGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUUAACGGAUACGCGAUGCUUACGUAAGU
.((((((((((((((.(((((((-(((.(((...((........))..)))....)))))).((((((.....)))))))))).....)).))))..)))))))).......((....)) ( -35.00)
>DroSec_CAF1 72726 119 - 1
GGCGUAUCUUAAGUGCUUCUGGC-GGGGGCAAUUGGAAUCAUUACUUAUGUAUCUCCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUUUUAACGGAUACGCGAUGCUUACGUAAGU
.((((((((.(((((.(((((((-(((((..((.((........)).))....)))))))).((((((.....)))))))))).....)))))....)))))))).......((....)) ( -37.80)
>DroSim_CAF1 71391 119 - 1
GGCGUAUCUUAAGUGCUUCUGGC-GGGGGCAAUUGGAAUCAUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUUAACGGAUACGCGAUGCUUACGUAAGU
.((((((((((((((.(((((((-(((.(((...((........))..)))....)))))).((((((.....)))))))))).....)).))))..)))))))).......((....)) ( -37.20)
>DroEre_CAF1 71922 118 - 1
GGCGUAUCUUAAGUGCUUCUGGC-GGGGGCAAUUGGAAUCAUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUGCAUCUUAACGGAUGCGCGGUGCAUGCGUAAG-
......(((....((((((....-.))))))...))).......((((((((((((((.((.((((((.....))))))))......((((((....))))))).)))).)))))))))- ( -41.20)
>DroYak_CAF1 75227 120 - 1
GGCGUAUCUUAAGUGCUUCUGGCUGGGGGCAAUUGGAAUCAUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUCAACGGCUGCGCUUCGCAUACGUAAGC
.((((((.(.((((((..(((..(((((((...(((...(((.....)))..)))...))).((((((.....))))))............)))).)))..)))))).).)))))).... ( -34.40)
>consensus
GGCGUAUCUUAAGUGCUUCUGGC_GGGGGCAAUUGGAAUCAUUACUUAUGUAUCACCCGCCAUCAACCAAAUUGGUUGAGGAACUUUUCAUCUUAACGGAUACGCGAUGCUUACGUAAGU
.((((((((((((((.(((((((.(((.(((...((........))..)))....)))))).((((((.....)))))))))).....)).))))..))))))))............... (-30.70 = -30.54 +  -0.16) 

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 09:43:33 2006