Locus 1398

Sequence ID 2L_DroMel_CAF1
Location 3,717,381 – 3,717,541
Length 160
Max. P 0.850565
window2280 window2281 window2282 window2283

overview

Window 0

Location 3,717,381 – 3,717,501
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -33.80
Consensus MFE -32.01
Energy contribution -31.79
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.95
SVM decision value 0.09
SVM RNA-class probability 0.579649
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3717381 120 + 22407834
AUGGUCUCCAAAGAUUCAUGCAUGGCAAACUGCUCUCGCUCCAUCCUGUCCAGCUUCUCAUCCUUUGACAGCUGCGAUGCCUUUAUGUUGGAAACGUCUGCUUUCAAGGCAUCCAGCUGG
........(((((......((.(((((....((....)).......)).)))))........))))).((((((.((((((((...((((....))...))....)))))))))))))). ( -33.34)
>DroSec_CAF1 179699 120 + 1
AUGGUCUUCAAAGAUUCCUGCAUGGCUAACUGCUCUCGCUCUAUCCUGUCCAGCUUAUCAUCCUUUGAUAGCUGCGAUGCCUUUAUGUUGGAAACGUCUGCUUUUAAGGCAUCCAGCUGG
.......((((((......((.((((.....((....))........).)))))........))))))((((((.((((((((...((((....))...))....)))))))))))))). ( -32.16)
>DroSim_CAF1 188578 120 + 1
AUGGUCUUCAAAGACUCCUGCAUGGCUGACUGCUCUCGCUCUAUCCUGUCCAGCUUAUCAUCCUUUGACAGCUGCGAUGCCUUUAUGUUGGAGACGUCUGCUUUUAAGGCAUCCAGCUGG
.......((((((.....((...(((((((.((....))........)).)))))...))..))))))((((((.((((((((...((((....))...))....)))))))))))))). ( -35.90)
>consensus
AUGGUCUUCAAAGAUUCCUGCAUGGCUAACUGCUCUCGCUCUAUCCUGUCCAGCUUAUCAUCCUUUGACAGCUGCGAUGCCUUUAUGUUGGAAACGUCUGCUUUUAAGGCAUCCAGCUGG
........(((((......((.((((.....((....))........).)))))........))))).((((((.((((((((...((((....))...))....)))))))))))))). (-32.01 = -31.79 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,717,381 – 3,717,501
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -35.19
Consensus MFE -33.90
Energy contribution -33.57
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -1.45
Structure conservation index 0.96
SVM decision value 0.06
SVM RNA-class probability 0.561954
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3717381 120 - 22407834
CCAGCUGGAUGCCUUGAAAGCAGACGUUUCCAACAUAAAGGCAUCGCAGCUGUCAAAGGAUGAGAAGCUGGACAGGAUGGAGCGAGAGCAGUUUGCCAUGCAUGAAUCUUUGGAGACCAU
.(((((((((((((((.((((....)))).))......))))))).))))))((.((((((.....(((((...((((...((....)).)))).))).))....)))))).))...... ( -37.30)
>DroSec_CAF1 179699 120 - 1
CCAGCUGGAUGCCUUAAAAGCAGACGUUUCCAACAUAAAGGCAUCGCAGCUAUCAAAGGAUGAUAAGCUGGACAGGAUAGAGCGAGAGCAGUUAGCCAUGCAGGAAUCUUUGAAGACCAU
..(((((((((((((.......((....)).......)))))))).))))).((((((.((.....(((((....(((...((....)).)))..))).))....))))))))....... ( -31.54)
>DroSim_CAF1 188578 120 - 1
CCAGCUGGAUGCCUUAAAAGCAGACGUCUCCAACAUAAAGGCAUCGCAGCUGUCAAAGGAUGAUAAGCUGGACAGGAUAGAGCGAGAGCAGUCAGCCAUGCAGGAGUCUUUGAAGACCAU
.((((((((((((((.......((....)).......)))))))).))))))(((((((.......(((((....(((...((....)).)))..))).)).....)))))))....... ( -36.74)
>consensus
CCAGCUGGAUGCCUUAAAAGCAGACGUUUCCAACAUAAAGGCAUCGCAGCUGUCAAAGGAUGAUAAGCUGGACAGGAUAGAGCGAGAGCAGUUAGCCAUGCAGGAAUCUUUGAAGACCAU
.((((((((((((((.......((....)).......)))))))).))))))((((((.((.....(((((....(((...((....)).)))..))).))....))))))))....... (-33.90 = -33.57 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,717,421 – 3,717,541
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -36.87
Consensus MFE -31.49
Energy contribution -31.27
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.45
Structure conservation index 0.85
SVM decision value 0.66
SVM RNA-class probability 0.815113
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3717421 120 + 22407834
CCAUCCUGUCCAGCUUCUCAUCCUUUGACAGCUGCGAUGCCUUUAUGUUGGAAACGUCUGCUUUCAAGGCAUCCAGCUGGAUAUUCAACUGGAUCUGAUCCUUGCGGGCUUCGUUCGCUA
..(((..((((((....(((.....)))((((((.((((((((...((((....))...))....)))))))))))))).........))))))..)))....((((((...)))))).. ( -40.30)
>DroSec_CAF1 179739 120 + 1
CUAUCCUGUCCAGCUUAUCAUCCUUUGAUAGCUGCGAUGCCUUUAUGUUGGAAACGUCUGCUUUUAAGGCAUCCAGCUGGACACUCAACUGGUUCUGAUCCUUGACGGUUUCGUUCGCUA
......((((((((((((((.....)))))).((.((((((((...((((....))...))....))))))))))))))))))......((((..(((.((.....))..)))...)))) ( -34.80)
>DroSim_CAF1 188618 120 + 1
CUAUCCUGUCCAGCUUAUCAUCCUUUGACAGCUGCGAUGCCUUUAUGUUGGAGACGUCUGCUUUUAAGGCAUCCAGCUGGACACUCAACUGGUUCUGAUCCUUGAGGGUUUCGUUCGCUA
....(((((((......(((.....))).(((((.((((((((...((((....))...))....))))))))))))))))))(((((..((.......)))))))))............ ( -35.50)
>consensus
CUAUCCUGUCCAGCUUAUCAUCCUUUGACAGCUGCGAUGCCUUUAUGUUGGAAACGUCUGCUUUUAAGGCAUCCAGCUGGACACUCAACUGGUUCUGAUCCUUGAGGGUUUCGUUCGCUA
.........((((....(((.....)))((((((.((((((((...((((....))...))....)))))))))))))).........))))....((.((.....))..))........ (-31.49 = -31.27 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,717,421 – 3,717,541
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -35.76
Consensus MFE -33.29
Energy contribution -33.07
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.03
Structure conservation index 0.93
SVM decision value 0.79
SVM RNA-class probability 0.850565
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3717421 120 - 22407834
UAGCGAACGAAGCCCGCAAGGAUCAGAUCCAGUUGAAUAUCCAGCUGGAUGCCUUGAAAGCAGACGUUUCCAACAUAAAGGCAUCGCAGCUGUCAAAGGAUGAGAAGCUGGACAGGAUGG
..((.......))((....))(((...(((((((...(((((((((((((((((((.((((....)))).))......))))))).)))))......)))))...)))))))...))).. ( -40.20)
>DroSec_CAF1 179739 120 - 1
UAGCGAACGAAACCGUCAAGGAUCAGAACCAGUUGAGUGUCCAGCUGGAUGCCUUAAAAGCAGACGUUUCCAACAUAAAGGCAUCGCAGCUAUCAAAGGAUGAUAAGCUGGACAGGAUAG
............((.....))(((....((((((...((((((((((((((((((.......((....)).......)))))))).)))))......)))))...))))))....))).. ( -33.64)
>DroSim_CAF1 188618 120 - 1
UAGCGAACGAAACCCUCAAGGAUCAGAACCAGUUGAGUGUCCAGCUGGAUGCCUUAAAAGCAGACGUCUCCAACAUAAAGGCAUCGCAGCUGUCAAAGGAUGAUAAGCUGGACAGGAUAG
............(((((((((.......))..)))))(((((((((.((((((((.......((....)).......)))))))).....(((((.....)))))))))))))))).... ( -33.44)
>consensus
UAGCGAACGAAACCCUCAAGGAUCAGAACCAGUUGAGUGUCCAGCUGGAUGCCUUAAAAGCAGACGUUUCCAACAUAAAGGCAUCGCAGCUGUCAAAGGAUGAUAAGCUGGACAGGAUAG
............((.....))(((....((((((...((((((((((((((((((.......((....)).......)))))))).)))))......)))))...))))))....))).. (-33.29 = -33.07 +  -0.22)

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 10:01:42 2006