Locus 3527

Sequence ID 3L_DroMel_CAF1
Location 10,345,177 – 10,345,268
Length 91
Max. P 0.938614
window5504 window5505

overview

Window 4

Location 10,345,177 – 10,345,268
Length 91
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 87.17
Mean single sequence MFE -30.25
Consensus MFE -26.67
Energy contribution -26.28
Covariance contribution -0.39
Combinations/Pair 1.16
Mean z-score -1.38
Structure conservation index 0.88
SVM decision value 0.02
SVM RNA-class probability 0.544695
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10345177 91 + 23771897
AGAGGGAGCGGCGCAAGAGGGAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCUGUUU---------------UUUUAGCCGCCACUG
...((..(((((.(((((((..(((.(((....)))..((....))....)))..))))).)).))...((((...---------------...)))))))..)). ( -29.40)
>DroSec_CAF1 219056 90 + 1
AGAGGGAGCGGCGCAAGAGGUAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCUGUUU----------------UUUAGCCGCCACUG
...((..(((((.((((((((.(((.(((....)))..((....))....))).)))))).)).))...((((...----------------..)))))))..)). ( -30.00)
>DroSim_CAF1 224984 90 + 1
AGAGGGAGCGGCACAAGAGGGAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCUGUUU----------------UUUAGCCGCCACUG
...((..(((((.(((((((..(((.(((....)))..((....))....)))..))))).))(((...)))....----------------....)))))..)). ( -29.00)
>DroEre_CAF1 232048 102 + 1
AGAGGCAGCGGCGCAAGAGGGAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCUGUUUUUUUUUUUU----UUUUUUAGCCGCCACUG
((((((((((((.(((((((..(((.(((....)))..((....))....)))..))))).)).))..)))))))))).......----................. ( -31.10)
>DroYak_CAF1 230119 89 + 1
AGAGGGAGCGGCGCAAGAGGGAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCUGUU-----------------UUUAGCCGCCACUG
...((..(((((.(((((((..(((.(((....)))..((....))....)))..))))).)).))...((((..-----------------..)))))))..)). ( -29.20)
>DroAna_CAF1 225604 106 + 1
AGGGCCAGUGGCACAAGAGGGAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCCGCUUAUGUUUUUUUUCGUUUGGUAGUUGCCACUG
.....(((((((((.(((((..(((.(((....)))..((....))....)))..)))))((((((......))))))..................).)))))))) ( -32.80)
>consensus
AGAGGGAGCGGCGCAAGAGGGAGGCAGAACUAGUUCAAGCAACUGUAAAAGCCAACCUCUAUGGGCUUCGCUGUUU________________UUUAGCCGCCACUG
...((..(((((.(((((((..(((.(((....)))..((....))....)))..))))).))(((...)))........................)))))..)). (-26.67 = -26.28 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,345,177 – 10,345,268
Length 91
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 87.17
Mean single sequence MFE -30.04
Consensus MFE -26.33
Energy contribution -26.52
Covariance contribution 0.20
Combinations/Pair 1.04
Mean z-score -2.20
Structure conservation index 0.88
SVM decision value 1.27
SVM RNA-class probability 0.938614
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10345177 91 - 23771897
CAGUGGCGGCUAAAA---------------AAACAGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUCCCUCUUGCGCCGCUCCCUCU
.((((((.(((....---------------....)))...((....(((((..(((....((((((.....)))).))...)))..))))).))))))))...... ( -29.20)
>DroSec_CAF1 219056 90 - 1
CAGUGGCGGCUAAA----------------AAACAGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUACCUCUUGCGCCGCUCCCUCU
.((((((.(((...----------------....)))...((....((((((.(((....((((((.....)))).))...))).)))))).))))))))...... ( -30.10)
>DroSim_CAF1 224984 90 - 1
CAGUGGCGGCUAAA----------------AAACAGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUCCCUCUUGUGCCGCUCCCUCU
.((((((((((...----------------.........))))((.(((((..(((....((((((.....)))).))...)))..))))))).))))))...... ( -28.80)
>DroEre_CAF1 232048 102 - 1
CAGUGGCGGCUAAAAAA----AAAAAAAAAAAACAGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUCCCUCUUGCGCCGCUGCCUCU
(((((((((((......----..................))))((.(((((..(((....((((((.....)))).))...)))..))))))).)))))))..... ( -30.76)
>DroYak_CAF1 230119 89 - 1
CAGUGGCGGCUAAA-----------------AACAGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUCCCUCUUGCGCCGCUCCCUCU
.((((((.(((...-----------------...)))...((....(((((..(((....((((((.....)))).))...)))..))))).))))))))...... ( -29.40)
>DroAna_CAF1 225604 106 - 1
CAGUGGCAACUACCAAACGAAAAAAAACAUAAGCGGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUCCCUCUUGUGCCACUGGCCCU
((((((((..........................(((...)))((.(((((..(((....((((((.....)))).))...)))..)))))))))))))))..... ( -32.00)
>consensus
CAGUGGCGGCUAAA________________AAACAGCGAAGCCCAUAGAGGUUGGCUUUUACAGUUGCUUGAACUAGUUCUGCCUCCCUCUUGCGCCGCUCCCUCU
.((((((((((............................))))((.(((((..(((....((((((.....)))).))...)))..))))))).))))))...... (-26.33 = -26.52 +   0.20)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:16 2006