Locus 1756

Sequence ID X_DroMel_CAF1
Location 4,871,693 – 4,871,802
Length 109
Max. P 0.998195
window2874 window2875

overview

Window 4

Location 4,871,693 – 4,871,802
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.55
Mean single sequence MFE -38.22
Consensus MFE -35.40
Energy contribution -35.08
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 0.93
SVM decision value 3.03
SVM RNA-class probability 0.998195
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4871693 109 + 22224390
GUUGCAGUUGCAAGGUGCAACAUGAGAGCCACUGGAGGCAGGCAGCUGUGCGCUCGCCACAAAUUGUUGUCCGCACAUUUUCCUCCUCUUUCGGCAUUAUUUCUGC---A--------CU
.((((....))))((((((..((((..(((...(((((.(((.((.((((((..((.((.....)).))..)))))).)).))))))))...))).))))...)))---)--------)) ( -38.10)
>DroSec_CAF1 23191 117 + 1
---GCAGUUGCAAGGUGCAACAUGAGAGCCACUGGAGGCAGGCAGCUGUGCGCUCGCCACAAAUUGUUGUCCGCGCAUUUUCCUCCUCUUUCGGCAUUAUUUCUGUGGCAGUGGCAGAGC
---((.(((((.....)))))......(((((((((((.(((.....((((((..((.((.....)).))..))))))...)))))))...(.(((.......))).))))))))...)) ( -42.00)
>DroSim_CAF1 23880 106 + 1
---GCAGUUGCAAGGUGCAACAUGAGAGCCACUGGAGGCAGGCAGCUGUGCGCUCGCCACAAAUUGUUGUCCGCACAUUUUCCUCCUCUUUCGGCAUUAUUUCUGC---A--------CU
---((((((((.....)))))......(((...(((((.(((.((.((((((..((.((.....)).))..)))))).)).))))))))...)))........)))---.--------.. ( -37.00)
>DroEre_CAF1 26076 106 + 1
---GCAGUUGCAAGGUGCAACAUGAGAGCCACUGGAGGCAGGCAGCUGUGCGCUCGCCACAAAUUGUUGUCCGCACAUUUUCCUCCUCUUUCGGCAUUAUUUCUGC---A--------CU
---((((((((.....)))))......(((...(((((.(((.((.((((((..((.((.....)).))..)))))).)).))))))))...)))........)))---.--------.. ( -37.00)
>DroYak_CAF1 23384 106 + 1
---GCAGUUGCAAGGUGCAACAUGAGAGCCACUGGAGGCAGGCAGCUGUGCGCUCGCCACAAAUUGUUGUCCGCACAUUUUCCUCCUCUUUCGGCAUUAUUUCUGC---A--------CU
---((((((((.....)))))......(((...(((((.(((.((.((((((..((.((.....)).))..)))))).)).))))))))...)))........)))---.--------.. ( -37.00)
>consensus
___GCAGUUGCAAGGUGCAACAUGAGAGCCACUGGAGGCAGGCAGCUGUGCGCUCGCCACAAAUUGUUGUCCGCACAUUUUCCUCCUCUUUCGGCAUUAUUUCUGC___A________CU
...((((((((.....)))))......(((...(((((.(((.((.((((((..((.((.....)).))..)))))).)).))))))))...)))........))).............. (-35.40 = -35.08 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,871,693 – 4,871,802
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.55
Mean single sequence MFE -35.74
Consensus MFE -32.20
Energy contribution -32.60
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.90
SVM decision value 0.76
SVM RNA-class probability 0.843584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4871693 109 - 22224390
AG--------U---GCAGAAAUAAUGCCGAAAGAGGAGGAAAAUGUGCGGACAACAAUUUGUGGCGAGCGCACAGCUGCCUGCCUCCAGUGGCUCUCAUGUUGCACCUUGCAACUGCAAC
.(--------(---((((.......((((...(((((((....((((((..(..((.....))..)..))))))....))).))))...)))).......)))))).((((....)))). ( -37.64)
>DroSec_CAF1 23191 117 - 1
GCUCUGCCACUGCCACAGAAAUAAUGCCGAAAGAGGAGGAAAAUGCGCGGACAACAAUUUGUGGCGAGCGCACAGCUGCCUGCCUCCAGUGGCUCUCAUGUUGCACCUUGCAACUGC---
.....((((((((((((((.......(((.....(.(......).).))).......))))))))(((.(((........)))))).))))))......(((((.....)))))...--- ( -36.24)
>DroSim_CAF1 23880 106 - 1
AG--------U---GCAGAAAUAAUGCCGAAAGAGGAGGAAAAUGUGCGGACAACAAUUUGUGGCGAGCGCACAGCUGCCUGCCUCCAGUGGCUCUCAUGUUGCACCUUGCAACUGC---
.(--------(---((((.......((((...(((((((....((((((..(..((.....))..)..))))))....))).))))...)))).......))))))...........--- ( -34.94)
>DroEre_CAF1 26076 106 - 1
AG--------U---GCAGAAAUAAUGCCGAAAGAGGAGGAAAAUGUGCGGACAACAAUUUGUGGCGAGCGCACAGCUGCCUGCCUCCAGUGGCUCUCAUGUUGCACCUUGCAACUGC---
.(--------(---((((.......((((...(((((((....((((((..(..((.....))..)..))))))....))).))))...)))).......))))))...........--- ( -34.94)
>DroYak_CAF1 23384 106 - 1
AG--------U---GCAGAAAUAAUGCCGAAAGAGGAGGAAAAUGUGCGGACAACAAUUUGUGGCGAGCGCACAGCUGCCUGCCUCCAGUGGCUCUCAUGUUGCACCUUGCAACUGC---
.(--------(---((((.......((((...(((((((....((((((..(..((.....))..)..))))))....))).))))...)))).......))))))...........--- ( -34.94)
>consensus
AG________U___GCAGAAAUAAUGCCGAAAGAGGAGGAAAAUGUGCGGACAACAAUUUGUGGCGAGCGCACAGCUGCCUGCCUCCAGUGGCUCUCAUGUUGCACCUUGCAACUGC___
..............((((.......((((...(((((((....((((((..(..((.....))..)..))))))....))).))))...)))).......((((.....))))))))... (-32.20 = -32.60 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:13 2006