Locus 3340

Sequence ID	3L_DroMel_CAF1
Location	9,811,504 – 9,811,664
Length	160
Max. P	0.961249

overview

Window 9

Location	9,811,504 – 9,811,624
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.17
Mean single sequence MFE	-43.78
Consensus MFE	-40.64
Energy contribution	-40.88
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.54
Structure conservation index	0.93
SVM decision value	1.52
SVM RNA-class probability	0.961249
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9811504 120 + 23771897
GCCUGUUCGGAGGUGAUGCGCUUGUUGGGAUCCAUUAGCAGCAGCUUCUGCAGCAGGUGAAAGGCCUUGCUGUCUGGCUUUAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUG
((((((((((((((..((((((...(((...)))..))).)))))))).(((((((((.....))).))))))((((((..((..((((......)))).))..))))))))))))))). ( -46.70)
>DroSec_CAF1 105730 120 + 1
GCCUGUUCAGAGGUGAUGCGCUUGUUGGGAUCCAUUAGCAGCAGUUUCUGCAGCAGGUGAAAGGCCUUGCUGUCCGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUG
((((((((.(((((....((((((((((...))....((((......))))))))))))....)))))((((...(((..........)))...(((......))).)))))))))))). ( -43.40)
>DroSim_CAF1 109040 120 + 1
GCCUGUUCAGAGGUGAUGCGCUUGUUGGGAUCCAUUAGCAGCAGUUUCUGUAGCAGAUGAAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUACUUGGCCAGCGAGCAGGUG
((((((((.((((((((.(........).)))((((.((.((((...)))).)).))))....)))))...(.((((((.......((((........))))..))))))))))))))). ( -39.20)
>DroEre_CAF1 108073 120 + 1
GCCUGUUCGGAGGUGAUGCGCUUGUUGGGGUCCAUUAGCAGUAGUUUCUGCAGCAGAUGAAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUG
(((((((((..(((((((((..((..(((((......((((......)))).(((((....(((((.........)))))...))))))))))..))))))))..)))..))))))))). ( -43.60)
>DroYak_CAF1 118629 120 + 1
GCCUGUUCGGAGGUGAUGCGCUUGUUGGGGUCCAUUAGCAGCAGUUUCUGCAGCAGGUGGAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUG
(((((((((..(((((((((..((..(((((((((..((.((((...)))).))..)))))(((((.........))))).........))))..))))))))..)))..))))))))). ( -46.00)
>consensus
GCCUGUUCGGAGGUGAUGCGCUUGUUGGGAUCCAUUAGCAGCAGUUUCUGCAGCAGGUGAAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUG
((((((((.(((((....((((((((((...))....((((......))))))))))))....)))))((((...(((..........)))...(((......))).)))))))))))). (-40.64 = -40.88 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	9,811,504 – 9,811,624
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.17
Mean single sequence MFE	-30.06
Consensus MFE	-27.82
Energy contribution	-28.06
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.21
Structure conservation index	0.93
SVM decision value	0.34
SVM RNA-class probability	0.694521
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9811504 120 - 23771897
CACCUGCUCGCUGGCCAAAUACAUGGAAAGGCACAAAAUAAAGCCAGACAGCAAGGCCUUUCACCUGCUGCAGAAGCUGCUGCUAAUGGAUCCCAACAAGCGCAUCACCUCCGAACAGGC
..((((.(((..(((((......)))...(((..........))).(.(((((.((.......)))))))).((.((.(((.....(((...)))...))))).)).))..))).)))). ( -30.60)
>DroSec_CAF1 105730 120 - 1
CACCUGCUCGCUGGCCAAAUACAUGGAAAGGCACAAAAUCAAGCCGGACAGCAAGGCCUUUCACCUGCUGCAGAAACUGCUGCUAAUGGAUCCCAACAAGCGCAUCACCUCUGAACAGGC
..((((.((((((.(((......)))...(((..........)))...))))..((...((((...((.((((...)))).))...))))..))..................)).)))). ( -29.50)
>DroSim_CAF1 109040 120 - 1
CACCUGCUCGCUGGCCAAGUACAUGGAAAGGCACAAAAUCAAGCCAGACAGCAAGGCCUUUCAUCUGCUACAGAAACUGCUGCUAAUGGAUCCCAACAAGCGCAUCACCUCUGAACAGGC
..((((.((((((.(((......)))...(((..........)))...))))..((...(((((..((..(((...)))..))..)))))..))..................)).)))). ( -28.60)
>DroEre_CAF1 108073 120 - 1
CACCUGCUCGCUGGCCAAAUACAUGGAAAGGCACAAAAUCAAGCCAGACAGCAAGGCCUUUCAUCUGCUGCAGAAACUACUGCUAAUGGACCCCAACAAGCGCAUCACCUCCGAACAGGC
..((((.(((..((...........(((((((......((......)).......)))))))....(((((((......))))...(((...)))...)))......))..))).)))). ( -29.62)
>DroYak_CAF1 118629 120 - 1
CACCUGCUCGCUGGCCAAAUACAUGGAAAGGCACAAAAUCAAGCCAGACAGCAAGGCCUUCCACCUGCUGCAGAAACUGCUGCUAAUGGACCCCAACAAGCGCAUCACCUCCGAACAGGC
..((((.((((((.(((......)))...(((..........)))...))))..((...((((...((.((((...)))).))...))))..))..................)).)))). ( -32.00)
>consensus
CACCUGCUCGCUGGCCAAAUACAUGGAAAGGCACAAAAUCAAGCCAGACAGCAAGGCCUUUCACCUGCUGCAGAAACUGCUGCUAAUGGAUCCCAACAAGCGCAUCACCUCCGAACAGGC
..((((.((((((.(((......)))...(((..........)))...))))..((...((((...((.((((...)))).))...))))..))..................)).)))). (-27.82 = -28.06 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	9,811,544 – 9,811,664
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.83
Mean single sequence MFE	-39.18
Consensus MFE	-36.32
Energy contribution	-35.68
Covariance contribution	-0.64
Combinations/Pair	1.15
Mean z-score	-1.27
Structure conservation index	0.93
SVM decision value	0.63
SVM RNA-class probability	0.806637
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9811544 120 + 23771897
GCAGCUUCUGCAGCAGGUGAAAGGCCUUGCUGUCUGGCUUUAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUGGAGUAUGUGGAGCGUUUAAAGUCCUUUGUCAGCGUAUGAU
..((((...(((((((((.....))).))))))..)))).....(..(((...(((((((((((.(((........))).)))))))))))((...((((....))))...)))))..). ( -38.60)
>DroSec_CAF1 105770 120 + 1
GCAGUUUCUGCAGCAGGUGAAAGGCCUUGCUGUCCGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUGGAGUAUGUGGAGCGUUUAAAGUCCUUUGUCAGCGUAUGAU
((.......(((((((((.....))).))))))..(((..(((((((.((..((((((((((((.(((........))).)))))))))))).)).)))))))....))).))....... ( -39.50)
>DroSim_CAF1 109080 120 + 1
GCAGUUUCUGUAGCAGAUGAAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUACUUGGCCAGCGAGCAGGUGGAGUAUGUGGAGCGUUUAAAGUCCUUUGUCAGCGUAUGAU
((((...)))).((.((..(((((((.........)))))(((((((.((..((((((((((((.(((........))).)))))))))))).)).))))))).))..)).))....... ( -38.20)
>DroEre_CAF1 108113 120 + 1
GUAGUUUCUGCAGCAGAUGAAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUGGAGUAUGUGGAGCGUUUAAAGUCUUUUGUCAGCGUAUGGU
((((...))))............(((.(((.(.(((((..(((((((.((..((((((((((((.(((........))).)))))))))))).)).)))))))....))))))))).))) ( -37.10)
>DroYak_CAF1 118669 120 + 1
GCAGUUUCUGCAGCAGGUGGAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUGGAGUAUGUGGAGCGCUUAAAGUCCUUUGUCAGGGUAUGAU
((((...))))(((((((.....))).)))).((((((..(((((((.((..((((((((((((.(((........))).)))))))))))).)).)))))))....))))))....... ( -42.50)
>consensus
GCAGUUUCUGCAGCAGGUGAAAGGCCUUGCUGUCUGGCUUGAUUUUGUGCCUUUCCAUGUAUUUGGCCAGCGAGCAGGUGGAGUAUGUGGAGCGUUUAAAGUCCUUUGUCAGCGUAUGAU
((((...)))).((.((..(((((((.........)))))(((((((.((..((((((((((((.(((........))).)))))))))))).)).))))))).))..)).))....... (-36.32 = -35.68 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:13 2006