Locus 4461

Sequence ID 3R_DroMel_CAF1
Location 11,810,430 – 11,810,655
Length 225
Max. P 0.558399
window7288 window7289 window7290 window7291

overview

Window 8

Location 11,810,430 – 11,810,538
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.12
Mean single sequence MFE -33.28
Consensus MFE -23.02
Energy contribution -22.94
Covariance contribution -0.08
Combinations/Pair 1.08
Mean z-score -1.98
Structure conservation index 0.69
SVM decision value 0.05
SVM RNA-class probability 0.558399
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11810430 108 - 27905053
AGACAUUGCGAUAAGGAUGCAAGGGUGCGGGUGCGGGUGCUGGACUAUCAGUAGUAG------CAGUA------GCAAAGUCCGGAAGAUGCCUUGUGGUCAGAAGAUAAAAGGCCAAAG
.(((.((((........((((....))))(.(((.(.(((((......))))).).)------)).).------)))).)))(....)..(((((...(((....)))..)))))..... ( -29.40)
>DroSec_CAF1 14706 107 - 1
AGACCUUGCGAUAAGAAUGCAAGGGUGCGGGUGCGGGUGCUGG-CUAUCAGUAGUUG------CAGUA------GCAAAGUCCGGAAGAUGCCUUGUGGUCAGAAGAUAAAAGGCCAAAG
...(((((((.......))))))).(((.(.(((((.(((((.-....))))).)))------)).).------))).....(....)..(((((...(((....)))..)))))..... ( -35.00)
>DroSim_CAF1 15104 107 - 1
AGACGUUGCGAUAAGGAUGCAAGGGUGCGGGUGCGGGUGCUGG-CUAUCAGUAGUUG------CAGUA------GCAAAGUCCGGAAGAUGCCUUGUGGUCAGAAGAUAAAAGGCCAAAG
.(((.((((........((((....))))(.(((((.(((((.-....))))).)))------)).).------)))).)))(....)..(((((...(((....)))..)))))..... ( -32.20)
>DroEre_CAF1 15059 107 - 1
AGUCAUUGCGAUAAGGAUGCAAGGGUGC------GGGUGCUGG-CUAUCAGCAGUAG------CAGUAGCAGUUGCAAAGUCCGGAAGAUGCCUUGUGGUCAAAAGAUAAAAGGCCAGAG
.(((.(((((.......)))))((((((------((.((((((-((((.....))))------)..))))).)))))...)))....)))(((((...(((....)))..)))))..... ( -31.00)
>DroYak_CAF1 15028 119 - 1
AGGCAUUGCGAUAAGGAUGCAAGGGUGCGGGUGCGGGUGCUGG-CUAUCAGUAGUAGCAGUGGCAGUAGCAGUUGCAAAGUCCGGAAGAUGCCUUGUGGUCAGAAGAUAAAAGGCCAAAG
(((((((.......((((.......(((((.(((.(.((((.(-((((.....)))))...)))).).))).)))))..))))....)))))))..(((((...........)))))... ( -38.80)
>consensus
AGACAUUGCGAUAAGGAUGCAAGGGUGCGGGUGCGGGUGCUGG_CUAUCAGUAGUAG______CAGUA______GCAAAGUCCGGAAGAUGCCUUGUGGUCAGAAGAUAAAAGGCCAAAG
.(((.((((.........(((....))).......(.((((((....)))))).)...................)))).)))(....)..(((((...(((....)))..)))))..... (-23.02 = -22.94 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,810,498 – 11,810,615
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.55
Mean single sequence MFE -36.30
Consensus MFE -28.90
Energy contribution -29.50
Covariance contribution 0.60
Combinations/Pair 1.08
Mean z-score -1.40
Structure conservation index 0.80
SVM decision value -0.03
SVM RNA-class probability 0.518759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11810498 117 + 27905053
GCACCCGCACCCGCACCCUUGCAUCCUUAUCGCAAUGUCUCCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC---UCUCCCUACUGGCUGGGUCGG
....(((.(((((((....))).........((...(((........)))((((..(((((.(((((.....))))))))))..))))........---...........)).))))))) ( -35.50)
>DroSec_CAF1 14773 117 + 1
GCACCCGCACCCGCACCCUUGCAUUCUUAUCGCAAGGUCUCCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC---UCUCCCUACUGGCUGGGUCGG
....(((.((((....((((((.........))))))..............(((..(((((.(((((.....))))))))))..)))(((......---..........))).))))))) ( -39.89)
>DroSim_CAF1 15171 117 + 1
GCACCCGCACCCGCACCCUUGCAUCCUUAUCGCAACGUCUCCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCAGCCUGUGGCCAGGGCCUCCUCC---UCUCCCUACUGGCUGGGUCGG
....(((.((((.(((((.(((...(.....)....(((........)))........))).)))))......((((.((((..((((.......)---)))..)))).))))))))))) ( -35.70)
>DroEre_CAF1 15132 114 + 1
GCACCC------GCACCCUUGCAUCCUUAUCGCAAUGACUCCUCCUCGACUACUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCCUCUCCUCUCUACUGGUUGGGUCGG
....((------(.((((((((.........))))............(((((....(((((.(((((.....))))))))))..((((.....))))...........)))))))))))) ( -30.60)
>DroYak_CAF1 15107 117 + 1
GCACCCGCACCCGCACCCUUGCAUCCUUAUCGCAAUGCCUACUCCUCGGCUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC---CCUCCCUACUAGCUGGGUCGG
....(((.((((((....((((.........))))............(((.(((..(((((.(((((.....))))))))))..))))))......---...........)).))))))) ( -39.80)
>consensus
GCACCCGCACCCGCACCCUUGCAUCCUUAUCGCAAUGUCUCCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC___UCUCCCUACUGGCUGGGUCGG
..........(((.((((..((..............(((........)))((((..(((((.(((((.....))))))))))..))))......................)).))))))) (-28.90 = -29.50 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,810,538 – 11,810,655
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.52
Mean single sequence MFE -43.42
Consensus MFE -33.00
Energy contribution -33.04
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.64
Structure conservation index 0.76
SVM decision value 0.03
SVM RNA-class probability 0.549291
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11810538 117 + 27905053
CCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC---UCUCCCUACUGGCUGGGUCGGAUCUUGGUCUGCCCGGCGAGGCGCCGACUUAAAGUUUUCC
.....(((...(((..(((((.(((((.....))))))))))..)))(((((....---.....(....)((((((.(((((....))))))))))))))))..)))............. ( -46.40)
>DroSec_CAF1 14813 112 + 1
CCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC---UCUCCCUACUGGCUGGGUCGGAUCUUGGUCUG-----CGAGGCGCCGACUUAAAGUUUUCC
.....(((.(.((((.(((((.(((((.....))))))))))((((((..(((..(---((..((....))..)))..)))))))))....-----.)))).).)))............. ( -38.80)
>DroSim_CAF1 15211 112 + 1
CCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCAGCCUGUGGCCAGGGCCUCCUCC---UCUCCCUACUGGCUGGGUCGGAUCUUGGUCUG-----CGAGGCGCCGACUUAAAGUUUUCC
.....(((.(.(((((((((..((....)).))((((.((((..((((.......)---)))..)))).))))))).(((((....)))))-----.)))).).)))............. ( -36.40)
>DroEre_CAF1 15166 120 + 1
CCUCCUCGACUACUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCCUCUCCUCUCUACUGGUUGGGUCGGAUCUCGGUCUGCCCGCCGAGGAGCCGACUUAAAGUUUUCC
.((((((.....((..(((((.(((((.....))))))))))..))(((..........((........))..(((.(((((....)))))))))))))))))................. ( -43.20)
>DroYak_CAF1 15147 117 + 1
ACUCCUCGGCUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC---CCUCCCUACUAGCUGGGUCGGAUCUUGGUCUGCCCGCCGAGGAGCCGACUUAAAGUUUUCC
.....((((((((((.(((((.(((((.....))))))))))...((((..((..(---(..(((........)))..)).....))...))))...))))))))))............. ( -52.30)
>consensus
CCUCCUCGACUCCUCCCCGCAUGGGUGACCCGCACCCUGUGGCCAGGGCCUCCUCC___UCUCCCUACUGGCUGGGUCGGAUCUUGGUCUGCCCG_CGAGGCGCCGACUUAAAGUUUUCC
...(((((........(((((.(((((.....))))))))))...(((((...(((......(((........)))..)))....)))))......)))))................... (-33.00 = -33.04 +   0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,810,538 – 11,810,655
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.52
Mean single sequence MFE -47.68
Consensus MFE -40.48
Energy contribution -40.92
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.24
Structure conservation index 0.85
SVM decision value 0.01
SVM RNA-class probability 0.539677
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11810538 117 - 27905053
GGAAAACUUUAAGUCGGCGCCUCGCCGGGCAGACCAAGAUCCGACCCAGCCAGUAGGGAGA---GGAGGAGGCCCUGGCCACAGGGUGCGGGUCACCCAUGCGGGGAGGAGUCGAGGAGG
......((((...(((((.((((((.(((..((((....(((..(((........)))...---)))....((((((....))))))...)))).)))..))))))....))))))))). ( -47.50)
>DroSec_CAF1 14813 112 - 1
GGAAAACUUUAAGUCGGCGCCUCG-----CAGACCAAGAUCCGACCCAGCCAGUAGGGAGA---GGAGGAGGCCCUGGCCACAGGGUGCGGGUCACCCAUGCGGGGAGGAGUCGAGGAGG
......((((...(((((.((((.-----..((((....(((..(((........)))...---)))....((((((....))))))...)))).(((....))))))).))))))))). ( -44.80)
>DroSim_CAF1 15211 112 - 1
GGAAAACUUUAAGUCGGCGCCUCG-----CAGACCAAGAUCCGACCCAGCCAGUAGGGAGA---GGAGGAGGCCCUGGCCACAGGCUGCGGGUCACCCAUGCGGGGAGGAGUCGAGGAGG
......((((...(((((.(((((-----((........(((..(((........)))...---)))((.((((((((((...))))).))))).))..)))))))....))))))))). ( -43.20)
>DroEre_CAF1 15166 120 - 1
GGAAAACUUUAAGUCGGCUCCUCGGCGGGCAGACCGAGAUCCGACCCAACCAGUAGAGAGGAGAGGAGGAGGCCCUGGCCACAGGGUGCGGGUCACCCAUGCGGGGAGUAGUCGAGGAGG
.................(((((((((((.....))..((((((((((..((........)).........(((....)))...)))).)))))).(((....))).....))))))))). ( -47.80)
>DroYak_CAF1 15147 117 - 1
GGAAAACUUUAAGUCGGCUCCUCGGCGGGCAGACCAAGAUCCGACCCAGCUAGUAGGGAGG---GGAGGAGGCCCUGGCCACAGGGUGCGGGUCACCCAUGCGGGGAGGAGCCGAGGAGU
.....(((((...((((((((((........((((....(((..(((..((....))..))---)..))).((((((....))))))...)))).(((....)))))))))))))))))) ( -55.10)
>consensus
GGAAAACUUUAAGUCGGCGCCUCG_CGGGCAGACCAAGAUCCGACCCAGCCAGUAGGGAGA___GGAGGAGGCCCUGGCCACAGGGUGCGGGUCACCCAUGCGGGGAGGAGUCGAGGAGG
......((((...(((((.((((..............((((((.(((........))).............((((((....)))))).)))))).(((....))))))).))))))))). (-40.48 = -40.92 +   0.44)

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 11:29:51 2006