Locus 1903

Sequence ID X_DroMel_CAF1
Location 5,278,457 – 5,278,615
Length 158
Max. P 0.999165
window3095 window3096 window3097 window3098

overview

Window 5

Location 5,278,457 – 5,278,575
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.36
Mean single sequence MFE -37.58
Consensus MFE -23.27
Energy contribution -23.67
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -2.33
Structure conservation index 0.62
SVM decision value 1.51
SVM RNA-class probability 0.959903
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5278457 118 + 22224390
GCUAAUGCUUAAUCCGCUCUUAAGCGCUUUUAAGAGAAAUACA-AAUACUGGGAACAGCAGUGGGAACACUAAGCGGCUGCGAACAC-UGUUCCCAGUACCCCAGGCAACUGUGCCCGAU
((....))........((((((((....)))))))).......-..((((((((((((.((((....))))..((....)).....)-))))))))))).....((((....)))).... ( -38.30)
>DroSec_CAF1 15517 107 + 1
GCUAAUGUUUAAGCCGCUCUUAAGCGCUUUUAAGAGAG--CCA-AAUACUGGGAACAGCAGUGGGAACACUAUGCGACUGGGAAC----------AGUACCCCAGGCAACUGUGCCCGAU
(((.......((((.(((....))))))).......))--)..-.....((((.((((.((((....)))).(((..(((((...----------.....)))))))).)))).)))).. ( -34.14)
>DroSim_CAF1 10171 107 + 1
GCUAAUGUUUAAGCCGCUCUUAAGCGCUUUUAAGAGAG--CCA-AAUACUGGGAACAGCAGUGGGAACACUGCGCGACUGUGAAC----------AGUACCCCAGGCAACUGUGCCCGAU
(((.......((((.(((....))))))).......))--)..-....(((((....((((((....))))))...((((....)----------)))..)))))(((....)))..... ( -36.24)
>DroEre_CAF1 15105 112 + 1
---AAAGUUUUCCGCGCUCUUAGGCGCUUUUAAGAGAG--CCA-AAUACUGGGAACAGCAGUGGGAACACCAUGCGGGUGGGAACACCU--UUGCAGUGCCCCAAGCAACUGUCCCCGAA
---..(((.((..((.((((((((....)))))))).)--)..-)).)))(((.((((...((((..(((..((((((((....)))))--..)))))).)))).....)))).)))... ( -38.70)
>DroYak_CAF1 11052 115 + 1
---AAAUUUUUUCCUGCUCUUAGGGCAUUUUAAGAGAG--CCAAAAUACUGGGAACAGUAGUGGGAACACCAUGCGGGUGGGAACACAUGCUUGCAGUACCCCAAGCCACUGUUCCCACA
---.........((..((((((((....)))))))).(--(.....(((((....)))))((((.....))))))))(((((((((...(((((........)))))...))))))))). ( -40.50)
>consensus
GCUAAUGUUUAACCCGCUCUUAAGCGCUUUUAAGAGAG__CCA_AAUACUGGGAACAGCAGUGGGAACACUAUGCGGCUGGGAACAC_U__U__CAGUACCCCAGGCAACUGUGCCCGAU
................((((((((....)))))))).............((((.((((..(((....)))...((..(((((..................)))))))..)))).)))).. (-23.27 = -23.67 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,278,457 – 5,278,575
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.36
Mean single sequence MFE -39.96
Consensus MFE -23.24
Energy contribution -24.04
Covariance contribution 0.80
Combinations/Pair 1.07
Mean z-score -2.48
Structure conservation index 0.58
SVM decision value 1.68
SVM RNA-class probability 0.971643
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5278457 118 - 22224390
AUCGGGCACAGUUGCCUGGGGUACUGGGAACA-GUGUUCGCAGCCGCUUAGUGUUCCCACUGCUGUUCCCAGUAUU-UGUAUUUCUCUUAAAAGCGCUUAAGAGCGGAUUAAGCAUUAGC
..((((((....))))))((((((((((((((-((....((....))..((((....)))))))))))))))))))-).................((((((.......))))))...... ( -42.40)
>DroSec_CAF1 15517 107 - 1
AUCGGGCACAGUUGCCUGGGGUACU----------GUUCCCAGUCGCAUAGUGUUCCCACUGCUGUUCCCAGUAUU-UGG--CUCUCUUAAAAGCGCUUAAGAGCGGCUUAAACAUUAGC
...(((.((((((((((((((....----------..))))))..))).((((....))))))))).))).((...-.((--(((((((((......))))))).))))...))...... ( -35.60)
>DroSim_CAF1 10171 107 - 1
AUCGGGCACAGUUGCCUGGGGUACU----------GUUCACAGUCGCGCAGUGUUCCCACUGCUGUUCCCAGUAUU-UGG--CUCUCUUAAAAGCGCUUAAGAGCGGCUUAAACAUUAGC
...(((.(((((.....((..((((----------((.(......).))))))..))....))))).))).((...-.((--(((((((((......))))))).))))...))...... ( -35.60)
>DroEre_CAF1 15105 112 - 1
UUCGGGGACAGUUGCUUGGGGCACUGCAA--AGGUGUUCCCACCCGCAUGGUGUUCCCACUGCUGUUCCCAGUAUU-UGG--CUCUCUUAAAAGCGCCUAAGAGCGCGGAAAACUUU---
...(((((((((....(((((((((((..--.((((....)))).))..)))).)))))..)))))))))(((.((-(.(--(.((((((........)))))).)).))).)))..--- ( -45.10)
>DroYak_CAF1 11052 115 - 1
UGUGGGAACAGUGGCUUGGGGUACUGCAAGCAUGUGUUCCCACCCGCAUGGUGUUCCCACUACUGUUCCCAGUAUUUUGG--CUCUCUUAAAAUGCCCUAAGAGCAGGAAAAAAUUU---
..((((((((((((..(((((....(((..((((((........)))))).))))))))))))))))))))...((((..--((((((((........)))))).))..))))....--- ( -41.10)
>consensus
AUCGGGCACAGUUGCCUGGGGUACUG__A__A_GUGUUCCCAGCCGCAUAGUGUUCCCACUGCUGUUCCCAGUAUU_UGG__CUCUCUUAAAAGCGCUUAAGAGCGGCUUAAACAUUAGC
...(((.(((((.((((((((.((...........))))))))..))..((((....))))))))).)))..............(((((((......)))))))................ (-23.24 = -24.04 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,278,497 – 5,278,615
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.60
Mean single sequence MFE -38.73
Consensus MFE -18.81
Energy contribution -19.60
Covariance contribution 0.79
Combinations/Pair 1.19
Mean z-score -2.42
Structure conservation index 0.49
SVM decision value 1.05
SVM RNA-class probability 0.906873
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5278497 118 + 22224390
ACA-AAUACUGGGAACAGCAGUGGGAACACUAAGCGGCUGCGAACAC-UGUUCCCAGUACCCCAGGCAACUGUGCCCGAUUUCUAAUUACUGUGUUGUUGGUUGGUUGGUGGGUGGUGGG
...-..((((((((((((.((((....))))..((....)).....)-)))))))))))((((((....))).(((((....((((((((......).)))))))....)))))...))) ( -45.90)
>DroEre_CAF1 15140 96 + 1
CCA-AAUACUGGGAACAGCAGUGGGAACACCAUGCGGGUGGGAACACCU--UUGCAGUGCCCCAAGCAACUGUCCCCGAACUCCAAUUACUGGGUAGGC---------------------
((.-.....((((.((((...((((..(((..((((((((....)))))--..)))))).)))).....)))).)))).((.(((.....))))).)).--------------------- ( -31.90)
>DroYak_CAF1 11087 99 + 1
CCAAAAUACUGGGAACAGUAGUGGGAACACCAUGCGGGUGGGAACACAUGCUUGCAGUACCCCAAGCCACUGUUCCCACAUUCUAAUUACUGGGUGGGC---------------------
(((...(((((....))))).))).....((((.((((((((((((...(((((........)))))...)))))))))..........))).))))..--------------------- ( -38.40)
>consensus
CCA_AAUACUGGGAACAGCAGUGGGAACACCAUGCGGGUGGGAACAC_UG_UUGCAGUACCCCAAGCAACUGUCCCCGAAUUCUAAUUACUGGGUAGGC_____________________
((.......((((.((((...((((.((.....(((.(((....))).))).....))..)))).....)))).))))(((((........)))))))...................... (-18.81 = -19.60 +   0.79)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,278,497 – 5,278,615
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 71.60
Mean single sequence MFE -36.40
Consensus MFE -23.64
Energy contribution -23.53
Covariance contribution -0.10
Combinations/Pair 1.21
Mean z-score -2.16
Structure conservation index 0.65
SVM decision value 3.41
SVM RNA-class probability 0.999165
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5278497 118 - 22224390
CCCACCACCCACCAACCAACCAACAACACAGUAAUUAGAAAUCGGGCACAGUUGCCUGGGGUACUGGGAACA-GUGUUCGCAGCCGCUUAGUGUUCCCACUGCUGUUCCCAGUAUU-UGU
......((((............((......))..........((((((....))))))))))((((((((((-((....((....))..((((....))))))))))))))))...-... ( -37.90)
>DroEre_CAF1 15140 96 - 1
---------------------GCCUACCCAGUAAUUGGAGUUCGGGGACAGUUGCUUGGGGCACUGCAA--AGGUGUUCCCACCCGCAUGGUGUUCCCACUGCUGUUCCCAGUAUU-UGG
---------------------.((.((((((...)))).))..(((((((((....(((((((((((..--.((((....)))).))..)))).)))))..)))))))))......-.)) ( -33.70)
>DroYak_CAF1 11087 99 - 1
---------------------GCCCACCCAGUAAUUAGAAUGUGGGAACAGUGGCUUGGGGUACUGCAAGCAUGUGUUCCCACCCGCAUGGUGUUCCCACUACUGUUCCCAGUAUUUUGG
---------------------..............(((((((((((((((((((..(((((....(((..((((((........)))))).)))))))))))))))))))).))))))). ( -37.60)
>consensus
_____________________GCCAACCCAGUAAUUAGAAUUCGGGAACAGUUGCUUGGGGUACUGCAA_CA_GUGUUCCCACCCGCAUGGUGUUCCCACUGCUGUUCCCAGUAUU_UGG
...........................................(((((((((.....((..(((((.......(((....))).....)))))..))....))))))))).......... (-23.64 = -23.53 +  -0.10)

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 10:21:32 2006