Locus 7167

Sequence ID 3R_DroMel_CAF1
Location 18,886,622 – 18,886,939
Length 317
Max. P 0.999992
window11590 window11591 window11592 window11593 window11594

overview

Window 0

Location 18,886,622 – 18,886,742
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.42
Mean single sequence MFE -53.12
Consensus MFE -49.66
Energy contribution -50.58
Covariance contribution 0.92
Combinations/Pair 1.07
Mean z-score -1.36
Structure conservation index 0.93
SVM decision value 1.12
SVM RNA-class probability 0.917636
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18886622 120 + 27905053
CAUGGUAGUAGUCCGGCUGCGAGUCCGUGCAGGAGUAGGUGUUCCGACUGGUGCUCGAGCUGCGCGGAUGGAACUCGCAGCUGGGCGAGGUGCUCGCACAGCGCUGCAGCGAUUUCUUCU
....(((((.((((((((((((((((((((((((((((((......)))..)))))...))))))))).....)))))))))))))(..(((....)))..))))))............. ( -55.80)
>DroSec_CAF1 886 120 + 1
CAUGGUAGUAGUCCGGCUGCGAGUCCGUGCAGGAGUAGGUGUUCCGACUGGUGCUCGAGCUGCGCGGAUGGAACUCGCAGCUGGGCGAGGUGCUCGCACAGCGCUGCAGCGACUUCUUCU
..........((((((((((((((((((((((((((((((......)))..)))))...))))))))).....)))))))))))))((((((((.(((......)))))).))))).... ( -57.50)
>DroSim_CAF1 531 119 + 1
CAUG-UAGUAGUCCGGCCGCGAGUCCGUGCAGGAGUAGGUGUUCCGACUCGUGCUCGAGCUGCACCAUUGGAACUUGCAGCUGGGGGAGGUGCUAGCACAGCGGCGCAGCGACUUCUUCU
....-......((((((.(((((((((((((((((((.(.((....)).).)))))...))))))....)).)))))).))))))(((((((((.((......))..))).))))))... ( -46.80)
>DroEre_CAF1 665 120 + 1
CAUGGUAGUAGUCCGGCUGCGAGUCCGUGCAGGAGUAGGUGUUCCGACUGGUGCUCGAGCUGCGCGGAUGGAACUCACAGCUGGGCGAGGUGCUGGCACAGCGCUGCAGCGACUUCUUCU
..........(((((((((.((((((((((((((((((((......)))..)))))...))))))))).....))).)))))))))(((((((((((.....))..)))).))))).... ( -52.10)
>DroYak_CAF1 528 120 + 1
CAUGAUAGUAGUCCGGCUGGGAGUCCGUGCAGGAGUAGGUGUUCCGACUGGUGCUCGAGCUGCGCGGAUGGAACUCGCAGCUGGGCGAGGUGCUGGCACAGCGCUGCAGCGACUUCUUCU
..........(((((((((.((((((((((((((((((((......)))..)))))...))))))))).....))).)))))))))(((((((((((.....))..)))).))))).... ( -53.40)
>consensus
CAUGGUAGUAGUCCGGCUGCGAGUCCGUGCAGGAGUAGGUGUUCCGACUGGUGCUCGAGCUGCGCGGAUGGAACUCGCAGCUGGGCGAGGUGCUCGCACAGCGCUGCAGCGACUUCUUCU
..........((((((((((((((((((((((((((((((......)))..)))))...)))))))).....))))))))))))))((((((((.(((......)))))).))))).... (-49.66 = -50.58 +   0.92)

alignment

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secondary structure

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Window 1

Location 18,886,702 – 18,886,819
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.08
Mean single sequence MFE -43.50
Consensus MFE -37.96
Energy contribution -37.56
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -1.22
Structure conservation index 0.87
SVM decision value 0.12
SVM RNA-class probability 0.595362
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18886702 117 + 27905053
CUGGGCGAGGUGCUCGCACAGCGCUGCAGCGAUUUCUUCUUGGCCCGCUGAUCGCU---CCACACAUUGAUCACCGAAAUAUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACG
.((((.(((((((......((((...(((((...((.....))..)))))..))))---..((((.....((((((.......)))))).))))..........)))))))))))..... ( -38.20)
>DroSec_CAF1 966 120 + 1
CUGGGCGAGGUGCUCGCACAGCGCUGCAGCGACUUCUUCUUGGCCCGCUGGUCGCUCGUCCACACAUUGAUCGCCGAAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACG
.(((((((((((((.....)))))..(((((.((.......))..)))))....))))))))......................(((((((.((.(........).))..)))))))... ( -41.00)
>DroSim_CAF1 610 120 + 1
CUGGGGGAGGUGCUAGCACAGCGGCGCAGCGACUUCUUCUUGGCCCGUUGGUCGCUAGUCCACACAUUGAUCGCCGAAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACG
.(((((((((..(((((.((((((.((...((.....))...))))))))...)))))..)((((.....((((((.......)))))).)))).............))))))))..... ( -45.60)
>DroEre_CAF1 745 120 + 1
CUGGGCGAGGUGCUGGCACAGCGCUGCAGCGACUUCUUCUUGGCACGCUGGUCGCUCGUCCACACAUUGAUCACCGGAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACG
.((((.(((((((.(((.(((((.(((...((.....))...)))))))))))........((((.....(((((((.....))))))).))))..........)))))))))))..... ( -46.10)
>DroYak_CAF1 608 120 + 1
CUGGGCGAGGUGCUGGCACAGCGCUGCAGCGACUUCUUCUUGGCACGCUGAUCGCUCGUCCACACAUUGAUCACCGGAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACG
.((((.(((((((.((.((((((...(((((.((.......))..)))))..)))).))))((((.....(((((((.....))))))).))))..........)))))))))))..... ( -46.60)
>consensus
CUGGGCGAGGUGCUCGCACAGCGCUGCAGCGACUUCUUCUUGGCCCGCUGGUCGCUCGUCCACACAUUGAUCACCGAAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACG
.((((.(((((((......((((...(((((...((.....))..)))))..)))).....((((.....((((((.......)))))).))))..........)))))))))))..... (-37.96 = -37.56 +  -0.40)

alignment

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secondary structure

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Window 2

Location 18,886,742 – 18,886,859
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -47.26
Consensus MFE -47.38
Energy contribution -46.90
Covariance contribution -0.48
Combinations/Pair 1.06
Mean z-score -3.52
Structure conservation index 1.00
SVM decision value 5.68
SVM RNA-class probability 0.999992
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18886742 117 + 27905053
UGGCCCGCUGAUCGCU---CCACACAUUGAUCACCGAAAUAUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGA
.(((.((.((((((..---........)))))).))........(((((((.((.(........).))..)))))))..)))...(((((((((((((........))))))))))))). ( -47.30)
>DroSec_CAF1 1006 120 + 1
UGGCCCGCUGGUCGCUCGUCCACACAUUGAUCGCCGAAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGA
.(((....(((.((.(((.........))).)))))........(((((((.((.(........).))..)))))))..)))...(((((((((((((........))))))))))))). ( -46.00)
>DroSim_CAF1 650 120 + 1
UGGCCCGUUGGUCGCUAGUCCACACAUUGAUCGCCGAAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGA
.(((.((.((((((...((....))..)))))).))........(((((((.((.(........).))..)))))))..)))...(((((((((((((........))))))))))))). ( -46.00)
>DroEre_CAF1 785 120 + 1
UGGCACGCUGGUCGCUCGUCCACACAUUGAUCACCGGAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGA
.(((...(((((.(.(((.........))).)))))).......(((((((.((.(........).))..)))))))..)))...(((((((((((((........))))))))))))). ( -48.40)
>DroYak_CAF1 648 120 + 1
UGGCACGCUGAUCGCUCGUCCACACAUUGAUCACCGGAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGA
.(((.((.((((((...((....))..)))))).))........(((((((.((.(........).))..)))))))..)))...(((((((((((((........))))))))))))). ( -48.60)
>consensus
UGGCCCGCUGGUCGCUCGUCCACACAUUGAUCACCGAAAUCUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGA
.(((.((.((((((.............)))))).))........(((((((.((.(........).))..)))))))..)))...(((((((((((((........))))))))))))). (-47.38 = -46.90 +  -0.48)

alignment

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secondary structure

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Window 3

Location 18,886,779 – 18,886,899
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.67
Mean single sequence MFE -47.40
Consensus MFE -47.34
Energy contribution -47.34
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 1.00
SVM decision value 3.75
SVM RNA-class probability 0.999585
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18886779 120 + 27905053
AUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUA
(((((((((((.((.(........).))..)))))))..((....(((((((((((((........))))))))))))).((((((........))).)))...)).))))......... ( -47.80)
>DroSec_CAF1 1046 120 + 1
CUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUA
.((((((((((.((.(........).))..)))))))..((....(((((((((((((........))))))))))))).((((((........))).)))...)).))).......... ( -47.30)
>DroSim_CAF1 690 120 + 1
CUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUA
.((((((((((.((.(........).))..)))))))..((....(((((((((((((........))))))))))))).((((((........))).)))...)).))).......... ( -47.30)
>DroEre_CAF1 825 120 + 1
CUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUA
.((((((((((.((.(........).))..)))))))..((....(((((((((((((........))))))))))))).((((((........))).)))...)).))).......... ( -47.30)
>DroYak_CAF1 688 120 + 1
CUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUA
.((((((((((.((.(........).))..)))))))..((....(((((((((((((........))))))))))))).((((((........))).)))...)).))).......... ( -47.30)
>consensus
CUCCGGUGGGGUGUCCUUCUUCAUGUACUUCCCCACCACGCCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUA
.((((((((((.((.(........).))..)))))))..((....(((((((((((((........))))))))))))).((((((........))).)))...)).))).......... (-47.34 = -47.34 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,886,819 – 18,886,939
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.33
Mean single sequence MFE -42.40
Consensus MFE -41.40
Energy contribution -41.44
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.38
Structure conservation index 0.98
SVM decision value 0.55
SVM RNA-class probability 0.779722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18886819 120 + 27905053
CCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUAGUUCAUGCAGACUAUGUUUCCGCUCGGAUUCCGGAUCGCU
.....(((((((((((((........)))))))))))))(((....((((..(((((((((...)))(((.....(.((((((......)))))).).))))).))))..))))...))) ( -41.60)
>DroSec_CAF1 1086 120 + 1
CCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUAGUUCAUGCAGACUCUGUUUCCGCUCGGAUUCCGGAUCGUU
.....(((((((((((((........)))))))))))))(((....((((..(((((..((..(((((..((((..((....))..)).))..)))))...)))))))..))))...))) ( -40.80)
>DroSim_CAF1 730 120 + 1
CCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUAGUUCAUGCAGACUCUGUUUCCGCUCGGAUUCCGGAUCGCU
.....(((((((((((((........)))))))))))))(((....((((..(((((..((..(((((..((((..((....))..)).))..)))))...)))))))..))))...))) ( -43.20)
>DroEre_CAF1 865 120 + 1
CCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUAGUUCAUGCAGACUCUGUUUCCGCUCGGAUUCCGGAUCGCU
.....(((((((((((((........)))))))))))))(((....((((..(((((..((..(((((..((((..((....))..)).))..)))))...)))))))..))))...))) ( -43.20)
>DroYak_CAF1 728 120 + 1
CCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUAGUUCAUGCAGACUCUGUUUCCGCUCGGAUUCCGGAUCGCU
.....(((((((((((((........)))))))))))))(((....((((..(((((..((..(((((..((((..((....))..)).))..)))))...)))))))..))))...))) ( -43.20)
>consensus
CCCUCCUUGUGCUGGGACUUCUCCUUGUUCCGGCGCGAGAGCAUCGUCGGUUUUCGGUUGCACAGCAGGAUCGUUAGAUAGUUCAUGCAGACUCUGUUUCCGCUCGGAUUCCGGAUCGCU
.....(((((((((((((........)))))))))))))(((....((((..(((((..((..(((((..((((..((....))..)).))..)))))...)))))))..))))...))) (-41.40 = -41.44 +   0.04)

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 12:39:04 2006