Locus 5940

Sequence ID 3R_DroMel_CAF1
Location 15,658,136 – 15,658,235
Length 99
Max. P 0.971677
window9695 window9696

overview

Window 5

Location 15,658,136 – 15,658,235
Length 99
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 75.18
Mean single sequence MFE -25.49
Consensus MFE -10.77
Energy contribution -11.38
Covariance contribution 0.61
Combinations/Pair 1.20
Mean z-score -2.60
Structure conservation index 0.42
SVM decision value 1.68
SVM RNA-class probability 0.971677
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15658136 99 + 27905053
AUUCUAGUUCAAGAGAAGAUA----AAUUUG--UAUU---UAUUUUCCCCGUUAAGUGUCUGACGUUCAUUGUCGUGUUGACACUUGUCACAAGAUUGAACGAGAAUA
(((((.((((((..(((((((----(((...--.)))---)))))))...(.(((((((((((((.....)))))....)))))))).)......)))))).))))). ( -29.40)
>DroGri_CAF1 221326 92 + 1
AU-----CUCACAUGGUCUUAGACUAAUUUAGGCAUUGCGU--UC-----ACUUGGCUUGUGAUUUU--GGCUCAACGUCACACAAGUCACAAGAUUGAAGGUGAA--
..-----......(((((...)))))..............(--((-----((((..(((((((((((--(((.....))))...)))))))))).....)))))))-- ( -22.80)
>DroSec_CAF1 186127 99 + 1
AUUUUAGUUCACGAGAAGAUA----AAUUUG--UAUU---UAUUUUCCCCGUUAAGUGUCUGACGUUCAUUGUCGUGUUGACACUUGUCACAAGAUUGAACGAGAAUA
(((((.(((((((.(((((((----(((...--.)))---)))))))..)))(((((((((((((.....)))))....))))))))..........)))).))))). ( -26.10)
>DroSim_CAF1 181838 99 + 1
AUUCUAGUUCAAGAGAAGAUA----AAUUUG--UAUU---UAUUUUCCCCGUUAAGUGUCUGACGUUCAUUGUCGUGUUGACACUUGUCACAAGAUUGAACGAGAAUA
(((((.((((((..(((((((----(((...--.)))---)))))))...(.(((((((((((((.....)))))....)))))))).)......)))))).))))). ( -29.40)
>DroEre_CAF1 163706 93 + 1
------GUUCAAGAGAAGAUA----AAUUUG--UAUU---UAUUUUCCCCGUUAAGAGUCUGACGUUCAUUGUCGUGUUGACACUUGUCACAAGAUUGAACGAGAAUA
------((((....(((((((----(((...--.)))---)))))))................((((((..(((.(((.(((....)))))).))))))))).)))). ( -22.80)
>DroAna_CAF1 180803 94 + 1
AUUCUAGUUCAAGAAAAGAUA----CAUUUU--UAUU-------U-UACUGUUUAGUGUCUGACGCUCAUUGUCUUGUUGACACUUGUCACAAGAUUGAACGAGAACA
......((((......(((((----(.....--....-------.-.........))))))..((.(((..(((((((.(((....))))))))))))).)).)))). ( -22.41)
>consensus
AUUCUAGUUCAAGAGAAGAUA____AAUUUG__UAUU___UAUUUUCCCCGUUAAGUGUCUGACGUUCAUUGUCGUGUUGACACUUGUCACAAGAUUGAACGAGAAUA
......(((((..........................................((((((((((((.....)))))....)))))))(((....))))))))....... (-10.77 = -11.38 +   0.61)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,658,136 – 15,658,235
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 75.18
Mean single sequence MFE -21.47
Consensus MFE -8.61
Energy contribution -8.87
Covariance contribution 0.25
Combinations/Pair 1.24
Mean z-score -2.45
Structure conservation index 0.40
SVM decision value 1.20
SVM RNA-class probability 0.929334
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15658136 99 - 27905053
UAUUCUCGUUCAAUCUUGUGACAAGUGUCAACACGACAAUGAACGUCAGACACUUAACGGGGAAAAUA---AAUA--CAAAUU----UAUCUUCUCUUGAACUAGAAU
.(((((.((((((...(((...(((((((...(((........)))..))))))).)))(((((.(((---(((.--...)))----))).))))))))))).))))) ( -25.90)
>DroGri_CAF1 221326 92 - 1
--UUCACCUUCAAUCUUGUGACUUGUGUGACGUUGAGCC--AAAAUCACAAGCCAAGU-----GA--ACGCAAUGCCUAAAUUAGUCUAAGACCAUGUGAG-----AU
--(((((......(((((.((((.((..(.(((((....--....((((.......))-----))--...))))).)...)).)))))))))....)))))-----.. ( -16.30)
>DroSec_CAF1 186127 99 - 1
UAUUCUCGUUCAAUCUUGUGACAAGUGUCAACACGACAAUGAACGUCAGACACUUAACGGGGAAAAUA---AAUA--CAAAUU----UAUCUUCUCGUGAACUAAAAU
.......(((((....(((...(((((((...(((........)))..))))))).)))(((((.(((---(((.--...)))----))).))))).)))))...... ( -22.20)
>DroSim_CAF1 181838 99 - 1
UAUUCUCGUUCAAUCUUGUGACAAGUGUCAACACGACAAUGAACGUCAGACACUUAACGGGGAAAAUA---AAUA--CAAAUU----UAUCUUCUCUUGAACUAGAAU
.(((((.((((((...(((...(((((((...(((........)))..))))))).)))(((((.(((---(((.--...)))----))).))))))))))).))))) ( -25.90)
>DroEre_CAF1 163706 93 - 1
UAUUCUCGUUCAAUCUUGUGACAAGUGUCAACACGACAAUGAACGUCAGACUCUUAACGGGGAAAAUA---AAUA--CAAAUU----UAUCUUCUCUUGAAC------
...(((((((((.((.((((((....))).))).))...))))))..)))........((((((.(((---(((.--...)))----))).)))))).....------ ( -19.40)
>DroAna_CAF1 180803 94 - 1
UGUUCUCGUUCAAUCUUGUGACAAGUGUCAACAAGACAAUGAGCGUCAGACACUAAACAGUA-A-------AAUA--AAAAUG----UAUCUUUUCUUGAACUAGAAU
((((..((((((.(((((((((....))).))))))...))))))...))))..........-.-------....--......----......((((......)))). ( -19.10)
>consensus
UAUUCUCGUUCAAUCUUGUGACAAGUGUCAACACGACAAUGAACGUCAGACACUUAACGGGGAAAAUA___AAUA__CAAAUU____UAUCUUCUCUUGAACUAGAAU
.......(((((.((....)).(((((((.....(((.......))).)))))))..........................................)))))...... ( -8.61 =  -8.87 +   0.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:31 2006