Locus 7305

Sequence ID 3R_DroMel_CAF1
Location 19,283,257 – 19,283,385
Length 128
Max. P 0.994747
window11812 window11813 window11814 window11815

overview

Window 2

Location 19,283,257 – 19,283,348
Length 91
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -29.65
Consensus MFE -17.80
Energy contribution -16.92
Covariance contribution -0.89
Combinations/Pair 1.29
Mean z-score -1.65
Structure conservation index 0.60
SVM decision value 0.14
SVM RNA-class probability 0.600675
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19283257 91 + 27905053
CGGUCAAUUUGUGGUUUCUUUGUUUCCUGACUGCGUCCCA----AAUGGCCGUGCUAGUUGGCCGCUAAUUUGGCCAGCAUUUAAGCCGGUC--------------AGU
((((((....(..(.....)..)....)))))).......----..((((((.(((.((((((((......)))))))).....))))))))--------------).. ( -29.70)
>DroPse_CAF1 94436 90 + 1
----CAAUUUGUGGUUUCUUUGUUUCCUGACCGAGUCCCCAUAUAAUGGCCACGUUAGUUGGCCGUUAAUUUGGCCAGUC-AAAUGACUGCG--------------AGG
----...((((..(((..((((....(((.((((((.......((((((((((....).))))))))))))))).))).)-))).)))..))--------------)). ( -28.21)
>DroEre_CAF1 80383 91 + 1
CGGUCAAUUUGUGGUUUCUUUGUUUCCUGACUGCGUCCCA----AAUGGCCAUGCUAGUUGGCCGCUAAUUUGGCCAGCAUUUAAGCCGGUC--------------AGC
(((((((((.((((((..((((...((.....).)...))----)).))))))...))))))))).....((((((.((......)).))))--------------)). ( -26.10)
>DroYak_CAF1 83676 91 + 1
CGGUCAAUUUGUGGUUUCUUUGUUUCCUGACUGCGUCCCA----AAUGGCCAUGCUAGUUGGCCACUAAUUUGGCCAGCAUUUAAGCCGGUC--------------AGG
.........................((((((((.((....----..((((...))))((((((((......))))))))......)))))))--------------))) ( -28.40)
>DroAna_CAF1 80482 108 + 1
GGGUCAAUUUGUGGUUUCUUUGUUUCCUGGCUGCGUCCCA-UAUAAUGGCCACGUUAGUUGGCCGCUAAUUUGGCCAGCAUUUAAGGCGGCCUGUGUGUGGCUGCGAGG
.(((((....(..(.....)..)....)))))(((..(((-((((..((((.(.(((((((((((......))))))))...))).).))))..))))))).))).... ( -37.30)
>DroPer_CAF1 94542 90 + 1
----CAAUUUGUGGUUUCUUUGUUUCCUGACCGAGUCCCCAUAUAAUGGCCACGUUAGUUGGCCGUUAAUUUGGCCAGUC-AAAUGACUGCG--------------AGG
----...((((..(((..((((....(((.((((((.......((((((((((....).))))))))))))))).))).)-))).)))..))--------------)). ( -28.21)
>consensus
CGGUCAAUUUGUGGUUUCUUUGUUUCCUGACUGCGUCCCA____AAUGGCCACGCUAGUUGGCCGCUAAUUUGGCCAGCAUUUAAGCCGGCC______________AGG
..........((((((............(((...)))..........))))))....((((((((......)))))))).............................. (-17.80 = -16.92 +  -0.89)

alignment

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secondary structure

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Window 3

Location 19,283,257 – 19,283,348
Length 91
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -25.32
Consensus MFE -15.23
Energy contribution -14.87
Covariance contribution -0.36
Combinations/Pair 1.25
Mean z-score -1.76
Structure conservation index 0.60
SVM decision value 0.30
SVM RNA-class probability 0.677744
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19283257 91 - 27905053
ACU--------------GACCGGCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAGCACGGCCAUU----UGGGACGCAGUCAGGAAACAAAGAAACCACAAAUUGACCG
.((--------------(((((((......)))).((((((....((((.........)))))))----)))......))))).......................... ( -22.90)
>DroPse_CAF1 94436 90 - 1
CCU--------------CGCAGUCAUUU-GACUGGCCAAAUUAACGGCCAACUAACGUGGCCAUUAUAUGGGGACUCGGUCAGGAAACAAAGAAACCACAAAUUG----
(((--------------(((((((....-)))))...........(((((.(....))))))......)))))....(((..(....)......)))........---- ( -24.20)
>DroEre_CAF1 80383 91 - 1
GCU--------------GACCGGCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAGCAUGGCCAUU----UGGGACGCAGUCAGGAAACAAAGAAACCACAAAUUGACCG
(((--------------(((((((......))))).....)))))(((((.......)))))...----((((((...))).(....).......)))........... ( -25.40)
>DroYak_CAF1 83676 91 - 1
CCU--------------GACCGGCUUAAAUGCUGGCCAAAUUAGUGGCCAACUAGCAUGGCCAUU----UGGGACGCAGUCAGGAAACAAAGAAACCACAAAUUGACCG
(((--------------(((((((......)))).((((....(((((((.......))))))))----)))......))))))......................... ( -27.90)
>DroAna_CAF1 80482 108 - 1
CCUCGCAGCCACACACAGGCCGCCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAACGUGGCCAUUAUA-UGGGACGCAGCCAGGAAACAAAGAAACCACAAAUUGACCC
(((.((.(((.......)))(((((...(((.((((((..((((.......))))..)))))).))).-.))).))..)).)))......................... ( -27.30)
>DroPer_CAF1 94542 90 - 1
CCU--------------CGCAGUCAUUU-GACUGGCCAAAUUAACGGCCAACUAACGUGGCCAUUAUAUGGGGACUCGGUCAGGAAACAAAGAAACCACAAAUUG----
(((--------------(((((((....-)))))...........(((((.(....))))))......)))))....(((..(....)......)))........---- ( -24.20)
>consensus
CCU______________GACCGGCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAACAUGGCCAUU____UGGGACGCAGUCAGGAAACAAAGAAACCACAAAUUGACCG
.................(((((.((((.....((((((..((((.......))))..))))))......)))).))..))).(....)..................... (-15.23 = -14.87 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,283,292 – 19,283,385
Length 93
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 76.61
Mean single sequence MFE -28.37
Consensus MFE -17.04
Energy contribution -16.80
Covariance contribution -0.25
Combinations/Pair 1.40
Mean z-score -3.11
Structure conservation index 0.60
SVM decision value 2.51
SVM RNA-class probability 0.994747
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19283292 93 + 27905053
UCCCA----AAUGGCCGUGCUAGUUGGCCGCUAAUUUGGCCAGCAUUUAAGCCGGUC--------------AGUCUUUAAUUAAC-AAAGGCCACACUCUAAUUGAUAAAUU
...((----(.((((((.(((.((((((((......)))))))).....))))))))--------------)((((((.......-))))))..........)))....... ( -27.80)
>DroVir_CAF1 98621 96 + 1
UCCCCA--UAACGGCCACCUUGGUUGGCCACUAAUUUGGCCGGCAAUAAGACCACGC----------UAC-AUGGCUUAAUUAAA---AAGUAACUCUCUAAUUGAUUAAUU
...(((--(...(((...((((((((((((......))))))))..)))).....))----------)..-)))).((((((((.---.((.......))..)))))))).. ( -20.20)
>DroPse_CAF1 94467 97 + 1
UCCCCAUAUAAUGGCCACGUUAGUUGGCCGUUAAUUUGGCCAGUC-AAAUGACUGCG--------------AGGCUUUAAUUAAAAAAAGGCCACACUCUAAUUGAUAAAUU
...(((..((((((((((....).)))))))))...)))((((((-....))))).)--------------.((((((.........))))))................... ( -27.30)
>DroYak_CAF1 83711 93 + 1
UCCCA----AAUGGCCAUGCUAGUUGGCCACUAAUUUGGCCAGCAUUUAAGCCGGUC--------------AGGCUUUAAUUAAC-AAAGGCCACACUCUAAUUGAUAAAUU
.....----..(((((......((((((((......))))))))(((.(((((....--------------.))))).)))....-...))))).................. ( -30.10)
>DroAna_CAF1 80517 110 + 1
UCCCA-UAUAAUGGCCACGUUAGUUGGCCGCUAAUUUGGCCAGCAUUUAAGGCGGCCUGUGUGUGGCUGCGAGGCUUUAAUUAAC-AAAGGCCACACUCUAAUUGAUAAAUU
..(((-((((..((((.(.(((((((((((......))))))))...))).).))))..)))))))......((((((.......-.))))))................... ( -37.50)
>DroPer_CAF1 94573 97 + 1
UCCCCAUAUAAUGGCCACGUUAGUUGGCCGUUAAUUUGGCCAGUC-AAAUGACUGCG--------------AGGCUUUAAUUAAAAAAAGGCCACACUCUAAUUGAUAAAUU
...(((..((((((((((....).)))))))))...)))((((((-....))))).)--------------.((((((.........))))))................... ( -27.30)
>consensus
UCCCA___UAAUGGCCACGUUAGUUGGCCGCUAAUUUGGCCAGCAUUAAAGCCGGCC______________AGGCUUUAAUUAAA_AAAGGCCACACUCUAAUUGAUAAAUU
...........(((((......((((((((......))))))))..........((.................))..............))))).................. (-17.04 = -16.80 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,283,292 – 19,283,385
Length 93
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 76.61
Mean single sequence MFE -27.02
Consensus MFE -13.28
Energy contribution -14.00
Covariance contribution 0.72
Combinations/Pair 1.15
Mean z-score -1.89
Structure conservation index 0.49
SVM decision value 0.21
SVM RNA-class probability 0.635299
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19283292 93 - 27905053
AAUUUAUCAAUUAGAGUGUGGCCUUU-GUUAAUUAAAGACU--------------GACCGGCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAGCACGGCCAUU----UGGGA
.................((((((..(-(((((((......(--------------(.(((((......))))).))))))))))((......))..)))))).----..... ( -23.20)
>DroVir_CAF1 98621 96 - 1
AAUUAAUCAAUUAGAGAGUUACUU---UUUAAUUAAGCCAU-GUA----------GCGUGGUCUUAUUGCCGGCCAAAUUAGUGGCCAACCAAGGUGGCCGUUA--UGGGGA
........((((((((((...)))---)))))))...((..-(((----------((.(((((........))))).......(((((.(....))))))))))--)..)). ( -26.60)
>DroPse_CAF1 94467 97 - 1
AAUUUAUCAAUUAGAGUGUGGCCUUUUUUUAAUUAAAGCCU--------------CGCAGUCAUUU-GACUGGCCAAAUUAACGGCCAACUAACGUGGCCAUUAUAUGGGGA
...............(((.(((.(((........)))))).--------------)))((((....-))))..(((...(((.(((((.(....)))))).)))..)))... ( -24.80)
>DroYak_CAF1 83711 93 - 1
AAUUUAUCAAUUAGAGUGUGGCCUUU-GUUAAUUAAAGCCU--------------GACCGGCUUAAAUGCUGGCCAAAUUAGUGGCCAACUAGCAUGGCCAUU----UGGGA
.................((((((..(-(((((((.(((((.--------------....))))).)))..((((((......))))))..))))).)))))).----..... ( -29.40)
>DroAna_CAF1 80517 110 - 1
AAUUUAUCAAUUAGAGUGUGGCCUUU-GUUAAUUAAAGCCUCGCAGCCACACACAGGCCGCCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAACGUGGCCAUUAUA-UGGGA
......(((......(((((((((((-(.....))))).......)))))))...((((((.(((...(.(((((........))))).)))).))))))......-))).. ( -33.31)
>DroPer_CAF1 94573 97 - 1
AAUUUAUCAAUUAGAGUGUGGCCUUUUUUUAAUUAAAGCCU--------------CGCAGUCAUUU-GACUGGCCAAAUUAACGGCCAACUAACGUGGCCAUUAUAUGGGGA
...............(((.(((.(((........)))))).--------------)))((((....-))))..(((...(((.(((((.(....)))))).)))..)))... ( -24.80)
>consensus
AAUUUAUCAAUUAGAGUGUGGCCUUU_GUUAAUUAAAGCCU______________GGCCGGCUUAAAUGCUGGCCAAAUUAGCGGCCAACUAACGUGGCCAUUA___GGGGA
.................((((((...............................................(((((........)))))((....)))))))).......... (-13.28 = -14.00 +   0.72)

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 12:42:36 2006