Locus 1812

Sequence ID X_DroMel_CAF1
Location 5,019,246 – 5,019,394
Length 148
Max. P 0.991345
window2953 window2954 window2955

overview

Window 3

Location 5,019,246 – 5,019,356
Length 110
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 92.86
Mean single sequence MFE -18.99
Consensus MFE -15.68
Energy contribution -15.93
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -2.51
Structure conservation index 0.83
SVM decision value 1.25
SVM RNA-class probability 0.935682
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5019246 110 + 22224390
UGCAACAUGUUCAAUGCAAAAACAAGCAUAUUUCUUCUUACUCCAA----ACUUAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUAAAAUAACUCACAUUUAUGCACAUU
((((..((((...((((........)))).........(((((.((----(((((...(((.....))).......))))))))))))...........))))...)))).... ( -16.90)
>DroSec_CAF1 85163 110 + 1
UGCAACAUGUUCAAUGCAUAAACAAGCAUAUUUCUUCUUACUCCAA----ACUCAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUGAAAUAACUCACAUUUAUGCACAUU
..............((((((((......((((((....(((((.((----(((((...(((.....))).......)))))))))))).)))))).......)))))))).... ( -22.62)
>DroEre_CAF1 89506 110 + 1
UGCAACAUGUUCAAUGCAUAAACAAGCAUAUUUUAUCUUACUCCGA----ACUCAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUGAAAUAACUCACACUUAUGCACAUU
.......((((((((((........))))...............((----(.......)))....)))))).(.(((((((.(((((........))))).))))))))..... ( -20.30)
>DroYak_CAF1 86582 114 + 1
UGCAACAUGUUCAACGCAUAAACAAGCAUAUUUCAUCUUACUUCGUAUACACUCAAAUUUCACCAUGAAUAAGACAUGAGUUCGAGUAUGAAAUAACUCACACUUAUGCACAUU
...............((((((.......(((((((...((((.((.....(((((...(((.....))).......))))).)))))))))))))........))))))..... ( -16.16)
>consensus
UGCAACAUGUUCAAUGCAUAAACAAGCAUAUUUCAUCUUACUCCAA____ACUCAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUGAAAUAACUCACACUUAUGCACAUU
((((.((((((..((((........)))).............................(((.....)))...))))))(((.(((((........))))).)))..)))).... (-15.68 = -15.93 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,019,246 – 5,019,356
Length 110
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 92.86
Mean single sequence MFE -25.85
Consensus MFE -19.90
Energy contribution -19.65
Covariance contribution -0.25
Combinations/Pair 1.15
Mean z-score -1.84
Structure conservation index 0.77
SVM decision value 0.09
SVM RNA-class probability 0.580167
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5019246 110 - 22224390
AAUGUGCAUAAAUGUGAGUUAUUUUAUACUCAAACUCAUGUCUUAUUCAUGGUGAAAUUUAAGU----UUGGAGUAAGAAGAAAUAUGCUUGUUUUUGCAUUGAACAUGUUGCA
....(((((((((.(((((........))))).((.((((.......))))))...))))).((----(..(.(((((((.((......)).))))))).)..)))....)))) ( -21.70)
>DroSec_CAF1 85163 110 - 1
AAUGUGCAUAAAUGUGAGUUAUUUCAUACUCAAACUCAUGUCUUAUUCAUGGUGAAAUUUGAGU----UUGGAGUAAGAAGAAAUAUGCUUGUUUAUGCAUUGAACAUGUUGCA
...((((((((((..((((((((((.((((((((((((.((.((((.....)))).)).)))))----)).)))))....)))))).))))))))))))))............. ( -29.50)
>DroEre_CAF1 89506 110 - 1
AAUGUGCAUAAGUGUGAGUUAUUUCAUACUCAAACUCAUGUCUUAUUCAUGGUGAAAUUUGAGU----UCGGAGUAAGAUAAAAUAUGCUUGUUUAUGCAUUGAACAUGUUGCA
....((((.(((((((..((((((..(((((.((((((.((.((((.....)))).)).)))))----)..)))))))))))..)))))))(((((.....)))))....)))) ( -25.50)
>DroYak_CAF1 86582 114 - 1
AAUGUGCAUAAGUGUGAGUUAUUUCAUACUCGAACUCAUGUCUUAUUCAUGGUGAAAUUUGAGUGUAUACGAAGUAAGAUGAAAUAUGCUUGUUUAUGCGUUGAACAUGUUGCA
..(((((...((((((((....))))))))...(((((.((.((((.....)))).)).))))))))))....((((.(((....((((........))))....))).)))). ( -26.70)
>consensus
AAUGUGCAUAAAUGUGAGUUAUUUCAUACUCAAACUCAUGUCUUAUUCAUGGUGAAAUUUGAGU____UCGGAGUAAGAAGAAAUAUGCUUGUUUAUGCAUUGAACAUGUUGCA
....((((...((((...((((((((.(((((((((((((.......))))).)...))))))).....))))))))........((((........))))...))))..)))) (-19.90 = -19.65 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,019,280 – 5,019,394
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.49
Mean single sequence MFE -28.27
Consensus MFE -25.25
Energy contribution -25.62
Covariance contribution 0.38
Combinations/Pair 1.11
Mean z-score -2.74
Structure conservation index 0.89
SVM decision value 2.26
SVM RNA-class probability 0.991345
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5019280 114 + 22224390
UUCUUACUCCAA----ACUUAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUAAAAUAACUCACAUUUAUGCACAUUCAGUUGCCAGACAGUUUGAAUUG--CUCUUCGGGGUAACU
.........(((----(((............(((((..(.(((((((.(((((........))))).))))))))..)))))(((....)))))))))..(((--(((....)))))).. ( -27.20)
>DroSec_CAF1 85197 116 + 1
UUCUUACUCCAA----ACUCAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUGAAAUAACUCACAUUUAUGCACAUUCAGUUGCCAGACAGUUUGAAUUGGCUUUUUUGGGGUAACU
...(((((((((----(..............(((((..(.(((((((.(((((........))))).))))))))..)))))...(((((..........)))))...)))))))))).. ( -29.00)
>DroEre_CAF1 89540 115 + 1
AUCUUACUCCGA----ACUCAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUGAAAUAACUCACACUUAUGCACAUUCAGUUGCCAGACAGCUUGAAUUGG-CUCUUCGGGGUAACU
...(((((((((----(.((((..((((...(((((..(.(((((((.(((((........))))).))))))))..)))))((((.....)))).))))))))-...)))))))))).. ( -33.30)
>DroYak_CAF1 86616 119 + 1
AUCUUACUUCGUAUACACUCAAAUUUCACCAUGAAUAAGACAUGAGUUCGAGUAUGAAAUAACUCACACUUAUGCACAUUCAGUUGCCAGACAGUUUGAAUUGG-CUCUUCGGUGUAACU
..........((.((((((............(((((..(.(((((((..((((........))))..))))))))..)))))...(((((..........))))-).....)))))))). ( -23.60)
>consensus
AUCUUACUCCAA____ACUCAAAUUUCACCAUGAAUAAGACAUGAGUUUGAGUAUGAAAUAACUCACACUUAUGCACAUUCAGUUGCCAGACAGUUUGAAUUGG_CUCUUCGGGGUAACU
...(((((((((......((((..((((...(((((..(.(((((((.(((((........))))).))))))))..)))))(((....)))....)))))))).....))))))))).. (-25.25 = -25.62 +   0.38)

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 10:19:24 2006