Locus 7009

Sequence ID X_DroMel_CAF1
Location 17,554,291 – 17,554,434
Length 143
Max. P 0.954791
window11452 window11453 window11454

overview

Window 2

Location 17,554,291 – 17,554,397
Length 106
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 87.42
Mean single sequence MFE -26.50
Consensus MFE -18.42
Energy contribution -19.67
Covariance contribution 1.25
Combinations/Pair 1.08
Mean z-score -2.30
Structure conservation index 0.70
SVM decision value 0.74
SVM RNA-class probability 0.838749
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17554291 106 + 22224390
UGAGUUGCGUGUAGAUAACACGACUAUGUCUGCUAGAUUGUAAACUUACACGAAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGCAGCACUUUUCCAA
.((((.((((((.....)))).....((((((((.((.((((((.((.....)).)))))).))..((((((........))))))))))))))))))))...... ( -25.50)
>DroSec_CAF1 6195 106 + 1
UGAGUUGCGUGUAGAUAACACGACCAUGUCUAGAAAGAUGUAAACUUACACGCAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGAAGCACUUUUCCAA
((((.(((((((((......)....((((((....)))))).....)))))))).))))....(((((((((........))))).))))(((((....))))).. ( -23.60)
>DroSim_CAF1 6030 106 + 1
UACGUGGCGUGUAGAUAACACGACCAUGUCUAGAAAGAUGUAAACUUACAGGAAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGCAGCACUUUUCCAA
.(((((((((((.....))))).)))))).(((..(((((((((.((.....)).))))))))).)))..(((((...((((((....)))))).....))))).. ( -33.00)
>DroEre_CAF1 10771 106 + 1
UAUGUUGCGUGUAGAGAACACGACCAUGUCCAUAAAUAUGUAAUUUUACGCGCAUUUUACAUUCGCUUUAGGAAAUAAUGCCUAAAAGUAGGCAGCGUUUUACCAA
.(((((((((((((((.....(((...)))(((....)))...)))))))))))....)))).........(((((..((((((....))))))..)))))..... ( -23.90)
>consensus
UAAGUUGCGUGUAGAUAACACGACCAUGUCUAGAAAGAUGUAAACUUACACGAAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGCAGCACUUUUCCAA
......((((((.....))))..............(((((((((...........)))))))))))....(((((...((((((....)))))).....))))).. (-18.42 = -19.67 +   1.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,554,291 – 17,554,397
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 87.42
Mean single sequence MFE -23.50
Consensus MFE -16.02
Energy contribution -16.83
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value 0.04
SVM RNA-class probability 0.555608
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17554291 106 - 22224390
UUGGAAAAGUGCUGCCUACUUAUAGGCAUUAUUUCCUAUAGCAAAUGUAAAAUUCGUGUAAGUUUACAAUCUAGCAGACAUAGUCGUGUUAUCUACACGCAACUCA
..((((..(((.((((((....)))))).)))))))....((.............((((..(((........)))..))))....((((.....))))))...... ( -21.30)
>DroSec_CAF1 6195 106 - 1
UUGGAAAAGUGCUUCCUACUUAUAGGCAUUAUUUCCUAUAGCAAAUGUAAAAUGCGUGUAAGUUUACAUCUUUCUAGACAUGGUCGUGUUAUCUACACGCAACUCA
..((((((((((((.........))))))).)))))................((((((((..(..((((....(((....)))..)))).)..))))))))..... ( -24.30)
>DroSim_CAF1 6030 106 - 1
UUGGAAAAGUGCUGCCUACUUAUAGGCAUUAUUUCCUAUAGCAAAUGUAAAAUUCCUGUAAGUUUACAUCUUUCUAGACAUGGUCGUGUUAUCUACACGCCACGUA
(((((((..((......(((((((((....((((..((((.....)))))))).)))))))))...))..)))))))((.(((.(((((.....)))))))).)). ( -26.30)
>DroEre_CAF1 10771 106 - 1
UUGGUAAAACGCUGCCUACUUUUAGGCAUUAUUUCCUAAAGCGAAUGUAAAAUGCGCGUAAAAUUACAUAUUUAUGGACAUGGUCGUGUUCUCUACACGCAACAUA
.........(((((((((....))))).(((.....))))))).((((....((((.(((((((.....))))..((((((....))))))..))).)))))))). ( -22.10)
>consensus
UUGGAAAAGUGCUGCCUACUUAUAGGCAUUAUUUCCUAUAGCAAAUGUAAAAUGCGUGUAAGUUUACAUCUUUCUAGACAUGGUCGUGUUAUCUACACGCAACUCA
..((((..(((.((((((....)))))).)))))))....((..((((........((((....)))).........))))....((((.....))))))...... (-16.02 = -16.83 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,554,331 – 17,554,434
Length 103
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 77.63
Mean single sequence MFE -27.30
Consensus MFE -12.83
Energy contribution -13.03
Covariance contribution 0.20
Combinations/Pair 1.30
Mean z-score -2.35
Structure conservation index 0.47
SVM decision value 1.45
SVM RNA-class probability 0.954791
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17554331 103 + 22224390
UAAACUUACACGAAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGCAGCACUUUUC-CAA---UAGCUGCUUAAGGCAUUCGCCAACAGGUGGCGCCACU
........................(((((.(((((...((((((....)))))).....))))-).)---)))).......(((..(((((....))))).)))... ( -30.00)
>DroSec_CAF1 6235 103 + 1
UAAACUUACACGCAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGAAGCACUUUUC-CAA---UAGCUGCUUAAGACAUUCGCCCACAGGUGGCGCCACU
..........(((.(((((.....(((((.(((((.....((((....)))).......))))-).)---))))....)))))....((((....)))))))..... ( -22.70)
>DroSim_CAF1 6070 103 + 1
UAAACUUACAGGAAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGCAGCACUUUUC-CAA---UAGCUGCUUAAGACAUUCGCCAACAGGUGGCGCCACU
..........((..(((((.....(((((.(((((...((((((....)))))).....))))-).)---))))....)))))....(((((.....)))))))... ( -28.40)
>DroEre_CAF1 10811 103 + 1
UAAUUUUACGCGCAUUUUACAUUCGCUUUAGGAAAUAAUGCCUAAAAGUAGGCAGCGUUUUAC-CAA---AUGCCGCUUAAGGCGCUUGCCAACAGGUGGCGCCACU
.........((((...........((((((((......((((((....))))))((((((...-.))---))))..))))))))(((((....))))).)))).... ( -31.40)
>DroAna_CAF1 12806 99 + 1
----UUUACAUGGUUUCUACAUUUG-UGUAAAAAGUAAAGCCUACAAGCAGGCAGUGGUUUUUGUAAAUGUAGUUUCUUU---UGCUCAGCGUUAGAUGGCGCCACA
----......((((..(((((((((-..((((((.((..((((......))))..)).)))))))))))))))..(((..---(((...)))..)))....)))).. ( -24.00)
>consensus
UAAACUUACACGAAUUUUACAUUUGCUAUAGGAAAUAAUGCCUAUAAGUAGGCAGCACUUUUC_CAA___UAGCUGCUUAAGACAUUCGCCAACAGGUGGCGCCACU
...................((((((.((((((........))))))..((((((((................)))))))).............))))))........ (-12.83 = -13.03 +   0.20)

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 12:28:01 2006