Locus 3068

Sequence ID 3L_DroMel_CAF1
Location 8,857,144 – 8,857,294
Length 150
Max. P 0.999185
window4786 window4787 window4788

overview

Window 6

Location 8,857,144 – 8,857,237
Length 93
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 79.02
Mean single sequence MFE -21.57
Consensus MFE -15.65
Energy contribution -15.77
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -3.24
Structure conservation index 0.73
SVM decision value 3.42
SVM RNA-class probability 0.999185
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8857144 93 + 23771897
------CCUUUACACAGUAGAAGUUGAUUUUCUC-----------------UUCUGAAAAUCUACAUAACUCAAUAUUUGAGUAGCAGGUUCGUUUACUUUUGCCCUGUGUAAAUC
------..((((((((((((((((.(((((((..-----------------....)))))))......(((((.....))))).............))))))))..)))))))).. ( -24.80)
>DroSec_CAF1 117047 110 + 1
AAGAACUGCUUACACAGUAG------AUUUUCUCUUUACCCAACUAACUUCUUUUGAAAAUCUACAUAACUCAAUAUUUAAGUAGCAAGUUCUUUUACUUUUGCCCUGUGUAAAUC
.........(((((((((((------((((((.......................))))))))))................((((.((((......))))))))..)))))))... ( -20.90)
>DroSim_CAF1 113475 116 + 1
AAGUACUGCUUACACAGUAGAAGUUGAUUUUCUCUUUACCCAACUAACUUCUUUUGAAAAUCUACAUAACUCAAUAUUUAAGUAGCAAGUUCUUUUACUUUUGCCCUGUGUAAAUC
.........((((((((.....((.(((((((.......................))))))).))................((((.((((......)))))))).))))))))... ( -19.00)
>consensus
AAG_ACUGCUUACACAGUAGAAGUUGAUUUUCUCUUUACCCAACUAACUUCUUUUGAAAAUCUACAUAACUCAAUAUUUAAGUAGCAAGUUCUUUUACUUUUGCCCUGUGUAAAUC
.........((((((((........(((((((.......................)))))))...................((((.((((......)))))))).))))))))... (-15.65 = -15.77 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,857,144 – 8,857,237
Length 93
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 79.02
Mean single sequence MFE -22.83
Consensus MFE -18.64
Energy contribution -18.87
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -2.02
Structure conservation index 0.82
SVM decision value 1.74
SVM RNA-class probability 0.974912
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8857144 93 - 23771897
GAUUUACACAGGGCAAAAGUAAACGAACCUGCUACUCAAAUAUUGAGUUAUGUAGAUUUUCAGAA-----------------GAGAAAAUCAACUUCUACUGUGUAAAGG------
..(((((((((.....((((.........(((.(((((.....)))))...)))(((((((....-----------------..))))))).))))...)))))))))..------ ( -24.60)
>DroSec_CAF1 117047 110 - 1
GAUUUACACAGGGCAAAAGUAAAAGAACUUGCUACUUAAAUAUUGAGUUAUGUAGAUUUUCAAAAGAAGUUAGUUGGGUAAAGAGAAAAU------CUACUGUGUAAGCAGUUCUU
(.(((((((((((((..(((......)))))))(((((.....)))))....(((((((((.......................))))))------)))))))))))))....... ( -21.90)
>DroSim_CAF1 113475 116 - 1
GAUUUACACAGGGCAAAAGUAAAAGAACUUGCUACUUAAAUAUUGAGUUAUGUAGAUUUUCAAAAGAAGUUAGUUGGGUAAAGAGAAAAUCAACUUCUACUGUGUAAGCAGUACUU
(.(((((((((((((..(((......))))))).........(((((...........))))).(((((((.(((............))).))))))).))))))))))....... ( -22.00)
>consensus
GAUUUACACAGGGCAAAAGUAAAAGAACUUGCUACUUAAAUAUUGAGUUAUGUAGAUUUUCAAAAGAAGUUAGUUGGGUAAAGAGAAAAUCAACUUCUACUGUGUAAGCAGU_CUU
..(((((((((.(((..(((((......)))))(((((.....)))))..))).(((((((.......................)))))))........)))))))))........ (-18.64 = -18.87 +   0.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,857,201 – 8,857,294
Length 93
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 87.95
Mean single sequence MFE -22.52
Consensus MFE -16.16
Energy contribution -17.28
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -2.12
Structure conservation index 0.72
SVM decision value 0.57
SVM RNA-class probability 0.784696
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8857201 93 - 23771897
AAAGACCAAGCCCGUGACCAGGCACUAAAUAUCCAUUCUUAUGAAUGGGAAGUUUAGGAUUUACACAGGGC-AAAAGUAAACGAACCU---GCUACU
.........(((((((...(((..((((((.(((((((....)))))))..))))))..))).))).))))-...((((........)---)))... ( -24.00)
>DroSec_CAF1 117121 93 - 1
AAAGACCAAGCCCGUGACCAGGCACUAAAUAUCCAUUCUUAUGAAUGGGAAGUCAGGGAUUUACACAGGGC-AAAAGUAAAAGAACUU---GCUACU
.........(((((((...............(((((((....)))))))(((((...))))).))).))))-...(((((......))---)))... ( -22.40)
>DroSim_CAF1 113555 93 - 1
AAAGACCAAGCCCGUGACCAGGCACUAAAUAUCCAUUCUUAUGAAUGGGAAGUCAGGGAUUUACACAGGGC-AAAAGUAAAAGAACUU---GCUACU
.........(((((((...............(((((((....)))))))(((((...))))).))).))))-...(((((......))---)))... ( -22.40)
>DroEre_CAF1 121367 92 - 1
GAAGACCAAGCCCGUGACCAGAGACUAAAAAUCCAUUCUUAUGAAUGGGAAGUUUAGCAUUUACACAGGC--AAAAGUAAAAGAACUU---GUAACU
.........(((.(((...(((..(((((..(((((((....)))))))...)))))..))).))).)))--..((((......))))---...... ( -21.50)
>DroYak_CAF1 120396 97 - 1
GAAGACCAAGCCCGUGAGCAGACACUAAAUAUCCAUUCUUAUGAAUGGGAAGUUUGGGAUUUACACAGGGAGAAAAGUCAACAAAAGUAGGGUAACG
...(((....((((((...(((..((((((.(((((((....)))))))..))))))..))).))).)))......))).................. ( -22.30)
>consensus
AAAGACCAAGCCCGUGACCAGGCACUAAAUAUCCAUUCUUAUGAAUGGGAAGUUUGGGAUUUACACAGGGC_AAAAGUAAAAGAACUU___GCUACU
.........(((((((...(((..((((((.(((((((....)))))))..))))))..))).))).)))).......................... (-16.16 = -17.28 +   1.12)

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 10:48:47 2006