Locus 2987

Sequence ID X_DroMel_CAF1
Location 7,946,985 – 7,947,118
Length 133
Max. P 0.912087
window4898 window4899

overview

Window 8

Location 7,946,985 – 7,947,088
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -21.23
Consensus MFE -13.89
Energy contribution -14.95
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.65
SVM decision value 0.27
SVM RNA-class probability 0.663628
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7946985 103 + 22224390
G-AGAGAGCACUGUAUCUAA----------AAAGUAUGAGCGACAAAUUGUUGUUGCACAG------AUAUACAUAUGUGUUUACAACAACAACAAUAACAAACUAUUCCACACCCAAAA
.-.(.(((((((((((((..----------.......(.(((((((....))))))).)))------))))).....)))))).)................................... ( -14.60)
>DroSec_CAF1 9334 119 + 1
G-AGAGAACACUGUACGUAAAAUCAGGCAAAAAGUAUGAGCGACAAAUUGUUGUUGCGUAGCGUAGUACAGAUAUAUGUGUUUGCAACAACAACAAUAACAAACUAUUCCACACCCAAAA
(-((((.....(((.(((....(((.((.....)).)))))))))..(((((((((((..(((((.........)))))...)))))))))))..........)).)))........... ( -23.10)
>DroSim_CAF1 4007 120 + 1
CCAGAGAACACUGUACGUAAAAUCAGGCAAAAAGUAUGAGCGACAAAUUGUUGUUGCAUAGCGUAGCACAGAUAUAUGUGUUUGCAACAACAACAAUAACAAACUAUUCCACACCCAAAA
...(.(((...(((.(((....(((.((.....)).))))))))).((((((((((....(((.((((((......)))))))))..)))))))))).........)))).......... ( -24.70)
>DroYak_CAF1 5216 98 + 1
U-AGAGAGCACCGUACGUAAA---------------------ACGAAUUGUUGUUGCAUAGCGUAGCAUAGGUAUAUGUGUUUGCAACAACAACAAAAACAAGCGAUUCCACACCCAAAA
.-.(((.((..(((.......---------------------)))..(((((((((((..(((((((....)).)))))...))))))))))).........))..)))........... ( -22.50)
>consensus
G_AGAGAACACUGUACGUAAA_________AAAGUAUGAGCGACAAAUUGUUGUUGCAUAGCGUAGCACAGAUAUAUGUGUUUGCAACAACAACAAUAACAAACUAUUCCACACCCAAAA
...............................................(((((((((((..(((((.........)))))...)))))))))))........................... (-13.89 = -14.95 +   1.06)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 7,947,014 – 7,947,118
Length 104
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 88.50
Mean single sequence MFE -19.50
Consensus MFE -15.69
Energy contribution -16.75
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -2.12
Structure conservation index 0.80
SVM decision value 1.08
SVM RNA-class probability 0.912087
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7947014 104 + 22224390
CGACAAAUUGUUGUUGCACAG------AUAUACAUAUGUGUUUACAACAACAACAAUAACAAACUAUUCCACACCCAAAA-AAAAGCCGCAAGCUAACA-----CACACGCGCACA
......((((((((((...((------(((((....)))))))....)))))))))).......................-....((.((.........-----.....))))... ( -14.74)
>DroSec_CAF1 9373 111 + 1
CGACAAAUUGUUGUUGCGUAGCGUAGUACAGAUAUAUGUGUUUGCAACAACAACAAUAACAAACUAUUCCACACCCAAAAAAAAAGCCGCAAGCUAACA-----CACACGCGCACA
.......(((((((((((..(((((.........)))))...)))))))))))................................((.((.........-----.....))))... ( -19.84)
>DroSim_CAF1 4047 110 + 1
CGACAAAUUGUUGUUGCAUAGCGUAGCACAGAUAUAUGUGUUUGCAACAACAACAAUAACAAACUAUUCCACACCCAAAA-AAAAGCCGCAAGCUAACA-----CACACGCGCACA
......((((((((((....(((.((((((......)))))))))..)))))))))).......................-....((.((.........-----.....))))... ( -21.44)
>DroYak_CAF1 5236 113 + 1
--ACGAAUUGUUGUUGCAUAGCGUAGCAUAGGUAUAUGUGUUUGCAACAACAACAAAAACAAGCGAUUCCACACCCAAAA-AAAAGCCGCAAGCUAACACCUCACACACGCGCACA
--.....(((((((((((..(((((((....)).)))))...))))))))))).........(((...............-...((.(....))).........(....))))... ( -22.00)
>consensus
CGACAAAUUGUUGUUGCAUAGCGUAGCACAGAUAUAUGUGUUUGCAACAACAACAAUAACAAACUAUUCCACACCCAAAA_AAAAGCCGCAAGCUAACA_____CACACGCGCACA
.......(((((((((((..(((((.........)))))...)))))))))))...............................((.(....)))..................... (-15.69 = -16.75 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:23 2006