Locus 7433

Sequence ID 2L_DroMel_CAF1
Location 20,628,371 – 20,628,483
Length 112
Max. P 0.842051
window11947 window11948

overview

Window 7

Location 20,628,371 – 20,628,473
Length 102
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 74.72
Mean single sequence MFE -18.62
Consensus MFE -6.60
Energy contribution -6.36
Covariance contribution -0.24
Combinations/Pair 1.29
Mean z-score -1.96
Structure conservation index 0.35
SVM decision value 0.75
SVM RNA-class probability 0.842051
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20628371 102 - 22407834
CAAAGCAAAUCGAUGGAUAUGCACAUGCAUAUUAAGCAUAUUAAAUAGAUUAAGCUUAAAUACUUAAGCCAUGCAAAGCAACUGC---------------GGUUAAAAAAACCUUAU
....(((((((....(((((((.............))))))).....))))..((((((....))))))..)))...((....))---------------((((.....)))).... ( -20.72)
>DroSec_CAF1 186676 96 - 1
CAAAACAAAUCGAUGGAUAUG------CAUAUUAAGCAUAUUAAAUAGAUUAAACUUAAAUACUUAAGCCAUGCAAAGAAACUGC---------------GGGUAAAAUCACUUUAU
.......((((....((((((------(.......))))))).....))))................(((.((((.......)))---------------))))............. ( -15.50)
>DroSim_CAF1 179080 96 - 1
CAAACCAAAUCGAUGGAUAUG------CAUAUUAAGCAUAUUAAAUAGAUUAAACUUAAAUACUUAAGCCAUGCAAAGAAACUGC---------------GGGUAAAAACACUUUAU
.......((((....((((((------(.......))))))).....))))................(((.((((.......)))---------------))))............. ( -15.50)
>DroEre_CAF1 127515 101 - 1
CAAAACAAAUCGAUGGAUAUGCUUU---AUGUCGAGCAUAUCAAAUAGGUUAAUGAUUAAUACCUAAGCCAUGGAAAGAAACUCCU-------------CUGGUCAAAAAGCGUUAU
...........(((((((((((((.---.....)))))))))...(((((...........))))).((((.(((.......))).-------------.)))).......)))).. ( -21.60)
>DroYak_CAF1 131675 117 - 1
CGAAUCAAAUCGAUGGAUAUGCUUUAGUAUGUCAAGCAUAUUAAACAGCUUAACCCUUAUUACUAAAGCCAUGAAAAGAAACUUCUUCAGGUCCUAAUACUUGUUAAGUAAUAAUAU
(((......)))...(((((((....)))))))....((((((....(((((((...(((((.....(((.(((..(((....)))))))))..)))))...)))))))..)))))) ( -19.80)
>consensus
CAAAACAAAUCGAUGGAUAUGC_____CAUAUUAAGCAUAUUAAAUAGAUUAAACUUAAAUACUUAAGCCAUGCAAAGAAACUGC_______________GGGUAAAAAAACUUUAU
.......((((....(((((((.............))))))).....)))).....................(((.......)))................................ ( -6.60 =  -6.36 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,628,393 – 20,628,483
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 81.79
Mean single sequence MFE -16.50
Consensus MFE -6.90
Energy contribution -7.00
Covariance contribution 0.10
Combinations/Pair 1.25
Mean z-score -2.40
Structure conservation index 0.42
SVM decision value 0.23
SVM RNA-class probability 0.643785
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20628393 90 - 22407834
CUACAAAGGGCAAAGCAAAUCGAUGGAUAUGCACAUGCAUAUUAAGCAUAUUAAAUAGAUUAAGCUUAAAUACUUAAGCCAUGCAAAGCA
.........((...(((((((....(((((((.............))))))).....))))..((((((....))))))..)))...)). ( -17.62)
>DroSec_CAF1 186698 83 - 1
CUA-AAAGGGCAAAACAAAUCGAUGGAUAUG------CAUAUUAAGCAUAUUAAAUAGAUUAAACUUAAAUACUUAAGCCAUGCAAAGAA
...-.....(((.....((((....((((((------(.......))))))).....))))...(((((....)))))...)))...... ( -13.60)
>DroSim_CAF1 179102 83 - 1
CUA-AAAGGGCAAACCAAAUCGAUGGAUAUG------CAUAUUAAGCAUAUUAAAUAGAUUAAACUUAAAUACUUAAGCCAUGCAAAGAA
...-.....(((.....((((....((((((------(.......))))))).....))))...(((((....)))))...)))...... ( -13.60)
>DroEre_CAF1 127539 86 - 1
CGA-CAAGGGCAAAACAAAUCGAUGGAUAUGCUUU---AUGUCGAGCAUAUCAAAUAGGUUAAUGAUUAAUACCUAAGCCAUGGAAAGAA
...-(...(((..............(((((((((.---.....)))))))))...(((((...........))))).)))...)...... ( -20.70)
>DroYak_CAF1 131712 89 - 1
CUA-CAAGGCCGAAUCAAAUCGAUGGAUAUGCUUUAGUAUGUCAAGCAUAUUAAACAGCUUAACCCUUAUUACUAAAGCCAUGAAAAGAA
...-((.((((((......)))..((.((.(((((((((((.....))))))))..))).)).))............))).))....... ( -17.00)
>consensus
CUA_AAAGGGCAAAACAAAUCGAUGGAUAUGC_____CAUAUUAAGCAUAUUAAAUAGAUUAAACUUAAAUACUUAAGCCAUGCAAAGAA
........(((....((......))(((((((....)))))))..................................))).......... ( -6.90 =  -7.00 +   0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:44 2006