Locus 9243

Sequence ID 3R_DroMel_CAF1
Location 24,654,826 – 24,654,971
Length 145
Max. P 0.875047
window14775 window14776

overview

Window 5

Location 24,654,826 – 24,654,942
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.38
Mean single sequence MFE -31.14
Consensus MFE -21.20
Energy contribution -20.08
Covariance contribution -1.12
Combinations/Pair 1.36
Mean z-score -2.55
Structure conservation index 0.68
SVM decision value 0.89
SVM RNA-class probability 0.875047
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24654826 116 + 27905053
---CACCAGGUAAUCUCUUUCUUUAUCUCAGAGAGCAGAGCAGGGCAAACG-AAAGAUGUGGGAUUAAUGACAUAAUUUACAAAUCCCCGAACGUUUUCAUUGACUUGCCCAAUACCCGU
---.....((((.(((((((((.......)))))).)))...((((((.((-((((((((((((((..(((......)))..))))))...)))))))..)))..))))))..))))... ( -30.70)
>DroSec_CAF1 13951 119 + 1
AAACACCAGGUAAUCUCUUUCUUUAUCUCAGAGAGCAGAGCAGGGCAAACG-AAAGAUGUGGGAUUAAUGACAUAAUUUACAGAUCCCCAAACGUUUUCAUCGACUUGCCCAAUACCCGU
........((((.(((((((((.......)))))).)))...((((((.((-((((((((((((((..(((......)))..))))))...)))))))..)))..))))))..))))... ( -33.20)
>DroSim_CAF1 14204 119 + 1
AAACACCAGGUAAUCUCUUUCUUUAUCUCAGAGAGCAGAGCAGGGCAAGCG-AAAGAUGUGGGAUUAAUGACAUAAUUUACAGAUUCCCGAACGUUUUCAUCGACUUGCCCAAUACCCGU
........((((.(((((((((.......)))))).)))...(((((((((-((((((((((((....((..........))...))))..)))))))..))).)))))))..))))... ( -35.70)
>DroEre_CAF1 14115 114 + 1
-AACACCAGGUAAUCCCUUUCUUUAUCUCAGAGAGC-----AGGGCAUAUGAAAAGGUCUGGGAUUAAUGACAUAAUUUACAGAUCCCUGAACGUUUUCAUCGAGUUGCCUAAUACUCGU
-......(((((((((((((((((.....)))))).-----))))...(((((((.(((.((((((..(((......)))..)))))).).)).)))))))...)))))))......... ( -30.90)
>DroYak_CAF1 14359 114 + 1
-AACACCAGUUAAUCCCUUUCUUUAUCUCAGGAAGC-----AGGGCAUACGCAGAGGUCUGGGAUUAAAGACAUAAUUUACAGAUCUCUUAACAUUUUCAUCAAGUUGCCUAAUACUUGU
-.......(((((.(((((((((......)))))..-----))))........((((((((((((((......)))))).)))))))))))))........(((((........))))). ( -25.20)
>consensus
_AACACCAGGUAAUCUCUUUCUUUAUCUCAGAGAGCAGAGCAGGGCAAACG_AAAGAUGUGGGAUUAAUGACAUAAUUUACAGAUCCCCGAACGUUUUCAUCGACUUGCCCAAUACCCGU
........((((....((((((.......)))))).......(((((..((..(((((((((((((..(((......)))..))))))...)))))))...))...)))))..))))... (-21.20 = -20.08 +  -1.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,654,863 – 24,654,971
Length 108
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 87.29
Mean single sequence MFE -26.88
Consensus MFE -18.72
Energy contribution -17.48
Covariance contribution -1.24
Combinations/Pair 1.39
Mean z-score -1.92
Structure conservation index 0.70
SVM decision value 0.21
SVM RNA-class probability 0.633834
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24654863 108 + 27905053
CAGGGCAAACG-AAAGAUGUGGGAUUAAUGACAUAAUUUACAAAUCCCCGAACGUUUUCAUUGACUUGCCCAAUACCCGUAGCUUCAGUGAAUCAAAAGCAGAGACUAA
..((((((.((-((((((((((((((..(((......)))..))))))...)))))))..)))..))))))..........((((..(.....)..))))......... ( -23.10)
>DroSec_CAF1 13991 108 + 1
CAGGGCAAACG-AAAGAUGUGGGAUUAAUGACAUAAUUUACAGAUCCCCAAACGUUUUCAUCGACUUGCCCAAUACCCGUAGCUUCAGUGAAUCAAAAGCAGAGACUAA
..((((((.((-((((((((((((((..(((......)))..))))))...)))))))..)))..))))))..........((((..(.....)..))))......... ( -25.60)
>DroSim_CAF1 14244 108 + 1
CAGGGCAAGCG-AAAGAUGUGGGAUUAAUGACAUAAUUUACAGAUUCCCGAACGUUUUCAUCGACUUGCCCAAUACCCGUAGCUUCAGUGAAUCAAAAGCAGAGAAUAA
..(((((((((-((((((((((((....((..........))...))))..)))))))..))).)))))))..........((((..(.....)..))))......... ( -28.10)
>DroEre_CAF1 14150 108 + 1
-AGGGCAUAUGAAAAGGUCUGGGAUUAAUGACAUAAUUUACAGAUCCCUGAACGUUUUCAUCGAGUUGCCUAAUACUCGUAGCUUCAGUGAAUCAAAAGCAGAGCCCAU
-.((((..(((((((.(((.((((((..(((......)))..)))))).).)).)))))))(((((........)))))..((((..(.....)..))))...)))).. ( -31.90)
>DroYak_CAF1 14394 108 + 1
-AGGGCAUACGCAGAGGUCUGGGAUUAAAGACAUAAUUUACAGAUCUCUUAACAUUUUCAUCAAGUUGCCUAAUACUUGUAGCUACAGUGAAUCAAUGGCAGAGACCAU
-.((......(((((((((((((((((......)))))).)))))))))...(((((((((..((((((.........))))))...)))))..)))))).....)).. ( -25.70)
>consensus
CAGGGCAAACG_AAAGAUGUGGGAUUAAUGACAUAAUUUACAGAUCCCCGAACGUUUUCAUCGACUUGCCCAAUACCCGUAGCUUCAGUGAAUCAAAAGCAGAGACUAA
..(((((..((..(((((((((((((..(((......)))..))))))...)))))))...))...)))))..........((((..(.....)..))))......... (-18.72 = -17.48 +  -1.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:41 2006