Locus 8478

Sequence ID 3L_DroMel_CAF1
Location 22,277,767 – 22,277,926
Length 159
Max. P 0.991027
window13867 window13868 window13869

overview

Window 7

Location 22,277,767 – 22,277,887
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.42
Mean single sequence MFE -42.86
Consensus MFE -39.86
Energy contribution -40.06
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.93
SVM decision value 2.24
SVM RNA-class probability 0.991027
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22277767 120 + 23771897
ACGCGCUGCCGAGUGAAAUAUGUUAAUUAAAUUAAGGGCUGGGUGGUGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCA
.......((((((((.................((((((((((((.((..........)).)).)))))).))))(((((((((..(..........)..))))))))).)))..))))). ( -43.60)
>DroSec_CAF1 36149 120 + 1
ACGCGCUGCCGAGUGAAAUAUGUUAAUUAAAUUAAGGGCUGGUUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCA
.......((((((((....................((((.((((((....(((.....)))..)))))))))).(((((((((..(..........)..))))))))).)))..))))). ( -41.70)
>DroSim_CAF1 27750 120 + 1
ACGCGCUGCCGAGUGAAAUAUGUUAAUUAAAUUAAGGGCUGGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCA
.......((((((((.................((((((((((((.(............).)).)))))).))))(((((((((..(..........)..))))))))).)))..))))). ( -41.50)
>DroEre_CAF1 34917 120 + 1
ACCCGCUGCCGAUUGAAAUAUGUUAAUUAAAUUAAGGGCUGGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCA
.(((((((((.((((.................((((((((((((.(............).)).)))))).))))(((....))).)))).)))))))))....((((.........)))) ( -46.00)
>DroYak_CAF1 964 120 + 1
ACUCGCUGCCGAGUGAAAUAUGUUAAUUAAAUUAAGGGCUGGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCA
.......((((((((.................((((((((((((.(............).)).)))))).))))(((((((((..(..........)..))))))))).)))..))))). ( -41.50)
>consensus
ACGCGCUGCCGAGUGAAAUAUGUUAAUUAAAUUAAGGGCUGGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCA
.......((((((((.................((((((((((.((.....(((.....))))))))))).))))(((((((((..(..........)..))))))))).)))..))))). (-39.86 = -40.06 +   0.20)

alignment

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secondary structure

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Window 8

Location 22,277,767 – 22,277,887
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.42
Mean single sequence MFE -36.86
Consensus MFE -35.34
Energy contribution -35.34
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.96
SVM decision value 1.14
SVM RNA-class probability 0.921238
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22277767 120 - 23771897
UGCCGAAGGUGUUGGCAUGCCCCCGCUGCCCAUUGUUGGCAUGCCACAAGCAGCUGGUGUCGCUUUUCGAUUCACCACCCAGCCCUUAAUUUAAUUAACAUAUUUCACUCGGCAGCGCGU
((((((((.((((((((((((...((........)).)))))))))...))).))(((((((.....)))..))))................................))))))...... ( -35.70)
>DroSec_CAF1 36149 120 - 1
UGCCGAAGGUGUUGGCAUGCCCCCGCUGCCCAUUGUUGGCAUGCCACAAGCAGCUGGUGUCGCUUUUCGAUUCCCCAACCAGCCCUUAAUUUAAUUAACAUAUUUCACUCGGCAGCGCGU
((((((..(((.(((((((((...((........)).))))))))).(((..((((((((((.....))))......)))))).)))..................)))))))))...... ( -37.60)
>DroSim_CAF1 27750 120 - 1
UGCCGAAGGUGUUGGCAUGCCCCCGCUGCCCAUUGUUGGCAUGCCACAAGCAGCUGGUGUCGCUUUUCGAUUCCCCACCCAGCCCUUAAUUUAAUUAACAUAUUUCACUCGGCAGCGCGU
((((((..(((.(((((((((...((........)).))))))))).(((..(((((.((((.....)))).......))))).)))..................)))))))))...... ( -35.50)
>DroEre_CAF1 34917 120 - 1
UGCCGAAGGUGUUGGCAUGCCCCCGCUGCCCAUUGUUGGCAUGCCACAAGCAGCUGGUGUCGCUUUUCGAUUCCCCACCCAGCCCUUAAUUUAAUUAACAUAUUUCAAUCGGCAGCGGGU
((((((.....))))))....(((((((((.((((.(((....))).(((..(((((.((((.....)))).......))))).)))..................)))).))))))))). ( -40.00)
>DroYak_CAF1 964 120 - 1
UGCCGAAGGUGUUGGCAUGCCCCCGCUGCCCAUUGUUGGCAUGCCACAAGCAGCUGGUGUCGCUUUUCGAUUCCCCACCCAGCCCUUAAUUUAAUUAACAUAUUUCACUCGGCAGCGAGU
((((((..(((.(((((((((...((........)).))))))))).(((..(((((.((((.....)))).......))))).)))..................)))))))))...... ( -35.50)
>consensus
UGCCGAAGGUGUUGGCAUGCCCCCGCUGCCCAUUGUUGGCAUGCCACAAGCAGCUGGUGUCGCUUUUCGAUUCCCCACCCAGCCCUUAAUUUAAUUAACAUAUUUCACUCGGCAGCGCGU
((((((..((..(((((((((...((........)).)))))))))...)).(((((.((((.....)))).......))))).........................))))))...... (-35.34 = -35.34 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,277,807 – 22,277,926
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.55
Mean single sequence MFE -43.44
Consensus MFE -42.06
Energy contribution -41.42
Covariance contribution -0.64
Combinations/Pair 1.14
Mean z-score -1.40
Structure conservation index 0.97
SVM decision value 1.34
SVM RNA-class probability 0.944403
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22277807 119 + 23771897
GGGUGGUGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCAGCGGCAAAUUCUUCCUCUACCCCCCUU-CUUCGCACUUGA
((((((.((((((.....)))..((.(((((((((((((((((..(..........)..)))))))).))).....)))))))).......)))..)))))).....-............ ( -40.00)
>DroSec_CAF1 36189 120 + 1
GGUUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCAGCGGCAAAUUCCUCCUCCAACCCCCUCCCUUCGCACUUGA
(((((((((.(((.....)))..((.(((((((((((((((((..(..........)..)))))))).))).....))))))))........))).)))))).................. ( -43.20)
>DroSim_CAF1 27790 120 + 1
GGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCAGCGGCAAAUUCCUCCUCCACCCCCCUCCCUGCGCACUUGA
(((((((((.(((.....)))..((.(((((((((((((((((..(..........)..)))))))).))).....))))))))........))).)))))).................. ( -45.60)
>DroEre_CAF1 34957 115 + 1
GGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCAGC----AAUGCUUCCUCCACCCCU-GCCCUUCUCCCUUGA
(((((((((((((.....))).....(((((((((((((((((..(..........)..)))))))).))).....))))))----.....)))).))))))..-............... ( -45.40)
>DroYak_CAF1 1004 114 + 1
GGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCAGC----AAUUCUUCCCCUACCUCU--CCCUUCUCACUUGA
(((((((((((((.....))).....(((((((((((((((((..(..........)..)))))))).))).....))))))----.....)))))).))))..--.............. ( -43.00)
>consensus
GGGUGGGGAAUCGAAAAGCGACACCAGCUGCUUGUGGCAUGCCAACAAUGGGCAGCGGGGGCAUGCCAACACCUUCGGCAGCGGCAAAUUCUUCCUCCACCCCCCUCCCUUCGCACUUGA
((((((((..(((.....))).....(((((((((((((((((..(..........)..)))))))).))).....))))))............)))))))).................. (-42.06 = -41.42 +  -0.64)

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 13:16:30 2006