Locus 2488

Sequence ID 3R_DroMel_CAF1
Location 6,818,843 – 6,819,000
Length 157
Max. P 0.976018
window4075 window4076 window4077

overview

Window 5

Location 6,818,843 – 6,818,960
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -22.56
Consensus MFE -21.64
Energy contribution -21.76
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.48
Structure conservation index 0.96
SVM decision value 1.76
SVM RNA-class probability 0.976018
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6818843 117 - 27905053
AAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC---UGUUUGUACAAAACGCAUAACCGUUAAGAUGAAUUUUUAAUAGAAUUUGACGAGGCUUAACUUU
((((((((((......((((((((....(((..(((((....)))))..))).---))))))))...((((......))))))))))))))................(((......))). ( -22.80)
>DroSim_CAF1 83868 117 - 1
AAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC---UGUUUGUACAAAACGCAUAACCGUUAAGAUGAAUUUUUAAUAGAAUUUGACGAGGCUUAACUUU
((((((((((......((((((((....(((..(((((....)))))..))).---))))))))...((((......))))))))))))))................(((......))). ( -22.80)
>DroEre_CAF1 62875 117 - 1
AAUUCAUUUUAAUAUUUACAAACAUUUUUUUCCCGGCUCCUUAGCCACUCGAC---UGUUUGUACAAAACGCAUAACCGUUAAGAUGAAUUUUUAAUACAAUUUGACGAGGCUUAACUUU
((((((((((......((((((((.((.......((((....))))....)).---))))))))...((((......))))))))))))))................(((......))). ( -18.20)
>DroYak_CAF1 76123 117 - 1
AAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC---UGUUUGUACAAAACGCAUAACCGUUAAGAUGAAUUUUUAAUACAAUUUGACGAGGCUUAACUUU
((((((((((......((((((((....(((..(((((....)))))..))).---))))))))...((((......))))))))))))))................(((......))). ( -22.80)
>DroAna_CAF1 34498 120 - 1
AAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCAAGCUCCUUGGCUGCGCGACGGUUGUUUGUACAAAACGCAUAACCGUUAAGAUGAAUUUUUAAUAGAAUUUGACGCGGCUCGACUUU
((((((((((....................((((((...)))))).....(((((((((.(((.....))).))))))))))))))))))).......(((.((((......)))).))) ( -26.20)
>consensus
AAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC___UGUUUGUACAAAACGCAUAACCGUUAAGAUGAAUUUUUAAUAGAAUUUGACGAGGCUUAACUUU
((((((((((......((((((((....(((..(((((....)))))..)))....))))))))...((((......))))))))))))))............................. (-21.64 = -21.76 +   0.12)

alignment

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secondary structure

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Window 6

Location 6,818,883 – 6,819,000
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.59
Mean single sequence MFE -25.66
Consensus MFE -19.97
Energy contribution -20.17
Covariance contribution 0.20
Combinations/Pair 1.10
Mean z-score -1.86
Structure conservation index 0.78
SVM decision value 0.38
SVM RNA-class probability 0.711055
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6818883 117 + 27905053
ACGGUUAUGCGUUUUGUACAAACA---GUCGAGCGGCUAAGGAGCCGGGCAAAAAAUGUUUGUAAAUAUUAAAAUGAAUUUAUGUGCAGAGCAAAAGUUUUUAAUUAAGUGAAAAGCGAA
.......(((((((((((((....---.(((..(((((....))))).(((((.....)))))...........))).....)))))))))).....((((((......))))))))).. ( -26.40)
>DroSim_CAF1 83908 117 + 1
ACGGUUAUGCGUUUUGUACAAACA---GUCGAGCGGCUAAGGAGCCGGGCAAAAAAUGUUUGUAAAUAUUAAAAUGAAUUUAUGUGCAGAGCAAAAGUUUUUAAUUAAGUGAAAAGCGAA
.......(((((((((((((....---.(((..(((((....))))).(((((.....)))))...........))).....)))))))))).....((((((......))))))))).. ( -26.40)
>DroEre_CAF1 62915 117 + 1
ACGGUUAUGCGUUUUGUACAAACA---GUCGAGUGGCUAAGGAGCCGGGAAAAAAAUGUUUGUAAAUAUUAAAAUGAAUUUAUGUGCAGAGCAAAAGUUUUUAAUUAAGUGAAAAGCGAA
.......(((((((((((((....---.(((..(((((....))))).......((((((....))))))....))).....)))))))))).....((((((......))))))))).. ( -23.20)
>DroYak_CAF1 76163 117 + 1
ACGGUUAUGCGUUUUGUACAAACA---GUCGAGCGGCUAAGGAGCCGGGCAAAAAAUGUUUGUAAAUAUUAAAAUGAAUUUAUGUGCAGAGCAAAAGUUUUUAAUUAAGUGAAAAGCGAA
.......(((((((((((((....---.(((..(((((....))))).(((((.....)))))...........))).....)))))))))).....((((((......))))))))).. ( -26.40)
>DroAna_CAF1 34538 119 + 1
ACGGUUAUGCGUUUUGUACAAACAACCGUCGCGCAGCCAAGGAGCUUGGCAAAAAAUGUUUGUAAAUAUUAAAAUGAAUUUAUGUGCAGCGG-AAAGUUUUUAAUUAAGUGAAAAACAGA
..........(((((.(((((((..((((.(((((((((((...))))))....((((((....))))))............))))).))))-...))))........))).)))))... ( -25.90)
>consensus
ACGGUUAUGCGUUUUGUACAAACA___GUCGAGCGGCUAAGGAGCCGGGCAAAAAAUGUUUGUAAAUAUUAAAAUGAAUUUAUGUGCAGAGCAAAAGUUUUUAAUUAAGUGAAAAGCGAA
..........((((((((((((((.........(((((....))))).........)))))((((((..........)))))))))))))))....((((((.........))))))... (-19.97 = -20.17 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,818,883 – 6,819,000
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.59
Mean single sequence MFE -17.32
Consensus MFE -15.94
Energy contribution -16.06
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.56
Structure conservation index 0.92
SVM decision value 1.66
SVM RNA-class probability 0.970567
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6818883 117 - 27905053
UUCGCUUUUCACUUAAUUAAAAACUUUUGCUCUGCACAUAAAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC---UGUUUGUACAAAACGCAUAACCGU
...((......................(((...)))....................((((((((....(((..(((((....)))))..))).---))))))))......))........ ( -16.80)
>DroSim_CAF1 83908 117 - 1
UUCGCUUUUCACUUAAUUAAAAACUUUUGCUCUGCACAUAAAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC---UGUUUGUACAAAACGCAUAACCGU
...((......................(((...)))....................((((((((....(((..(((((....)))))..))).---))))))))......))........ ( -16.80)
>DroEre_CAF1 62915 117 - 1
UUCGCUUUUCACUUAAUUAAAAACUUUUGCUCUGCACAUAAAUUCAUUUUAAUAUUUACAAACAUUUUUUUCCCGGCUCCUUAGCCACUCGAC---UGUUUGUACAAAACGCAUAACCGU
...((......................(((...)))....................((((((((.((.......((((....))))....)).---))))))))......))........ ( -12.20)
>DroYak_CAF1 76163 117 - 1
UUCGCUUUUCACUUAAUUAAAAACUUUUGCUCUGCACAUAAAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC---UGUUUGUACAAAACGCAUAACCGU
...((......................(((...)))....................((((((((....(((..(((((....)))))..))).---))))))))......))........ ( -16.80)
>DroAna_CAF1 34538 119 - 1
UCUGUUUUUCACUUAAUUAAAAACUUU-CCGCUGCACAUAAAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCAAGCUCCUUGGCUGCGCGACGGUUGUUUGUACAAAACGCAUAACCGU
...((((((.........))))))...-.(((.(((..((((.....))))...................((((((...))))))))))))((((((((.(((.....))).)))))))) ( -24.00)
>consensus
UUCGCUUUUCACUUAAUUAAAAACUUUUGCUCUGCACAUAAAUUCAUUUUAAUAUUUACAAACAUUUUUUGCCCGGCUCCUUAGCCGCUCGAC___UGUUUGUACAAAACGCAUAACCGU
................................(((...((((.....)))).....((((((((....(((..(((((....)))))..)))....))))))))......)))....... (-15.94 = -16.06 +   0.12)

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 10:37:40 2006