Locus 1669

Sequence ID 3R_DroMel_CAF1
Location 4,796,551 – 4,796,743
Length 192
Max. P 0.999986
window2754 window2755 window2756

overview

Window 4

Location 4,796,551 – 4,796,663
Length 112
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -33.92
Consensus MFE -31.30
Energy contribution -31.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.22
Structure conservation index 0.92
SVM decision value 4.49
SVM RNA-class probability 0.999909
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4796551 112 + 27905053
---UGUUGUUGUUGUGGCUCGGCAUGGUAAUGAGCUGAGCAGCCAAGAAACAGAAACAGAGUCUGAUUAUCAUGAGUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAA
---...........((((((..((((((((((.(((....))))......((((.......))))))))))))).((((((((....)))))))))))))).............. ( -31.30)
>DroSec_CAF1 31915 109 + 1
---UGUU---GUUGUGGCUCGGCAUGGUAAUGAGCUGAGCAGCCAAGAAACAGAAACAGAGUCUGAUUAUCAUGAGUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAA
---....---....((((((..((((((((((.(((....))))......((((.......))))))))))))).((((((((....)))))))))))))).............. ( -31.30)
>DroSim_CAF1 27970 112 + 1
---UGUUGUUGUUGUGGCUCGGCAUGGUAAUGAGCUGAGCAGCCAAGAAACAGAAACAGAGUCUGAUUAUCAUGAGUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAA
---...........((((((..((((((((((.(((....))))......((((.......))))))))))))).((((((((....)))))))))))))).............. ( -31.30)
>DroEre_CAF1 32672 115 + 1
AGUUGUUUUUGUUGUGGCUCGGCAUGGUAAUGAGCUGAGCAGCCAAGAAACAGAAACAGAGUCUGAUUAUCAUGAGUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAA
..(..((((((((.((((((..((((((((((.(((....))))......((((.......))))))))))))).((((((((....)))))))))))))).)).))))))..). ( -35.30)
>DroYak_CAF1 33096 115 + 1
AGUUGUUUUUGCUGUGGCUCGGCAUGGUAAUGAGCUGAGCAGCCAAGAAACAGAAACAGAGUCUGAUUAUCAUGAGUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAA
..(..((((((((.((((((..((((((((((.(((....))))......((((.......))))))))))))).((((((((....))))))))))))))..))))))))..). ( -40.40)
>consensus
___UGUUGUUGUUGUGGCUCGGCAUGGUAAUGAGCUGAGCAGCCAAGAAACAGAAACAGAGUCUGAUUAUCAUGAGUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAA
..............((((((..((((((((((.(((....))))......((((.......))))))))))))).((((((((....)))))))))))))).............. (-31.30 = -31.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,796,551 – 4,796,663
Length 112
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -24.40
Consensus MFE -24.40
Energy contribution -24.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.14
Structure conservation index 1.00
SVM decision value 5.41
SVM RNA-class probability 0.999986
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4796551 112 - 27905053
UUCACUUUUACUCUCGGCUCAUAAGCAUAAUCAUGCUUACUCAUGAUAAUCAGACUCUGUUUCUGUUUCUUGGCUGCUCAGCUCAUUACCAUGCCGAGCCACAACAACAACA---
...............(((((.(((((((....)))))))..((((.((((((((.......))))......((((....)))).)))).))))..)))))............--- ( -24.40)
>DroSec_CAF1 31915 109 - 1
UUCACUUUUACUCUCGGCUCAUAAGCAUAAUCAUGCUUACUCAUGAUAAUCAGACUCUGUUUCUGUUUCUUGGCUGCUCAGCUCAUUACCAUGCCGAGCCACAAC---AACA---
...............(((((.(((((((....)))))))..((((.((((((((.......))))......((((....)))).)))).))))..))))).....---....--- ( -24.40)
>DroSim_CAF1 27970 112 - 1
UUCACUUUUACUCUCGGCUCAUAAGCAUAAUCAUGCUUACUCAUGAUAAUCAGACUCUGUUUCUGUUUCUUGGCUGCUCAGCUCAUUACCAUGCCGAGCCACAACAACAACA---
...............(((((.(((((((....)))))))..((((.((((((((.......))))......((((....)))).)))).))))..)))))............--- ( -24.40)
>DroEre_CAF1 32672 115 - 1
UUCACUUUUACUCUCGGCUCAUAAGCAUAAUCAUGCUUACUCAUGAUAAUCAGACUCUGUUUCUGUUUCUUGGCUGCUCAGCUCAUUACCAUGCCGAGCCACAACAAAAACAACU
...............(((((.(((((((....)))))))..((((.((((((((.......))))......((((....)))).)))).))))..)))))............... ( -24.40)
>DroYak_CAF1 33096 115 - 1
UUCACUUUUACUCUCGGCUCAUAAGCAUAAUCAUGCUUACUCAUGAUAAUCAGACUCUGUUUCUGUUUCUUGGCUGCUCAGCUCAUUACCAUGCCGAGCCACAGCAAAAACAACU
...............(((((.(((((((....)))))))..((((.((((((((.......))))......((((....)))).)))).))))..)))))............... ( -24.40)
>consensus
UUCACUUUUACUCUCGGCUCAUAAGCAUAAUCAUGCUUACUCAUGAUAAUCAGACUCUGUUUCUGUUUCUUGGCUGCUCAGCUCAUUACCAUGCCGAGCCACAACAAAAACA___
...............(((((.(((((((....)))))))..((((.((((((((.......))))......((((....)))).)))).))))..)))))............... (-24.40 = -24.40 +   0.00)

alignment

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secondary structure

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Window 6

Location 4,796,623 – 4,796,743
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -32.91
Consensus MFE -29.32
Energy contribution -29.27
Covariance contribution -0.05
Combinations/Pair 1.11
Mean z-score -1.72
Structure conservation index 0.89
SVM decision value 1.26
SVM RNA-class probability 0.937775
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4796623 120 + 27905053
GUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAAAGAGGCGGAGAAUGUGUGUGUAAAGAAUGCCUUGAGUGUCUGAGUGCCUCGUAUGUAGGCCAAGUCUAUUAUGCGGCUAG
((((((((....)))))))).(((((((.(((..((.....((((((....................))))))......))...))))))((((((((((...))))).))))))))).. ( -34.05)
>DroSec_CAF1 31984 116 + 1
GUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAAAGAGGCGGAGAGUG----UGUAAAGAAUGCCUUGAGUGUCUGAGUGCCUCGUAUGUAGGCCAAGUCUAUUAUGCGGCUAG
((((((((....)))))))).(((((((.(((..((.....((((((.......----.........))))))......))...))))))((((((((((...))))).))))))))).. ( -34.29)
>DroSim_CAF1 28042 118 + 1
GUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAAAGAGGCGGAGAGUG--UGUGUAAAGAAUGCCUUGAGUGUCUGAGUGCCUCGUAUGUAGGCCAAGUCUAUUAUGCGGCUAG
((((((((....)))))))).(((((((.(((........(((.((...(((.(--(((.......)))))))..)).)))...))))))((((((((((...))))).))))))))).. ( -34.60)
>DroEre_CAF1 32747 118 + 1
GUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAAAGAGGCGGAGAGUG--UGUGUAAAGAAUGCCUUGAGUGUCUGAGUGCCUCGUAUGUAGGCCAAGUCUAUUAUGCGGCUAG
((((((((....)))))))).(((((((.(((........(((.((...(((.(--(((.......)))))))..)).)))...))))))((((((((((...))))).))))))))).. ( -34.60)
>DroYak_CAF1 33171 118 + 1
GUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAAAGAGGCGGAGAGUG--UGUGUAAAGAAUGCCUUGAGUGUCUGAGUGCCUCGUAUGUAGGCCAAGUCUAUUAUGCGGCUAG
((((((((....)))))))).(((((((.(((........(((.((...(((.(--(((.......)))))))..)).)))...))))))((((((((((...))))).))))))))).. ( -34.60)
>DroAna_CAF1 31654 116 + 1
GUAAGCAUGAUUAUGCUUAUGAGCAGAGAGUAAAAGUGACUGACGGAACGAGCG--AGUG-AAAGAAUGCCUUGAGUGUCUGAGUGUUUUGUAUGUAGGCCAAGUCUAUUAUGCGGCUA-
((((((((....)))))))).(((.............(((...((((.((..((--((.(-........)))))..))))))...))).(((((((((((...))))).))))))))).- ( -25.30)
>consensus
GUAAGCAUGAUUAUGCUUAUGAGCCGAGAGUAAAAGUGAAAGAGGCGGAGAGUG__UGUGUAAAGAAUGCCUUGAGUGUCUGAGUGCCUCGUAUGUAGGCCAAGUCUAUUAUGCGGCUAG
((((((((....)))))))).(((((((.(((..((.....((((((....................))))))......))...))))))((((((((((...))))).))))))))).. (-29.32 = -29.27 +  -0.05)

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 10:16:27 2006