Locus 5357

Sequence ID 2R_DroMel_CAF1
Location 17,297,722 – 17,297,906
Length 184
Max. P 0.983561
window8560 window8561

overview

Window 0

Location 17,297,722 – 17,297,833
Length 111
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 74.29
Mean single sequence MFE -31.40
Consensus MFE -17.11
Energy contribution -17.75
Covariance contribution 0.64
Combinations/Pair 1.26
Mean z-score -2.33
Structure conservation index 0.54
SVM decision value 1.95
SVM RNA-class probability 0.983561
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17297722 111 - 20766785
UUUACACUACACCAUAUCAUUCACAAUUC------UCUAGGCACUUUCACAGCAUGGAGGUGUUUGCCACCUUUGAUAUCUUCAAUUUAAGAGGAAUCAAAGUGGCUCAGGGACACA
...........................((------((((((((((((((.....)))))))))))(((((.((((((.(((((.......))))))))))))))))..))))).... ( -32.70)
>DroGri_CAF1 302 109 - 1
CUUAAGAUAUAAUAUAU-AUUCUCCUC-------UUGCAGGCACUUUCACAGCAUGGAAGUGUUUGCCACCUUUGACAUAUUCGAUGCAGAGGGUCGCAAAGUUGCCCAGGGCCACA
.....(((.........-.........-------..(((((((((((((.....)))))))))))))..((((((.(((.....)))))))))))).....((.(((...))).)). ( -31.30)
>DroSec_CAF1 21834 111 - 1
CUUACACCAAACCAUAUCUUUCACAAUUC------UCUAGGCAUUUUCACAGCAUGGAGGUGUUUGCCACCUUUGAUAUCUUCGAUUUAAGAGGACACAAAGUGGCUCAGGGACACA
...........................((------((((((((((((((.....)))))))))))(((((.((((...(((((.......)))))..)))))))))..))))).... ( -27.40)
>DroSim_CAF1 23721 107 - 1
UUUACACCAUUUC----CUAUCGAAAUUC------CUUAGGCAUUUUCACAGCAUGGAGGUGUUUGCCACCUUUGAUAUCUUCGAUUUAAGAGGACACAAAGUGGCUCAGGGACACA
........(((((----.....)))))((------((((((((((((((.....)))))))))))(((((.((((...(((((.......)))))..)))))))))..))))).... ( -28.20)
>DroAna_CAF1 8376 108 - 1
CUUACUCUACCUAA---UAUUCCAUCUUC------CCCAGGCACUAUCACAGCAUGGAGGUGUUUGCCACUUUUGACAUCUUCGACCUGAGUGGCCGGAAAGUGGCCCAGGGCCACA
..............---..((((......------...(((((((.(((.....))).)))))))(((((((((((.....))))...))))))).)))).((((((...)))))). ( -32.70)
>DroPer_CAF1 24207 117 - 1
CGUUGAACACUCAAGAGCACUCUCAUUUCUCUCUUACCAGGCACUUUCACAGCAUGGAAGUGUUUGCCACCUUUGACAUCUUCGAUUUGAGCGGUCGGAAGGUCGCUCAGGGCCACA
.((..((.....(((((.............)))))..((((((((((((.....)))))))))))).....))..))........((((((((..(....)..))))))))...... ( -36.12)
>consensus
CUUACACCACACCAUAUCAUUCACAAUUC______UCCAGGCACUUUCACAGCAUGGAGGUGUUUGCCACCUUUGACAUCUUCGAUUUAAGAGGACGCAAAGUGGCUCAGGGACACA
...................................((((((((((((((.....)))))))))))(((((.((((....((((.......))))...)))))))))...)))..... (-17.11 = -17.75 +   0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,297,802 – 17,297,906
Length 104
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 60.52
Mean single sequence MFE -23.59
Consensus MFE -9.29
Energy contribution -8.77
Covariance contribution -0.53
Combinations/Pair 1.36
Mean z-score -1.68
Structure conservation index 0.39
SVM decision value 0.58
SVM RNA-class probability 0.788379
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17297802 104 - 20766785
GAAGAGCCAAUGGGAGUGGCACAUGUGCCAUAUGUGAGUACACAGUGAAAAAUAGUGGCAUACCUAUAAACUAUUUACACUACACCAUAUCAUUCACAAUUC------UC
(((((....((((..((((((....))))))..(((....)))((((..(((((((.............))))))).))))...)))).)).))).......------.. ( -22.42)
>DroGri_CAF1 382 94 - 1
GAAGAGCCAGUGGGAGUGGCAUAUGUGUCAUAUGUAAGCAUA--AUGAUUAGUUA-GC-----CCAACUUGUGCUUAAGAUAUAAUAUAU-AUUCUCCUC-------UUG
...........(((((..(.((((((((.((((.((((((((--......((((.-..-----..))))))))))))..)))).))))))-)).)..)))-------)). ( -22.50)
>DroSec_CAF1 21914 104 - 1
GAAGAGCCAAUGGGAGUGGCACAUGUGCCAUAUGUGAGUACACAGUGAAAAAUUCUGGCAAACCUAUAUACUACUUACACCAAACCAUAUCUUUCACAAUUC------UC
(((((....((((..((((((....)))))).((((((((......((.....)).((....)).......)))))))).....)))).)))))........------.. ( -21.40)
>DroSim_CAF1 23801 96 - 1
GAAGAGCCAAUGGGAGUGGCACAUGUGCCAUAUGUGAGUACACAGUGAAAAAUACUGGCAAAUCUAUAC----UUUACACCAUUUC----CUAUCGAAAUUC------CU
(((........(((((((((((((((...)))))))......(((((.....)))))............----......)))))))----)........)))------.. ( -20.39)
>DroAna_CAF1 8456 81 - 1
GAAGAGCCAGUGGGAGUGGCACAUGUGUCACAUGUAAGUGU-CAG-----------------CCUAAGGAC--CUUACUCUACCUAA---UAUUCCAUCUUC------CC
(((((.....((((.((((((....))))))..(((((.((-(..-----------------......)))--)))))....)))).---.......)))))------.. ( -24.32)
>DroPer_CAF1 24287 92 - 1
GAAGAGUCAGUGGGAGUGGCACAUGUGCCACAUGUGAGUAGAU---------UACUGUU----CU-----CUCCGUUGAACACUCAAGAGCACUCUCAUUUCUCUCUUAC
.(((((..((((((((((.((((((.....)))))).......---------...((((----(.-----.......)))))........))))))))))...))))).. ( -30.50)
>consensus
GAAGAGCCAAUGGGAGUGGCACAUGUGCCAUAUGUGAGUACACAGUGAAAAAUACUGGC___CCUAUAUACU_CUUACACCACACCAUAUCAUUCACAAUUC______UC
...(((((....)).((((((....)))))).............................................................)))............... ( -9.29 =  -8.77 +  -0.53)

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 11:43:00 2006