Locus 3384

Sequence ID 2R_DroMel_CAF1
Location 11,445,374 – 11,445,509
Length 135
Max. P 0.936644
window5529 window5530 window5531

overview

Window 9

Location 11,445,374 – 11,445,469
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.63
Mean single sequence MFE -24.07
Consensus MFE -14.52
Energy contribution -14.64
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -2.11
Structure conservation index 0.60
SVM decision value 1.25
SVM RNA-class probability 0.936644
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11445374 95 + 20766785
----AUGUAUUAGGCAUAUGAGUUAAGCUA-AAAGGGCACUUAAAACCUUAAUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU--------------------UUACAAGUGAUUA
----.......(((....(((((...(((.-....))))))))...)))((((((((((((((((((((....))))))).......--------------------))))))))))))) ( -24.51)
>DroSec_CAF1 64254 95 + 1
----AUGUAUUAGGCAUAUGAGUUAAGCUA-AAAGGGCACUUAAAACCUUAUUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU--------------------UUACGAGUGAUUA
----.......(((....(((((...(((.-....))))))))...)))...(((((((((((((((((....))))))).......--------------------))))))))))... ( -21.51)
>DroSim_CAF1 54263 95 + 1
----AUGUAUUAGACAUAUGAGUAAAGCUA-AAAGGUCACUUAAAACCUUAUUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU--------------------UUACAAGUGAUUA
----........(((.....((.....)).-....)))..............(((((((((((((((((....))))))).......--------------------))))))))))... ( -20.81)
>DroEre_CAF1 61268 119 + 1
AGCAAUGUAUCAGGUAUAUGAAUAAGGCUUAAAAGGCUAUUUAAAACCUUAUUCACUUGUAAUGCGCUUAAAUGGGUUUAAUGAACUCCGCGAAUGG-GGCAGCGAAUUACAAGUGAUUA
...........((((...(((((..((((.....)))))))))..))))...(((((((((((.((((.....((((((...)))).))((......-.)))))).)))))))))))... ( -30.40)
>DroYak_CAF1 59935 120 + 1
AGAAAUGUAUAAGGCAUAUGAAUAAAACGAAAAAGGGCACUUAAAACCUUAUUCACUCGUAAUGAGCUUUAAUGGGUUUAAUGAACUCCACAAAUGGGGGCAGCGAAAUACAAGUGUGUU
............(((((((.........(((.((((..........)))).)))..((((..(((((((....))))))).....(((((....)))))...)))).......))))))) ( -23.10)
>consensus
____AUGUAUUAGGCAUAUGAGUAAAGCUA_AAAGGGCACUUAAAACCUUAUUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU____________________UUACAAGUGAUUA
....((((.....))))...............((((..........))))..(((((((((((((((((....)))))))...........................))))))))))... (-14.52 = -14.64 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,445,374 – 11,445,469
Length 95
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.63
Mean single sequence MFE -20.79
Consensus MFE -8.28
Energy contribution -9.24
Covariance contribution 0.96
Combinations/Pair 1.15
Mean z-score -2.26
Structure conservation index 0.40
SVM decision value 1.11
SVM RNA-class probability 0.916944
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11445374 95 - 20766785
UAAUCACUUGUAA--------------------AGUUCAUUAAACCCAUUUAGGCUCAUUACAAGUGAUUAAGGUUUUAAGUGCCCUUU-UAGCUUAACUCAUAUGCCUAAUACAU----
(((((((((((((--------------------.(....(((((....)))))...).)))))))))))))((((.((((((.......-..)))))).......)))).......---- ( -19.80)
>DroSec_CAF1 64254 95 - 1
UAAUCACUCGUAA--------------------AGUUCAUUAAACCCAUUUAGGCUCAUUACAAGUGAAUAAGGUUUUAAGUGCCCUUU-UAGCUUAACUCAUAUGCCUAAUACAU----
.........(((.--------------------.(((.....)))....((((((((((.....))))...(((((..(((....))).-.))))).........)))))))))..---- ( -13.00)
>DroSim_CAF1 54263 95 - 1
UAAUCACUUGUAA--------------------AGUUCAUUAAACCCAUUUAGGCUCAUUACAAGUGAAUAAGGUUUUAAGUGACCUUU-UAGCUUUACUCAUAUGUCUAAUACAU----
...((((((((((--------------------.(....(((((....)))))...).)))))))))).(((((((..(((....))).-.)))))))..................---- ( -17.90)
>DroEre_CAF1 61268 119 - 1
UAAUCACUUGUAAUUCGCUGCC-CCAUUCGCGGAGUUCAUUAAACCCAUUUAAGCGCAUUACAAGUGAAUAAGGUUUUAAAUAGCCUUUUAAGCCUUAUUCAUAUACCUGAUACAUUGCU
..((((((((((((.((((((.-......))((.(((.....))))).....)))).)))))))))(((((((((((.(((......))))))))))))))........)))........ ( -32.40)
>DroYak_CAF1 59935 120 - 1
AACACACUUGUAUUUCGCUGCCCCCAUUUGUGGAGUUCAUUAAACCCAUUAAAGCUCAUUACGAGUGAAUAAGGUUUUAAGUGCCCUUUUUCGUUUUAUUCAUAUGCCUUAUACAUUUCU
....((((((((....(((..........((((.(((.....)))))))...)))....)))))))).(((((((..............................)))))))........ ( -20.83)
>consensus
UAAUCACUUGUAA____________________AGUUCAUUAAACCCAUUUAGGCUCAUUACAAGUGAAUAAGGUUUUAAGUGCCCUUU_UAGCUUUACUCAUAUGCCUAAUACAU____
...((((((((((.............................................)))))))))).(((((((..(((....)))...)))))))...................... ( -8.28 =  -9.24 +   0.96)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,445,409 – 11,445,509
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -26.31
Consensus MFE -12.98
Energy contribution -14.22
Covariance contribution 1.24
Combinations/Pair 1.08
Mean z-score -2.34
Structure conservation index 0.49
SVM decision value 1.10
SVM RNA-class probability 0.914994
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11445409 100 + 20766785
UUAAAACCUUAAUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU--------------------UUACAAGUGAUUAAUCAAAAUCUAUAAGCAAUGUUUUGACAGUAACUUCUGUG
........(((((((((((((((((((((....))))))).......--------------------)))))))))))))).((((((...........))))))((((......)))). ( -24.61)
>DroSec_CAF1 64289 100 + 1
UUAAAACCUUAUUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU--------------------UUACGAGUGAUUAAUGAAAAUCUAUAAGCAAAGUUUUGUCAGUAACUUCUGUG
......(.(((.(((((((((((((((((....))))))).......--------------------)))))))))).))).)...........((((((((........))))).))). ( -21.01)
>DroSim_CAF1 54298 100 + 1
UUAAAACCUUAUUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU--------------------UUACAAGUGAUUAAUGAAAAGCUACAAGCAAAGUUUUGACAGUAACUUCUGUG
.((((((.(((.(((((((((((((((((....))))))).......--------------------)))))))))).)))......((.....))...))))))((((......)))). ( -24.81)
>DroEre_CAF1 61308 115 + 1
UUAAAACCUUAUUCACUUGUAAUGCGCUUAAAUGGGUUUAAUGAACUCCGCGAAUGG-GGCAGCGAAUUACAAGUGAUUAAUGCAAAUCUGUAAG----GGGUUGACAGUAACUUCUGUG
....((((((..(((((((((((.((((.....((((((...)))).))((......-.)))))).)))))))))))....((((....)))).)----))))).((((......)))). ( -33.10)
>DroYak_CAF1 59975 116 + 1
UUAAAACCUUAUUCACUCGUAAUGAGCUUUAAUGGGUUUAAUGAACUCCACAAAUGGGGGCAGCGAAAUACAAGUGUGUUAUGCAAAUCUGUAAG----GUUUUGACAGUAACUGCUUCG
((((((((((((....((((..(((((((....))))))))))).(((((....)))))...(((.(((((....))))).)))......)))))----))))))).............. ( -28.00)
>consensus
UUAAAACCUUAUUCACUUGUAAUGAGCCUAAAUGGGUUUAAUGAACU____________________UUACAAGUGAUUAAUGAAAAUCUAUAAGCAA_GUUUUGACAGUAACUUCUGUG
........(((.(((((((((((((((((....)))))))...........................)))))))))).)))........................((((......)))). (-12.98 = -14.22 +   1.24)

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 10:54:14 2006