Locus 5525

Sequence ID 3L_DroMel_CAF1
Location 15,170,162 – 15,170,284
Length 122
Max. P 0.984902
window8727 window8728 window8729

overview

Window 7

Location 15,170,162 – 15,170,252
Length 90
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 72.29
Mean single sequence MFE -18.71
Consensus MFE -13.16
Energy contribution -14.47
Covariance contribution 1.31
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.70
SVM decision value 1.99
SVM RNA-class probability 0.984902
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15170162 90 - 23771897
AAAUGGCUUUAGCUUAAGCUCUACAAAAACAGUUUAUAGUAUAACCAUUUCCGGAAAGUAUCCAAUUUGAA-----------------------AACU-A----AAAACUUCUUAAUU
((((((.((..(((((((((..........)))))).)))..))))))))..(((.....)))........-----------------------....-.----.............. (  -9.40)
>DroSec_CAF1 59875 113 - 1
AAAUGGUUUUAGCUUAAGCUCUACAAAAAGAGUUUAUAGUAAAACCAUUUCCGGUAAGAACCCAAUUUGAAAUACCUCGUUAAUCUGUACAGAAAACU-A----AAAACUUUUUUAAA
(((((((((((.((((((((((......)))))))).)))))))))))))..((((................))))..(((..(((....))).))).-.----.............. ( -21.09)
>DroSim_CAF1 61139 114 - 1
AAAUGGUUUUAGCUUAAGCUCUACAAAAAGAGUUUAUAGCAUAACCAUUUCCGGAAAGAUUCCAAUUUGAAAUACCUAUUUAAUCUGCACAGAAAUCUGA----AAAACUUCAUAAAA
((((((((...(((((((((((......)))))))).)))..))))))))..(((.....)))..........................(((....))).----.............. ( -23.00)
>DroEre_CAF1 60884 115 - 1
AAAUGGUUUAAGCUUAAGCUCUACCAGAAAC-CUUAAAGCAUACCCAUUUCCGGAAAGUAUCCACUUUUAAUUACCUUCUAUAUCUUUGCGGAAAACU-ACCCGAAAG-UGCUUAGAA
...((((...(((....)))..)))).....-....(((((......((((((.((((..........................)))).))))))...-...(....)-))))).... ( -21.37)
>consensus
AAAUGGUUUUAGCUUAAGCUCUACAAAAAGAGUUUAUAGCAUAACCAUUUCCGGAAAGAAUCCAAUUUGAAAUACCU__UUAAUCUGUACAGAAAACU_A____AAAACUUCUUAAAA
((((((((...(((((((((((......)))))))).)))..))))))))..(((.....)))....................................................... (-13.16 = -14.47 +   1.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,170,181 – 15,170,284
Length 103
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 82.95
Mean single sequence MFE -22.03
Consensus MFE -14.68
Energy contribution -15.68
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -1.57
Structure conservation index 0.67
SVM decision value -0.01
SVM RNA-class probability 0.527041
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15170181 103 + 23771897
-------UUCAAAUUGGAUACUUUCCGGAAAUGGUUAUACUAUAAACUGUUUUUGUAGAGCUUAAGCUAAAGCCAUUUAAACGCAAAUAUAAUCACUUUGUUUUUUUGCC
-------......(((((.....)))))((((((((...(((((((.....)))))))(((....)))..))))))))....(((((.((((.....))))...))))). ( -22.10)
>DroSec_CAF1 59910 104 + 1
GAGGUAUUUCAAAUUGGGUUCUUACCGGAAAUGGUUUUACUAUAAACUCUUUUUGUAGAGCUUAAGCUAAAACCAUUUAAAUGCAA-----AUCACACUGUUU-UUUGCC
((.((((((.......(((....)))..(((((((((((((.(((.((((......)))).))))).)))))))))))))))))..-----.)).........-...... ( -22.70)
>DroSim_CAF1 61175 109 + 1
UAGGUAUUUCAAAUUGGAAUCUUUCCGGAAAUGGUUAUGCUAUAAACUCUUUUUGUAGAGCUUAAGCUAAAACCAUUUAAAUGCAAAUAUAAUCACACUGUUU-UUUGCC
...((((((....(((((.....)))))((((((((..(((.(((.((((......)))).))))))...))))))))))))))...................-...... ( -21.60)
>DroEre_CAF1 60922 108 + 1
AAGGUAAUUAAAAGUGGAUACUUUCCGGAAAUGGGUAUGCUUUAAG-GUUUCUGGUAGAGCUUAAGCUUAAACCAUUUAAAUGCAAAUAUAAUCACAUUGUUU-UUUGCC
..(((((..((.(((((((....((((....))))..(((((((((-.....((((.((((....))))..)))))))))).)))......))).)))).)).-.))))) ( -21.70)
>consensus
_AGGUAUUUCAAAUUGGAUACUUUCCGGAAAUGGUUAUACUAUAAACUCUUUUUGUAGAGCUUAAGCUAAAACCAUUUAAAUGCAAAUAUAAUCACACUGUUU_UUUGCC
..............((((.....)))).((((((((...(((((((.....)))))))(((....)))..))))))))....(((((...(((......)))..))))). (-14.68 = -15.68 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,170,181 – 15,170,284
Length 103
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 82.95
Mean single sequence MFE -20.12
Consensus MFE -16.79
Energy contribution -18.10
Covariance contribution 1.31
Combinations/Pair 1.10
Mean z-score -1.58
Structure conservation index 0.83
SVM decision value 0.31
SVM RNA-class probability 0.683392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15170181 103 - 23771897
GGCAAAAAAACAAAGUGAUUAUAUUUGCGUUUAAAUGGCUUUAGCUUAAGCUCUACAAAAACAGUUUAUAGUAUAACCAUUUCCGGAAAGUAUCCAAUUUGAA-------
..((((......(((((.(((((((.((((((....(((((......)))))......)))).))....))))))).)))))..(((.....)))..))))..------- ( -14.80)
>DroSec_CAF1 59910 104 - 1
GGCAAA-AAACAGUGUGAU-----UUGCAUUUAAAUGGUUUUAGCUUAAGCUCUACAAAAAGAGUUUAUAGUAAAACCAUUUCCGGUAAGAACCCAAUUUGAAAUACCUC
.(((((-..((...))..)-----))))....(((((((((((.((((((((((......)))))))).)))))))))))))..((((................)))).. ( -24.29)
>DroSim_CAF1 61175 109 - 1
GGCAAA-AAACAGUGUGAUUAUAUUUGCAUUUAAAUGGUUUUAGCUUAAGCUCUACAAAAAGAGUUUAUAGCAUAACCAUUUCCGGAAAGAUUCCAAUUUGAAAUACCUA
((....-....((((..(......)..)))).((((((((...(((((((((((......)))))))).)))..))))))))))(((.....)))............... ( -25.40)
>DroEre_CAF1 60922 108 - 1
GGCAAA-AAACAAUGUGAUUAUAUUUGCAUUUAAAUGGUUUAAGCUUAAGCUCUACCAGAAAC-CUUAAAGCAUACCCAUUUCCGGAAAGUAUCCACUUUUAAUUACCUU
......-.......(((((((....(((.(((((.((((...(((....)))..)))).....-.))))))))...........(((.....))).....)))))))... ( -16.00)
>consensus
GGCAAA_AAACAAUGUGAUUAUAUUUGCAUUUAAAUGGUUUUAGCUUAAGCUCUACAAAAAGAGUUUAUAGCAUAACCAUUUCCGGAAAGAAUCCAAUUUGAAAUACCU_
((.........((((..(......)..)))).((((((((...(((((((((((......)))))))).)))..))))))))))(((.....)))............... (-16.79 = -18.10 +   1.31)

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 11:52:22 2006