Locus 1121

Sequence ID 3L_DroMel_CAF1
Location 3,287,459 – 3,287,608
Length 149
Max. P 0.999969
window1741 window1742 window1743

overview

Window 1

Location 3,287,459 – 3,287,569
Length 110
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 92.69
Mean single sequence MFE -26.36
Consensus MFE -20.02
Energy contribution -20.50
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -3.03
Structure conservation index 0.76
SVM decision value 1.70
SVM RNA-class probability 0.972705
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3287459 110 + 23771897
UUUUCCCGACCCGCAC------CCUUUCUUCUCUUUCGACCAUUGUGACUGUGCACAAUUAACUUGCAUACAUACGUGUAUGUAUGUACACACUCUGUUUGUAUGUAUGCGUGCCA
............((((------...................((((((......))))))......((((((((((((((((....))))))((...))..)))))))))))))).. ( -27.80)
>DroSec_CAF1 17256 110 + 1
UUUUCCCGACCCUCCU------CCUUUCUUCUUUCACGACCAUUGUGACUGUGCACAAUUAACUUGCAUACAUACGUGUAUGUAUGUACACACUCUGUUUGUAUGUAUGCGUGCCA
................------............(((....((((((......))))))......((((((((((((((((....))))))((...))..)))))))))))))... ( -24.70)
>DroSim_CAF1 18101 110 + 1
UUUUCCCGACCCUCCC------CCUUUCUUCUUUCACGACCAUUGUGACUGUGCACAAUUAACUUGCAUACAUACGCGUAUGUAUGUACACACUCUGUUUGUAUGUAUGCGUGCCA
................------...........((((((...)))))).((((((.........))))))..((((((((((((((.(((.....))).))))))))))))))... ( -22.80)
>DroEre_CAF1 19280 114 + 1
UUUUCCCGACCCGCACCCGCCCCCUUUCUUCUCU--CGUCCAUUGUGACUGUGCACAAUUAACUUGCAUACAUACGUAUAUGUAUGUACACACUCUGUUUGUAUGUAUGCGUGCCA
............((((..................--.((..((((((......))))))..))..(((((((((((((((....)))))((.....))..)))))))))))))).. ( -27.50)
>DroYak_CAF1 19875 108 + 1
UUUUCCCGACCCGCAC------CCUUUCUUCUCU--CGUCCAUUGUGACUGUGCACAAUUAACUUGCAUACAUACGUAUAUGUAUGUACACACUCUGUUCGUAUGUAUGCGUGCCA
............((((------............--.((..((((((......))))))..))..(((((((((((.(((.(..((....))..)))).))))))))))))))).. ( -29.00)
>consensus
UUUUCCCGACCCGCAC______CCUUUCUUCUCU__CGACCAUUGUGACUGUGCACAAUUAACUUGCAUACAUACGUGUAUGUAUGUACACACUCUGUUUGUAUGUAUGCGUGCCA
............((((.........................((((((......))))))......(((((((((((..((.(..((....))..)))..))))))))))))))).. (-20.02 = -20.50 +   0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,287,459 – 3,287,569
Length 110
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 92.69
Mean single sequence MFE -29.26
Consensus MFE -24.96
Energy contribution -24.72
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -2.16
Structure conservation index 0.85
SVM decision value 2.39
SVM RNA-class probability 0.993279
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3287459 110 - 23771897
UGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUGGUCGAAAGAGAAGAAAGG------GUGCGGGUCGGGAAAA
.(((.((((..(.........((.((((((((((((((....))))))))(((.....))))))))).)).......((....)).......).------.)))).)))....... ( -31.00)
>DroSec_CAF1 17256 110 - 1
UGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUGGUCGUGAAAGAAGAAAGG------AGGAGGGUCGGGAAAA
...(((((((((((((.....(.((((((....)))))).)))))))))))..(...((((((......))))))...))))............------................ ( -25.70)
>DroSim_CAF1 18101 110 - 1
UGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACGCGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUGGUCGUGAAAGAAGAAAGG------GGGAGGGUCGGGAAAA
...(((((((((((((.......((((((....))))))..))))))))))..(...((((((......))))))...))))............------................ ( -26.30)
>DroEre_CAF1 19280 114 - 1
UGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUAUACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUGGACG--AGAGAAGAAAGGGGGCGGGUGCGGGUCGGGAAAA
.(((.((((..(............(((((((((((......))))))))))).(((.((((((......)))))).))).--................)..)))).)))....... ( -30.80)
>DroYak_CAF1 19875 108 - 1
UGGCACGCAUACAUACGAACAGAGUGUGUACAUACAUAUACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUGGACG--AGAGAAGAAAGG------GUGCGGGUCGGGAAAA
..(((((((((((((((......((((((....)))))).)))))))))))..(((.((((((......)))))).))).--............------))))............ ( -32.50)
>consensus
UGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUGGUCG__AGAGAAGAAAGG______GUGCGGGUCGGGAAAA
.(((..((((((((((.....(.((((((....)))))).)))))))))))..(...((((((......))))))...)...........................)))....... (-24.96 = -24.72 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,287,493 – 3,287,608
Length 115
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 96.20
Mean single sequence MFE -33.52
Consensus MFE -33.02
Energy contribution -32.78
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -2.72
Structure conservation index 0.99
SVM decision value 5.03
SVM RNA-class probability 0.999969
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3287493 115 - 23771897
AAAUUCCUUUGCUUCUCC-UUUUUCCGCCUCAAUUGGGGGUGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUG
..........((((....-.....(((((((.....)))))))...((((((((((.....(.((((((....)))))).)))))))))))))))..((((((......)))))). ( -33.20)
>DroSec_CAF1 17290 115 - 1
AAAUUCCUUCGCUUCUCC-UUUUUCCGCCUCAAUUGGGGGUGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUG
..........((((....-.....(((((((.....)))))))...((((((((((.....(.((((((....)))))).)))))))))))))))..((((((......)))))). ( -33.30)
>DroSim_CAF1 18135 115 - 1
AAAUUCCUUCGCUUCUCC-UUUUUCCGCCUCAAUUGGGGGUGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACGCGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUG
..........((((....-.....(((((((.....)))))))...((((((((((.......((((((....))))))..))))))))))))))..((((((......)))))). ( -33.90)
>DroEre_CAF1 19318 116 - 1
AAAUUCCUUCGCUUUUCCCUGUUUCCGCCUCACUUGGGGGUGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUAUACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUG
..........((((......((..(((((((.....))))))).))((((((((((.....(.((((((....)))))).)))))))))))))))..((((((......)))))). ( -32.20)
>DroYak_CAF1 19907 116 - 1
AAAUUCCUUCGCUUUUCCCUGCUUCCGCCUCAAUUGGGGGUGGCACGCAUACAUACGAACAGAGUGUGUACAUACAUAUACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUG
..........((((.....((((.((.((......)).)).)))).(((((((((((......((((((....)))))).)))))))))))))))..((((((......)))))). ( -35.00)
>consensus
AAAUUCCUUCGCUUCUCC_UUUUUCCGCCUCAAUUGGGGGUGGCACGCAUACAUACAAACAGAGUGUGUACAUACAUACACGUAUGUAUGCAAGUUAAUUGUGCACAGUCACAAUG
..........((((..........(((((((.....)))))))...((((((((((.....(.((((((....)))))).)))))))))))))))..((((((......)))))). (-33.02 = -32.78 +  -0.24)

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 09:59:39 2006