Locus 5107

Sequence ID 3R_DroMel_CAF1
Location 13,450,491 – 13,450,623
Length 132
Max. P 0.528836
window8328 window8329

overview

Window 8

Location 13,450,491 – 13,450,595
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.01
Mean single sequence MFE -20.90
Consensus MFE -16.10
Energy contribution -16.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.99
Structure conservation index 0.77
SVM decision value -0.06
SVM RNA-class probability 0.505006
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13450491 104 + 27905053
-----UGAAAAACUAAAAAAUA----CUGACACAAU-CUUUUGUG------UAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
-----.................----(((.(((((.-...)))))------))).....((((((((.((......)))))))(((((.....))))).................))).. ( -22.50)
>DroPse_CAF1 5275 103 + 1
GCUUUUAAAAAAGUAUAAUAUAGCCACUUAGAC-----------A------AAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
(((((....)))))........(((........-----------.------..)))...((((((((.((......)))))))(((((.....))))).................))).. ( -20.00)
>DroSec_CAF1 1629 104 + 1
-----UGAAAAACAAAAAAAUA----CAAAGACAAG-CUCGUGUG------UAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
-----.................----.......(((-(.(.(((.------(((....(((.(((((.((......))))))))))....))).))).).))))................ ( -21.90)
>DroSim_CAF1 623 104 + 1
-----UGAAAAACAAAAAAAUA----UUGACACAAG-CUCUUGUG------UAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
-----.................----(((....(((-(.(((((.------(((....(((.(((((.((......))))))))))....))).))))).))))....)))......... ( -24.00)
>DroAna_CAF1 955 110 + 1
-----UA-CAAACAAAUAAAAA----AAGAAGCAAUGCUUAUAUUUCCUCAAAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
-----..-..............----..(((((...((((............))))....(((((((.((......)))))))(((((.....))))))))))))............... ( -18.60)
>DroPer_CAF1 1912 103 + 1
GCUUUUAAAAAUGUAUAAUAUAUCCACUUAGAC-----------G------AAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
((((((......((...........))......-----------)------)))))...((((((((.((......)))))))(((((.....))))).................))).. ( -18.40)
>consensus
_____UAAAAAACAAAAAAAUA____CUGAGACAA__CU__UGUG______AAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCAC
...........................................................((((((((.((......)))))))(((((.....))))).................))).. (-16.10 = -16.10 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 9

Location 13,450,521 – 13,450,623
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.58
Mean single sequence MFE -27.77
Consensus MFE -25.33
Energy contribution -24.88
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.01
Structure conservation index 0.91
SVM decision value -0.01
SVM RNA-class probability 0.528836
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13450521 102 + 27905053
UUGUG------UAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUGCGUUAUAUGCCUGACCAAA------------
(((..------(((((...((((((((.((......)))))))(((((.....))))).................)))..(((((...)))))....)))))..))).------------ ( -28.30)
>DroPse_CAF1 5308 110 + 1
----A------AAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAACUGACUCCGCCGUGUCCAACCACCAUCAAUUA
----.------..(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).)))....(((........)))................ ( -27.00)
>DroSec_CAF1 1659 102 + 1
GUGUG------UAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUACGUUGUUCGUCUGACCAAU------------
..(((------(.(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).)))))))((((.((....)).))))------------ ( -28.90)
>DroSim_CAF1 653 102 + 1
UUGUG------UAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUGCGUUGUUCGUCUGACCAAU------------
(((..------(((((...((((((((.((......)))))))(((((.....))))).................)))(((((((...)))))))..)))))..))).------------ ( -28.70)
>DroAna_CAF1 985 115 + 1
AUAUUUCCUCAAAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAGAUGAAAUUCACUUGUCCAAAAAGCUAC-----
..(((((.((...(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).))).)).)))))....................----- ( -27.00)
>DroPer_CAF1 1945 110 + 1
----G------AAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAACUGAUUCCGCCGUGUCCAACCACCAAUAAUUA
----.------..((.(.(((((((((.((......))))))).((((.....))))((((((.................))))))..........)))).).))............... ( -26.73)
>consensus
_UGUG______AAGGCCCCGGCGAGAUUCGAACUCACGAUCUCCUGUUUACUAGACAGGCGCUUUAACCAACUAAGCCACGGCGCCAUACGAUAUUCGCCUGACCAAA____________
.............(((.((((((((((.((......)))))))(((((.....)))))))((((.........))))..))).)))....(((........)))................ (-25.33 = -24.88 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:24 2006