Locus 6548

Sequence ID	2R_DroMel_CAF1
Location	20,476,683 – 20,476,868
Length	185
Max. P	0.694889

overview

Window 7

Location	20,476,683 – 20,476,773
Length	90
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	81.93
Mean single sequence MFE	-20.78
Consensus MFE	-14.55
Energy contribution	-14.80
Covariance contribution	0.25
Combinations/Pair	1.17
Mean z-score	-1.75
Structure conservation index	0.70
SVM decision value	0.34
SVM RNA-class probability	0.694889
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20476683 90 + 20766785
UGUCUAUUCGACCAUUUAGACCAUU---UCUACUCACGCGAGUUUGUGUUAGCGAUCUCGUUGAUUUCAUUGGGAUCCAACCAGACCUUCUUC
.(((((..........)))))....---.............(((((.(((.(.(((((((.((....)).))))))))))))))))....... ( -18.80)
>DroSim_CAF1 533 90 + 1
UGUCUAUUCGACCAUUUAGUCCAUU---UCUACUCACGCGAGUUUGUGUUAGCGAUCUCGUUGAUUUCAUUGGGGUCCAACCAGACCUUCUUC
.((((.((.((((.......(((..---.....(((.(((((.((((....)))).))))))))......))))))).))..))))....... ( -18.93)
>DroEre_CAF1 533 87 + 1
UUACACUUCG---UGUUGGACCAUU---UCUACUCACGCGAAUUUGUGUUGGCGAUCUCGUUGAUUUCAUUGGGAUCCAACCAGACCUUCUUC
......((((---(((((((.....---))))...)))))))((((.(((((..((((((.((....)).)))))))))))))))........ ( -22.30)
>DroYak_CAF1 751 87 + 1
UCUCACUCCA---UGUUGAACCAUU---UCUACUCACGCGAGUUUGUGUUGGCGAUCUCGUUGAUUUCAUUGGGAUCCAACCAGACCUUCUUC
..........---.((((..(((..---...((((....))))......))).(((((((.((....)).)))))))))))............ ( -17.50)
>DroMoj_CAF1 532 92 + 1
UC-UUAUUCGCACAUUUCCUCCAUUUGGUAUACUUACGCGAGUUUGUGUUGGCGAUCUCAUUAAUUUCAUUGGGAUCCAACCAAACCUUCUUC
..-....((((.........((....)).........))))(((((.(((((..((((((..........))))))))))))))))....... ( -21.37)
>DroAna_CAF1 532 80 + 1
CGGCU---CA---ACUGGGGCC-------UUACUUACGCGAGUUUGUGUUGGCGAUCUCGUUGAUUUCAUUGGGAUCCAACCAGACCUUCUUC
.....---..---.((((.(((-------.(((..((....))..)))..)))(((((((.((....)).)))))))...))))......... ( -25.80)
>consensus
UGUCUAUUCG___AUUUGGACCAUU___UCUACUCACGCGAGUUUGUGUUGGCGAUCUCGUUGAUUUCAUUGGGAUCCAACCAGACCUUCUUC
.........................................(((((.((((..(((((((.((....)).))))))))))))))))....... (-14.55 = -14.80 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	20,476,773 – 20,476,868
Length	95
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-26.10
Consensus MFE	-17.18
Energy contribution	-17.85
Covariance contribution	0.67
Combinations/Pair	1.10
Mean z-score	-1.30
Structure conservation index	0.66
SVM decision value	-0.01
SVM RNA-class probability	0.528429
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20476773 95 - 20766785
GCUACUUUCGAAAUGAUGGACUAACAAGUUA---CCCUCCUUUGCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCCGUGCUGCGAUGCGGCAA
(((...............((((....)))).---..(((.((((.((((......)))).)))).)))(((((((((......))))))).))))).. ( -26.30)
>DroVir_CAF1 5990 83 - 1
GCUGCAUUCUAAU-GU-G-------------AUGUCUCUCUUUCCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCAGUGCUGCGUUGCGGCAA
((((((.......-..-(-------------(.((((((((....((((......))))..)).))))))))(((((......)))))..)))))).. ( -27.50)
>DroPse_CAF1 627 89 - 1
GCUGUUUUC------AUGAACUAAUGCUUGU---CCAUUAUUUGCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCUGUACUGCGUUGCGGCAA
(((((...(------......(((((.....---.)))))...(((((.((((........)))((((((.....))))))).))))))..))))).. ( -24.30)
>DroEre_CAF1 620 95 - 1
GCUACUUUCGAAAUGAUGGACUAACAAGUAC---CCCUCCUUUGCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCCGUGCUGCGAUGCGGCAA
(((..............(((((....))).)---).(((.((((.((((......)))).)))).)))(((((((((......))))))).))))).. ( -27.10)
>DroYak_CAF1 838 95 - 1
GCUACUUUCGAAAUGAUGGACUAACAAGUAC---CCCUCCUUUGCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCCGUGCUGCGAUGCGGCAA
(((..............(((((....))).)---).(((.((((.((((......)))).)))).)))(((((((((......))))))).))))).. ( -27.10)
>DroPer_CAF1 627 89 - 1
GCUGUUUUC------AUGAACUAAUGCUUGU---CCAUUAUUUGCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCUGUACUGCGUUGCGGCAA
(((((...(------......(((((.....---.)))))...(((((.((((........)))((((((.....))))))).))))))..))))).. ( -24.30)
>consensus
GCUACUUUCGAAA_GAUGGACUAACAAGUAC___CCCUCCUUUGCAGUUCUCUAAAGCUCCAGAAGAGGCUCGCAGCCUCCGUGCUGCGAUGCGGCAA
(((................................((((.((((.((((......)))).)))).))))..((((((......))))))....))).. (-17.18 = -17.85 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:34 2006