Locus 3801

Sequence ID	3L_DroMel_CAF1
Location	10,972,320 – 10,972,417
Length	97
Max. P	0.945393

overview

Window 4

Location	10,972,320 – 10,972,417
Length	97
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	85.44
Mean single sequence MFE	-23.00
Consensus MFE	-17.72
Energy contribution	-19.38
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.76
Structure conservation index	0.77
SVM decision value	0.62
SVM RNA-class probability	0.802824
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10972320 97 + 23771897
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAAAAAA----------AAAGUAAGACUGAAA-AAAGUGGCAACCCACUGUGGUUUACUUUAACCAAGCC-CAAAG
((((((...(((..(((((.....)))))..)))......----------((((((.(((((...-..(((((....))))).)))))))))))..)))))).-..... ( -24.00)
>DroSec_CAF1 104463 92 + 1
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAA--------------AAAGUAAGACUGAAA--AAGUGGCAGCCCACUGUGGUUUACUUUAACCAAGCC-CAAAG
((((((...(((..(((((.....)))))..)))..--------------((((((.(((((...--.(((((....))))).)))))))))))..)))))).-..... ( -24.70)
>DroSim_CAF1 102674 93 + 1
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAA--------------AAAGUAAGACUGAAA-AAAGUGGCAGCCCACUGUGGUUUACUUUAACCAAGCC-CAAAG
((((((...(((..(((((.....)))))..)))..--------------((((((.(((((...-..(((((....))))).)))))))))))..)))))).-..... ( -24.00)
>DroEre_CAF1 105132 94 + 1
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAA--------------AAAGUAAGACUGAAA-AAAGUGGCAGCCCACUGUGGUUUACUUUAACCAAGCCCCCAAG
((((((...(((..(((((.....)))))..)))..--------------((((((.(((((...-..(((((....))))).)))))))))))..))))))....... ( -24.00)
>DroYak_CAF1 107821 108 + 1
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAAAAAAAAAAUGGAAAAAAGUAAGACUGAAAAAAAGUGGCAAACCACUGUGGUUUACUUUAACCAAGCC-CAAAG
((((((...(((..(((((.....)))))..)))................((((((.(((((......(((((....))))).)))))))))))..)))))).-..... ( -23.70)
>DroAna_CAF1 98489 74 + 1
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAA--------------AAAGGA---------------G---GCACACUGUGGUUUACUUUAACCAAGCC-C--AG
.((.(((((((((..((((.................--------------))))..---------------)---))))....(((((......)))))))))-.--)) ( -17.63)
>consensus
GCUUGGCUGUGUCAACUUUCAAUCAAAGUCAACAAA______________AAAGUAAGACUGAAA_AAAGUGGCAGCCCACUGUGGUUUACUUUAACCAAGCC_CAAAG
((((((...(((..(((((.....)))))..)))................((((((.(((((......(((((....))))).)))))))))))..))))))....... (-17.72 = -19.38 +   1.67)

alignment

secondary structure

dotplot

Window 5

Location	10,972,320 – 10,972,417
Length	97
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	85.44
Mean single sequence MFE	-26.03
Consensus MFE	-22.35
Energy contribution	-23.02
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.54
Structure conservation index	0.86
SVM decision value	1.35
SVM RNA-class probability	0.945393
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10972320 97 - 23771897
CUUUG-GGCUUGGUUAAAGUAAACCACAGUGGGUUGCCACUUU-UUUCAGUCUUACUUU----------UUUUUUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
.....-.(((((((((((((((((...(((((....)))))..-.....)).)))))))----------......(((..(((((.....)))))..))).)))))))) ( -27.10)
>DroSec_CAF1 104463 92 - 1
CUUUG-GGCUUGGUUAAAGUAAACCACAGUGGGCUGCCACUU--UUUCAGUCUUACUUU--------------UUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
.....-.(((((((((((((((((...(((((....))))).--.....)).)))))))--------------..(((..(((((.....)))))..))).)))))))) ( -27.70)
>DroSim_CAF1 102674 93 - 1
CUUUG-GGCUUGGUUAAAGUAAACCACAGUGGGCUGCCACUUU-UUUCAGUCUUACUUU--------------UUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
.....-.(((((((((((((((((...(((((....)))))..-.....)).)))))))--------------..(((..(((((.....)))))..))).)))))))) ( -27.10)
>DroEre_CAF1 105132 94 - 1
CUUGGGGGCUUGGUUAAAGUAAACCACAGUGGGCUGCCACUUU-UUUCAGUCUUACUUU--------------UUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
.......(((((((((((((((((...(((((....)))))..-.....)).)))))))--------------..(((..(((((.....)))))..))).)))))))) ( -27.10)
>DroYak_CAF1 107821 108 - 1
CUUUG-GGCUUGGUUAAAGUAAACCACAGUGGUUUGCCACUUUUUUUCAGUCUUACUUUUUUCCAUUUUUUUUUUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
.....-.((((((((...(((((((.....)))))))......................................(((..(((((.....)))))..))).)))))))) ( -27.40)
>DroAna_CAF1 98489 74 - 1
CU--G-GGCUUGGUUAAAGUAAACCACAGUGUGC---C---------------UCCUUU--------------UUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
..--.-.((((((((...(((.((....)).)))---.---------------......--------------..(((..(((((.....)))))..))).)))))))) ( -19.80)
>consensus
CUUUG_GGCUUGGUUAAAGUAAACCACAGUGGGCUGCCACUUU_UUUCAGUCUUACUUU______________UUUGUUGACUUUGAUUGAAAGUUGACACAGCCAAGC
.......((((((((............(((((....)))))..................................(((..(((((.....)))))..))).)))))))) (-22.35 = -23.02 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:58 2006