Locus 7272

Sequence ID	2L_DroMel_CAF1
Location	20,358,889 – 20,358,992
Length	103
Max. P	0.875118

overview

Window 7

Location	20,358,889 – 20,358,992
Length	103
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-39.38
Consensus MFE	-25.75
Energy contribution	-25.03
Covariance contribution	-0.71
Combinations/Pair	1.41
Mean z-score	-2.42
Structure conservation index	0.65
SVM decision value	0.79
SVM RNA-class probability	0.851528
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20358889 103 + 22407834
UACGGUUACAA-AGUUGCUGCUAAAGUGGU------UGCCGCAAGUUGCACGUUGCAG---GUUGCUGUUGCAGA-UGUACUUGUACUUGCACUUGCAGUUGCUGCGGCAACCG
..((((.((..-.)).)))).......(((------(((((((.((((((.((.((((---((.((...(((...-.)))...)))))))))).))))...)))))))))))). ( -37.90)
>DroSec_CAF1 15765 103 + 1
UACGGUUACAG-AGUUGCUGUUAAAGUGGC------UGCCGCAAGUUGCACGUUGCAG---GUUGCUGUUGCAGA-UGUACUUGUACUUGCACUUGCAGUUGCUGCGGCAACCG
..........(-.((((((((...((..((------(((.((((((.(((.((.(((.---.((((....)))).-))))).)))))))))....)))))..))))))))))). ( -40.60)
>DroSim_CAF1 14844 103 + 1
UACGGUUACAA-AGUUGCUGCUAAAGCGGC------UGCCGCAAGUUGCACGUUGCAG---GUUGCUGUUGCAGA-UGUACUUGUACUUGCACUUGCAGUUGCUGCGGCAACCG
...........-.((((((((...((((((------(((.((((((.(((.((.(((.---.((((....)))).-))))).)))))))))....))))))))))))))))).. ( -43.00)
>DroEre_CAF1 16395 104 + 1
UACGGUUGCAACAGUCGCUGCCAAAGUGGU------UUCCGCAUGUGGCACGUUGCAG---GCUGCCGUUGCAGA-UGUACUUGUACUUGCACUUGCAGUUGCUGCGGCAACCG
..(((((((..((((.(((((((..((((.------..))))...)))))...(((((---(.(((...(((((.-.....)))))...))))))))))).))))..))))))) ( -43.70)
>DroYak_CAF1 15663 104 + 1
UACGGUUACAAAAGUCGCUGCCAAAGUGGU------UUCCGCAUGUGGCACGUUGCAG---GUUGCUGUUGCAGA-UGUACUUGUACUUGCACUUGCAGUUGCUGCAGCAACCG
.............((.(((((((..((((.------..))))...))))).)).)).(---((((((((.((((.-((((..(((....)))..)))).)))).))))))))). ( -40.70)
>DroPer_CAF1 15819 109 + 1
UACGGUUACAGUAGUCGUUACUAAAGUUGUGCCAGUGGCAGCUAGUUCUGGGGUUGAGGCAGUGGCUGUUGCUCGUAGUACUUG---UUGUACUUGUUGUGGCA--AGCAAGCG
.(((..((...))..)))(((..((((..(((.((..(((((((.(.((........)).).)))))))..)).)))..)))).---..)))((((((......--)))))).. ( -30.40)
>consensus
UACGGUUACAA_AGUCGCUGCUAAAGUGGU______UGCCGCAAGUUGCACGUUGCAG___GUUGCUGUUGCAGA_UGUACUUGUACUUGCACUUGCAGUUGCUGCGGCAACCG
..(((((......((.(((((....(((((.......))))).....))).)).))........(((((.(((...((((..(((....)))..))))..))).)))))))))) (-25.75 = -25.03 +  -0.71)

alignment

secondary structure

dotplot

Window 8

Location	20,358,889 – 20,358,992
Length	103
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	81.52
Mean single sequence MFE	-33.35
Consensus MFE	-19.80
Energy contribution	-21.08
Covariance contribution	1.28
Combinations/Pair	1.24
Mean z-score	-2.81
Structure conservation index	0.59
SVM decision value	0.89
SVM RNA-class probability	0.875118
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20358889 103 - 22407834
CGGUUGCCGCAGCAACUGCAAGUGCAAGUACAAGUACA-UCUGCAACAGCAAC---CUGCAACGUGCAACUUGCGGCA------ACCACUUUAGCAGCAACU-UUGUAACCGUA
.(((((((((((....((((..((((.(((....))).-..(((....)))..---.))))...))))..))))))))------)))......((((.....-))))....... ( -34.20)
>DroSec_CAF1 15765 103 - 1
CGGUUGCCGCAGCAACUGCAAGUGCAAGUACAAGUACA-UCUGCAACAGCAAC---CUGCAACGUGCAACUUGCGGCA------GCCACUUUAACAGCAACU-CUGUAACCGUA
.(((((((((((....((((..((((.(((....))).-..(((....)))..---.))))...))))..))))))))------)))......((((.....-))))....... ( -35.70)
>DroSim_CAF1 14844 103 - 1
CGGUUGCCGCAGCAACUGCAAGUGCAAGUACAAGUACA-UCUGCAACAGCAAC---CUGCAACGUGCAACUUGCGGCA------GCCGCUUUAGCAGCAACU-UUGUAACCGUA
.(((((((((((....((((..((((.(((....))).-..(((....)))..---.))))...))))..))))))))------)))(((.....)))....-........... ( -35.90)
>DroEre_CAF1 16395 104 - 1
CGGUUGCCGCAGCAACUGCAAGUGCAAGUACAAGUACA-UCUGCAACGGCAGC---CUGCAACGUGCCACAUGCGGAA------ACCACUUUGGCAGCGACUGUUGCAACCGUA
(((((((.((((((.((((...((((.(((....))).-..))))...)))).---.)))..(((((((..((.(...------.)))...))))).))..))).))))))).. ( -40.80)
>DroYak_CAF1 15663 104 - 1
CGGUUGCUGCAGCAACUGCAAGUGCAAGUACAAGUACA-UCUGCAACAGCAAC---CUGCAACGUGCCACAUGCGGAA------ACCACUUUGGCAGCGACUUUUGUAACCGUA
((((((((((((....(((...((((.(((....))).-..))))...)))..---))))).(((((((..((.(...------.)))...))))).))......))))))).. ( -34.40)
>DroPer_CAF1 15819 109 - 1
CGCUUGCU--UGCCACAACAAGUACAA---CAAGUACUACGAGCAACAGCCACUGCCUCAACCCCAGAACUAGCUGCCACUGGCACAACUUUAGUAACGACUACUGUAACCGUA
.(((((((--((........(((((..---...))))).))))))..)))...((((.......(((......))).....))))..((..((((....))))..))....... ( -19.10)
>consensus
CGGUUGCCGCAGCAACUGCAAGUGCAAGUACAAGUACA_UCUGCAACAGCAAC___CUGCAACGUGCAACUUGCGGCA______ACCACUUUAGCAGCAACU_UUGUAACCGUA
((((((((((((((..((((.((((........))))....(((....)))......))))...)))....))))))................((((......))))))))).. (-19.80 = -21.08 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:01 2006