Locus 8336

Sequence ID	3R_DroMel_CAF1
Location	22,252,491 – 22,252,621
Length	130
Max. P	0.969222

overview

Window 9

Location	22,252,491 – 22,252,594
Length	103
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	77.58
Mean single sequence MFE	-22.74
Consensus MFE	-8.79
Energy contribution	-11.28
Covariance contribution	2.49
Combinations/Pair	1.04
Mean z-score	-2.13
Structure conservation index	0.39
SVM decision value	0.78
SVM RNA-class probability	0.848870
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22252491 103 - 27905053
UGGAAUCGGGGAAAACCCAGUUUCUGUACAUAAUUGUUUCAAGUGCUC---AUAAAGUGCUGAUAAAGGUUGGAAGAAACAGAUGCCAAAAUACUAAUUAAUUAUU
(((.((((((.....))).((((((...((...((...(((.(..((.---....))..))))..))...))..)))))).))).))).................. ( -24.30)
>DroSec_CAF1 25181 102 - 1
CGGAAUCGGGGAAAACCCAGAUUCUGUACAUAAUUGUUUCAAAUGCUC---AUA-AGUGCUGAUAAAGGUUGGAACACACAAAUGCCAAAAUACUGAUUAAUUAUU
((((((((((.....))).)))))))...(((((((..(((...((..---...-...)).......(((((.......))...))).......))).))))))). ( -19.80)
>DroSim_CAF1 25305 102 - 1
CGGAAUCGGGGAAAACCCAGAUUCUGUACAUAAUUGUUUCAAGUGCUC---AUA-AGUGCUGAUAAAGGUUGGAACACACAAAUGCCAAAAUACUGAUUAAUUAUU
((((((((((.....))).)))))))...(((((((..(((((..((.---...-))..))......(((((.......))...))).......))).))))))). ( -23.00)
>DroEre_CAF1 34286 79 - 1
----AUCGGGGAAAUACCAGAUUCUGUACAUAAUUGUUUCCA-------------------GAUAAGUGCUGGAACCAAAAAAUUCUAAAAUACUGUAUA-GU---
----(((.((......)).))).(((((((...(((.(((((-------------------(.......)))))).)))...(((....)))..))))))-).--- ( -15.20)
>DroYak_CAF1 30188 104 - 1
UGGAAUCGGGGUAAGCCCAGAUUCUGUUCCUAAUUGUUUCAAGUGCUAAUCACA-AUUGCUGAUUAGUGCUGGAACAAACAAACACCAAAAUACUGAUUA-UUAUU
.((((((.(((....))).))))))........((((((((.(..((((((((.-...).)))))))..)))))))))......................-..... ( -31.40)
>consensus
CGGAAUCGGGGAAAACCCAGAUUCUGUACAUAAUUGUUUCAAGUGCUC___AUA_AGUGCUGAUAAAGGUUGGAACAAACAAAUGCCAAAAUACUGAUUAAUUAUU
(((((((.(((....))).)))))))........(((((((((((((........)))))).........)))))))............................. ( -8.79 = -11.28 +   2.49)

alignment

secondary structure

dotplot

Window 0

Location	22,252,531 – 22,252,621
Length	90
Sequences	4
Columns	94
Reading direction	reverse
Mean pairwise identity	88.52
Mean single sequence MFE	-23.82
Consensus MFE	-20.01
Energy contribution	-20.82
Covariance contribution	0.81
Combinations/Pair	1.08
Mean z-score	-2.39
Structure conservation index	0.84
SVM decision value	1.64
SVM RNA-class probability	0.969222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22252531 90 - 27905053
GCAUUUGAUUUACGUCACAAA-ACUGUUUGGAAUCGGGGAAAACCCAGUUUCUGUACAUAAUUGUUUCAAGUGCUC---AUAAAGUGCUGAUAA
((((((((........((((.-..(((..(((((.(((.....))).)))))...)))...)))).))))))))..---............... ( -19.90)
>DroSec_CAF1 25221 89 - 1
GCAUUUGAUUUACGCCACAAA-ACUGUUCGGAAUCGGGGAAAACCCAGAUUCUGUACAUAAUUGUUUCAAAUGCUC---AUA-AGUGCUGAUAA
((((((((........((((.-..(((.((((((((((.....))).))))))).)))...)))).))))))))..---...-........... ( -25.30)
>DroSim_CAF1 25345 89 - 1
GCAUUUGAUUUACGCCACAAA-UCUGUUCGGAAUCGGGGAAAACCCAGAUUCUGUACAUAAUUGUUUCAAGUGCUC---AUA-AGUGCUGAUAA
((((((((........((((.-(.(((.((((((((((.....))).))))))).))).).)))).))))))))..---...-........... ( -25.30)
>DroYak_CAF1 30227 93 - 1
GCAUUUGAUUUACGCCCCAAAAGCUCUUUGGAAUCGGGGUAAGCCCAGAUUCUGUUCCUAAUUGUUUCAAGUGCUAAUCACA-AUUGCUGAUUA
((((((((...((((.......)).....((((((.(((....))).))))))..........)).))))))))(((((((.-...).)))))) ( -24.80)
>consensus
GCAUUUGAUUUACGCCACAAA_ACUGUUCGGAAUCGGGGAAAACCCAGAUUCUGUACAUAAUUGUUUCAAGUGCUC___AUA_AGUGCUGAUAA
((((((((........((((....(((.(((((((.(((....))).))))))).)))...)))).)))))))).................... (-20.01 = -20.82 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:09 2006