Locus 6204

Sequence ID	2R_DroMel_CAF1
Location	19,530,178 – 19,530,378
Length	200
Max. P	0.926450

overview

Window 3

Location	19,530,178 – 19,530,298
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.64
Mean single sequence MFE	-32.75
Consensus MFE	-29.06
Energy contribution	-30.00
Covariance contribution	0.94
Combinations/Pair	1.09
Mean z-score	-1.80
Structure conservation index	0.89
SVM decision value	0.85
SVM RNA-class probability	0.866857
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19530178 120 - 20766785
AUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUUUACACUUCAUUCCGUACAUAUUUAGGUCCGCCGGAAACGUUUUGUGUUUCUGGCUGAUUAAAGUCUUAAAGCUGUUCUUG
...(((((((.(....).)))))))..(((((((..(((((..((........)).........((((.((((((((((.....)))))))))).)))).)))))....))))))).... ( -34.50)
>DroAna_CAF1 641 117 - 1
AUCAGGGUGACAUUCUCCUGAUCCUCCAACAGCUGCGAUUUGCACUUCAUUCCGUACAUAUUCAGGUCCGCCGGAAAAGUUUUGUGUUUUUGGCUAAUU---GUUUUGAAGCUGUAUUUU
(((((((.(.....))))))))......((((((.(((...(((.......((...........))...((((((((.........))))))))....)---)).))).))))))..... ( -25.10)
>DroEre_CAF1 8 120 - 1
AUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUUUACACUUCAUUCCGUACAUAUUGAGGUCCGCCGGAAACGUUUUGUGUUUCUGGCUGAUUAAAGUCUUAAAGCUGUUCUUG
...(((((((.(....).)))))))..(((((((..(((((..((((((............))))))..((((((((((.....))))))))))......)))))....))))))).... ( -36.80)
>DroYak_CAF1 21 120 - 1
AUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUUUACACUUCAUUCCGUACAUAUUGAUGUCCGCCGGAAACGUUUUGUGUUUCUGGCUGAUUAAAGUCUUAAAGCUGUUCUUG
...(((((((.(....).)))))))..(((((((..(((((.....(((....(.((((....)))).)((((((((((.....)))))))))))))...)))))....))))))).... ( -34.60)
>consensus
AUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUUUACACUUCAUUCCGUACAUAUUGAGGUCCGCCGGAAACGUUUUGUGUUUCUGGCUGAUUAAAGUCUUAAAGCUGUUCUUG
(((((((........)))))))......((((((..(((((..((((((............))))))..((((((((((.....))))))))))......)))))....))))))..... (-29.06 = -30.00 +   0.94)

alignment

secondary structure

dotplot

Window 4

Location	19,530,258 – 19,530,378
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.08
Mean single sequence MFE	-41.28
Consensus MFE	-31.46
Energy contribution	-32.14
Covariance contribution	0.68
Combinations/Pair	1.24
Mean z-score	-2.22
Structure conservation index	0.76
SVM decision value	1.18
SVM RNA-class probability	0.926450
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19530258 120 - 20766785
GCUUCUUUUGCCACCUGCAACGCAGCAGGGUCCAAGCCCAACUCUUCGGCUUCUGGCGGAUUGAGUUCCGCCGAUUGAUGAUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUU
.......((((.....))))((((((.((((....)))).........(((..(((((((......)))))))...((.((((((((........)))))))).)).))).))))))... ( -46.20)
>DroPse_CAF1 20 120 - 1
GUUUCUUUUGCCAUCUGCAGCGAAGUACGUUCCAGGUCCAACUCUUUGGUUUGGGACGAACGGAAUUUCGACGAUUGAUGAUUAAUGUCACAUUUUCCUGUUCCUCCAAUAACUGCGACU
...............(((((....((.(((((((((.((((....))))))))))))).))(((((...((.((.((.((((....)))))).))))..)))))........)))))... ( -30.30)
>DroAna_CAF1 718 120 - 1
GCUUUUUCUGCCACCUGCACCGCAGCAGGGUCCACGUCCAGCUCUUCGGCUUCCGUUGAAUUGAGUUCCGUCGAUUGAUGAUCAGGGUGACAUUCUCCUGAUCCUCCAACAGCUGCGAUU
........(((.....))).((((((..((((.(((...(((((((((((....))))))..))))).))).))))((.((((((((.(.....))))))))).)).....))))))... ( -37.50)
>DroEre_CAF1 88 120 - 1
GCUUCUUUUGCCACCUGCAACGCAGCAGGGUCCAAGCCCAAUUCUUCGGCUUCUGGCGGAUUGAGUUCCGCCGAUUGAUGAUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUU
.......((((.....))))((((((.((((....)))).........(((..(((((((......)))))))...((.((((((((........)))))))).)).))).))))))... ( -46.20)
>DroYak_CAF1 101 120 - 1
GCUUCUUUUGCCACCUGCAACGCAGCAGGGUCCAAGCCCAACUCUUCGGCUUCUGGCGGAUUGAGUUCCGCCGAUUGAUGAUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUU
.......((((.....))))((((((.((((....)))).........(((..(((((((......)))))))...((.((((((((........)))))))).)).))).))))))... ( -46.20)
>consensus
GCUUCUUUUGCCACCUGCAACGCAGCAGGGUCCAAGCCCAACUCUUCGGCUUCUGGCGGAUUGAGUUCCGCCGAUUGAUGAUCAGGGUCACGUUCUCCUGAUCCUCCAGCAGCUGCGAUU
.......((((.....))))((((((.((((....)))).........(((...((((((......))))))....((.((((((((........)))))))).)).))).))))))... (-31.46 = -32.14 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:25 2006