Locus 4192

Sequence ID	3R_DroMel_CAF1
Location	11,345,173 – 11,345,306
Length	133
Max. P	0.794265

overview

Window 2

Location	11,345,173 – 11,345,280
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.96
Mean single sequence MFE	-32.30
Consensus MFE	-21.15
Energy contribution	-22.23
Covariance contribution	1.08
Combinations/Pair	1.13
Mean z-score	-2.13
Structure conservation index	0.65
SVM decision value	0.27
SVM RNA-class probability	0.662048
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345173 107 - 27905053
ACCUAUAUUCCUGCAGCUUAGAGUUUUCGUGCAUUUUGCAUUCAACUUUUUGCUGAUAUAGCUGAUUCUCAGAGA-------------AUUGCGGUUUGCUGGGAUUUAGUUAGAGGUCU
((((.........((((..((((((...((((.....))))..))))))..))))...(((((((.((((((..(-------------((....)))..)))))).))))))).)))).. ( -34.30)
>DroSec_CAF1 84040 107 - 1
ACCUAUAUUCCAGCAGCUUAGAGUUUUCGUUCAUUUUGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCUCUGAGA-------------AUUGCGGUUUGCUGGGAUUUAGUUAGAGGUCU
..(((.(((((((((((((((((...((((.......))..(((((.....))))).......))..))))))).-------------........)))))))))).))).......... ( -30.00)
>DroSim_CAF1 82587 106 - 1
ACCUAUAUUCCAGCAGCUUAGAGUUUUCGUUCAUUUUGCAUUCAGCUU-UUGCUGAUAUAGCUGAUUCUCAGAGA-------------AUUGCGGUUUGCUGGGAUUUAGUUAGAGGUCU
..(((.((((((((((((...(((((((.........((..(((((..-..)))))....)).........))))-------------)))..)).)))))))))).))).......... ( -30.07)
>DroEre_CAF1 80312 120 - 1
AUGUAUAUCCCUGCAGCUCAGAGUUUUCGUGCAUUUGGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCCCGGAGAAGGAAGACGUUGAAGUGCGGUUUGCUGGCAUUUAUUUAGAGGUUU
((((......(((((..((((.((((((.(...(((((...((((((............))))))...)))))..).)))))).))))..))))).......)))).............. ( -31.12)
>DroYak_CAF1 82399 120 - 1
ACCUAUAUCCCUGCAGCUCAGAGUUUUCGUGCAUUUUGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCCCGCAGAAGGGAGACGUUGAAGUGCGGUUUGCUGGGAUUUAUUUAGAGGUUU
((((..(((((.((((..(.(......)..(((((((((..(((((.....)))))....))...(((((......))))).....))))))))..)))).)))))........)))).. ( -36.00)
>consensus
ACCUAUAUUCCUGCAGCUUAGAGUUUUCGUGCAUUUUGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCUCAGAGA_____________AUUGCGGUUUGCUGGGAUUUAGUUAGAGGUCU
((((.........((((..((((((...((((.....))))..))))))..))))...(((((((.((((((...........................)))))).))))))).)))).. (-21.15 = -22.23 +   1.08)

alignment

secondary structure

dotplot

Window 3

Location	11,345,205 – 11,345,306
Length	101
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	83.58
Mean single sequence MFE	-23.45
Consensus MFE	-16.70
Energy contribution	-18.32
Covariance contribution	1.62
Combinations/Pair	1.08
Mean z-score	-1.88
Structure conservation index	0.71
SVM decision value	0.60
SVM RNA-class probability	0.794265
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11345205 101 - 27905053
UCAGCUGUAUCUGUAUCUGUAUCUGUACCUAUAUUCCUGCAGCUUAGAGUUUUCGUGCAUUUUGCAUUCAACUUUUUGCUGAUAUAGCUGAUUCUCAGAGA-----
(((((((((((.(((...((((........))))...)))(((..((((((...((((.....))))..))))))..))))))))))))))..........----- ( -28.90)
>DroSec_CAF1 84072 95 - 1
GCAGCUGUAUCU------GUAUCUGUACCUAUAUUCCAGCAGCUUAGAGUUUUCGUUCAUUUUGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCUCUGAGA-----
.(((((((((((------(...((((............))))..))))...................(((((.....)))))))))))))...........----- ( -21.50)
>DroSim_CAF1 82619 94 - 1
GCAGCUGUAUCU------GUAUCUGUACCUAUAUUCCAGCAGCUUAGAGUUUUCGUUCAUUUUGCAUUCAGCUU-UUGCUGAUAUAGCUGAUUCUCAGAGA-----
.(((((((((((------(...((((............))))..))))...................(((((..-..)))))))))))))...........----- ( -21.50)
>DroEre_CAF1 80352 94 - 1
----CUGCAUCC------GUACCU--AUGUAUAUCCCUGCAGCUCAGAGUUUUCGUGCAUUUGGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCCCGGAGAAGGAA
----.....(((------((((..--..)))).(((...(((((..........((((.....))))(((((.....)))))...)))))......)))...))). ( -21.90)
>consensus
GCAGCUGUAUCU______GUAUCUGUACCUAUAUUCCAGCAGCUUAGAGUUUUCGUGCAUUUUGCAUUCAGCUUUUUGCUGAUAUAGCUGAUUCUCAGAGA_____
.((((((((((.......(((....)))............(((..((((((...((((.....))))..))))))..)))))))))))))................ (-16.70 = -18.32 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:08 2006