Locus 5649

Sequence ID	2R_DroMel_CAF1
Location	17,953,156 – 17,953,309
Length	153
Max. P	0.951326

overview

Window 5

Location	17,953,156 – 17,953,271
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.60
Mean single sequence MFE	-32.18
Consensus MFE	-30.83
Energy contribution	-31.07
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.96
SVM decision value	0.16
SVM RNA-class probability	0.609962
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17953156 115 - 20766785
AUGAAUGGGAAGCCGCAAGACAAAUCCCCGCGAUCUGCAAUUUGUAAUUCAAAUUGCCAGCCGACCAAUGUGGGCUUAUGGACUUUGUUUGUCGCCCCGUCUAAUUACAGAAAUA-----
....(((((..((.(((.(((((((((.........((((((((.....)))))))).((((.((....)).))))...))).))))))))).)))))))...............----- ( -32.00)
>DroSec_CAF1 10413 115 - 1
AUGAAUGGGAAGCCGCAAGACAAAUCCCCGCGAUCUGCAAUUUGUAAUUCAAAUUGCCAGCCGACCAAUGUGGGCUUAUGGACUUUGUUUGUCGCCCCGUCAAAUUACAGAAAUA-----
.(((.((((..((.(((.(((((((((.........((((((((.....)))))))).((((.((....)).))))...))).))))))))).))))))))).............----- ( -33.40)
>DroSim_CAF1 6163 115 - 1
AUGAAUGGGAAGCCGCAAGACAAAUCCCCGCGAUCUGCAAUUUGUAAUUCAAAUUGCCAGCCGACCAAUGUGGGCUUAUGGACUUUGUUUGUCGCCCCGUCUAAUUACAGAAAUA-----
....(((((..((.(((.(((((((((.........((((((((.....)))))))).((((.((....)).))))...))).))))))))).)))))))...............----- ( -32.00)
>DroEre_CAF1 15170 120 - 1
AUGAAUGGGAAGCCGCAAGACAAAUCCCAGCGAUCUGCAAUUUGUAAUUCAAAUUGCCAGCCGACCAAUGUGGGCUUAUGGACUUUGUUUGUCGCGCCGUCUAAUUACAGAAAUACUUGC
.(((.((((..((((..(((((((..(((.......((((((((.....)))))))).((((.((....)).))))..)))..)))))))..)).))..)))).)))............. ( -31.30)
>consensus
AUGAAUGGGAAGCCGCAAGACAAAUCCCCGCGAUCUGCAAUUUGUAAUUCAAAUUGCCAGCCGACCAAUGUGGGCUUAUGGACUUUGUUUGUCGCCCCGUCUAAUUACAGAAAUA_____
..((.((((..((.(((.(((((((((.........((((((((.....)))))))).((((.((....)).))))...))).))))))))).))))))))................... (-30.83 = -31.07 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	17,953,191 – 17,953,309
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	95.20
Mean single sequence MFE	-33.77
Consensus MFE	-31.27
Energy contribution	-31.52
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.93
SVM decision value	1.41
SVM RNA-class probability	0.951326
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17953191 118 + 20766785
CAUAAGCCCACAUUGGUCGGCUGGCAAUUUGAAUUACAAAUUGCAGAUCGCGGGGAUUUGUCUUGCGGCUUCCCAUUCAUUUCCUUUGGCAACCCUCCCAUCAGAGUCAGCGAUUUUU
....((((.((....)).)))).((((((((.....))))))))(((((((.((((...(((....))).)))).........((((((...........))))))...))))))).. ( -33.70)
>DroSec_CAF1 10448 118 + 1
CAUAAGCCCACAUUGGUCGGCUGGCAAUUUGAAUUACAAAUUGCAGAUCGCGGGGAUUUGUCUUGCGGCUUCCCAUUCAUUUCCUUUGGUAACCAUCCCAUCAGUGUCAGCGAUUUUU
....((((.((....)).)))).((((((((.....))))))))(((((((.((((...(((....))).))))...((((.....(((........)))..))))...))))))).. ( -32.90)
>DroSim_CAF1 6198 118 + 1
CAUAAGCCCACAUUGGUCGGCUGGCAAUUUGAAUUACAAAUUGCAGAUCGCGGGGAUUUGUCUUGCGGCUUCCCAUUCAUUUCCUUUGGUAACCAUCCCAUCAGUGUCAGCGAUUUUU
....((((.((....)).)))).((((((((.....))))))))(((((((.((((...(((....))).))))...((((.....(((........)))..))))...))))))).. ( -32.90)
>DroEre_CAF1 15210 113 + 1
CAUAAGCCCACAUUGGUCGGCUGGCAAUUUGAAUUACAAAUUGCAGAUCGCUGGGAUUUGUCUUGCGGCUUCCCAUUCAUUUCCUUUG-----CCUCCCAUCAGAACCAGCGAUUUUU
....((((.((....)).)))).((((((((.....))))))))((((((((((..((((....(.(((..................)-----)).)....)))).)))))))))).. ( -35.57)
>consensus
CAUAAGCCCACAUUGGUCGGCUGGCAAUUUGAAUUACAAAUUGCAGAUCGCGGGGAUUUGUCUUGCGGCUUCCCAUUCAUUUCCUUUGGUAACCAUCCCAUCAGAGUCAGCGAUUUUU
....((((.((....)).)))).((((((((.....))))))))(((((((.((((...(((....))).))))............(((........))).........))))))).. (-31.27 = -31.52 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:59 2006