Locus 5617

Sequence ID	2R_DroMel_CAF1
Location	17,881,773 – 17,881,968
Length	195
Max. P	0.891020

overview

Window 6

Location	17,881,773 – 17,881,888
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.75
Mean single sequence MFE	-38.20
Consensus MFE	-29.40
Energy contribution	-29.84
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.29
Structure conservation index	0.77
SVM decision value	0.33
SVM RNA-class probability	0.689712
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17881773 115 + 20766785
ACCCACUUACCAGCGUGCAGACAAAUGUUUGCCUAUUACAGGGUACACAAAGUCAGCAUUCCCGCCCAGCCAUUCGGUAUCAUCAUGCAAAUUGAAGGGGG----CUGG-GAUAGGGAUA
..............((((.(((...(((.(((((......))))).)))..))).))))((((.(((((((.((((((............))))))...))----))))-)...)))).. ( -39.40)
>DroSec_CAF1 46741 115 + 1
ACCCACUUACCAGCGUGCAGACAGAUGUUUGCCUAUUACAGGGUACACAAAGUCAGCAUUCCCGCCCAGCCAUUCGGUAUCAUCAUGCAAAUUGAAGGGGG----CUGG-GAUAGGGAUA
..............((((.(((...(((.(((((......))))).)))..))).))))((((.(((((((.((((((............))))))...))----))))-)...)))).. ( -39.40)
>DroSim_CAF1 47104 115 + 1
ACCCACUUACCAGCGUGCAGACAAAUGUUUGCCUAUUACAGGGUACACAAAGUCAGCAUUCCCGCCCAGCCAUUCGGUAUCAUCAUGCAAAUUGAAGGGGG----CUGG-GAUAGGGAUA
..............((((.(((...(((.(((((......))))).)))..))).))))((((.(((((((.((((((............))))))...))----))))-)...)))).. ( -39.40)
>DroEre_CAF1 49175 119 + 1
ACCCACUUACCACCGUGCAGAUAAAUGUUUGCCUAUUACAGGGUACACAAAGUCAGCAUUCCCGCCCAGCCAUUCGCUAUCAUCAUGCAAAUUGAAGGGGGGGUGCUGG-GAUAGGGAUA
..............((((.(((...(((.(((((......))))).)))..))).))))((((.((((((.((((.((....(((.......)))..)).)))))))))-)...)))).. ( -37.30)
>DroYak_CAF1 46418 116 + 1
ACCCACUUACCAGCGUGCAGACAAAUGUUUGCCUAUUACAGGGUACACAAAGUCAGCAUUCCCGCCCAGCCAUUCGCUAUCAUCAUGCAAAUUGAAGGGGG----CUGGAGAUAGGGAUA
.(((..((.(((((((((.(((...(((.(((((......))))).)))..))).))))((((....(((.....)))....(((.......))).)))))----)))).))..)))... ( -35.50)
>consensus
ACCCACUUACCAGCGUGCAGACAAAUGUUUGCCUAUUACAGGGUACACAAAGUCAGCAUUCCCGCCCAGCCAUUCGGUAUCAUCAUGCAAAUUGAAGGGGG____CUGG_GAUAGGGAUA
.(((..((.((((.((((.(((...(((.(((((......))))).)))..))).))))..((.(((.(((....)))....(((.......))).)))))....)))).))..)))... (-29.40 = -29.84 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	17,881,853 – 17,881,968
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.82
Mean single sequence MFE	-43.22
Consensus MFE	-30.08
Energy contribution	-31.36
Covariance contribution	1.28
Combinations/Pair	1.07
Mean z-score	-3.33
Structure conservation index	0.70
SVM decision value	0.96
SVM RNA-class probability	0.891020
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17881853 115 + 20766785
CAUCAUGCAAAUUGAAGGGGG----CUGG-GAUAGGGAUAAUGGGGAUGCCGAAAUUUGCAUUUCAAUUCUGCCGCCGCCGGCAUUUCCAUUCCCCUGCACCUCCACCCACGUCCCCACC
..(((.......))).(((((----((((-(.(((((..(((((..((((((......(((.........)))......))))))..))))).)))))........)))).))))))... ( -43.60)
>DroSec_CAF1 46821 115 + 1
CAUCAUGCAAAUUGAAGGGGG----CUGG-GAUAGGGAUAAUGGGGAUGCCGAAAUUUGCAUUUCAAUUCUGCCGUCGCCGGCAUUUCCAUUCCCCUGCACCUCCACUCACGUCCCCACC
..(((.......))).(((((----(.((-..(((((..(((((..((((((......(((.........)))......))))))..))))).)))))..)).........))))))... ( -41.30)
>DroSim_CAF1 47184 115 + 1
CAUCAUGCAAAUUGAAGGGGG----CUGG-GAUAGGGAUAAUGGGGAUGCCGAAAUUUGCAUUUCAAUUCUGCCGUCGCCGGCAUUUCCAUUCCCCUGCACCUCCACCCACGUCCCCACC
..(((.......))).(((((----((((-(.(((((..(((((..((((((......(((.........)))......))))))..))))).)))))........)))).))))))... ( -43.60)
>DroEre_CAF1 49255 113 + 1
CAUCAUGCAAAUUGAAGGGGGGGUGCUGG-GAUAGGGAUAAUGGGGAUGCCAAAAUUUGCAUUUAAAUUCUGCCGUCGCCGGCAUUUCCAUUCCCCUGCUCCUCCACCC-----CCC-AC
..(((.......)))..((((((((..((-..(((((..(((((..(((((.......(((.........))).......)))))..))))).)))))..))..)))))-----)))-.. ( -50.74)
>DroYak_CAF1 46498 111 + 1
CAUCAUGCAAAUUGAAGGGGG----CUGGAGAUAGGGAUAAUGGGGAUGCCAAAAUUUGCAUUUCAAUUCUGCCGUCGCCGGCAUUUCCAUUCCUCCGCUCUUCCGCAC-----CCGAAC
..(((.......))).(((.(----(.(((((..(((..(((((..(((((.......(((.........))).......)))))..)))))..)))..))))).)).)-----)).... ( -36.84)
>consensus
CAUCAUGCAAAUUGAAGGGGG____CUGG_GAUAGGGAUAAUGGGGAUGCCGAAAUUUGCAUUUCAAUUCUGCCGUCGCCGGCAUUUCCAUUCCCCUGCACCUCCACCCACGUCCCCACC
..(((.......))).(((((.....(((...(((((..(((((..((((((......(((.........)))......))))))..))))).))))).....)))......)))))... (-30.08 = -31.36 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:12 2006