Locus 178

Sequence ID	4_DroMel_CAF1
Location	1,102,421 – 1,102,581
Length	160
Max. P	0.990532

overview

Window 3

Location	1,102,421 – 1,102,541
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-31.91
Consensus MFE	-26.10
Energy contribution	-26.34
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	0.82
SVM decision value	0.70
SVM RNA-class probability	0.825915
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1102421 120 - 1281640
GAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
(((((((......)))))))....((((((((..(..(((((((((...........(((((..........)))))............)))))))))..)..))))).)))........ ( -31.80)
>DroSec_CAF1 16185 120 - 1
GAGCCAAUCUUAUUUGGCUUCUAAUCGGACUCGUCUGGUUUGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
..((..(((((((((((((((.(((((((....))))))).))))))).((.........))))))))))..)).(((((..........(((((....)))))..........))))). ( -34.85)
>DroSim_CAF1 6819 119 - 1
GAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGU-UGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
..((..(((((((((((((((.(((..((....))..))-)))))))).((.........))))))))))..)).(((((..........(((((....)))))..........))))). ( -32.75)
>DroEre_CAF1 15694 120 - 1
GAGCUAAUCUUAUUUGGCUUCUCAUUGGACUUGUCUGGUUUGAAGUCAAAUUAAUAAAUUGCAAUGGGAUAAGCAGUAGUAAUUACUAUACUUCUAAUUUGGAGACACACAAGGGCUGCA
..(((.(((((((((((((((..((..((....))..))..)))))))((((....))))..)))))))).))).(((((..........((((......))))..........))))). ( -31.05)
>DroYak_CAF1 7682 120 - 1
GAGCCAAUCUUAUAUGGCUUCUCAUUGGACUCGUCUGGUUUGAAGUCAAACUAAUAAAUUGCAAUGGAAUCAGCAGUAGUAAUUACUAUGCUUCGAAUUUGGAGACACAUAAGGGCUGCA
.((((...(((((.((.((((((((((.(......(((((((....)))))))......).))))))....((((.((((....))))))))........)))).)).)))))))))... ( -29.10)
>consensus
GAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGUAAUUAUUAUGCUUCGAAUUUGGAGAGUCACAAGGGCUGCA
..((..(((((((((((((((..((((((....))))))..)))))))..............))))))))..)).(((((..........((((......))))..........))))). (-26.10 = -26.34 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	1,102,461 – 1,102,581
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.33
Mean single sequence MFE	-30.56
Consensus MFE	-27.70
Energy contribution	-27.38
Covariance contribution	-0.32
Combinations/Pair	1.12
Mean z-score	-1.78
Structure conservation index	0.91
SVM decision value	2.22
SVM RNA-class probability	0.990532
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 1102461 120 - 1281640
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
..((((((..(((((....(((....)))...)))))...))))))......(((((((((.(((..((....))..))).))))))))).......(((((..........)))))... ( -32.10)
>DroSec_CAF1 16225 120 - 1
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUCGGACUCGUCUGGUUUGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
..((((((..(((((....(((....)))...)))))...))))))(((((((((((((((.(((((((....))))))).))))))).((.........)))))))))).......... ( -34.20)
>DroSim_CAF1 6859 119 - 1
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGU-UGAAGUCAAGCUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
..((((((..(((((....(((....)))...)))))...))))))(((((((((((((((.(((..((....))..))-)))))))).((.........)))))))))).......... ( -32.10)
>DroEre_CAF1 15734 120 - 1
CAAGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCUAAUCUUAUUUGGCUUCUCAUUGGACUUGUCUGGUUUGAAGUCAAAUUAAUAAAUUGCAAUGGGAUAAGCAGUAGU
...(((((..(((((....(((....)))...)))))...)))))......((((((((((..((..((....))..))..))))))))))......(((((..........)))))... ( -28.30)
>DroYak_CAF1 7722 120 - 1
CAAGGCUCAGUACGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUAUGGCUUCUCAUUGGACUCGUCUGGUUUGAAGUCAAACUAAUAAAUUGCAAUGGAAUCAGCAGUAGU
...(((((.((.(((....(((....)))...)))..)).))))).........(((((((..((..((....))..))..))))))).........(((((..........)))))... ( -26.10)
>consensus
CAUGGUUCAAUGCGUAACUGUUCAAAGAUUAAACGCAAUAGAGCCAAUCUUAUUUGGCUUCUAAUUGGACUCGUCUGGUUUGAAGUCAAACUUAUAAAUUGCAAUGGGAUCAGCAGUAGU
...(((((..(((((....(((....)))...)))))...))))).......(((((((((..((((((....))))))..))))))))).......(((((..........)))))... (-27.70 = -27.38 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:16 2006