Locus 3112

Sequence ID	3R_DroMel_CAF1
Location	8,204,272 – 8,204,432
Length	160
Max. P	0.567281

overview

Window 9

Location	8,204,272 – 8,204,392
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-44.48
Consensus MFE	-38.37
Energy contribution	-39.50
Covariance contribution	1.13
Combinations/Pair	1.08
Mean z-score	-1.48
Structure conservation index	0.86
SVM decision value	0.07
SVM RNA-class probability	0.567281
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8204272 120 - 27905053
AGUUGGUCACCCUCCAUCGUGUUGAUCAACUUGGAGUUCAGCUCCAGACCCAAAGCCUUGGCCACCAUCUGGAUGGCGCGACUGGCCGGCGCCAUGGGGAAAUUGUAGAGAUCCAAGUUC
.((((((((.((......).).))))))))(((((.(((.((......((((..((.(((((((((((....))))......))))))).))..))))......)).))).))))).... ( -39.60)
>DroSim_CAF1 19948 120 - 1
AGUUGGUCACCCUCCAUCGUGUUGAUCACCUUGGAGUUCAGCUCCAGACCCAAAGCCUUGGCCACCAUCUGGAUGGCGCGACUGGCCGGCGACAUGGGGAAAUUGUACAGAUCCAUGUUU
.((((((((..(((((..(((.....)))..))))).((.((((((((......((....)).....))))))..))..)).))))))))((((((((.............)))))))). ( -40.02)
>DroEre_CAF1 16790 120 - 1
AAUUGGUCACCCUCCAUAGUAUUGAUCAGCUUGGAGUUCAGCUCCAGUCCCAGAGCCUUGGCCACCAUCUGGAUGGCGCGACUGGCCGGGGCCUUGGGGAAAUUGUAGAGAUCCAAGUUU
...((((((..((....))...))))))(((((((.(((.((.....((((((.((((((((((((((....))))......)))))))))).)))))).....)).))).))))))).. ( -47.70)
>DroYak_CAF1 25810 120 - 1
AGUUGGUCACCCUCCAUCGUGUUGAUCAGCUUGGAGUUCAGCUCCAGACCCAGAGCCUUGGCCACCAUCUGGAUGGCGCGACUGGCCGGGGCUAUGGGGAAAUUGUAGAGAUCCAGGCUU
...((((((.((......).).))))))(((((((.(((.((......((((.(((((((((((((((....))))......))))))))))).))))......)).))).))))))).. ( -50.60)
>consensus
AGUUGGUCACCCUCCAUCGUGUUGAUCAGCUUGGAGUUCAGCUCCAGACCCAAAGCCUUGGCCACCAUCUGGAUGGCGCGACUGGCCGGCGCCAUGGGGAAAUUGUAGAGAUCCAAGUUU
...((((((.............))))))(((((((.(((.((......((((..((((((((((((((....))))......))))))))))..))))......)).))).))))))).. (-38.37 = -39.50 +   1.13)

alignment

secondary structure

dotplot

Window 0

Location	8,204,312 – 8,204,432
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.86
Mean single sequence MFE	-42.15
Consensus MFE	-38.42
Energy contribution	-40.68
Covariance contribution	2.25
Combinations/Pair	1.15
Mean z-score	-1.45
Structure conservation index	0.91
SVM decision value	0.06
SVM RNA-class probability	0.565812
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8204312 120 + 27905053
CGCGCCAUCCAGAUGGUGGCCAAGGCUUUGGGUCUGGAGCUGAACUCCAAGUUGAUCAACACGAUGGAGGGUGACCAACUGAAGCCAGAGUUCGUGAGGAUUAACCCACAGCACACCAUU
.(.((((((.....)))))))...(((.(((((.(((((.....)))))...(((((..(((((....((....))..(((....)))...)))))..)))))))))).)))........ ( -43.70)
>DroSim_CAF1 19988 120 + 1
CGCGCCAUCCAGAUGGUGGCCAAGGCUUUGGGUCUGGAGCUGAACUCCAAGGUGAUCAACACGAUGGAGGGUGACCAACUGAAGCCGGAGUUCGUGAAGAUCAACCCACAGCACACCAUU
.(.((((((.....)))))))...(((.(((((.(((((.....)))))...(((((..(((((....((....))..(((....)))...)))))..)))))))))).)))........ ( -44.70)
>DroEre_CAF1 16830 120 + 1
CGCGCCAUCCAGAUGGUGGCCAAGGCUCUGGGACUGGAGCUGAACUCCAAGCUGAUCAAUACUAUGGAGGGUGACCAAUUGAAGCCGGAUUUCGUGAAGAUCAACCCGCAGCACACCAUU
.(.((((((.....)))))))...(((.((((..(((((.....)))))...(((((..(((......((....))....((((.....)))))))..))))).)))).)))........ ( -36.30)
>DroYak_CAF1 25850 120 + 1
CGCGCCAUCCAGAUGGUGGCCAAGGCUCUGGGUCUGGAGCUGAACUCCAAGCUGAUCAACACGAUGGAGGGUGACCAACUGAAGCCGGAGUUCGUGAAGAUCAACCCGCAGCACACCAUU
.(.((((((.....)))))))...(((.(((((.(((((.....)))))...(((((..(((((....((....))..(((....)))...)))))..)))))))))).)))........ ( -43.90)
>consensus
CGCGCCAUCCAGAUGGUGGCCAAGGCUCUGGGUCUGGAGCUGAACUCCAAGCUGAUCAACACGAUGGAGGGUGACCAACUGAAGCCGGAGUUCGUGAAGAUCAACCCACAGCACACCAUU
.(.((((((.....)))))))...(((.((((..(((((.....)))))...(((((..(((((....((....))..(((....)))...)))))..))))).)))).)))........ (-38.42 = -40.68 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:24 2006