Locus 5204

Sequence ID	2L_DroMel_CAF1
Location	14,717,161 – 14,717,287
Length	126
Max. P	0.880051

overview

Window 3

Location	14,717,161 – 14,717,270
Length	109
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	80.93
Mean single sequence MFE	-37.04
Consensus MFE	-21.19
Energy contribution	-21.47
Covariance contribution	0.28
Combinations/Pair	1.13
Mean z-score	-1.83
Structure conservation index	0.57
SVM decision value	-0.00
SVM RNA-class probability	0.532904
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14717161 109 - 22407834
AUAAUGGG--GAUCCCAACUCCUCUACCACAUCCUCCUCUUCCGCCCACUUCCUUCUCG-GGGCGGAGCCCUAA--GUGGGCGUGGCCAGAUCCAGUUGAAGCCAAAAGGCCAA
........--.....(((((..(((.((((..........(((((((............-)))))))((((...--..))))))))..)))...)))))..(((....)))... ( -37.20)
>DroSec_CAF1 74136 88 - 1
AUAAUGGG--GAUCC---------------------CUCUGCCGCCCACUUCCUUCUCG-GGGCGGAGCCCUAA--GAGGGCGUGGCCAGAUCCAGUUGAAGCCAAAAGGCCAA
.((((..(--((((.---------------------....(((((......((((((..-((((...))))..)--))))).)))))..))))).))))..(((....)))... ( -33.60)
>DroSim_CAF1 74112 105 - 1
AUAAUGGGGGGAUCCCUCCUCCU------CAUCCUCCUCUGCCGCCCACUUCCUUCUCG-GGGCGGAGCCCUAA--GAGGGCGUGGCCAGAUCCAGUUGAAGCCAAAAGGCCAA
.....(((((....)))))...(------((......((((..(((.((..((((((..-((((...))))..)--))))).)))))))))......))).(((....)))... ( -38.50)
>DroEre_CAF1 73713 112 - 1
AUAAUAGG--GAUGCCUCCUCCUACUCCUCUUCCUCCUCUUUUGGCCACUUCCUUCGCAGGGGCGGUACCCGAAAGGAGGGCGUGGCCAGAUCCAGUUGAAGCCAAAAGGCCAA
....((((--(........)))))......(((..(....(((((((((.((((((...(((......)))....)))))).)))))))))....)..)))(((....)))... ( -38.20)
>DroYak_CAF1 73294 103 - 1
AUAAUAGG--GA---CUUCUCCUACUC----UCCUCCUCUUCCGCCCACUUCCUUCUCGGGGGCGGAACCCGGA--GAGGGCGUGGCCAGAUCCAGUUGAAGCCAAAAGGCCAA
....((((--(.---....)))))(((----(((.....((((((((.((........))))))))))...)))--)))(((.(((((((......)))..))))....))).. ( -37.70)
>consensus
AUAAUGGG__GAUCCCUCCUCCU___C__C_UCCUCCUCUUCCGCCCACUUCCUUCUCG_GGGCGGAGCCCUAA__GAGGGCGUGGCCAGAUCCAGUUGAAGCCAAAAGGCCAA
.........................................((((((.............)))))).((((.......)))).(((((....................))))). (-21.19 = -21.47 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	14,717,197 – 14,717,287
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	76.95
Mean single sequence MFE	-32.55
Consensus MFE	-18.29
Energy contribution	-18.65
Covariance contribution	0.36
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.56
SVM decision value	0.91
SVM RNA-class probability	0.880051
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14717197 90 + 22407834
AC--UUAGGGCUCCGCCC-CGAGAAGGAAGUGGGCGGAAGAGGAGGAUGUGGUAGAGGAGUUGGGAUC--CCCAUUAUACCGCCGACUUUCUAUG
.(--(..((((...))))-..)).(((((((.(((((..((((.((((.(.(.........).).)))--))).))...))))).)))))))... ( -34.60)
>DroSec_CAF1 74172 69 + 1
UC--UUAGGGCUCCGCCC-CGAGAAGGAAGUGGGCGGCAGAG---------------------GGAUC--CCCAUUAUACCGCCGACUUUCUAUG
((--(..((((...))))-..)))(((((((.(((((..(((---------------------((...--))).))...))))).)))))))... ( -31.50)
>DroSim_CAF1 74148 86 + 1
UC--UUAGGGCUCCGCCC-CGAGAAGGAAGUGGGCGGCAGAGGAGGAUG------AGGAGGAGGGAUCCCCCCAUUAUACCGCCGACUUUCUAUG
((--(..((((...))))-..)))(((((((.(((((........((((------.((.(((....))).))))))...))))).)))))))... ( -37.50)
>DroEre_CAF1 73749 93 + 1
UCCUUUCGGGUACCGCCCCUGCGAAGGAAGUGGCCAAAAGAGGAGGAAGAGGAGUAGGAGGAGGCAUC--CCUAUUAUACCGCCGACUUUCUAUG
((((((..((..((((.(((....)))..))))))...)))))).........((((((((.(((...--...........)))..)))))))). ( -25.64)
>DroYak_CAF1 73330 84 + 1
UC--UCCGGGUUCCGCCCCCGAGAAGGAAGUGGGCGGAAGAGGAGGA----GAGUAGGAGAAG---UC--CCUAUUAUACCGCCGACUUUCUAUG
((--((.(((......))).))))(((((((.(((((......(((.----((.(......).---))--)))......))))).)))))))... ( -33.50)
>consensus
UC__UUAGGGCUCCGCCC_CGAGAAGGAAGUGGGCGGAAGAGGAGGA_G__G___AGGAGGAGGGAUC__CCCAUUAUACCGCCGACUUUCUAUG
.......((((...))))......(((((((.(((((..........................................))))).)))))))... (-18.29 = -18.65 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:34 2006