Locus 4490

Sequence ID	2L_DroMel_CAF1
Location	12,870,862 – 12,870,962
Length	100
Max. P	0.968839

overview

Window 2

Location	12,870,862 – 12,870,962
Length	100
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.01
Mean single sequence MFE	-26.77
Consensus MFE	-12.94
Energy contribution	-13.94
Covariance contribution	1.00
Combinations/Pair	1.21
Mean z-score	-2.64
Structure conservation index	0.48
SVM decision value	1.63
SVM RNA-class probability	0.968839
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12870862 100 + 22407834
CCCUAUUC-CCUUUCCCUUACCCUCACU-GGGAGAAAGUUCCUCUACUCACUUUCUCCC---UGGCUCCCACUUUUCCAUGAUUUUCGCCCGACAGGGGCAAAGG
........-((((((((((.........-((((((((((..........))))))))))---.(((.....................)))....))))).))))) ( -27.30)
>DroSec_CAF1 49956 100 + 1
CCCUAUUC-CCUUUCCAUUACCCGCUGU-GGGGGCAAGUUCCUCUACUCACUUUCUCCA---UGGCUCCCACUUUUCCAUGAUUUUCGCCCGACAGGAGCAAAGG
........-(((((.........(((((-(((((.((((..........))))))))))---)))).....................((((....)).))))))) ( -22.50)
>DroSim_CAF1 52548 100 + 1
CCCUAUUC-CCUUUCCAUUACCCGCUCU-GGGGGAAAGUUCCUCUACUCACUUUCUCCC---UGGCUCCCACUUUUCCAUGAUUUUCGCCCGACAGGAGCAAAGG
........-(((((.........(((..-((((((((((..........))))))))))---.))).....................((((....)).))))))) ( -24.80)
>DroEre_CAF1 55939 97 + 1
CCCCUUUG-CCUGUCCCUCCCCCGC----GGGGGAAAGUUCCCACACUCACUUUCUCCC---GGGCACCCGCUUUUCCAUGAUUUUAGUCCGACAGGAGCAAAGG
..((((((-((((((........((----((((((((((..........))))))))))---((....))))........(((....))).)))))..))))))) ( -34.30)
>DroYak_CAF1 52105 100 + 1
CCCCUUUUCCCUUUCCCACCCCCCC--UGGGGGGAAAGUUCCUACACUCACUUUCUCCG---GGGCACCCACUUUUCCUUGAUUUUAGCCCGACAGGAGCAAAGG
..........(((((((.(((....--.))))))))))............((((((((.---((((.....................))))....)))).)))). ( -29.20)
>DroAna_CAF1 73017 97 + 1
CUCUACCC-CCACCUCGUUGCGAUC----CGGGGAAAGUUCCUCAACUCACUUUCUCCUCCCGCCCGGUCGGUCCUCCACGAUUC---CCCGCCAGAUGCAAAGG
........-...(((..((((.(((----.(((((((((..........))))))))).......(((..((((......)))).---.)))...)))))))))) ( -22.50)
>consensus
CCCUAUUC_CCUUUCCCUUACCCGC__U_GGGGGAAAGUUCCUCUACUCACUUUCUCCC___GGGCUCCCACUUUUCCAUGAUUUUCGCCCGACAGGAGCAAAGG
.........(((((................(((((((((..........)))))))))......(((((..........................)))))))))) (-12.94 = -13.94 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	12,870,862 – 12,870,962
Length	100
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	77.01
Mean single sequence MFE	-33.76
Consensus MFE	-16.35
Energy contribution	-17.58
Covariance contribution	1.23
Combinations/Pair	1.32
Mean z-score	-2.16
Structure conservation index	0.48
SVM decision value	0.70
SVM RNA-class probability	0.825764
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12870862 100 - 22407834
CCUUUGCCCCUGUCGGGCGAAAAUCAUGGAAAAGUGGGAGCCA---GGGAGAAAGUGAGUAGAGGAACUUUCUCCC-AGUGAGGGUAAGGGAAAGG-GAAUAGGG
(((((((((......(((.....((((......))))..))).---((((((((((..........))))))))))-.....))))))))).....-........ ( -37.50)
>DroSec_CAF1 49956 100 - 1
CCUUUGCUCCUGUCGGGCGAAAAUCAUGGAAAAGUGGGAGCCA---UGGAGAAAGUGAGUAGAGGAACUUGCCCCC-ACAGCGGGUAAUGGAAAGG-GAAUAGGG
((.((((((((((.(((......((((((...........)))---))).....(..(((......)))..)))).-)))).)))))).)).....-........ ( -28.50)
>DroSim_CAF1 52548 100 - 1
CCUUUGCUCCUGUCGGGCGAAAAUCAUGGAAAAGUGGGAGCCA---GGGAGAAAGUGAGUAGAGGAACUUUCCCCC-AGAGCGGGUAAUGGAAAGG-GAAUAGGG
(((((((((((.((.(((.....((((......))))..))).---....)).)).)))))))))..(((((((((-.....)))....)))))).-........ ( -32.10)
>DroEre_CAF1 55939 97 - 1
CCUUUGCUCCUGUCGGACUAAAAUCAUGGAAAAGCGGGUGCCC---GGGAGAAAGUGAGUGUGGGAACUUUCCCCC----GCGGGGGAGGGACAGG-CAAAGGGG
(((((((..(((((...(((...((((.......(((....))---).......))))...)))...((((((((.----..))))))))))))))-)))))).. ( -38.74)
>DroYak_CAF1 52105 100 - 1
CCUUUGCUCCUGUCGGGCUAAAAUCAAGGAAAAGUGGGUGCCC---CGGAGAAAGUGAGUGUAGGAACUUUCCCCCCA--GGGGGGGUGGGAAAGGGAAAAGGGG
(((((((((((.(((((.((...(((........))).)).))---)))....)).)))).......((((((((((.--....))).)))))))...))))).. ( -34.30)
>DroAna_CAF1 73017 97 - 1
CCUUUGCAUCUGGCGGG---GAAUCGUGGAGGACCGACCGGGCGGGAGGAGAAAGUGAGUUGAGGAACUUUCCCCG----GAUCGCAACGAGGUGG-GGGUAGAG
.((((((.(((.((((.---...))))...)))((.(((..((((..((.((((((..........)))))).)).----..)))).....))).)-).)))))) ( -31.40)
>consensus
CCUUUGCUCCUGUCGGGCGAAAAUCAUGGAAAAGUGGGAGCCA___GGGAGAAAGUGAGUAGAGGAACUUUCCCCC_A__GCGGGUAAGGGAAAGG_GAAUAGGG
(((((((((((.((.........((((......))))...((.....)).)).)).)))))))))..(((((((((......)))....)))))).......... (-16.35 = -17.58 +   1.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:04 2006