Locus 4760

Sequence ID	3L_DroMel_CAF1
Location	13,372,865 – 13,373,012
Length	147
Max. P	0.662864

overview

Window 1

Location	13,372,865 – 13,372,977
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.71
Mean single sequence MFE	-31.47
Consensus MFE	-15.90
Energy contribution	-15.93
Covariance contribution	0.03
Combinations/Pair	1.08
Mean z-score	-3.06
Structure conservation index	0.51
SVM decision value	0.27
SVM RNA-class probability	0.662864
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13372865 112 - 23771897
AAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGUGCGGU---GGGGGGCAUAACU----CGCC-CUCGAAGAUUUAUGUACAAAUUACAAUCAUA
...((((((((((((....)..(((....((((((((((....)))))))))).....))))))---))(((((......----.)))-))....))))))((((.....))))...... ( -31.90)
>DroPse_CAF1 21293 111 - 1
AAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUGGGG-GAGUGUGGG--------GCGCUAGGGACACUCUUUCGGAGGAUUUAUGUACAAAUUACAAUCAUA
......(((((..((...((((((..((..(((((((((....)))))))))..-)))))))).--------.))...))))).(((.....)))(((...((((.....)))))))... ( -28.10)
>DroEre_CAF1 44677 108 - 1
AAUUAAGUCCCAGCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGGCAGUGCGGUGGG----GGCAU---G----CCCC-CCCGAAGAUUUAUGUACAAAUUACAAUCAUA
...((((((((.(((......))).....((((((((((....)))))))))))).....(((.(((----((...---.----))))-))))..))))))((((.....))))...... ( -35.50)
>DroYak_CAF1 46174 111 - 1
AAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGUGCGUAGGU----GGUAUUUCG----CCCC-CCCGAAGAUUUAUGUACAAAUUACAAUCAUA
...((((((...(((.....(((((....((((((((((....)))))))))).....))))).(((----((....)))----))..-..))).))))))((((.....))))...... ( -28.50)
>DroAna_CAF1 43790 119 - 1
AAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGGCAGUAUGGGGGCACUGGGCACUAGGUGCCCCCC-CUGGAAGAUUUAUGUACAAAUUACAAUCAUA
...(((((((((..........((.....((((((((((....)))))))))).)).....(((((((((........))))))))).-.)))..))))))((((.....))))...... ( -36.70)
>DroPer_CAF1 21336 111 - 1
AAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUGGGG-GAGUGUGGG--------GCGCUAGGGACACUCUUUCGGAGGAUUUAUGUACAAAUUACAAUCAUA
......(((((..((...((((((..((..(((((((((....)))))))))..-)))))))).--------.))...))))).(((.....)))(((...((((.....)))))))... ( -28.10)
>consensus
AAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCG_CAGUGCGGG_______GGCACUAGG____CCCC_CCCGAAGAUUUAUGUACAAAUUACAAUCAUA
...((((((.....(....).((((....((((((((((....)))))))))).....)))).................................))))))((((.....))))...... (-15.90 = -15.93 +   0.03)

alignment

secondary structure

dotplot

Window 2

Location	13,372,900 – 13,373,012
Length	112
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	82.35
Mean single sequence MFE	-29.36
Consensus MFE	-17.82
Energy contribution	-18.51
Covariance contribution	0.69
Combinations/Pair	1.05
Mean z-score	-2.04
Structure conservation index	0.61
SVM decision value	0.08
SVM RNA-class probability	0.571842
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13372900 112 - 23771897
AUACAAGCCAAACCGAUAGAGCUCUAUGGAAAUUCAAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGUGCGGU---GGGGGGCAUAACU
......(((...((.((((....)))))).............((((((((....)..(((....((((((((((....)))))))))).....))))))---)))))))...... ( -33.70)
>DroSec_CAF1 44456 115 - 1
AUACAAGCCAAACCGAUAGAGCUCUAUGGAAAUUCAAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGCGCGGGCGGGGGGUGUACAACU
.((((.......((.((((....)))))).............((((.(((...((.(((.....((((((((((....))))))))))....))).)).)))))))))))..... ( -29.50)
>DroSim_CAF1 44320 115 - 1
AUACAAGCCAAACCGAUAGAGCUCUAUGGAAAUUCAAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGCGCGGGCGGGGGGUGUACAACU
.((((.......((.((((....)))))).............((((.(((...((.(((.....((((((((((....))))))))))....))).)).)))))))))))..... ( -29.50)
>DroEre_CAF1 44712 98 - 1
----------AGCCGAUAGAGCGCCAUGGAAAUUCAAUUAAGUCCCAGCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGGCAGUGCGGUGGG----GGCAU---G
----------.(((....).))(((.(((....))).......((((.((....(((((.....((((((((((....)))))))))).)).))))).))))----)))..---. ( -28.70)
>DroYak_CAF1 46209 111 - 1
CUGCAAGCCAAGCCGAUAGAGCUCUAUGGAAAUUCAAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGUGCGUAGGU----GGUAUUUCG
......(((..(((....((..((.((((...............)))).))..))(((((....((((((((((....)))))))))).....))))).)))----)))...... ( -28.76)
>DroAna_CAF1 43829 102 - 1
-------------UGAUAGAGCUCUAUGGAAAUUCAAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGGCAGUAUGGGGGCACUGGGCACUAGG
-------------...(((.((((..(((....))).....(((((...(....)..((.....((((((((((....)))))))))).))......)))))...)))).))).. ( -26.00)
>consensus
AUACAAGCCAAACCGAUAGAGCUCUAUGGAAAUUCAAUUAAGUCCCAUCGAAAUCACGCAAUUAGUUAAUCAAAUAAUUUUGAUUAGCGCCAGUGCGGGGGGGGGGGGCACAACG
..................((..((.((((...............)))).))..)).((((....((((((((((....)))))))))).....)))).................. (-17.82 = -18.51 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:28 2006