Locus 5271

Sequence ID	2R_DroMel_CAF1
Location	17,132,001 – 17,132,159
Length	158
Max. P	0.982948

overview

Window 7

Location	17,132,001 – 17,132,121
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.86
Mean single sequence MFE	-46.05
Consensus MFE	-38.22
Energy contribution	-38.73
Covariance contribution	0.50
Combinations/Pair	1.17
Mean z-score	-2.51
Structure conservation index	0.83
SVM decision value	1.91
SVM RNA-class probability	0.982418
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17132001 120 - 20766785
AUGCGGUUAAAUUAGGUACAACGUUGCCAGGUCUUGGUGCAGUUAGUCUGCGGCCUGGCAGCACGGUAAGCAAUGAAGGCAUUGCCGGAUCGAUUACAUACGCGGUCUGGUAGCCCUCCA
.(((............(((...(((((((((((.....((((.....)))))))))))))))...))).)))..((.(((..((((((((((..........))))))))))))).)).. ( -45.62)
>DroSec_CAF1 67891 120 - 1
AUGCGGUUAAACUAGGGCCAACGUUGCCAGGUCUUGCUGCAGUAUGUCUGCGGCCUGGCAUCACGCUUGGUAAAGAAGGCAUUGCCGGAUUGAUUACAUACGCGGUCUGGCAGCCCUCCA
..............(((((((((((((((((((.....((((.....)))))))))))))..))).)))))......(((..((((((((((..........)))))))))))))..)). ( -47.60)
>DroSim_CAF1 58734 120 - 1
AUGCGGUUAAAUUAGGGCCAAUGUUGCCAGGUCUUGCUGCAGUAGGUCUGCGGCCUGGCAUCACGCUUGGCAAUGAAGGCAUUGCCGGAUCGAUUACAUACGCAGUCUGGCAGCCCUCCA
....((.....(((..(((((((((((((((((.....((((.....)))))))))))))..))).)))))..))).(((..((((((((((........))..)))))))))))..)). ( -46.50)
>DroYak_CAF1 75311 119 - 1
UUGCGGCUUAAUUAGCGACAACGUUGCCAGUUCCAAUUGCAGUAAGUCUGCGAUCUGGCAACAAUGUUA-UAAUGCAGACAUUGCCGGAUCGAUUACAUACGCGGUCUGGCAGCUCCCCA
((((((((.....)))((((..((((((((.....(((((((.....)))))))))))))))..)))).-...)))))...(((((((((((..........)))))))))))....... ( -44.50)
>consensus
AUGCGGUUAAAUUAGGGACAACGUUGCCAGGUCUUGCUGCAGUAAGUCUGCGGCCUGGCAUCACGCUUAGCAAUGAAGGCAUUGCCGGAUCGAUUACAUACGCGGUCUGGCAGCCCUCCA
....((................(((((((((((.....((((.....)))))))))))))))...............(((..((((((((((..........)))))))))))))..)). (-38.22 = -38.73 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	17,132,041 – 17,132,159
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	77.59
Mean single sequence MFE	-34.33
Consensus MFE	-21.55
Energy contribution	-22.05
Covariance contribution	0.50
Combinations/Pair	1.13
Mean z-score	-2.39
Structure conservation index	0.63
SVM decision value	1.93
SVM RNA-class probability	0.982948
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17132041 118 - 20766785
ACCUAUUCUUUCUUUUUAUUUUAAAAGAC-ACUUGAA-AAAUGCGGUUAAAUUAGGUACAACGUUGCCAGGUCUUGGUGCAGUUAGUCUGCGGCCUGGCAGCACGGUAAGCAAUGAAGGC
.(((......((((((......)))))).-.......-...(((............(((...(((((((((((.....((((.....)))))))))))))))...))).)))....))). ( -32.32)
>DroSec_CAF1 67931 118 - 1
AUCUAUUCUUUCUUUUUAUUUUAAUAGAC-ACUUGAA-AAAUGCGGUUAAACUAGGGCCAACGUUGCCAGGUCUUGCUGCAGUAUGUCUGCGGCCUGGCAUCACGCUUGGUAAAGAAGGC
.......(((((((((((.((((((.(.(-(.((...-.))))).)))))).))).(((((((((((((((((.....((((.....)))))))))))))..))).))))))))))))). ( -36.20)
>DroSim_CAF1 58774 119 - 1
AUCUAUUCUUUCUAUUUAUUUUAAUAGAC-ACUUGAAAAAAUGCGGUUAAAUUAGGGCCAAUGUUGCCAGGUCUUGCUGCAGUAGGUCUGCGGCCUGGCAUCACGCUUGGCAAUGAAGGC
.......(((((..((((.((((((.(.(-(.((....)).))).)))))).))))(((((((((((((((((.....((((.....)))))))))))))..))).)))))...))))). ( -36.00)
>DroYak_CAF1 75351 109 - 1
AUCUAUUAAU---------UUUUAAAUAUGAAUGGAA-AUUUGCGGCUUAAUUAGCGACAACGUUGCCAGUUCCAAUUGCAGUAAGUCUGCGAUCUGGCAACAAUGUUA-UAAUGCAGAC
.((((((.((---------........)).)))))).-.(((((((((.....)))((((..((((((((.....(((((((.....)))))))))))))))..)))).-...)))))). ( -32.80)
>consensus
AUCUAUUCUUUCUUUUUAUUUUAAAAGAC_ACUUGAA_AAAUGCGGUUAAAUUAGGGACAACGUUGCCAGGUCUUGCUGCAGUAAGUCUGCGGCCUGGCAUCACGCUUAGCAAUGAAGGC
..............................................................(((((((((((.....((((.....))))))))))))))).................. (-21.55 = -22.05 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:52 2006