Locus 6443

Sequence ID	3L_DroMel_CAF1
Location	17,224,548 – 17,224,707
Length	159
Max. P	0.985034

overview

Window 1

Location	17,224,548 – 17,224,667
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.90
Mean single sequence MFE	-29.22
Consensus MFE	-23.56
Energy contribution	-23.96
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-1.35
Structure conservation index	0.81
SVM decision value	-0.05
SVM RNA-class probability	0.506390
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17224548 119 - 23771897
UAUUACGUUACGGCACACACCAACUCAUGGCCCGACCAGAACCAUAACAAAGGAGAGCACUGGCUGCAUAAUCAAAUAGAAAAUGUUCGAGCCAAGCGCACUGGGAGAAAUCAGGU-CAA
...........((......))......(((((...((((..((........))...((.((((((((((..((.....))..))))...)))).)).)).))))((....)).)))-)). ( -28.00)
>DroSec_CAF1 108015 120 - 1
UAUUACGUUACGGCACACACUAACUCAUGGCCCGACCAGAACCAUAACAAAGGAGAGCACUGGCUGCAUAAUCAAAUAGAAAAUGUUCGAGCCAAGCGCACUGGGAGAAACCAGUUGCAA
............((.........(((.(((.....)))...((........)).)))...(((((((((..((.....))..))))...))))).))(((((((......)))).))).. ( -26.10)
>DroSim_CAF1 101736 120 - 1
UAUUACGUUACGGCACACACCAACUCAUGGCCCGACCAGAACCAUAACAAAGGAGAGCACUGGCUGCAUAAUCAAAUAGAAAAUGUUCGAGCCAAGUGCACUGGGAGAAAUCAGGUGCAA
............((((...(((.....)))..(..((((..((........))...(((((((((((((..((.....))..))))...)))).))))).))))..).......)))).. ( -31.70)
>DroEre_CAF1 111763 113 - 1
UAUUACGUUACGGCACACACCAACUCAUGGCCCGACCAGAACCAUAACAAAGGAGAGCACUGGCUGCAUAAUCAAAUAGAA-ACGUUCGAGCCAAGUGCACUGGGAGAAAUC------AA
...........(((.((..........)))))...((((..((........))...(((((((((................-.......)))).))))).))))((....))------.. ( -23.80)
>DroYak_CAF1 114484 119 - 1
UAUUACGUUACGGCACACACCGACUGGUGGCCCGACCAGAACCAUAACAAAGGAGAGCACUGGCUGCAUAAUCAAAUAGAA-AUGUUCGAGCCAAGUGCACUGGGCGAAAGUAUGGGUAA
.................((((....))))(((((.((((..((........))...(((((((((((((..((.....)).-))))...)))).))))).))))((....)).))))).. ( -36.50)
>consensus
UAUUACGUUACGGCACACACCAACUCAUGGCCCGACCAGAACCAUAACAAAGGAGAGCACUGGCUGCAUAAUCAAAUAGAAAAUGUUCGAGCCAAGUGCACUGGGAGAAAUCAGGUGCAA
...........(((.((..........)))))...((((..((........))...(((((((((((((..((.....))..))))...)))).))))).))))((....))........ (-23.56 = -23.96 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	17,224,587 – 17,224,707
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-37.16
Consensus MFE	-34.10
Energy contribution	-34.90
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.92
SVM decision value	1.99
SVM RNA-class probability	0.985034
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17224587 120 + 23771897
UCUAUUUGAUUAUGCAGCCAGUGCUCUCCUUUGUUAUGGUUCUGGUCGGGCCAUGAGUUGGUGUGUGCCGUAACGUAAUAUGGAGCAGAAACAAUAGUUUCGGCCUCAUCAUCAUCCAAC
......((((.(((..(((..((((((....(((((((((......((.((((.....)))).)).)))))))))......))))))(((((....))))))))..))).))))...... ( -38.60)
>DroSec_CAF1 108055 120 + 1
UCUAUUUGAUUAUGCAGCCAGUGCUCUCCUUUGUUAUGGUUCUGGUCGGGCCAUGAGUUAGUGUGUGCCGUAACGUAAUAUGGAGAAGAAACAAUAGUUUCGGCCUAAUCAUCAUCCAAC
......((((((....(((.....(((((..(((((((((.(((((((.....))).)))).....)))))))))......))))).(((((....)))))))).))))))......... ( -30.80)
>DroSim_CAF1 101776 120 + 1
UCUAUUUGAUUAUGCAGCCAGUGCUCUCCUUUGUUAUGGUUCUGGUCGGGCCAUGAGUUGGUGUGUGCCGUAACGUAAUAUGGAGCAGAAACAAUAGUUUCGGCCUCAUCAUCAUCCAAC
......((((.(((..(((..((((((....(((((((((......((.((((.....)))).)).)))))))))......))))))(((((....))))))))..))).))))...... ( -38.60)
>DroEre_CAF1 111796 120 + 1
UCUAUUUGAUUAUGCAGCCAGUGCUCUCCUUUGUUAUGGUUCUGGUCGGGCCAUGAGUUGGUGUGUGCCGUAACGUAAUAUGGAGCAGAAACAAUAGUUUCGGCCUCAUCAUCAUCCAAC
......((((.(((..(((..((((((....(((((((((......((.((((.....)))).)).)))))))))......))))))(((((....))))))))..))).))))...... ( -38.60)
>DroYak_CAF1 114523 120 + 1
UCUAUUUGAUUAUGCAGCCAGUGCUCUCCUUUGUUAUGGUUCUGGUCGGGCCACCAGUCGGUGUGUGCCGUAACGUAAUAUGGAGCAGAAACAAUAGUUUCGGCCUCAUCAUCAUCCAAC
......((((.(((..(((..((((((....(((((((((.((((..((....))..)))).....)))))))))......))))))(((((....))))))))..))).))))...... ( -39.20)
>consensus
UCUAUUUGAUUAUGCAGCCAGUGCUCUCCUUUGUUAUGGUUCUGGUCGGGCCAUGAGUUGGUGUGUGCCGUAACGUAAUAUGGAGCAGAAACAAUAGUUUCGGCCUCAUCAUCAUCCAAC
......((((.(((..(((..((((((....(((((((((......((.((((.....)))).)).)))))))))......))))))(((((....))))))))..))).))))...... (-34.10 = -34.90 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:57 2006