Locus 5362

Sequence ID	3R_DroMel_CAF1
Location	14,078,850 – 14,078,956
Length	106
Max. P	0.849992

overview

Window 8

Location	14,078,850 – 14,078,956
Length	106
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	75.52
Mean single sequence MFE	-30.67
Consensus MFE	-18.34
Energy contribution	-18.43
Covariance contribution	0.09
Combinations/Pair	1.37
Mean z-score	-1.58
Structure conservation index	0.60
SVM decision value	0.54
SVM RNA-class probability	0.776026
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14078850 106 + 27905053
GCCUUGGCCUCCUCGGGCGCCUCCGGACACAAAUUACCCAGUGCCGCCAGUUCGAAUUUGUGCAGCUUUUUCUGCAUCAGCAAGCUGAA--U--UUGAA-AUAAU---UGA-AUA
...(((((......(((....)))((.(((..........))))))))))((((((((.((((((......))))))(((....)))))--)--)))))-.....---...-... ( -24.70)
>DroVir_CAF1 2015 107 + 1
GCCUUGGCCUCCUCCGGCGCCUCCGGGCACAGAUUACCCAGUGCAGCCAGCUCGAACUUGUGCAGUUUCUUUUGCAUAAGCAAACUGGG--A--GUACACAAAAU---AAA-AUA
((((.(((((.....)).)))...))))........((((((((.....)).....(((((((((......)))))))))...))))))--.--...........---...-... ( -31.80)
>DroGri_CAF1 1864 108 + 1
GCUUUGGCUUCCUCCGGCGCCUCUGGGCACAGAUUGCCCAGGGCAGCUAGUUCGAAUUUGUGCAGCUUCUUUUGCAUUAGCAGACUGGG--A--AUAAUUCAAAU---AAAUAUA
..((((..((..(((((((((.(((((((.....)))))))))).)))(((..(.....((((((......))))))...)..))).))--)--..))..)))).---....... ( -34.40)
>DroWil_CAF1 1794 106 + 1
GCCUUGGCCUCUUCUGGAGCCUCCGGACACAGAUUGCCCAGUGCAGCCAAUUCGAAUUUGUGCAAUUUCUUUUGCAUUAGUAAACUGCAAAAAUAUGGA-AC--U---UU---UA
((((.(((.((((((((.....)))))...)))..))).)).))......((((.((((.((((.(((((........)).))).)))).)))).))))-..--.---..---.. ( -23.20)
>DroMoj_CAF1 1901 104 + 1
GCCUUAGCCUCUUCCGGCGCCUCCGGGCAGAGAUUGCCCAGAGCGGCAAGUUCGAAUUUGUGCAGUUUCUUUUGCAUAAGUAAACUAGA--A--ACAAG-AAAAU---UGA---A
(((...(((......)))((.((.((((((...)))))).))))))).((((...((((((((((......)))))))))).))))...--.--.(((.-....)---)).---. ( -33.00)
>DroAna_CAF1 1602 104 + 1
GCCUUGGCUUCUUCCGGAGCCUCUGGGCACAGAUUGCCUAGGGCGGCUAGCUCGAAUUUAUGCAAUUUCUUUUGCAUCAGCAAGCUGGA---------A-AAAAAUCAUUA-CUA
(((..((((((....)))))).(((((((.....))))))))))..((((((.(.....((((((......))))))...).)))))).---------.-...........-... ( -36.90)
>consensus
GCCUUGGCCUCCUCCGGCGCCUCCGGGCACAGAUUGCCCAGUGCAGCCAGUUCGAAUUUGUGCAGUUUCUUUUGCAUAAGCAAACUGGA__A__AUAAA_AAAAU___UAA_AUA
((((.(((.((....)).)))...(((((.....))))))).))..((((((.(.....((((((......))))))...).))))))........................... (-18.34 = -18.43 +   0.09)

alignment

secondary structure

dotplot

Window 9

Location	14,078,850 – 14,078,956
Length	106
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	75.52
Mean single sequence MFE	-31.27
Consensus MFE	-21.38
Energy contribution	-20.88
Covariance contribution	-0.50
Combinations/Pair	1.38
Mean z-score	-1.37
Structure conservation index	0.68
SVM decision value	0.78
SVM RNA-class probability	0.849992
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14078850 106 - 27905053
UAU-UCA---AUUAU-UUCAA--A--UUCAGCUUGCUGAUGCAGAAAAAGCUGCACAAAUUCGAACUGGCGGCACUGGGUAAUUUGUGUCCGGAGGCGCCCGAGGAGGCCAAGGC
...-...---.....-.....--.--....((((.((..(((((......)))))..........(.((((.(.((((..(.....)..)))).).)))).))).))))...... ( -27.80)
>DroVir_CAF1 2015 107 - 1
UAU-UUU---AUUUUGUGUAC--U--CCCAGUUUGCUUAUGCAAAAGAAACUGCACAAGUUCGAGCUGGCUGCACUGGGUAAUCUGUGCCCGGAGGCGCCGGAGGAGGCCAAGGC
...-...---.(((((.((.(--(--((.(((((((((.((((........)))).))))..)))))(((.((.(((((((.....)))))))..)))))))))...))))))). ( -36.60)
>DroGri_CAF1 1864 108 - 1
UAUAUUU---AUUUGAAUUAU--U--CCCAGUCUGCUAAUGCAAAAGAAGCUGCACAAAUUCGAACUAGCUGCCCUGGGCAAUCUGUGCCCAGAGGCGCCGGAGGAAGCCAAAGC
.......---.((((((((..--.--..((((.(((....)))......))))....))))))))(..((.((((((((((.....))))))).)))))..)............. ( -30.40)
>DroWil_CAF1 1794 106 - 1
UA---AA---A--GU-UCCAUAUUUUUGCAGUUUACUAAUGCAAAAGAAAUUGCACAAAUUCGAAUUGGCUGCACUGGGCAAUCUGUGUCCGGAGGCUCCAGAAGAGGCCAAGGC
..---..---(--((-((...((((.((((((((.((........)))))))))).))))..)))))((((...((((((..((((....)))).)).))))....))))..... ( -29.10)
>DroMoj_CAF1 1901 104 - 1
U---UCA---AUUUU-CUUGU--U--UCUAGUUUACUUAUGCAAAAGAAACUGCACAAAUUCGAACUUGCCGCUCUGGGCAAUCUCUGCCCGGAGGCGCCGGAAGAGGCUAAGGC
.---...---.....-.((((--.--..((((((.(((......))))))))).))))..........(((((((((((((.....)))))))).))(((......)))...))) ( -30.90)
>DroAna_CAF1 1602 104 - 1
UAG-UAAUGAUUUUU-U---------UCCAGCUUGCUGAUGCAAAAGAAAUUGCAUAAAUUCGAGCUAGCCGCCCUAGGCAAUCUGUGCCCAGAGGCUCCGGAAGAAGCCAAGGC
...-........(((-(---------(((((((((...((((((......)))))).....))))))....(((((.((((.....)))).)).)))...)))))))((....)) ( -32.80)
>consensus
UAU_UAA___AUUUU_UUUAU__U__UCCAGUUUGCUAAUGCAAAAGAAACUGCACAAAUUCGAACUGGCUGCACUGGGCAAUCUGUGCCCGGAGGCGCCGGAAGAGGCCAAGGC
.............................((((((....((((........))))......)))))).(((...(((((((.....))))))).(((..(....)..)))..))) (-21.38 = -20.88 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:55 2006