Locus 6238

Sequence ID 2L_DroMel_CAF1
Location 17,339,756 – 17,339,890
Length 134
Max. P 0.849945
window9969 window9970

overview

Window 9

Location 17,339,756 – 17,339,866
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.81
Mean single sequence MFE -38.02
Consensus MFE -25.40
Energy contribution -26.15
Covariance contribution 0.75
Combinations/Pair 1.23
Mean z-score -1.76
Structure conservation index 0.67
SVM decision value 0.05
SVM RNA-class probability 0.557274
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17339756 110 + 22407834
AUGUCCCUAGUGGCCACAUCCACGUCCCGUUUUUCGACGAAUACGUGAGGACGA-U------CGCAGGUCAUGGUCA-UGACCAUAAAGUGUUUCCCAA-GGAUUACUGGGGAAUAGA-U
...((((((((((((.......((((.........))))(((((((((......-)------))).((((((....)-))))).....)))))......-)).)))))))))).....-. ( -36.20)
>DroSec_CAF1 36078 110 + 1
AUGUCCCUAGUGGCCAUAUCCACGUCCCGUUUUUCGACGGAUACGUGAGGACGA-U------CGCAGGUCAUGGUCA-UGACCAUAAAGUGUUUCCCAA-GGAUUACUGGGGAAUAGA-U
...((((((((((((.....(((((.(((((....)))))..))))).(((...-.------(((.((((((....)-))))).....)))..)))...-)).)))))))))).....-. ( -39.00)
>DroSim_CAF1 38705 110 + 1
AUGUCCCUAGUGGCCAUAUCCACGUCCCGUUUUUCGACGGAUACGUGAGGACGA-U------CGCAGGUCAUGGUCA-UGACCAUAAAGUGUUUCCCAA-GGAUUACUGGGGAAUAGA-U
...((((((((((((.....(((((.(((((....)))))..))))).(((...-.------(((.((((((....)-))))).....)))..)))...-)).)))))))))).....-. ( -39.00)
>DroEre_CAF1 38205 109 + 1
AUGUCCCUAGUGGCCAUAUCCACGUCCCGUUUUUCGACGGAUACGUGAGGACGA-U------CGCAGGUCAUGGUCA-UGACCAUAAGGGAUUCCACAC-GGAUUACUGG-GAAUAGA-U
.(((.((((((((((.....(((((.(((((....)))))..))))).(((..(-(------(.(.((((((....)-)))))....).))))))....-)).)))))))-).)))..-. ( -36.90)
>DroYak_CAF1 33146 110 + 1
AUGUCCCUAGUGGCCAUAUCCACGUCCCGUUUUUCGACGGAUACGUGAGGAGGA-U------CGCAGGUCAUGGUCA-UGACCAUAAGGGAUUCCACGC-GGAUUACUGGGGAACCGA-U
...((((((((((((.....(((((.(((((....)))))..))))).((((..-(------(...((((((....)-)))))....))..))))....-)).)))))))))).....-. ( -43.30)
>DroAna_CAF1 43987 117 + 1
GUGUCCCUGUUGGCCAU--GCACGUUCCGUUUUUCGCCGCGUACGUGAGGAUGGGUUGCUCCUGAAGGCCAUGGGCAGUGCCUAGAAAGGGUGUUCUAGCAGAGAGCUUU-AAAAAUAUU
....((((..(((((..--.(((((..(((........))).)))))((((........))))...)))))(((((...)))))...)))).(((((.....)))))...-......... ( -33.70)
>consensus
AUGUCCCUAGUGGCCAUAUCCACGUCCCGUUUUUCGACGGAUACGUGAGGACGA_U______CGCAGGUCAUGGUCA_UGACCAUAAAGGGUUUCCCAA_GGAUUACUGGGGAAUAGA_U
...((((((((((((.....(((((.(((((....)))))..)))))....((.........))..))))((((((...))))))....................))))))))....... (-25.40 = -26.15 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,339,796 – 17,339,890
Length 94
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 81.34
Mean single sequence MFE -28.32
Consensus MFE -21.48
Energy contribution -21.68
Covariance contribution 0.20
Combinations/Pair 1.19
Mean z-score -1.87
Structure conservation index 0.76
SVM decision value 0.78
SVM RNA-class probability 0.849945
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17339796 94 + 22407834
AUACGUGAGGACGAUCGCAGGUCAUGGUCAUGACCAUAAAGUGUUUCCCAAGGAUUACUGGGGAAUAGAUUUCUUUGGUUUUAUCAUAAUAAAA----------------
......(((((.((((...((((((....))))))......(((((((((.(.....)))))))))))))))))))..................---------------- ( -24.70)
>DroSec_CAF1 36118 100 + 1
AUACGUGAGGACGAUCGCAGGUCAUGGUCAUGACCAUAAAGUGUUUCCCAAGGAUUACUGGGGAAUAGAUUUCUUUGGUUUUGUCAU---AAACAAGGAUU-------AA
....((((......)))).((((((....))))))......(((((((((.(.....))))))))))....((((((..........---...))))))..-------.. ( -27.02)
>DroSim_CAF1 38745 110 + 1
AUACGUGAGGACGAUCGCAGGUCAUGGUCAUGACCAUAAAGUGUUUCCCAAGGAUUACUGGGGAAUAGAUUUCUUUGGUUUUAUCAUAAUAAACUAGGACAAAUUCGCAA
....(((((((.((((...((((((....))))))......(((((((((.(.....))))))))))))))))((((((((.........)))))))).....))))).. ( -29.40)
>DroEre_CAF1 38245 109 + 1
AUACGUGAGGACGAUCGCAGGUCAUGGUCAUGACCAUAAGGGAUUCCACACGGAUUACUGG-GAAUAGAUUUCUUUAGUUCUAUCAUUAUAAAUUGGGACAUAUUCCUAA
...((((.(((..(((.(.((((((....))))))....).)))))).))))......(((-((((((....)....((((((...........)))))).)))))))). ( -29.50)
>DroYak_CAF1 33186 110 + 1
AUACGUGAGGAGGAUCGCAGGUCAUGGUCAUGACCAUAAGGGAUUCCACGCGGAUUACUGGGGAACCGAUUUCUCUAGCUUUAUCAUUAUAAAAUGGGAUACAAUCACAA
...((((.((((..((...((((((....))))))....))..)))).))))((((.((((((((.....)))))))).....(((((....))))).....)))).... ( -31.00)
>consensus
AUACGUGAGGACGAUCGCAGGUCAUGGUCAUGACCAUAAAGUGUUUCCCAAGGAUUACUGGGGAAUAGAUUUCUUUGGUUUUAUCAUAAUAAAAUAGGACA_A_UC__AA
.....((((((.((((...((((((....))))))......(((((((((.(.....))))))))))))))))))))................................. (-21.48 = -21.68 +   0.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:05 2006