Locus 2833

Sequence ID 2L_DroMel_CAF1
Location 8,115,906 – 8,116,038
Length 132
Max. P 0.995022
window4503 window4504

overview

Window 3

Location 8,115,906 – 8,115,998
Length 92
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 92.98
Mean single sequence MFE -9.20
Consensus MFE -8.80
Energy contribution -8.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.96
SVM decision value 2.35
SVM RNA-class probability 0.992761
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8115906 92 + 22407834
AGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCACAAAAA---AAA--AACAAAUAUUUUAAAGCAAGCGCUU
((((((((......))))))))..........................................---...--.............((((....)))) (  -8.90)
>DroSec_CAF1 71846 95 + 1
AGUUGAAACGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCACAAAAAAAAAAA--AACAAAUAUUUUAAAGCAAGCGCUU
((((((((......))))))))................................................--.............((((....)))) (  -8.60)
>DroSim_CAF1 71942 94 + 1
AGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCACAAAAAA-AAAA--AACAAAUAUUUUAAAGCAAGCGCUU
((((((((......))))))))...........................................-....--.............((((....)))) (  -8.90)
>DroEre_CAF1 72527 86 + 1
AGUUGAAAUGCAAAUUUCAGCUAAUUUAGAUUAAUAACAAAUAAAGACCGAAAAACCACAAAAAA-----------AAUAUUUUAAAGCAAGCGCUU
(((((((((....)))))))))...........................................-----------.........((((....)))) ( -10.70)
>DroYak_CAF1 73759 97 + 1
AGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCACAAAAAAAAAAAUCAACAAAUAUUUUAAAGCAAGCGCUU
((((((((......))))))))...............................................................((((....)))) (  -8.90)
>consensus
AGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCACAAAAAA_AAAA__AACAAAUAUUUUAAAGCAAGCGCUU
((((((((......))))))))...............................................................((((....)))) ( -8.80 =  -8.80 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,115,938 – 8,116,038
Length 100
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 83.81
Mean single sequence MFE -15.32
Consensus MFE -15.12
Energy contribution -15.15
Covariance contribution 0.03
Combinations/Pair 1.07
Mean z-score -2.50
Structure conservation index 0.99
SVM decision value 2.53
SVM RNA-class probability 0.995022
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8115938 100 + 22407834
AAUAACA---------AAUAAAGACCGAAAAACCACAAAAA---AAA--AACAAAUAUUUUA-AAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.......---------.........................---...--.............-......((((((((..((((((.........(....))))))))))))))). ( -15.60)
>DroGri_CAF1 74665 108 + 1
AGUAAUUGUAACAUUUAAUAAAAACGGAAACA-----ACAA--AAAACCAAAAAAUAUUUUAAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUUAGCGCC
.........................(....).-----....--..........................(((((.((((.(((((.........(....))))))))))))))). ( -14.70)
>DroSec_CAF1 71878 103 + 1
AAUAACA---------AAUAAAGACCGAAAAACCACAAAAAAAAAAA--AACAAAUAUUUUA-AAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.......---------...............................--.............-......((((((((..((((((.........(....))))))))))))))). ( -15.60)
>DroEre_CAF1 72559 94 + 1
AAUAACA---------AAUAAAGACCGAAAAACCACAAAAAA-----------AAUAUUUUA-AAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.......---------..........................-----------.........-......((((((((..((((((.........(....))))))))))))))). ( -15.60)
>DroYak_CAF1 73791 105 + 1
AAUAACA---------AAUAAAGACCGAAAAACCACAAAAAAAAAAAUCAACAAAUAUUUUA-AAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.......---------..............................................-......((((((((..((((((.........(....))))))))))))))). ( -15.60)
>DroAna_CAF1 74815 94 + 1
AAUAAUA---------AAAUCUGA--GAAAAAACCCAAAAAAA---------AAAUAUUUUA-AAGCAAGCGCUUGGAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.......---------........--.................---------..........-......((((((((..((((((.........(....))))))))))))))). ( -14.80)
>consensus
AAUAACA_________AAUAAAGACCGAAAAACCACAAAAAA__AAA__AACAAAUAUUUUA_AAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.....................................................................((((((((..((((((.........(....))))))))))))))). (-15.12 = -15.15 +   0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:24 2006