Locus 4087

Sequence ID	3R_DroMel_CAF1
Location	11,154,006 – 11,154,110
Length	104
Max. P	0.573071

overview

Window 7

Location	11,154,006 – 11,154,110
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	71.88
Mean single sequence MFE	-24.40
Consensus MFE	-14.61
Energy contribution	-16.35
Covariance contribution	1.74
Combinations/Pair	1.26
Mean z-score	-1.46
Structure conservation index	0.60
SVM decision value	0.08
SVM RNA-class probability	0.573071
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11154006 104 + 27905053
AAACAACAUUGCGAAUUCGGUCAUACUGUGUUGUUUGGCAACGCGACCGCUGCAAUUUAAACUGCGACUUUAAACUUUGCUUUAGGUCCGAUUUAAAGUCGGUA
.......((((((....(((((.....((((((.....))))))))))).))))))........((((((((((....((.....))....))))))))))... ( -27.30)
>DroSec_CAF1 11214 81 + 1
AAACAACAUUGCGAAUUCGGUCAUACUGCGUUGUUUGGCAACGCGACCGCUGCAAUUUAAACUGCGACUUU-----------------------AAAGUCGCUA
.......((((((....(((((.....((((((.....))))))))))).)))))).......((((((..-----------------------..)))))).. ( -27.10)
>DroSim_CAF1 6924 81 + 1
AAACAACAUUGCGAAUUCGGUCAUACUGCGUUGUUUGGCAACGCGACCGCUGUAAUUUAAACUGCGACUUU-----------------------AAAGUCGCUA
.......((((((....(((((.....((((((.....))))))))))).)))))).......((((((..-----------------------..)))))).. ( -25.10)
>DroEre_CAF1 6926 103 + 1
AAG-AACUUCAUAAAUUCGGUCAUACUGCGUUGGUUGGCAACGCGAGCGCUGCAAUUUGAACUGCAACUUUAAGCCUUGAUUGAAAUGCUUUUUUAGGUCGGUA
...-............(((..(.....((((((.....))))))(((((...(((((......((........))...)))))...))))).....)..))).. ( -21.40)
>DroYak_CAF1 6954 98 + 1
ACGGCACAUUGCGAAUUUGGUCCUACUGCGUUGGUUGGCAACGCGAGCGCUGCAAUUUAAA------CUUUAAACUUUGAUUAAAACCCGGCUUUAAGUCGGAU
.......((((((.....((.....))(((((.((.(....))).))))))))))).....------....................(((((.....))))).. ( -21.10)
>consensus
AAACAACAUUGCGAAUUCGGUCAUACUGCGUUGUUUGGCAACGCGACCGCUGCAAUUUAAACUGCGACUUUAA_C_UUG_UU_A____C___UUAAAGUCGGUA
.......((((((....(((((.....((((((.....))))))))))).))))))........((((((((((.................))))))))))... (-14.61 = -16.35 +   1.74)

alignment

secondary structure

dotplot

Window 8

Location	11,154,006 – 11,154,110
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	71.88
Mean single sequence MFE	-24.00
Consensus MFE	-12.04
Energy contribution	-14.96
Covariance contribution	2.92
Combinations/Pair	1.19
Mean z-score	-1.65
Structure conservation index	0.50
SVM decision value	0.08
SVM RNA-class probability	0.572147
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11154006 104 - 27905053
UACCGACUUUAAAUCGGACCUAAAGCAAAGUUUAAAGUCGCAGUUUAAAUUGCAGCGGUCGCGUUGCCAAACAACACAGUAUGACCGAAUUCGCAAUGUUGUUU
...(((((((((((..(........)...)))))))))))........(((((..((((((..(((..........)))..)))))).....)))))....... ( -24.20)
>DroSec_CAF1 11214 81 - 1
UAGCGACUUU-----------------------AAAGUCGCAGUUUAAAUUGCAGCGGUCGCGUUGCCAAACAACGCAGUAUGACCGAAUUCGCAAUGUUGUUU
..((((((..-----------------------..)))))).......(((((..((((((..((((........))))..)))))).....)))))....... ( -27.50)
>DroSim_CAF1 6924 81 - 1
UAGCGACUUU-----------------------AAAGUCGCAGUUUAAAUUACAGCGGUCGCGUUGCCAAACAACGCAGUAUGACCGAAUUCGCAAUGUUGUUU
..((((((..-----------------------..))))))..........((((((((((..((((........))))..)))))(....).....))))).. ( -24.50)
>DroEre_CAF1 6926 103 - 1
UACCGACCUAAAAAAGCAUUUCAAUCAAGGCUUAAAGUUGCAGUUCAAAUUGCAGCGCUCGCGUUGCCAACCAACGCAGUAUGACCGAAUUUAUGAAGUU-CUU
.............(((.((((((.....((.(((..((((((((....))))))))(((.((((((.....))))))))).))))).......)))))).-))) ( -24.60)
>DroYak_CAF1 6954 98 - 1
AUCCGACUUAAAGCCGGGUUUUAAUCAAAGUUUAAAG------UUUAAAUUGCAGCGCUCGCGUUGCCAACCAACGCAGUAGGACCAAAUUCGCAAUGUGCCGU
....(((((.((((..(((....)))...)))).)))------))...(((((...(((.((((((.....))))))))).(((.....))))))))....... ( -19.20)
>consensus
UACCGACUUUAA___G____U_AA_CAA_G_UUAAAGUCGCAGUUUAAAUUGCAGCGGUCGCGUUGCCAAACAACGCAGUAUGACCGAAUUCGCAAUGUUGUUU
...(((((((((((...............)))))))))))........(((((..(((((((((((.....)))))).....))))).....)))))....... (-12.04 = -14.96 +   2.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:50 2006