Locus 4311

Sequence ID	3R_DroMel_CAF1
Location	11,435,686 – 11,435,806
Length	120
Max. P	0.999564

overview

Window 2

Location	11,435,686 – 11,435,806
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.83
Mean single sequence MFE	-31.72
Consensus MFE	-31.06
Energy contribution	-31.66
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.98
SVM decision value	3.73
SVM RNA-class probability	0.999564
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11435686 120 + 27905053
CUCAAGUCCCGGACAAAAUAUGUUUUUAAUAUGCAAAAACUUUUAGCCAAAUGGCUUUUAACUGUCAUUAGGCAACUGUUGCCCGAGCGGAUCCAAAGCCAGAAAAUGGCCAAUGAAAUU
.(((.(((((((.(((.....((((((.......)))))).....(((.((((((........)))))).))).....))).)))...)))).....((((.....))))...))).... ( -27.60)
>DroSec_CAF1 175795 120 + 1
CUCAAGUCCCGGGCAAAAUAUGUUUUUAAUAUGCAAAAACUUUUAGCCAAAUGGCUUUUAACUGUCAUUAGGCAACUGUUGCCCGAGCGGAUCCAAAGCCAGAAAAUGGCCAAUGAAAUU
.(((.(((((((((((.....((((((.......)))))).....(((.((((((........)))))).))).....)))))))...)))).....((((.....))))...))).... ( -34.70)
>DroSim_CAF1 169992 120 + 1
CUCAAGUCCCGGACAAAAUAUGUUUUUAAUAUGCAAAAACUUUUAGCCAAAUGGCUUUUAACUGUCAUUAGGCAACUGUUGCCCGAGCGGAUCCAAAGCCAGAAAAUGGCCAAUGAAAUU
.(((.(((((((.(((.....((((((.......)))))).....(((.((((((........)))))).))).....))).)))...)))).....((((.....))))...))).... ( -27.60)
>DroEre_CAF1 165377 120 + 1
CUCAAGUCCCGGGCAAAAUAUGUUUUUAAUAUGCAAAAACUUUUAGCCAAAUGGCUUUUAACUGUCAUUAGGCAACUGUUGCCCGAGCGGAUCCGAAGCCAGAAAAUGGCCAAUGAAAUU
.((..(((((((((((.....((((((.......)))))).....(((.((((((........)))))).))).....)))))))...))))..)).((((.....)))).......... ( -34.80)
>DroYak_CAF1 168181 120 + 1
CUCAAGUCCCGGGCAAAAUAUGUUUUUAAUAUGCAAAAACUUUUAGCCAAAUGGCUUUUAACUGUCAUUAGGCAACUGUUGCCCGAGCGGAGCCAAAGCCAGAAAAUGGCCAAUGAAAUU
.(((..((((((((((.....((((((.......)))))).....(((.((((((........)))))).))).....)))))))...)))......((((.....))))...))).... ( -33.90)
>consensus
CUCAAGUCCCGGGCAAAAUAUGUUUUUAAUAUGCAAAAACUUUUAGCCAAAUGGCUUUUAACUGUCAUUAGGCAACUGUUGCCCGAGCGGAUCCAAAGCCAGAAAAUGGCCAAUGAAAUU
.(((.(((((((((((.....((((((.......)))))).....(((.((((((........)))))).))).....)))))))...)))).....((((.....))))...))).... (-31.06 = -31.66 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	11,435,686 – 11,435,806
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.83
Mean single sequence MFE	-32.50
Consensus MFE	-31.32
Energy contribution	-31.28
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.92
Structure conservation index	0.96
SVM decision value	2.30
SVM RNA-class probability	0.991931
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11435686 120 - 27905053
AAUUUCAUUGGCCAUUUUCUGGCUUUGGAUCCGCUCGGGCAACAGUUGCCUAAUGACAGUUAAAAGCCAUUUGGCUAAAAGUUUUUGCAUAUUAAAAACAUAUUUUGUCCGGGACUUGAG
...((((..(((((.....))))).))))....(((((((((.....(((.((((.(........).)))).))).....(((((((.....))))))).....)))))))))....... ( -31.00)
>DroSec_CAF1 175795 120 - 1
AAUUUCAUUGGCCAUUUUCUGGCUUUGGAUCCGCUCGGGCAACAGUUGCCUAAUGACAGUUAAAAGCCAUUUGGCUAAAAGUUUUUGCAUAUUAAAAACAUAUUUUGCCCGGGACUUGAG
...((((..(((((.....))))).))))....(((((((((.....(((.((((.(........).)))).))).....(((((((.....))))))).....)))))))))....... ( -33.70)
>DroSim_CAF1 169992 120 - 1
AAUUUCAUUGGCCAUUUUCUGGCUUUGGAUCCGCUCGGGCAACAGUUGCCUAAUGACAGUUAAAAGCCAUUUGGCUAAAAGUUUUUGCAUAUUAAAAACAUAUUUUGUCCGGGACUUGAG
...((((..(((((.....))))).))))....(((((((((.....(((.((((.(........).)))).))).....(((((((.....))))))).....)))))))))....... ( -31.00)
>DroEre_CAF1 165377 120 - 1
AAUUUCAUUGGCCAUUUUCUGGCUUCGGAUCCGCUCGGGCAACAGUUGCCUAAUGACAGUUAAAAGCCAUUUGGCUAAAAGUUUUUGCAUAUUAAAAACAUAUUUUGCCCGGGACUUGAG
....((...(((((.....)))))...))....(((((((((.....(((.((((.(........).)))).))).....(((((((.....))))))).....)))))))))....... ( -33.00)
>DroYak_CAF1 168181 120 - 1
AAUUUCAUUGGCCAUUUUCUGGCUUUGGCUCCGCUCGGGCAACAGUUGCCUAAUGACAGUUAAAAGCCAUUUGGCUAAAAGUUUUUGCAUAUUAAAAACAUAUUUUGCCCGGGACUUGAG
....(((..(((((.....))))).)))(((..(((((((((.....(((.((((.(........).)))).))).....(((((((.....))))))).....)))))))))....))) ( -33.80)
>consensus
AAUUUCAUUGGCCAUUUUCUGGCUUUGGAUCCGCUCGGGCAACAGUUGCCUAAUGACAGUUAAAAGCCAUUUGGCUAAAAGUUUUUGCAUAUUAAAAACAUAUUUUGCCCGGGACUUGAG
....((...(((((.....)))))...))....(((((((((.....(((.((((.(........).)))).))).....(((((((.....))))))).....)))))))))....... (-31.32 = -31.28 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:41 2006