Locus 3372

Sequence ID	2L_DroMel_CAF1
Location	9,778,004 – 9,778,094
Length	90
Max. P	0.998064

overview

Window 8

Location	9,778,004 – 9,778,094
Length	90
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	77.59
Mean single sequence MFE	-23.28
Consensus MFE	-9.63
Energy contribution	-10.43
Covariance contribution	0.80
Combinations/Pair	1.20
Mean z-score	-3.05
Structure conservation index	0.41
SVM decision value	3.00
SVM RNA-class probability	0.998064
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9778004 90 + 22407834
AGGGGAUAUUUCAAUUUCGUUGGAGU---GGUUCCCAUA-----AAAAUAGCACUUCCUUUUUUUUGGGGGCUUUCCACUCCAAUUAAAUUCCCAUUU
.(((((....))(((((.((((((((---((((((((.(-----((((.((......)).)))))))))))....)))))))))).)))))))).... ( -29.90)
>DroSec_CAF1 60272 83 + 1
AG--GAUAUUUCAAUUUCGUUGGAGU---GGUUUCCAUA-----GAAAUACCACUUCGUU---UUCGGGGGCUUUCCACUUCAAUUAAAUUCCCAU--
.(--((.......((((.((((((((---((..(((...-----((((.((......)))---)))..)))....)))))))))).)))))))...-- ( -19.91)
>DroSim_CAF1 59476 80 + 1
AG--GAUAUUUUAAUUUCGUUGGAGUGGUGGUUUCCAUA-----GAAAUACCACUU---------CGGGGGCUUUCCACUCCAAUUAAAUUCCCAU--
.(--((.......((((.((((((((((.(((..((..(-----(........)).---------.))..)))..)))))))))).)))))))...-- ( -27.61)
>DroEre_CAF1 59333 83 + 1
AG--GAUAUUUCAAUUUAGUUGGAGU---GGUUCCCAUA-----AAAAUACCACUUCGUU---U-GG-GGGGCUUCCAUUCAAAUGAAAUUCCCAAUA
.(--(..(((((.........(((((---(((.......-----.....))))))))(((---(-((-(((....)).))))))))))))..)).... ( -22.10)
>DroYak_CAF1 61508 88 + 1
AG--GAUAUUUCAAUUUAGUUCGAGU---GGUUCCCAAAAGAAAAAAAAAACACCUCGUU---U-GGCGGGGUUUCCAUGCCAAAUAAAUUCCC-AUA
.(--((........(((..(((...(---((...)))...)))..))).........(((---(-((((((....)).))))))))....))).-... ( -16.90)
>consensus
AG__GAUAUUUCAAUUUCGUUGGAGU___GGUUCCCAUA_____AAAAUACCACUUCGUU___U_CGGGGGCUUUCCACUCCAAUUAAAUUCCCAUU_
............(((((.((((((((...(((((((..............................)))))))....)))))))).)))))....... ( -9.63 = -10.43 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	9,778,004 – 9,778,094
Length	90
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	77.59
Mean single sequence MFE	-20.32
Consensus MFE	-5.24
Energy contribution	-5.88
Covariance contribution	0.64
Combinations/Pair	1.11
Mean z-score	-2.13
Structure conservation index	0.26
SVM decision value	0.95
SVM RNA-class probability	0.887358
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9778004 90 - 22407834
AAAUGGGAAUUUAAUUGGAGUGGAAAGCCCCCAAAAAAAAGGAAGUGCUAUUUU-----UAUGGGAACC---ACUCCAACGAAAUUGAAAUAUCCCCU
....((((((((..(((((((((......((((.(((((.((.....)).))))-----).))))..))---)))))))..)))).......)))).. ( -26.41)
>DroSec_CAF1 60272 83 - 1
--AUGGGAAUUUAAUUGAAGUGGAAAGCCCCCGAA---AACGAAGUGGUAUUUC-----UAUGGAAACC---ACUCCAACGAAAUUGAAAUAUC--CU
--..((((.(((((((....((((.......((..---..))..(((((..(((-----....))))))---))))))....)))))))...))--)) ( -17.80)
>DroSim_CAF1 59476 80 - 1
--AUGGGAAUUUAAUUGGAGUGGAAAGCCCCCG---------AAGUGGUAUUUC-----UAUGGAAACCACCACUCCAACGAAAUUAAAAUAUC--CU
--..((((((((..(((((((((...(((....---------....))).((((-----....))))...)))))))))..)))).......))--)) ( -20.91)
>DroEre_CAF1 59333 83 - 1
UAUUGGGAAUUUCAUUUGAAUGGAAGCCCC-CC-A---AACGAAGUGGUAUUUU-----UAUGGGAACC---ACUCCAACUAAAUUGAAAUAUC--CU
....((((((((((((((..(((.......-))-)---...(.((((((.(((.-----...))).)))---))).)...)))).)))))).))--)) ( -16.80)
>DroYak_CAF1 61508 88 - 1
UAU-GGGAAUUUAUUUGGCAUGGAAACCCCGCC-A---AACGAGGUGUUUUUUUUUUCUUUUGGGAACC---ACUCGAACUAAAUUGAAAUAUC--CU
...-((((((((.((((((..(....)...)))-)---))((((..((((((..........)))))).---.))))..........)))).))--)) ( -19.70)
>consensus
_AAUGGGAAUUUAAUUGGAGUGGAAAGCCCCCC_A___AACGAAGUGGUAUUUU_____UAUGGGAACC___ACUCCAACGAAAUUGAAAUAUC__CU
....(((..(((..........)))..)))................((((((((.......((((.........))))........)))))))).... ( -5.24 =  -5.88 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:52 2006