Locus 296

Sequence ID 3R_DroMel_CAF1
Location 1,128,936 – 1,129,029
Length 93
Max. P 0.500000
window504

overview

Window 4

Location 1,128,936 – 1,129,029
Length 93
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 68.02
Mean single sequence MFE -22.94
Consensus MFE -4.20
Energy contribution -5.16
Covariance contribution 0.96
Combinations/Pair 1.19
Mean z-score -1.91
Structure conservation index 0.18
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1128936 93 + 27905053
AAUGGCAGAAUGGCAGACAAGCCGA---AGUGAACU-GAGCGAGUGACUCAGUUU-UCGCUACGUAUACGUAAUGUGCGAUGCACGCACACAUAAUGU
.(((((....((((......)))).---.(.(((((-(((.......))))))))-.)))((((....)))).((((((.....)))))))))..... ( -27.00)
>DroSec_CAF1 62874 81 + 1
AAUGG--------CAGCCAAGACGAGCGAGUGAACU-GAGCGAGUGACUCAGUUU-UCGCUACGUAUACGUAAUGUG-----CACAAACACAUAAU--
.....--------..((....((((((((..(((((-(((.......))))))))-))))).)))....)).(((((-----......)))))...-- ( -22.80)
>DroSim_CAF1 63480 81 + 1
AAUGG--------CAGACAAGCCGAGCGAGUGAACU-GAGCGAGUGACUCAGUUU-UCGCUACGUAUACGUAAUGUG-----CACAAGCACAUAAU--
..(((--------(......))))(((((..(((((-(((.......))))))))-)))))(((....))).(((((-----(....))))))...-- ( -28.80)
>DroEre_CAF1 63551 71 + 1
--------------UGACAAACCAC---GUUGAACU--AGCGGGUGACUCAGUU--UGGCUACGUAUACGUAAUGUGCGAGGCACAA-AAC---AU--
--------------(((...(((.(---((((...)--)))))))...)))(((--(.(((.((((((.....)))))).)))...)-)))---..-- ( -19.70)
>DroAna_CAF1 59810 76 + 1
A------------CAGACGGUCCAA---GUUGAACUCAAGCCAAUGAGUCAGUGCCACGGUGCGUAUACGUAAUGUGCCUC--UCAACAAC---AU--
.------------............---((((((((((......)))))..(.(.((((.((((....)))).)))).).)--)))))...---..-- ( -16.40)
>consensus
AAUGG________CAGACAAGCCGA___AGUGAACU_GAGCGAGUGACUCAGUUU_UCGCUACGUAUACGUAAUGUGC____CACAAACACAUAAU__
...............................(((((.(((.......)))))))).....((((....)))).((((.....))))............ ( -4.20 =  -5.16 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:45 2006