Locus 2225

Sequence ID	3L_DroMel_CAF1
Location	6,156,408 – 6,156,556
Length	148
Max. P	0.890790

overview

Window 7

Location	6,156,408 – 6,156,516
Length	108
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	88.27
Mean single sequence MFE	-41.65
Consensus MFE	-32.83
Energy contribution	-34.67
Covariance contribution	1.84
Combinations/Pair	1.09
Mean z-score	-3.03
Structure conservation index	0.79
SVM decision value	0.82
SVM RNA-class probability	0.857951
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6156408 108 - 23771897
AAGGCGGAGGCGGAGCUCCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGUCGAACACUUACGACGGCUUCUACGCGCAGAAGGCGGAG
....(((((((((..((((((.....)).)))).))))))))).((((((.....))))))((((((.((((........)))).)))))).(((.......)))... ( -50.90)
>DroSec_CAF1 7805 108 - 1
AAGGCGGAGGCGGAGCUCCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGACGAACACGUACGACGGCUUCUACGCGCAGAAGGCGGAG
....(((((((((..((((((.....)).)))).))))))))).((((((.....))))))((((((.((((....))).)....)))))).(((.......)))... ( -46.40)
>DroSim_CAF1 7844 108 - 1
AAGGCGGAGGCGGAGCUCCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGACGAACACGUACGACGGCUUCUACGCGCAGAAAGCGGAG
....(((((((((..((((((.....)).)))).))))))))).((((((.....))))))((((((.((((....))).)....)))))).(((.......)))... ( -47.00)
>DroEre_CAF1 7958 108 - 1
AAGGCAGAGGCGGAGCUUCGGAAAAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGACAAACACGUACGAUGGCUUCUACGCUCAGAAGGCGGAG
....(..((((((..((((((.....)).)))).))))))..).((((((.....))))))((((((.(((......)).)....)))))).((((.....))))... ( -37.90)
>DroWil_CAF1 8673 108 - 1
AAGGCUGAAAUUGAGCUUAAGAAGAUCCAAGAGGCGGCCUUCGAGCAGCUAAAUAAGCUGCAAAAGCAACAGAAUACCUACGAUGGCUUCUAUGCCCAAAAGAACGCC
.(((((.......)))))..............((((..(((...((((((.....))))))....(((..((((..((......)).)))).)))....)))..)))) ( -26.60)
>DroYak_CAF1 7961 108 - 1
AAGGCGGAGGCGGAGCUUCGCAAGAUCCAGGAGGCUGCCUUCGAGCAGCUGAACAAGCUGCAGAAGCAGACAAACACGUACGAUGGCUUCUACGCUCAAAAGGCCGAG
..(((((((((((..((((..........)))).))))))))((((((((.....))))(.((((((.(((......)).)....)))))).))))).....)))... ( -41.10)
>consensus
AAGGCGGAGGCGGAGCUCCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGACGAACACGUACGACGGCUUCUACGCGCAGAAGGCGGAG
....(((((((((..((((((.....)).)))).))))))))).((((((.....))))))((((((...((........))...)))))).(((.......)))... (-32.83 = -34.67 +   1.84)

alignment

secondary structure

dotplot

Window 8

Location	6,156,445 – 6,156,556
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.11
Mean single sequence MFE	-42.72
Consensus MFE	-29.00
Energy contribution	-29.98
Covariance contribution	0.98
Combinations/Pair	1.28
Mean z-score	-2.88
Structure conservation index	0.68
SVM decision value	0.96
SVM RNA-class probability	0.890790
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6156445 111 - 23771897
GCUGCUGGCCUACCAGAUCGAGGAGAACGAGGCCAAGCGCAAGGCGGAGGCGGAGCUCCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGUC---------
(((((((((((....(.((.....)).).)))))...(....).(((((((((..((((((.....)).)))).))))))))).((((((.....))))))...)))))).--------- ( -52.00)
>DroGri_CAF1 5440 120 - 1
AUUGCUGGCACAACAGAUGGAGGAGAAUGAAGCGAAGCGCAAGGCAGAGGAGGAGACGCGCAAGAUUCAAGAGGCUGCAUGCGAGCAGCUCAACAGACUUCAAAAGCAGGUGCAGAGUGA
.(..((.((((......(((((.....(((.((....((((..((((.....(((...(....).)))......)))).))))....))))).....))))).......))))..))..) ( -32.52)
>DroSim_CAF1 7881 111 - 1
GCUGCUGGCCUACCAGAUCGAGGAGAACGAGGCCAAGCGGAAGGCGGAGGCGGAGCUCCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGAC---------
.((((((((((....(.((.....)).).))))).)))))...((((((((((..((((((.....)).)))).))))))))..((((((.....))))))....))....--------- ( -51.60)
>DroEre_CAF1 7995 111 - 1
GCUGCUGGCCUACCAAAUCGAGGAGAACGAGGCCAAGCGCAAGGCAGAGGCGGAGCUUCGGAAAAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGAC---------
((.((((((((......((.....))...))))).)))))...((.(((((((..((((((.....)).)))).)))))))...((((((.....))))))....))....--------- ( -42.70)
>DroWil_CAF1 8710 111 - 1
GCUGUUGGCAUUCCAAAUCGAAGAGAAUGAGGCUAAACGCAAGGCUGAAAUUGAGCUUAAGAAGAUCCAAGAGGCGGCCUUCGAGCAGCUAAAUAAGCUGCAAAAGCAACA---------
((((((..((((((........).))))).)))....((.(((((((...(((..((.....))...)))....))))))))).((((((.....))))))...)))....--------- ( -30.70)
>DroYak_CAF1 7998 111 - 1
ACUGCUGGCCUACCAGAUCGAGGAGAACGAGGCCAAGCGCAAGGCGGAGGCGGAGCUUCGCAAGAUCCAGGAGGCUGCCUUCGAGCAGCUGAACAAGCUGCAGAAGCAGAC---------
.((((((((((....(.((.....)).).)))))...(....).(((((((((..((((..........)))).))))))))).((((((.....))))))...)))))..--------- ( -46.80)
>consensus
GCUGCUGGCCUACCAGAUCGAGGAGAACGAGGCCAAGCGCAAGGCGGAGGCGGAGCUUCGGAAGAUCCAGGAGGCUGCCUUCGAGCAGCUAAACAAGCUGCAGAAGCAGAC_________
.((((((((((....(.((.....)).).)))))...((.(((((((....(((....(....).)))......))))))))).((((((.....))))))...)))))........... (-29.00 = -29.98 +   0.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:17 2006