Locus 3131

Sequence ID	3R_DroMel_CAF1
Location	8,243,834 – 8,243,940
Length	106
Max. P	0.795407

overview

Window 2

Location	8,243,834 – 8,243,940
Length	106
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	88.94
Mean single sequence MFE	-39.17
Consensus MFE	-28.00
Energy contribution	-29.25
Covariance contribution	1.25
Combinations/Pair	1.07
Mean z-score	-2.21
Structure conservation index	0.71
SVM decision value	0.60
SVM RNA-class probability	0.795407
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8243834 106 + 27905053
AAAUGGCUUCAGGAGAAUCCCUCCUUCGAGGUGCUGCCCUCAGGAACCGUUCAGUCAGCCGACGCAGAGAAGCGUUUGCUGAAAGGGGCACCGGAAGCCGCCACCU
....(((((((((((.....)))))....(((((..((((..(((....)))..(((((.(((((......))))).))))).))))))))).))))))....... ( -44.90)
>DroSec_CAF1 75 106 + 1
AAAUGGCUUCAGGAGAAUCCCACCUUCGAGGUGCUGCCCUCGGGAACCGUUCAGACAAUCGACGCAGAGAAGCGUUUGCUGAAACGGGCACCAGAAGCCACCACCU
...(((((((.((((........))))..(((((..((....))..((((((((.((...(((((......)))))))))).)))))))))).)))))))...... ( -42.20)
>DroEre_CAF1 75 103 + 1
AAAUGGCUUCAGGAGAAUCCCACCUUCGAGGUGCUGCCCUCAGGAACCGUUCAGUCAAUCGACGCAGAGAAGCGUCCGCUGAAACGGCCACAGGAAAC---CACCU
...(((.(((.((((........))))((((......)))).((..(((((((((.....(((((......))))).)))).)))))))....))).)---))... ( -31.00)
>DroYak_CAF1 81 103 + 1
AAAUGGCUACAGGAGAAUCCCACCUACGAGGUCCUGCCCUCGGGAACCGUUCAGUCCAUUGACGCAGAGAAGCGUCCGCUGAAACGGGCGCCGGAAGC---CACCU
...(((((...((......)).((..(((((......)))))((..(((((((((.....(((((......))))).)))).)))))...)))).)))---))... ( -38.60)
>consensus
AAAUGGCUUCAGGAGAAUCCCACCUUCGAGGUGCUGCCCUCAGGAACCGUUCAGUCAAUCGACGCAGAGAAGCGUCCGCUGAAACGGGCACCGGAAGC___CACCU
....((((((.((.........(((..((((......)))))))..(((((((((.....(((((......))))).)))).)))))...)).))))))....... (-28.00 = -29.25 +   1.25)

alignment

secondary structure

dotplot

Window 3

Location	8,243,834 – 8,243,940
Length	106
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	88.94
Mean single sequence MFE	-41.08
Consensus MFE	-30.90
Energy contribution	-32.02
Covariance contribution	1.13
Combinations/Pair	1.12
Mean z-score	-1.44
Structure conservation index	0.75
SVM decision value	-0.01
SVM RNA-class probability	0.527684
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8243834 106 - 27905053
AGGUGGCGGCUUCCGGUGCCCCUUUCAGCAAACGCUUCUCUGCGUCGGCUGACUGAACGGUUCCUGAGGGCAGCACCUCGAAGGAGGGAUUCUCCUGAAGCCAUUU
.......((((((.(((((((((((((((..((((......))))..)))))((....)).....)))))..)))))....(((((.....))))))))))).... ( -44.20)
>DroSec_CAF1 75 106 - 1
AGGUGGUGGCUUCUGGUGCCCGUUUCAGCAAACGCUUCUCUGCGUCGAUUGUCUGAACGGUUCCCGAGGGCAGCACCUCGAAGGUGGGAUUCUCCUGAAGCCAUUU
....(((((((((.(((((((..((((((((((((......))))...))).)))))(((...))).))))).((((.....)))).......)).))))))))). ( -42.30)
>DroEre_CAF1 75 103 - 1
AGGUG---GUUUCCUGUGGCCGUUUCAGCGGACGCUUCUCUGCGUCGAUUGACUGAACGGUUCCUGAGGGCAGCACCUCGAAGGUGGGAUUCUCCUGAAGCCAUUU
(((((---(((((..(..((((((.((((((((((......)))))...)).)))))))))..).((((((..((((.....)))).).)))))..)))))))))) ( -39.40)
>DroYak_CAF1 81 103 - 1
AGGUG---GCUUCCGGCGCCCGUUUCAGCGGACGCUUCUCUGCGUCAAUGGACUGAACGGUUCCCGAGGGCAGGACCUCGUAGGUGGGAUUCUCCUGUAGCCAUUU
(((((---((((((.((..(((((.((((.(((((......)))))....).))))))))....(((((......)))))...)).))).........)))))))) ( -38.40)
>consensus
AGGUG___GCUUCCGGUGCCCGUUUCAGCAAACGCUUCUCUGCGUCGAUUGACUGAACGGUUCCCGAGGGCAGCACCUCGAAGGUGGGAUUCUCCUGAAGCCAUUU
(((((...(((..(((...(((((.((((((((((......)))))...)).))))))))...)))..)))..)))))....((((((.....)))...))).... (-30.90 = -32.02 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:47 2006