Locus 7912

Sequence ID	3R_DroMel_CAF1
Location	21,229,692 – 21,229,805
Length	113
Max. P	0.999144

overview

Window 3

Location	21,229,692 – 21,229,805
Length	113
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	72.93
Mean single sequence MFE	-35.01
Consensus MFE	-14.38
Energy contribution	-15.94
Covariance contribution	1.56
Combinations/Pair	1.35
Mean z-score	-2.04
Structure conservation index	0.41
SVM decision value	1.15
SVM RNA-class probability	0.923451
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21229692 113 + 27905053
--CAGUACACCGACUUGCU-CGAAUGUGGGGGAAGCCGAAGCAAAGCACAUUAAGCCAAGAAAGAGGCUUCUGCGGAGUCGGUGGGAAAAAUGGAGCUGCAGUUGAAGCAGCGGCA
--..((.(((((((((((.-.....)).(.(((((((........((.......)).........))))))).).)))))))))...........(((((.......))))).)). ( -37.63)
>DroSim_CAF1 56608 113 + 1
--CAGUAUACCGACUUGCU-CGACUGUGGGGGAAGCCGAAGCAAAGCACAUUAAGCGAAGAAAGAGGCUUCUGUGGCGUUGGUGGGAAAAAUGGAGCUGCAGUUGAAGCAGCGGCA
--.......((..((..(.-((((.((.(.(((((((........((.......)).........))))))).).)))))))..)).........(((((.......))))))).. ( -35.83)
>DroEre_CAF1 57888 114 + 1
-CCAGUAUACCGACUUGCU-GGAAUGUGGGGGAAGUCGAAUCAAAGCACAUUAAGCCAAGAAAGAGGCCUCUGCGCCGUCGGUGGGAAAAAUGAAGCUGCAGUUGAAGCAGCGGCA
-((....(((((((..(((-..((((((...((.......))....)))))).))).........(((......))))))))))...........(((((.......))))))).. ( -32.70)
>DroYak_CAF1 58872 100 + 1
ACCGGUAUACCGACUUUCU-CUAAUGUGGGAGAAGU---------------UAAGCCAAGAAAGAGGCUCCUGCGCCGUCGGUGGGAAAAAUGAAGCUGCAGUUGAAGCAGCGGCA
.((....(((((((.((((-((......))))))((---------------..((((........))))...))...)))))))...........(((((.......))))))).. ( -32.80)
>DroAna_CAF1 50684 92 + 1
----GGGCGGCGA--UGCUGCGACGAU--GGGAAGCCACAUCGAAACACAUUAGGCCAAGGAAGCUGUUGC-----CAU-----GAAAAAAUGAAG------UUGCAGCAGCGCCA
----....((((.--((((((((((((--(((...)).))))...........(((..((....))...))-----)..-----...........)------)))))))).)))). ( -36.10)
>consensus
__CAGUAUACCGACUUGCU_CGAAUGUGGGGGAAGCCGAAGCAAAGCACAUUAAGCCAAGAAAGAGGCUUCUGCGCCGUCGGUGGGAAAAAUGAAGCUGCAGUUGAAGCAGCGGCA
....((.(((((((...............((....))................((((........))))........)))))))...........(((((.......))))).)). (-14.38 = -15.94 +   1.56)

alignment

secondary structure

dotplot

Window 4

Location	21,229,692 – 21,229,805
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	72.93
Mean single sequence MFE	-32.72
Consensus MFE	-12.54
Energy contribution	-13.38
Covariance contribution	0.84
Combinations/Pair	1.36
Mean z-score	-2.81
Structure conservation index	0.38
SVM decision value	3.40
SVM RNA-class probability	0.999144
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21229692 113 - 27905053
UGCCGCUGCUUCAACUGCAGCUCCAUUUUUCCCACCGACUCCGCAGAAGCCUCUUUCUUGGCUUAAUGUGCUUUGCUUCGGCUUCCCCCACAUUCG-AGCAAGUCGGUGUACUG--
....(((((.......)))))...........((((((((..((..(((((........)))))((((((....((....))......))))))..-.)).)))))))).....-- ( -39.10)
>DroSim_CAF1 56608 113 - 1
UGCCGCUGCUUCAACUGCAGCUCCAUUUUUCCCACCAACGCCACAGAAGCCUCUUUCUUCGCUUAAUGUGCUUUGCUUCGGCUUCCCCCACAGUCG-AGCAAGUCGGUAUACUG--
....(((((.......)))))............(((.((((.(((.((((..........))))..))))).(((((.(((((........)))))-))))))).)))......-- ( -28.70)
>DroEre_CAF1 57888 114 - 1
UGCCGCUGCUUCAACUGCAGCUUCAUUUUUCCCACCGACGGCGCAGAGGCCUCUUUCUUGGCUUAAUGUGCUUUGAUUCGACUUCCCCCACAUUCC-AGCAAGUCGGUAUACUGG-
..(((((((.......)))))............((((((((((((.(((((........)))))..))))))..((.......))...........-.....)))))).....))- ( -31.90)
>DroYak_CAF1 58872 100 - 1
UGCCGCUGCUUCAACUGCAGCUUCAUUUUUCCCACCGACGGCGCAGGAGCCUCUUUCUUGGCUUA---------------ACUUCUCCCACAUUAG-AGAAAGUCGGUAUACCGGU
.((((((((.......)))))............(((((((((.((((((.....)))))))))..---------------..(((((........)-)))).)))))).....))) ( -32.70)
>DroAna_CAF1 50684 92 - 1
UGGCGCUGCUGCAA------CUUCAUUUUUUC-----AUG-----GCAACAGCUUCCUUGGCCUAAUGUGUUUCGAUGUGGCUUCCC--AUCGUCGCAGCA--UCGCCGCCC----
.((((.((((((((------(..((((...((-----(.(-----((....)))....)))...)))).)))..(((((((....))--).))))))))))--.))))....---- ( -31.20)
>consensus
UGCCGCUGCUUCAACUGCAGCUUCAUUUUUCCCACCGACGCCGCAGAAGCCUCUUUCUUGGCUUAAUGUGCUUUGAUUCGGCUUCCCCCACAUUCG_AGCAAGUCGGUAUACUG__
(((((((((.......))))).........................(((((........))))).........................................))))....... (-12.54 = -13.38 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:53 2006