Locus 7571

Sequence ID	3R_DroMel_CAF1
Location	20,298,486 – 20,298,578
Length	92
Max. P	0.964920

overview

Window 3

Location	20,298,486 – 20,298,578
Length	92
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	77.79
Mean single sequence MFE	-26.98
Consensus MFE	-20.51
Energy contribution	-20.60
Covariance contribution	0.09
Combinations/Pair	1.27
Mean z-score	-2.08
Structure conservation index	0.76
SVM decision value	1.57
SVM RNA-class probability	0.964920
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20298486 92 + 27905053
-----AGAGGCACAUA-GUGAAAAGGGGCGGGGUUCUGGCCAAUUUAGUGGCCACAAACAAAUUGCUUUAGAUUUGUUUGCCCUACAAAGAGAGUCCA
-----...........-........((((((((...((((((......))))))((((((((((......)))))))))))))).(.....).)))). ( -27.10)
>DroSec_CAF1 107344 95 + 1
CA--GAGAGACGUACA-GUGAAAAGGGGCGGGGUUCUGGCCAAUUUAGUGGCCACAAACAAAUUGCUUUAGAUUUGUAUGCCCUACAAAGAAGGCCCA
..--............-........(((((((((..((((((......))))))...(((((((......)))))))..))))).(......))))). ( -27.20)
>DroSim_CAF1 115683 97 + 1
CAUACAGCGACACAGA-GCGAAAAGGGGCGGGGUUCUGGCCAAUUUAGUGGCCACAAACAAAUUGCUUUAGAUUUGUAUGCCCUACAAAGAGGGCCCA
.(((((((........-)).....(((((((.(((.((((((......))))))..)))...))))))).....)))))(((((......)))))... ( -29.30)
>DroEre_CAF1 110375 90 + 1
CA--------UACAAAAGGAAAAAGGGGCGGGGCAAUGGCCAAUUUAGUGGCCACAAGCAAAUUGCUUUAGAUUUGUAUGCCCUACAAAGUGGACUCA
..--------.................(..(((((.((((((......))))))...(((((((......))))))).)))))..)............ ( -25.50)
>DroYak_CAF1 112864 90 + 1
CA--------CACAAAGGGAAAAGAGGGCGGGGCUAUGGCCAAUUUAGUGGCCACAAACAAAUUGCUUUAGAUUUGUAUGCCCUACAAAGUGGGCUCA
..--------...............(((((((((..((((((......))))))...(((((((......)))))))..))))).(.....).)))). ( -27.00)
>DroPer_CAF1 130024 87 + 1
CA--------CACACA-GCGACAG--GGAGUGUUGUUGGCCAAUUUAGUGGCCACAAACAAAUUGCUCUAGAUCUGAGCACUCUUCCCAAUAGAUUCA
..--------......-......(--((((((((..((((((......))))))..))))...(((((.......)))))...))))).......... ( -25.80)
>consensus
CA________CACAAA_GCGAAAAGGGGCGGGGUUCUGGCCAAUUUAGUGGCCACAAACAAAUUGCUUUAGAUUUGUAUGCCCUACAAAGAGGGCCCA
.........................(((((((((..((((((......))))))...(((((((......)))))))..))))).........)))). (-20.51 = -20.60 +   0.09)

alignment

secondary structure

dotplot

Window 4

Location	20,298,486 – 20,298,578
Length	92
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	77.79
Mean single sequence MFE	-23.77
Consensus MFE	-16.51
Energy contribution	-16.73
Covariance contribution	0.22
Combinations/Pair	1.14
Mean z-score	-1.52
Structure conservation index	0.69
SVM decision value	0.81
SVM RNA-class probability	0.855449
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20298486 92 - 27905053
UGGACUCUCUUUGUAGGGCAAACAAAUCUAAAGCAAUUUGUUUGUGGCCACUAAAUUGGCCAGAACCCCGCCCCUUUUCAC-UAUGUGCCUCU-----
.((((.........(((((((((((((........)))))))))((((((......)))))).........))))......-...)).))...----- ( -23.67)
>DroSec_CAF1 107344 95 - 1
UGGGCCUUCUUUGUAGGGCAUACAAAUCUAAAGCAAUUUGUUUGUGGCCACUAAAUUGGCCAGAACCCCGCCCCUUUUCAC-UGUACGUCUCUC--UG
.((((...(..((..((((..((((((........))))))((.((((((......)))))).))....)))).....)).-.)...))))...--.. ( -22.30)
>DroSim_CAF1 115683 97 - 1
UGGGCCCUCUUUGUAGGGCAUACAAAUCUAAAGCAAUUUGUUUGUGGCCACUAAAUUGGCCAGAACCCCGCCCCUUUUCGC-UCUGUGUCGCUGUAUG
...(((((......)))))(((((........((.....((((.((((((......))))))))))...))........((-........))))))). ( -23.40)
>DroEre_CAF1 110375 90 - 1
UGAGUCCACUUUGUAGGGCAUACAAAUCUAAAGCAAUUUGCUUGUGGCCACUAAAUUGGCCAUUGCCCCGCCCCUUUUUCCUUUUGUA--------UG
............(..(((((..........((((.....))))(((((((......))))))))))))..).................--------.. ( -23.80)
>DroYak_CAF1 112864 90 - 1
UGAGCCCACUUUGUAGGGCAUACAAAUCUAAAGCAAUUUGUUUGUGGCCACUAAAUUGGCCAUAGCCCCGCCCUCUUUUCCCUUUGUG--------UG
...((((........))))(((((((...((((........(((((((((......))))))))).........))))....))))))--------). ( -25.03)
>DroPer_CAF1 130024 87 - 1
UGAAUCUAUUGGGAAGAGUGCUCAGAUCUAGAGCAAUUUGUUUGUGGCCACUAAAUUGGCCAACAACACUCC--CUGUCGC-UGUGUG--------UG
..........((((....(((((.......)))))...((((..((((((......))))))..)))).)))--)...(((-.....)--------)) ( -24.40)
>consensus
UGAGCCCACUUUGUAGGGCAUACAAAUCUAAAGCAAUUUGUUUGUGGCCACUAAAUUGGCCAGAACCCCGCCCCUUUUCAC_UGUGUG________UG
...............((((...........((((.....)))).((((((......)))))).......))))......................... (-16.51 = -16.73 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:13 2006