Locus 7388

Sequence ID 3R_DroMel_CAF1
Location 19,618,447 – 19,618,601
Length 154
Max. P 0.977656
window11943 window11944

overview

Window 3

Location 19,618,447 – 19,618,561
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.03
Mean single sequence MFE -19.76
Consensus MFE -9.49
Energy contribution -13.55
Covariance contribution 4.06
Combinations/Pair 1.07
Mean z-score -2.34
Structure conservation index 0.48
SVM decision value 1.80
SVM RNA-class probability 0.977656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19618447 114 - 27905053
AUCAUAAUUCGUAAAAAUAAAAUAGCAUUAAGCUGAUUAAACUUUCUCAGCAAGUGCAC------AUAGUGCACGUGACACAUUUGAUGAAAUAUGAAUAAUAUAUAAGAAGAAGAAGAA
.(((((.(((((...((.......((.....(((((..........)))))..((((((------...)))))))).......)).))))).)))))....................... ( -22.24)
>DroSec_CAF1 2805 102 - 1
AUCAUAAUUCGUAAAAA---AC-----UUGUUCACUUUAAACAUUCUCAGCAUGUGC--------AUAGUGCACGUGACACAUUUGAUGAAAUAUGAAUAAUAUAAAAGAUGA--AAGUA
.(((((.(((((.(((.---..-----.((((.......))))......((((((((--------.....))))))).)...))).))))).)))))................--..... ( -18.10)
>DroSim_CAF1 2834 90 - 1
AUCAUAAUUCGUCAAAA--------------------UAAACUUUUUCAGCAUGUGU--------AUAGUGCACGUGACACAUUUGAUGAAAUAUGAAUAAUAUAGAAGAAGA--AAGUA
.(((((.(((((((((.--------------------....((.....))(((((((--------.....))))))).....))))))))).)))))................--..... ( -19.60)
>DroEre_CAF1 2758 107 - 1
AUCAUAAUG---UAAAA-----UAGCAUUAAGCUGAGAGAAGUUUCUUUGCAAGUACAGUUGAUAACAAUCAACGUGACGCAUUUGAUGAAAUAUGAAUAAUGAAGAAGG-----AAAAA
((((.((((---(....-----..(((..(((((......)))))...)))..((...((((((....))))))...)))))))))))......................-----..... ( -19.10)
>consensus
AUCAUAAUUCGUAAAAA__________UUAAGCUGAUUAAACUUUCUCAGCAAGUGC________AUAGUGCACGUGACACAUUUGAUGAAAUAUGAAUAAUAUAGAAGAAGA__AAGAA
.(((((.(((((((((......((((.....))))..............(((((((((...........)))))))).)...))))))))).)))))....................... ( -9.49 = -13.55 +   4.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,618,487 – 19,618,601
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.41
Mean single sequence MFE -20.56
Consensus MFE -6.86
Energy contribution -9.02
Covariance contribution 2.16
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.33
SVM decision value 1.37
SVM RNA-class probability 0.946938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19618487 114 - 27905053
CACUAUACAUAUACGAAUUAAUGAGUCAAAUCUCUCAUGAAUCAUAAUUCGUAAAAAUAAAAUAGCAUUAAGCUGAUUAAACUUUCUCAGCAAGUGCAC------AUAGUGCACGUGACA
(((........(((((((((.(((.(((.........))).))))))))))))..................(((((..........)))))..((((((------...)))))))))... ( -27.40)
>DroSec_CAF1 2843 104 - 1
CGCUAUACAUAUACGAAUUAAUGAGUCAAAUCUAUCAUGAAUCAUAAUUCGUAAAAA---AC-----UUGUUCACUUUAAACAUUCUCAGCAUGUGC--------AUAGUGCACGUGACA
.(((.......(((((((((.(((.(((.........))).))))))))))))....---..-----.((((.......)))).....)))((((((--------.....)))))).... ( -22.00)
>DroSim_CAF1 2872 92 - 1
CGCUAUAAAUAUACGAAUUAAUGAGUCAAAUCUCUCAUGAAUCAUAAUUCGUCAAAA--------------------UAAACUUUUUCAGCAUGUGU--------AUAGUGCACGUGACA
............((((((((.(((.(((.........))).))))))))))).....--------------------............((((((((--------.....))))))).). ( -17.60)
>DroEre_CAF1 2793 112 - 1
CAAUAUAAACAUACAAAUUAAUGAGUCAAAUCCCUCAUGAAUCAUAAUG---UAAAA-----UAGCAUUAAGCUGAGAGAAGUUUCUUUGCAAGUACAGUUGAUAACAAUCAACGUGACG
....................(((((........)))))......(((((---(....-----..)))))).((.(((((....))))).))..((...((((((....))))))...)). ( -19.70)
>DroYak_CAF1 2851 113 - 1
AAAUAUACUUAUACAAAUUAAUGAGUCAAAUCCCUCAUGAAUCAUAAUGCGUUAACA-----UAUAAU--AACUGGUAGAAGUUUUUUAGCAAGUGCAGUUGAUGACAAUCAAUGUGACG
...........((((.....(((((........))))).........(((((((((.-----..(((.--((((......))))..)))((....)).))))))).)).....))))... ( -16.10)
>consensus
CACUAUACAUAUACGAAUUAAUGAGUCAAAUCUCUCAUGAAUCAUAAUUCGUAAAAA_____UA__AUU_AGCUGAUUAAACUUUCUCAGCAAGUGCA_______AUAGUGCACGUGACA
............((((((((.(((.(((.........))).))))))))))).....................................(((.(((((...........))))).)).). ( -6.86 =  -9.02 +   2.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:42 2006