Locus 5942

Sequence ID 2R_DroMel_CAF1
Location 18,743,927 – 18,744,020
Length 93
Max. P 0.998777
window9531 window9532

overview

Window 1

Location 18,743,927 – 18,744,020
Length 93
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 78.68
Mean single sequence MFE -28.27
Consensus MFE -19.50
Energy contribution -19.38
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.34
Structure conservation index 0.69
SVM decision value 1.96
SVM RNA-class probability 0.983995
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18743927 93 + 20766785
CGUCGCCGCU-----------GCUGCCGGUAAAUGUCUUUAUAGACAUUAUUCCCGC--AGUCGCCUCGUCUUGGCAAAGCUUUAAAUUUAUGGCAACGCAUUUGC
(((.((((..-----------(((((.((..(((((((....)))))))...)).))--))).(((.......)))...............)))).)))....... ( -29.00)
>DroEre_CAF1 109153 92 + 1
CGCCGUCGCC-----------GCUGCCGGUAAAUGUCUUUAUAGGCAUUAUUCCCGCACAGUCGCC---UCCUGGCAAAGCUUUAAAUUUAUGGCAACGCAUUUGC
.((.((.(((-----------(.(((.((..(((((((....)))))))...)).))))....(((---....)))................))).))))...... ( -25.90)
>DroYak_CAF1 109322 102 + 1
CGCCGUCGUUGCCGCAUUGGAGCUGCCGGUAAAUGUCUUUAUAGACAUUAUUCCCGC--CGUCGCCU--UCCUGGCAAAGCUUUAAAUUUAUGGCAACGCAUUUGC
....(.((((((((..((((((((((.((..(((((((....)))))))...)).))--....(((.--....)))..)))))))).....)))))))))...... ( -35.30)
>DroAna_CAF1 103492 75 + 1
---------------------GUUGCCGGUAAAUGUCUUCAUAGACAU---UCCCGG--AGUCGCCG-----CGGCAAAGCUUUAAAUUUAUGGCAACGCAUUUGC
---------------------((((((((..(((((((....))))))---).))((--(((.((..-----..))...)))))........))))))........ ( -22.90)
>consensus
CGCCGUCGCU___________GCUGCCGGUAAAUGUCUUUAUAGACAUUAUUCCCGC__AGUCGCCU__UCCUGGCAAAGCUUUAAAUUUAUGGCAACGCAUUUGC
.....................((((((((..(((((((....)))))))...)).........(((.......)))................))))..))...... (-19.50 = -19.38 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,743,927 – 18,744,020
Length 93
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 78.68
Mean single sequence MFE -31.25
Consensus MFE -23.56
Energy contribution -23.88
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.81
Structure conservation index 0.75
SVM decision value 3.22
SVM RNA-class probability 0.998777
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18743927 93 - 20766785
GCAAAUGCGUUGCCAUAAAUUUAAAGCUUUGCCAAGACGAGGCGACU--GCGGGAAUAAUGUCUAUAAAGACAUUUACCGGCAGC-----------AGCGGCGACG
((....))((((((...........((((((......))))))(.((--((.((...(((((((....)))))))..)).)))))-----------...)))))). ( -36.00)
>DroEre_CAF1 109153 92 - 1
GCAAAUGCGUUGCCAUAAAUUUAAAGCUUUGCCAGGA---GGCGACUGUGCGGGAAUAAUGCCUAUAAAGACAUUUACCGGCAGC-----------GGCGACGGCG
.......(((((((..............(((((....---)))))((((.(((....((((.((....)).))))..))))))).-----------)))))))... ( -28.20)
>DroYak_CAF1 109322 102 - 1
GCAAAUGCGUUGCCAUAAAUUUAAAGCUUUGCCAGGA--AGGCGACG--GCGGGAAUAAUGUCUAUAAAGACAUUUACCGGCAGCUCCAAUGCGGCAACGACGGCG
((.....(((((((..............(((((....--.))))).(--.(((....(((((((....)))))))..))).).((......)))))))))...)). ( -36.30)
>DroAna_CAF1 103492 75 - 1
GCAAAUGCGUUGCCAUAAAUUUAAAGCUUUGCCG-----CGGCGACU--CCGGGA---AUGUCUAUGAAGACAUUUACCGGCAAC---------------------
((....))((((((..............((((..-----..))))..--..((((---((((((....)))))))).))))))))--------------------- ( -24.50)
>consensus
GCAAAUGCGUUGCCAUAAAUUUAAAGCUUUGCCAGGA__AGGCGACU__GCGGGAAUAAUGUCUAUAAAGACAUUUACCGGCAGC___________AGCGACGGCG
((....))((((((..............(((((.......)))))......((....(((((((....)))))))..))))))))..................... (-23.56 = -23.88 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:37 2006