Locus 1539

Sequence ID 2L_DroMel_CAF1
Location 4,156,127 – 4,156,225
Length 98
Max. P 0.967844
window2488 window2489

overview

Window 8

Location 4,156,127 – 4,156,225
Length 98
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 78.33
Mean single sequence MFE -23.19
Consensus MFE -12.60
Energy contribution -15.16
Covariance contribution 2.56
Combinations/Pair 1.27
Mean z-score -2.69
Structure conservation index 0.54
SVM decision value 1.62
SVM RNA-class probability 0.967844
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4156127 98 + 22407834
UGCAGCAGCUGAGGGAAAAGAAAA---AAAAGCGUAAAA-AAAAG-GAAAAUGCAUAGAAAUUACGCAUACGCAGCGUGUGACGACGUUCAAGUUGCUGGUUG
..(((((((((((.(.........---....((((....-.....-....))))..........((((((((...)))))).)).).))).)))))))).... ( -24.52)
>DroSec_CAF1 284849 76 + 1
UGCA------------------------AAAGCGUAAAA-AAGAG-GAAAAUGCAUAGAAAUUACGCAUACGCAGCGUGUGACGACGUUCAAGUUGCUGGCU-
.((.------------------------...((((((..-.....-(......).......))))))....(((((...(((......))).)))))..)).- ( -15.44)
>DroSim_CAF1 289031 97 + 1
UGCAGCAGCUGAGCGAAAAGAAAA---AAAAGCGUAAAA-AAGAG-GAAAAUGCAUAGAAAUUACGCAUACGCAGCGUGUGACGACGUUCAAGUUGCUGGCU-
..(((((((((((((.........---....((((....-.....-....))))..........((((((((...)))))).)).))))).))))))))...- ( -28.42)
>DroEre_CAF1 300956 100 + 1
UGCAGCAGCUGAGCGAGCGGAAAA--AAAGAACGUAAAAUAAGAG-GAAAAUGCAUAGAAAUUACGCAUACGCAGCGUGUGACGACGCUCAAGUUGCUGGCUG
..(((((((((((((.(((.....--......)))..........-..................((((((((...)))))).)).))))).)))))))).... ( -30.20)
>DroYak_CAF1 308055 103 + 1
UGCAGCAGCUGAGCGAAAUGAAAAGAAAAAAACGUAAAAAAAAAGGGAAAAUGCAUAGAAAUUACGCAUACGCAGCGUGUGACGACGCUCAAGUUGCUGGCUG
..(((((((((((((..................(((...............)))..........((((((((...)))))).)).))))).)))))))).... ( -27.86)
>DroAna_CAF1 334736 80 + 1
UGCAGCAGUUGAACAAAA------------AAC---AAA-AAGAG-GAAAAUAUAUAGAAAAUACGCAUACGCAGUGUAU------GCUAAAGUUGUUGGAUG
.(((((.(((........------------)))---...-.....-...................((((((.....))))------))....)))))...... ( -12.70)
>consensus
UGCAGCAGCUGAGCGAAA_GAAAA___AAAAACGUAAAA_AAGAG_GAAAAUGCAUAGAAAUUACGCAUACGCAGCGUGUGACGACGCUCAAGUUGCUGGCUG
..(((((((((((((................((((...............))))........(((((.......)))))......))))).)))))))).... (-12.60 = -15.16 +   2.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,156,127 – 4,156,225
Length 98
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 78.33
Mean single sequence MFE -17.70
Consensus MFE -9.44
Energy contribution -10.55
Covariance contribution 1.11
Combinations/Pair 1.11
Mean z-score -1.81
Structure conservation index 0.53
SVM decision value 0.10
SVM RNA-class probability 0.583892
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4156127 98 - 22407834
CAACCAGCAACUUGAACGUCGUCACACGCUGCGUAUGCGUAAUUUCUAUGCAUUUUC-CUUUU-UUUUACGCUUUU---UUUUCUUUUCCCUCAGCUGCUGCA
....(((((.((.((.(((......)))..(((((((((((.....)))))).....-.....-...)))))....---............)))).))))).. ( -16.91)
>DroSec_CAF1 284849 76 - 1
-AGCCAGCAACUUGAACGUCGUCACACGCUGCGUAUGCGUAAUUUCUAUGCAUUUUC-CUCUU-UUUUACGCUUU------------------------UGCA
-.((.(((.......((((.((.....)).))))(((((((.....)))))))....-.....-......)))..------------------------.)). ( -13.70)
>DroSim_CAF1 289031 97 - 1
-AGCCAGCAACUUGAACGUCGUCACACGCUGCGUAUGCGUAAUUUCUAUGCAUUUUC-CUCUU-UUUUACGCUUUU---UUUUCUUUUCGCUCAGCUGCUGCA
-.((.((((.((.((.((............(((((((((((.....)))))).....-.....-...)))))....---.........)).)))).)))))). ( -19.22)
>DroEre_CAF1 300956 100 - 1
CAGCCAGCAACUUGAGCGUCGUCACACGCUGCGUAUGCGUAAUUUCUAUGCAUUUUC-CUCUUAUUUUACGUUCUUU--UUUUCCGCUCGCUCAGCUGCUGCA
..((.((((.((.(((((.((.........(((((((((((.....)))))).....-.........))))).....--.....))..))))))).)))))). ( -24.84)
>DroYak_CAF1 308055 103 - 1
CAGCCAGCAACUUGAGCGUCGUCACACGCUGCGUAUGCGUAAUUUCUAUGCAUUUUCCCUUUUUUUUUACGUUUUUUUCUUUUCAUUUCGCUCAGCUGCUGCA
..((.((((.((.(((((.((.....))..(((((((((((.....))))))...............)))))................))))))).)))))). ( -22.46)
>DroAna_CAF1 334736 80 - 1
CAUCCAACAACUUUAGC------AUACACUGCGUAUGCGUAUUUUCUAUAUAUUUUC-CUCUU-UUU---GUU------------UUUUGUUCAACUGCUGCA
((...(((((.....((------((((.....))))))((((.....))))......-.....-.))---)))------------...))............. (  -9.10)
>consensus
CAGCCAGCAACUUGAACGUCGUCACACGCUGCGUAUGCGUAAUUUCUAUGCAUUUUC_CUCUU_UUUUACGCUUUU___UUUUC_UUUCGCUCAGCUGCUGCA
....(((((......((((.((.....)).))))(((((((.....)))))))...........................................))))).. ( -9.44 = -10.55 +   1.11)

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 10:05:02 2006