Locus 5297

Sequence ID 3L_DroMel_CAF1
Location 14,651,696 – 14,651,792
Length 96
Max. P 0.730736
window8372 window8373

overview

Window 2

Location 14,651,696 – 14,651,792
Length 96
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 86.71
Mean single sequence MFE -26.12
Consensus MFE -20.79
Energy contribution -21.68
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -2.35
Structure conservation index 0.80
SVM decision value 0.42
SVM RNA-class probability 0.730736
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14651696 96 + 23771897
AAAGUUCACACAGGCACA---CAAAAAUCGGAA-AAAAGAAGAUAAAAACUCACAAGUUUUGGGCAGCUGGAAGUGCGUGCCUCGCCUGGCGAACUAUCU
..(((((.(.(((((...---............-...........((((((....))))))(((((((.......)).))))).)))))).))))).... ( -26.90)
>DroSec_CAF1 1531 96 + 1
AAAGUUCACACAGGCACA---CAAAAAUCGGGA-CAAAGAAGAUAAAAACUCACAAGUUUUGGGCAGCUGGAAGUGCGUGCCUCGCCUGGCGAACUAUCU
..(((((.(.(((((...---............-...........((((((....))))))(((((((.......)).))))).)))))).))))).... ( -26.90)
>DroSim_CAF1 1524 96 + 1
AAAGUUCACACAGGCACA---CAAAAAUCGGAA-CAAAGAAGAUAAAAACUCACAAGUUUUGGGCAGCUGGAAGUGCGUGCCUCGCCUGGCGAACUAUCU
..(((((.(.(((((...---............-...........((((((....))))))(((((((.......)).))))).)))))).))))).... ( -26.90)
>DroEre_CAF1 1868 96 + 1
UAAGUUCACACAGGCACU---CAACAAUCGGAA-CAAAAAAGAUAAAAACUCACAAGUUUUGGGCAGCUGCAAGUGCGUGCCUCGCCUGGCGAACUCGCU
..(((((.(.(((((...---............-...........((((((....))))))(((((((.......)).))))).)))))).))))).... ( -26.30)
>DroYak_CAF1 1520 96 + 1
UAAGUUCACACGGGCACA---CAAAAAUCGGCAAAAAAAAAGAUA-AAACUCAAAAGUUUUGGGCAGCUGGAAAUGCGUGCCUCGCCUGGCGAACUCGCU
..(((((.(.(((((...---......................((-(((((....)))))))((((((.......)).))))..)))))).))))).... ( -26.00)
>DroAna_CAF1 1709 97 + 1
AAAGUUCACAGAGGCAUAUAGCAAGAAGCCAUA-AAAAAACGACAAAAAGUCACAAGUUUUUGGGA--CAGAAGUGCGUGUCUCGCCUGGCGAACUAGUU
..(((((.(..((((.(((.((.....)).)))-.(((((((((.....)))....))))))((((--((........)))))))))).).))))).... ( -23.70)
>consensus
AAAGUUCACACAGGCACA___CAAAAAUCGGAA_AAAAAAAGAUAAAAACUCACAAGUUUUGGGCAGCUGGAAGUGCGUGCCUCGCCUGGCGAACUAGCU
..(((((.(.(((((..............................((((((....))))))(((((((.......)).))))).)))))).))))).... (-20.79 = -21.68 +   0.89)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,651,696 – 14,651,792
Length 96
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 86.71
Mean single sequence MFE -28.53
Consensus MFE -21.63
Energy contribution -22.97
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.76
SVM decision value 0.02
SVM RNA-class probability 0.541843
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14651696 96 - 23771897
AGAUAGUUCGCCAGGCGAGGCACGCACUUCCAGCUGCCCAAAACUUGUGAGUUUUUAUCUUCUUUU-UUCCGAUUUUUG---UGUGCCUGUGUGAACUUU
....(((((((((((((.((((.((.......))))))(((((.(((.(((...............-)))))).)))))---..)))))).))))))).. ( -29.46)
>DroSec_CAF1 1531 96 - 1
AGAUAGUUCGCCAGGCGAGGCACGCACUUCCAGCUGCCCAAAACUUGUGAGUUUUUAUCUUCUUUG-UCCCGAUUUUUG---UGUGCCUGUGUGAACUUU
....(((((((((((((.((((.((.......)))))))((((((....))))))...........-............---...))))).))))))).. ( -28.20)
>DroSim_CAF1 1524 96 - 1
AGAUAGUUCGCCAGGCGAGGCACGCACUUCCAGCUGCCCAAAACUUGUGAGUUUUUAUCUUCUUUG-UUCCGAUUUUUG---UGUGCCUGUGUGAACUUU
....(((((((((((((.((((.((.......))))))(((((.(((.(((...............-)))))).)))))---..)))))).))))))).. ( -28.76)
>DroEre_CAF1 1868 96 - 1
AGCGAGUUCGCCAGGCGAGGCACGCACUUGCAGCUGCCCAAAACUUGUGAGUUUUUAUCUUUUUUG-UUCCGAUUGUUG---AGUGCCUGUGUGAACUUA
...((((((((((((((.((((.((.......)))))))((((((....))))))...........-............---...))))).)))))))). ( -30.20)
>DroYak_CAF1 1520 96 - 1
AGCGAGUUCGCCAGGCGAGGCACGCAUUUCCAGCUGCCCAAAACUUUUGAGUUU-UAUCUUUUUUUUUGCCGAUUUUUG---UGUGCCCGUGUGAACUUA
...((((((((...(((.((((((((..((..((.....((((((....)))))-)............)).))....))---))))))))))))))))). ( -27.43)
>DroAna_CAF1 1709 97 - 1
AACUAGUUCGCCAGGCGAGACACGCACUUCUG--UCCCAAAAACUUGUGACUUUUUGUCGUUUUUU-UAUGGCUUCUUGCUAUAUGCCUCUGUGAACUUU
....(((((((.((((((((.(((.((....(--((.(((....))).))).....))))).))))-((((((.....)))))).))))..))))))).. ( -27.10)
>consensus
AGAUAGUUCGCCAGGCGAGGCACGCACUUCCAGCUGCCCAAAACUUGUGAGUUUUUAUCUUCUUUG_UUCCGAUUUUUG___UGUGCCUGUGUGAACUUU
....(((((((((((((.((((.((.......)))))).((((((....)))))).............................)))))).))))))).. (-21.63 = -22.97 +   1.33)

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 11:46:37 2006