Locus 8573

Sequence ID 3R_DroMel_CAF1
Location 22,902,860 – 22,902,956
Length 96
Max. P 0.965417
window13772 window13773

overview

Window 2

Location 22,902,860 – 22,902,956
Length 96
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 77.19
Mean single sequence MFE -20.79
Consensus MFE -11.72
Energy contribution -12.50
Covariance contribution 0.78
Combinations/Pair 1.24
Mean z-score -2.39
Structure conservation index 0.56
SVM decision value 1.58
SVM RNA-class probability 0.965417
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22902860 96 + 27905053
GUGUCGGCCAACUA---AAAAAAAAA---AAAAACAAAACCUAUCAAAGCGAAGAGGCUAGGAUGGGAAAAUGG-UUUUGGCAAAUAUUGGCCAACAGUUCAA
.(((.((((((...---.........---..........((((((..(((......)))..))))))......(-(....)).....)))))).)))...... ( -23.80)
>DroSec_CAF1 19863 82 + 1
GUGUCGGCCAACUA---AAA-----------------AACCUAUCAAAGCGAAGAGGCUAGGAUGGGAAAAUGG-UUUUGGCAAAUAUUGGCCAACAGUUCAA
.(((.((((((...---...-----------------..((((((..(((......)))..))))))......(-(....)).....)))))).)))...... ( -23.80)
>DroSim_CAF1 20544 85 + 1
GUGUCGGCCAACUA---AAAAAA--------------AAGCUAUCAAAGCGAAGAGGCUAGGAUGGGAAAAUGG-UUUUGGCAAAUAUUGGCCAACAGUUCAA
.(((.((((((...---......--------------..(((.....)))......((((((((.(.....).)-))))))).....)))))).)))...... ( -22.40)
>DroEre_CAF1 49691 84 + 1
GUGUCGGCCAACUA---AAA----------------AAACCCAUCAAAGAGAAGAGGCUAGGAUGGUAAAAUGGAUUUUGGCCAAUAUUGGCCAAUAGUUCAA
..............---...----------------....(((((..((........))..))))).....(((((((((((((....))))))).)))))). ( -21.00)
>DroYak_CAF1 20560 99 + 1
GUGUCGGCCAACUA---AAAAAAAAACUAUAAAAAAAAACCAAUCAAAGAGAAGCGGCUAGGAUGGGAAAAUGG-UUUUGGCAAAUAUUGGCCAAUAGUUCAA
.....((((((...---.....((((((((.........(((.((..((........))..)))))....))))-))))........)))))).......... ( -17.81)
>DroAna_CAF1 32782 92 + 1
GUGUUGACAAACUGCUGAAA-AAACACAAAAAACAAAGACCAAUCGAGGGGA----GCUA-----GGGAAGUGG-CGUUGGCAAAUAUUGGCCAAUAGUUCAG
(((((..((......))...-.)))))............((......))(((----((((-----......)))-)((((((........))))))..))).. ( -15.90)
>consensus
GUGUCGGCCAACUA___AAA_AA_____________AAACCUAUCAAAGCGAAGAGGCUAGGAUGGGAAAAUGG_UUUUGGCAAAUAUUGGCCAACAGUUCAA
.(((.((((((............................((((((..((........))..))))))((((....))))........)))))).)))...... (-11.72 = -12.50 +   0.78)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,902,860 – 22,902,956
Length 96
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 77.19
Mean single sequence MFE -18.51
Consensus MFE -9.58
Energy contribution -10.00
Covariance contribution 0.42
Combinations/Pair 1.22
Mean z-score -2.26
Structure conservation index 0.52
SVM decision value 1.10
SVM RNA-class probability 0.915151
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22902860 96 - 27905053
UUGAACUGUUGGCCAAUAUUUGCCAAAA-CCAUUUUCCCAUCCUAGCCUCUUCGCUUUGAUAGGUUUUGUUUUU---UUUUUUUUU---UAGUUGGCCGACAC
......(((((((((((.......((((-.((....((.(((..(((......)))..))).))...)).))))---.........---..))))))))))). ( -22.17)
>DroSec_CAF1 19863 82 - 1
UUGAACUGUUGGCCAAUAUUUGCCAAAA-CCAUUUUCCCAUCCUAGCCUCUUCGCUUUGAUAGGUU-----------------UUU---UAGUUGGCCGACAC
......(((((((((((.(((....)))-.......((.(((..(((......)))..))).))..-----------------...---..))))))))))). ( -21.50)
>DroSim_CAF1 20544 85 - 1
UUGAACUGUUGGCCAAUAUUUGCCAAAA-CCAUUUUCCCAUCCUAGCCUCUUCGCUUUGAUAGCUU--------------UUUUUU---UAGUUGGCCGACAC
......(((((((((((.(((....)))-..........(((..(((......)))..))).....--------------......---..))))))))))). ( -19.10)
>DroEre_CAF1 49691 84 - 1
UUGAACUAUUGGCCAAUAUUGGCCAAAAUCCAUUUUACCAUCCUAGCCUCUUCUCUUUGAUGGGUUU----------------UUU---UAGUUGGCCGACAC
........(((((((((..(((.......))).....(((((..((........))..)))))....----------------...---..)))))))))... ( -20.10)
>DroYak_CAF1 20560 99 - 1
UUGAACUAUUGGCCAAUAUUUGCCAAAA-CCAUUUUCCCAUCCUAGCCGCUUCUCUUUGAUUGGUUUUUUUUUAUAGUUUUUUUUU---UAGUUGGCCGACAC
........(((((((((.......((((-(.((...........(((((..((.....)).))))).......)).))))).....---..)))))))))... ( -16.71)
>DroAna_CAF1 32782 92 - 1
CUGAACUAUUGGCCAAUAUUUGCCAACG-CCACUUCCC-----UAGC----UCCCCUCGAUUGGUCUUUGUUUUUUGUGUUU-UUUCAGCAGUUUGUCAACAC
(((((...(((((........)))))..-.(((.....-----.(((----...((......)).....)))....)))...-.))))).............. ( -11.50)
>consensus
UUGAACUAUUGGCCAAUAUUUGCCAAAA_CCAUUUUCCCAUCCUAGCCUCUUCGCUUUGAUAGGUUU_____________UU_UUU___UAGUUGGCCGACAC
........(((((((((...((........))............(((((..((.....)).))))).........................)))))))))... ( -9.58 = -10.00 +   0.42)

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 13:14:24 2006