Locus 1890

Sequence ID 2L_DroMel_CAF1
Location 5,190,684 – 5,190,779
Length 95
Max. P 0.828999
window3035 window3036

overview

Window 5

Location 5,190,684 – 5,190,779
Length 95
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 76.25
Mean single sequence MFE -30.57
Consensus MFE -14.79
Energy contribution -15.27
Covariance contribution 0.48
Combinations/Pair 1.43
Mean z-score -1.91
Structure conservation index 0.48
SVM decision value 0.26
SVM RNA-class probability 0.656392
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5190684 95 + 22407834
UUGGCCGCAGCUCUAAAGGAGCAGUCUUCAACUCCGACUGGAGCUUCGGUUGCUGAAGAUGUUCA--GA------CUCAGCCUGAGGAAAUUGUUCUUGAGGA
..(((((.(((((((..((((..(....)..))))...))))))).))))).(((((....))))--).------.....(((.(((((....))))).))). ( -33.00)
>DroSec_CAF1 67853 95 + 1
UUGGCUGCAGCUCUAAGGGAGCAGUCUUCAACUCCGACUGUAGCUUCAGUUGCUGAAGAUGUUCA--GA------CUCAUCCUGAGGAAAUUGUUCUUGAGGA
..(((((..((((.....)))).(((((((....((((((......)))))).)))))))...))--).------))..((((.(((((....))))).)))) ( -29.30)
>DroSim_CAF1 40653 95 + 1
UUGGCCGCAGCUCUAAAGGAGCAGUCUUCAACUCCGACUGGAGCUUCAGUUGCUGAAGAUGUUCA--GA------CUCAGCCUGAGGAAAUAGUUCUUGAGGA
(((..(...((((.....)))).(((((((....(((((((....))))))).))))))))..))--).------.....(((.(((((....))))).))). ( -28.50)
>DroEre_CAF1 70166 95 + 1
UUGGCCGCAGCUCUAAAGGAGCAGUCUUCAACUCCGACUGAAGCUUCGGUGGUUGAAGAUGUGCA--GG------CUCAGCCGGAGGAAAUUGUUCUGGAGGA
...((((((((((.....)))).((((((((((((((........)))).)))))))))).))).--))------)((..((((((.......))))))..)) ( -38.20)
>DroYak_CAF1 69618 101 + 1
UUGGCCGCAGCUCUUCAGGAGCAGUCUUCAACUCCCACCGAAGCAUCGGUUGUUGAAGAUGUAAA--GGAAAUUGUUCAGCCCAAAGAAAUUGUUCUUGAAGA
...........(((((((((((((((((((((....(((((....))))).))))))))).....--((............))........)))))))))))) ( -32.30)
>DroPer_CAF1 81087 86 + 1
UUGGCCGGAGCCUUGAAGGAACAGC----AA-----ACCGUACCUAAAGUAGAAGAAGCA--UCAACCA------UUCAAGUUGAGACAGUUGUUCCUGCAGA
..(((....)))(((.(((((((((----..-----....(((.....)))......(..--(((((..------.....)))))..).))))))))).))). ( -22.10)
>consensus
UUGGCCGCAGCUCUAAAGGAGCAGUCUUCAACUCCGACUGAAGCUUCAGUUGCUGAAGAUGUUCA__GA______CUCAGCCUGAGGAAAUUGUUCUUGAGGA
..(((....)))((..((((((((((((((.(....(((((....))))).).)))))))...............(((.....))).....)))))))..)). (-14.79 = -15.27 +   0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,190,684 – 5,190,779
Length 95
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 76.25
Mean single sequence MFE -26.50
Consensus MFE -16.15
Energy contribution -17.77
Covariance contribution 1.62
Combinations/Pair 1.33
Mean z-score -1.65
Structure conservation index 0.61
SVM decision value 0.71
SVM RNA-class probability 0.828999
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5190684 95 - 22407834
UCCUCAAGAACAAUUUCCUCAGGCUGAG------UC--UGAACAUCUUCAGCAACCGAAGCUCCAGUCGGAGUUGAAGACUGCUCCUUUAGAGCUGCGGCCAA
.....................(((((((------((--((((((((((((((..((((........)))).)))))))).))....)))))).)).))))).. ( -27.50)
>DroSec_CAF1 67853 95 - 1
UCCUCAAGAACAAUUUCCUCAGGAUGAG------UC--UGAACAUCUUCAGCAACUGAAGCUACAGUCGGAGUUGAAGACUGCUCCCUUAGAGCUGCAGCCAA
((((...(((....)))...))))((.(------.(--((....((((((((.((((......))))....))))))))..((((.....))))..)))))). ( -21.70)
>DroSim_CAF1 40653 95 - 1
UCCUCAAGAACUAUUUCCUCAGGCUGAG------UC--UGAACAUCUUCAGCAACUGAAGCUCCAGUCGGAGUUGAAGACUGCUCCUUUAGAGCUGCGGCCAA
.....................(((((((------((--(......((((((...))))))((((....))))....)))))((((.....))))..))))).. ( -27.50)
>DroEre_CAF1 70166 95 - 1
UCCUCCAGAACAAUUUCCUCCGGCUGAG------CC--UGCACAUCUUCAACCACCGAAGCUUCAGUCGGAGUUGAAGACUGCUCCUUUAGAGCUGCGGCCAA
.....................(((((((------((--((((..((((((((..((((........)))).)))))))).)))......)).))).))))).. ( -28.50)
>DroYak_CAF1 69618 101 - 1
UCUUCAAGAACAAUUUCUUUGGGCUGAACAAUUUCC--UUUACAUCUUCAACAACCGAUGCUUCGGUGGGAGUUGAAGACUGCUCCUGAAGAGCUGCGGCCAA
.....(((((....)))))..(((((..........--......((((((((.(((((....)))))....))))))))..((((.....))))..))))).. ( -30.10)
>DroPer_CAF1 81087 86 - 1
UCUGCAGGAACAACUGUCUCAACUUGAA------UGGUUGA--UGCUUCUUCUACUUUAGGUACGGU-----UU----GCUGUUCCUUCAAGGCUCCGGCCAA
..((.((((((((((((....(((((((------(((..((--....))..))).))))))))))))-----..----..))))))).)).(((....))).. ( -23.70)
>consensus
UCCUCAAGAACAAUUUCCUCAGGCUGAG______UC__UGAACAUCUUCAGCAACCGAAGCUACAGUCGGAGUUGAAGACUGCUCCUUUAGAGCUGCGGCCAA
.....................(((((..................((((((((.((((......))))....))))))))..((((.....))))..))))).. (-16.15 = -17.77 +   1.62)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:50 2006