Locus 1797

Sequence ID 3R_DroMel_CAF1
Location 5,128,879 – 5,128,973
Length 94
Max. P 0.962386
window2961 window2962

overview

Window 1

Location 5,128,879 – 5,128,973
Length 94
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 62.83
Mean single sequence MFE -32.08
Consensus MFE -13.26
Energy contribution -14.86
Covariance contribution 1.60
Combinations/Pair 1.25
Mean z-score -2.32
Structure conservation index 0.41
SVM decision value 1.54
SVM RNA-class probability 0.962386
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5128879 94 + 27905053
GAGCCAGGCCAAGUUGAA--CGCAUGGGCCAACUGAAGGCA---------UAGGCAAUAGCCAA-GGAAAAGGCAGGGCACGCGACUUGGGCAC-----GCAACUUGGCCA
......((((((((((..--.((....(((.......))).---------...)).....((((-(......((...))......)))))....-----.)))))))))). ( -33.60)
>DroSec_CAF1 10663 89 + 1
GAGCCUGGCCAAGUUGAA--CGAAUGGGCCAA-------------------AGGCAAUAGCCAA-GGAAAAGGCAGGGCACGCGACUUGGCCAACUUGGCCAACUUGGCCA
......((((((((((..--(((...((((((-------------------..((....(((..-......))).(....)))...))))))...)))..)))))))))). ( -37.90)
>DroSim_CAF1 7353 80 + 1
GAGCCUGGCCAAGUUGAA--CGAAUGGGCCAA-------------------AGGCAAUAGCCAA-GUGAAAGGCAGGGCACGCGACUUGGCCAACUU---------GGCCA
......((((((((((..--.......(((..-------------------.)))....(((((-((.....((...)).....)))))))))))))---------)))). ( -32.10)
>DroYak_CAF1 8048 76 + 1
GAGCCGGGCAAAGUUGAA--CGAAUG------------GCA---------UAGGCAAUCGCCAAGGAAAAGGACAGGGCACGCGACUAGG------------ACUUUGCCC
.....((((((((((...--.((...------------((.---------...))..))(((..(........)..)))..........)------------))))))))) ( -22.70)
>DroAna_CAF1 30139 102 + 1
GCGUUGCCAAAAGUUGAGUUCGAAUUGGCCAGCCGGCAGCAAGCAGCCAGCAGCUAGCAGCCGG---CGAAAACAGAGCACGCGACUUGGACGA-----G-GACUUGGGCA
....((((..(((((..((((((.((((((.((((((.((.(((........))).)).)))))---)(....).).))...))).))))))..-----.-))))).)))) ( -34.10)
>consensus
GAGCCGGGCCAAGUUGAA__CGAAUGGGCCAA______GCA__________AGGCAAUAGCCAA_GGAAAAGGCAGGGCACGCGACUUGGCCAA________ACUUGGCCA
......(((((((((.....................................(((....)))...........((((........))))............))))))))). (-13.26 = -14.86 +   1.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,128,879 – 5,128,973
Length 94
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 62.83
Mean single sequence MFE -30.85
Consensus MFE -10.86
Energy contribution -12.10
Covariance contribution 1.24
Combinations/Pair 1.27
Mean z-score -2.15
Structure conservation index 0.35
SVM decision value 0.51
SVM RNA-class probability 0.762179
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5128879 94 - 27905053
UGGCCAAGUUGC-----GUGCCCAAGUCGCGUGCCCUGCCUUUUCC-UUGGCUAUUGCCUA---------UGCCUUCAGUUGGCCCAUGCG--UUCAACUUGGCCUGGCUC
.((((((((((.-----.(((((((.(.((((((...(((......-..)))....))..)---------)))....).)))).....)))--..))))))))))...... ( -31.90)
>DroSec_CAF1 10663 89 - 1
UGGCCAAGUUGGCCAAGUUGGCCAAGUCGCGUGCCCUGCCUUUUCC-UUGGCUAUUGCCU-------------------UUGGCCCAUUCG--UUCAACUUGGCCAGGCUC
(((((((((((..(.(((.(((((((..(((......(((......-..)))...))).)-------------------)))))).))).)--..)))))))))))..... ( -39.60)
>DroSim_CAF1 7353 80 - 1
UGGCC---------AAGUUGGCCAAGUCGCGUGCCCUGCCUUUCAC-UUGGCUAUUGCCU-------------------UUGGCCCAUUCG--UUCAACUUGGCCAGGCUC
(((((---------(((((((((((((.(((.....))).....))-)))))....(((.-------------------..))).......--..)))))))))))..... ( -31.30)
>DroYak_CAF1 8048 76 - 1
GGGCAAAGU------------CCUAGUCGCGUGCCCUGUCCUUUUCCUUGGCGAUUGCCUA---------UGC------------CAUUCG--UUCAACUUUGCCCGGCUC
(((((((((------------.(.(((.(((((..(.(((((.......)).))).)..))---------)))------------.))).)--....)))))))))..... ( -20.50)
>DroAna_CAF1 30139 102 - 1
UGCCCAAGUC-C-----UCGUCCAAGUCGCGUGCUCUGUUUUCG---CCGGCUGCUAGCUGCUGGCUGCUUGCUGCCGGCUGGCCAAUUCGAACUCAACUUUUGGCAACGC
..........-.-----...........((((...........(---(((((.((.(((........))).)).))))))..(((((..............))))).)))) ( -30.94)
>consensus
UGGCCAAGU________UUGGCCAAGUCGCGUGCCCUGCCUUUUCC_UUGGCUAUUGCCU__________UGC______UUGGCCCAUUCG__UUCAACUUGGCCAGGCUC
(((((((((...................(((.....)))..........(((....)))......................................)))))))))..... (-10.86 = -12.10 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:48 2006