Locus 5068

Sequence ID 3R_DroMel_CAF1
Location 13,360,268 – 13,360,387
Length 119
Max. P 0.895509
window8264 window8265

overview

Window 4

Location 13,360,268 – 13,360,387
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.71
Mean single sequence MFE -34.65
Consensus MFE -20.35
Energy contribution -23.76
Covariance contribution 3.41
Combinations/Pair 1.27
Mean z-score -2.06
Structure conservation index 0.59
SVM decision value 0.89
SVM RNA-class probability 0.875402
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13360268 119 + 27905053
AAGAGUUUAGUGGUACCGUGUGCGGAAGUAAGUUUCAUCUCCAGUUUAGUGUUACCAGA-GUCUAUGUUGGCUUCCUCACCACGUGGUGAAGGAGGGAAACUUUGCUGCAUACGGUGAGA
.............((((((((((((....(((((((.(((((...............((-(((......)))))..(((((....))))).))))))))))))..))))))))))))... ( -45.90)
>DroSec_CAF1 105295 119 + 1
AGGAAUUUAGUGGUACCGUGUGCAGAAAUUAGUUUCAUCUCCAAUUUAGUGUUACCAGA-GUCUAUGUUGUCUUGCUCACCACGUGGUGAAGGAGGGAAACUUUGCUGCAUACGGUGAAA
.............((((((((((((.....((((((.(((((...............((-(.(......).)))..(((((....))))).)))))))))))...))))))))))))... ( -42.70)
>DroSim_CAF1 110917 119 + 1
AGGAAUUUAGUGGUACCGUGUGCAGAAAUUAGUUUCAUCUCCAAUUUAGUGUUACCAGA-GUCUAUGUUGUCUUGCUCACCACGUGGUGAAGGAGGGAAACUUUGCUACAUACGGUAAAA
.............(((((((((.((.....((((((.(((((...............((-(.(......).)))..(((((....))))).)))))))))))...)).)))))))))... ( -36.40)
>DroEre_CAF1 112909 107 + 1
AAGAUGUUAGUGGUACCAUAUGCGGAAACUAGUUUCAUC-CCAAUUCAGUGUUACCAGA-GAUUAAGGUGUCUUCCUCACCACGUGGUGA-----GAAAAUUCAAUAAAAAU-----U-A
..((((..(.((((.((......))..)))).)..))))-.................((-(((......))))).((((((....)))))-----)................-----.-. ( -20.40)
>DroYak_CAF1 129800 119 + 1
AAGAAGUUAGUGGUACCAUAUGUUGAAACUAGUUUUAUCCCCAAUUCAGCGUUACCUCUCUGGUAUGUUGUCUUUCUCACCACGUGGUGUAGGACGGAAACUUAGCUACAGUAGGUGA-A
.........(((....))).(((((((.................)))))))((((((((.((((.....(((((...((((....)))).)))))(....)...)))).)).))))))-. ( -27.83)
>consensus
AAGAAUUUAGUGGUACCGUGUGCAGAAAUUAGUUUCAUCUCCAAUUUAGUGUUACCAGA_GUCUAUGUUGUCUUCCUCACCACGUGGUGAAGGAGGGAAACUUUGCUACAUACGGUGA_A
.............((((((((((((.....((((((.(((((..............((....))............(((((....))))).)))))))))))...))))))))))))... (-20.35 = -23.76 +   3.41)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,360,268 – 13,360,387
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.71
Mean single sequence MFE -29.02
Consensus MFE -13.36
Energy contribution -15.00
Covariance contribution 1.64
Combinations/Pair 1.23
Mean z-score -2.28
Structure conservation index 0.46
SVM decision value 0.99
SVM RNA-class probability 0.895509
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13360268 119 - 27905053
UCUCACCGUAUGCAGCAAAGUUUCCCUCCUUCACCACGUGGUGAGGAAGCCAACAUAGAC-UCUGGUAACACUAAACUGGAGAUGAAACUUACUUCCGCACACGGUACCACUAAACUCUU
....(((((.(((.(..(((((((..((((.((((....))))))))............(-((..((........))..)))..)))))))....).))).))))).............. ( -33.90)
>DroSec_CAF1 105295 119 - 1
UUUCACCGUAUGCAGCAAAGUUUCCCUCCUUCACCACGUGGUGAGCAAGACAACAUAGAC-UCUGGUAACACUAAAUUGGAGAUGAAACUAAUUUCUGCACACGGUACCACUAAAUUCCU
....(((((.(((((.((((((((.((..((((((....))))))..))..........(-((..((........))..)))..))))))..)).))))).))))).............. ( -33.50)
>DroSim_CAF1 110917 119 - 1
UUUUACCGUAUGUAGCAAAGUUUCCCUCCUUCACCACGUGGUGAGCAAGACAACAUAGAC-UCUGGUAACACUAAAUUGGAGAUGAAACUAAUUUCUGCACACGGUACCACUAAAUUCCU
...((((((.(((((.((((((((.((..((((((....))))))..))..........(-((..((........))..)))..))))))..)).))))).))))))............. ( -32.50)
>DroEre_CAF1 112909 107 - 1
U-A-----AUUUUUAUUGAAUUUUC-----UCACCACGUGGUGAGGAAGACACCUUAAUC-UCUGGUAACACUGAAUUGG-GAUGAAACUAGUUUCCGCAUAUGGUACCACUAACAUCUU
.-.-----............(((((-----(((((....))))))))))...........-..(((((.....(((((((-.......)))))))(((....)))))))).......... ( -21.60)
>DroYak_CAF1 129800 119 - 1
U-UCACCUACUGUAGCUAAGUUUCCGUCCUACACCACGUGGUGAGAAAGACAACAUACCAGAGAGGUAACGCUGAAUUGGGGAUAAAACUAGUUUCAACAUAUGGUACCACUAACUUCUU
.-..(((...((((((((.((((..(((((.((((....))))............((((.....))))...........))))).)))))))))...)))...))).............. ( -23.60)
>consensus
U_UCACCGUAUGUAGCAAAGUUUCCCUCCUUCACCACGUGGUGAGCAAGACAACAUAGAC_UCUGGUAACACUAAAUUGGAGAUGAAACUAAUUUCCGCACACGGUACCACUAAAUUCUU
....(((((.(((......((((((.....(((((....)))))...................(((.....)))....))))))((((....)))).))).))))).............. (-13.36 = -15.00 +   1.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:25 2006