Locus 1348

Sequence ID 2L_DroMel_CAF1
Location 3,579,679 – 3,579,799
Length 120
Max. P 0.728865
window2203 window2204

overview

Window 3

Location 3,579,679 – 3,579,799
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.50
Mean single sequence MFE -46.32
Consensus MFE -33.63
Energy contribution -33.58
Covariance contribution -0.05
Combinations/Pair 1.39
Mean z-score -1.55
Structure conservation index 0.73
SVM decision value 0.13
SVM RNA-class probability 0.597652
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3579679 120 + 22407834
AAAUAGGAUUCCAGGGCCUGGAGAUUAAGAGCUGCUGCUGCCGCCGAAUUGGCCGGCAGUAGGGCGGCCUGCUGCAAACUGCUGACCAUGGUUCCUUGCAGCGAAAGAACGACCGCAGCA
........((((((...)))))).......(((((((((((((((.....)).))))))))((.((..(((((((((...(((......)))...)))))))...))..)).))))))). ( -48.40)
>DroVir_CAF1 54731 120 + 1
AAAUAGGAUUCGAGUGCCUGCAAGUUGAGCGCUGCUGCUGCUGCCGAAUUGGCCGGCAGCAAUGCCGCCUGCUGCAGGCUGCUGACCAUGGUGCCCUGCAGCGAGAGCACCACAGCAGCU
......(.(((((.((....))..))))))(((((((.((((((((.......)))))))).....((((((((((((..(((......)))..)))))))).)).))....))))))). ( -52.90)
>DroGri_CAF1 56059 120 + 1
AAAUACGAUUCGAGCGCCUGUAAAUUGAGUGCUGCUGCUGCCGCUGAAUUUGCCGGCAGCAAUGCCGCUUGCUGUAGGCUGCUGACCAUGGUGCCCUGUAGUGAGAGGACGACAGCAGCA
............((((((........).)))))(((((((.((((........(((((....)))))((..(((((((..(((......)))..)))))))..)).)).)).))))))). ( -45.40)
>DroWil_CAF1 74291 120 + 1
AAAUAGGAUUCCAAUGCUUGGAGAUUGAGGGCAGCUGCUGCUGCUGAAUUGGCCGGCAAAAGGGCAGCUUGUUGUAGACUGCUAACCAUUGUGCCUUGCAAUGAUAGAACAACAGCAGCA
........(((((.....)))))..........(((((((.(((((.......)))))....(((((((......)).)))))...((((((.....)))))).........))))))). ( -34.30)
>DroMoj_CAF1 62400 120 + 1
AAAUAGGAUUCGAGCGCCUGCAAAUUGAGUGCUGCUGCUGCUGCUGAAUUGGCCGGCAGCAAUGCCGCCUGCUGCAGGCUGCUGACCAUGGUGCCCUGCAGCGACAGAACGACAGCGGCA
............((((((........).)))))((((((((..(((....(((.((((....)))))))(((((((((..(((......)))..))))))))).)))...).))))))). ( -52.90)
>DroAna_CAF1 51512 120 + 1
AGAUAGGAUUCCAAAGCCUGCAGGUUAAGAGCUGCUGCUGCUGCAGAGUUGGCCGGCAACAGAGCGGCCUGUUGCAGGCUGCUGACCAUGGUUCCUUGCAGCGACAGGACAACAGCGGCC
..............((((....))))....(((((((.((((((((....(((((.(......))))))..))))))(((((.(((....)))....))))).......)).))))))). ( -44.00)
>consensus
AAAUAGGAUUCCAGCGCCUGCAAAUUGAGAGCUGCUGCUGCUGCUGAAUUGGCCGGCAGCAAUGCCGCCUGCUGCAGGCUGCUGACCAUGGUGCCCUGCAGCGACAGAACGACAGCAGCA
...((((.........))))..........(((((((((((((((.....)).)))))))).........((((((((.((((......)))).))))))))............))))). (-33.63 = -33.58 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,579,679 – 3,579,799
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.50
Mean single sequence MFE -45.60
Consensus MFE -30.78
Energy contribution -31.73
Covariance contribution 0.95
Combinations/Pair 1.26
Mean z-score -2.17
Structure conservation index 0.68
SVM decision value 0.42
SVM RNA-class probability 0.728865
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3579679 120 - 22407834
UGCUGCGGUCGUUCUUUCGCUGCAAGGAACCAUGGUCAGCAGUUUGCAGCAGGCCGCCCUACUGCCGGCCAAUUCGGCGGCAGCAGCAGCUCUUAAUCUCCAGGCCCUGGAAUCCUAUUU
.((((((((((......)(((((((.(.((....))...)...))))))).))))......((((((.((.....))))))))..)))))........(((((...)))))......... ( -42.70)
>DroVir_CAF1 54731 120 - 1
AGCUGCUGUGGUGCUCUCGCUGCAGGGCACCAUGGUCAGCAGCCUGCAGCAGGCGGCAUUGCUGCCGGCCAAUUCGGCAGCAGCAGCAGCGCUCAACUUGCAGGCACUCGAAUCCUAUUU
.((((((((((((((((......)))))))))))).)))).((((((((..((((((.((((((((((.....))))))))))..))..))))....))))))))............... ( -61.40)
>DroGri_CAF1 56059 120 - 1
UGCUGCUGUCGUCCUCUCACUACAGGGCACCAUGGUCAGCAGCCUACAGCAAGCGGCAUUGCUGCCGGCAAAUUCAGCGGCAGCAGCAGCACUCAAUUUACAGGCGCUCGAAUCGUAUUU
(((((((((((((((........))))).............(((..((((((......))))))..))).........))))))))))((.((........))))............... ( -40.00)
>DroWil_CAF1 74291 120 - 1
UGCUGCUGUUGUUCUAUCAUUGCAAGGCACAAUGGUUAGCAGUCUACAACAAGCUGCCCUUUUGCCGGCCAAUUCAGCAGCAGCAGCUGCCCUCAAUCUCCAAGCAUUGGAAUCCUAUUU
.((((((((((((.....((((...((((.((.((...((((.((......)))))))))).))))...))))..))))))))))))...........((((.....))))......... ( -36.50)
>DroMoj_CAF1 62400 120 - 1
UGCCGCUGUCGUUCUGUCGCUGCAGGGCACCAUGGUCAGCAGCCUGCAGCAGGCGGCAUUGCUGCCGGCCAAUUCAGCAGCAGCAGCAGCACUCAAUUUGCAGGCGCUCGAAUCCUAUUU
.((((((((.((((((..((((((((((((....))..))..)))))))).(((((((....)))).)))....))).))).))))).(((.......))).)))............... ( -48.40)
>DroAna_CAF1 51512 120 - 1
GGCCGCUGUUGUCCUGUCGCUGCAAGGAACCAUGGUCAGCAGCCUGCAACAGGCCGCUCUGUUGCCGGCCAACUCUGCAGCAGCAGCAGCUCUUAACCUGCAGGCUUUGGAAUCCUAUCU
((((((((((((...((.(((((..(....)...).)))).(((.((((((((....)))))))).)))..))...)))))))).((((........)))).)))).............. ( -44.60)
>consensus
UGCUGCUGUCGUUCUCUCGCUGCAAGGCACCAUGGUCAGCAGCCUGCAGCAGGCGGCACUGCUGCCGGCCAAUUCAGCAGCAGCAGCAGCACUCAAUCUGCAGGCACUCGAAUCCUAUUU
.(((((((((((......(((((..(....)...).)))).(((.(((((((......))))))).))).......))))))))))).((.((........))))............... (-30.78 = -31.73 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:18 2006