Locus 1352

Sequence ID 2L_DroMel_CAF1
Location 3,587,186 – 3,587,356
Length 170
Max. P 0.642295
window2210 window2211

overview

Window 0

Location 3,587,186 – 3,587,297
Length 111
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 82.41
Mean single sequence MFE -26.00
Consensus MFE -23.30
Energy contribution -23.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.90
SVM decision value 0.23
SVM RNA-class probability 0.642295
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3587186 111 - 22407834
AAA-CUCAAGACUCAAGACCACAGACCCCCAGACCCCAGACCACAAGACACCCAAAGCCCCGAGACAGGGAGGAGCACUCUUGAGAGACCCUCGUGCUCGUGCCCCGUUUCA
...-.........................................................(((((.((((.((((((....(((.....))))))))).).))).))))). ( -23.30)
>DroSec_CAF1 54913 104 - 1
AAA-CUCAAGACUCGAGACCACAUACCCCC-------AGACCACAAGACACCCAAAGCCCCGAGACAGGGAGGAGCACUCUUGAGAGACCCUCGUGCUCGUGCCCCGUUUCA
...-(((.......))).............-------........................(((((.((((.((((((....(((.....))))))))).).))).))))). ( -25.00)
>DroSim_CAF1 58328 104 - 1
AAA-CUCAAGACUCGAGACCACAGAUCCCC-------AGACCACAAGACACCCAAAGCCCCGAGACAGGGAGGAGCACUCUUGAGAGACCCUCGUGCUCGUGCCCCGUUUCA
...-(((.......))).............-------........................(((((.((((.((((((....(((.....))))))))).).))).))))). ( -25.00)
>DroAna_CAF1 59570 91 - 1
AAAACUAAAGA-----AAAAAC---------------UGAAAACU-GAAAACCCAGGCCUCGAGACAGGGAGGAGCACUCUUGAGAGACCCUCGUGCUCGUGCCCUGUUUCA
...........-----......---------------.((...((-(......)))...))((((((((((.((((((....(((.....))))))))).).))))))))). ( -30.70)
>consensus
AAA_CUCAAGACUCGAGACCACAGACCCCC_______AGACCACAAGACACCCAAAGCCCCGAGACAGGGAGGAGCACUCUUGAGAGACCCUCGUGCUCGUGCCCCGUUUCA
.............................................................(((((.((((.((((((....(((.....))))))))).).))).))))). (-23.30 = -23.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,587,258 – 3,587,356
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 90.94
Mean single sequence MFE -21.47
Consensus MFE -18.45
Energy contribution -19.23
Covariance contribution 0.78
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.86
SVM decision value 0.09
SVM RNA-class probability 0.578855
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3587258 98 - 22407834
GACUCGAGUGCUUGGGGAAUGGACGAGACUCCACCUCAAGAUUCAAGCCCCAAAACUCAAAACUCAAGACUCAAGACCACAGACCCCCAGACCCCAGA
.....((((..((((((..((((.(((.......)))....))))..)))))).))))........................................ ( -19.80)
>DroSec_CAF1 54985 91 - 1
GACUCGAGUGCUUGGGAAAUGGACGAGACUCCACCUCAAGAUCCAAGCCCCAAAACUCAAAACUCAAGACUCGAGACCACAUACCCCC-------AGA
..(((((((.((((((...((((.(((.......)))....))))((........)).....))))))))))))).............-------... ( -21.50)
>DroSim_CAF1 58400 91 - 1
GACUCGAGUGCUUGGGGAAUGGACGAGACUCCACCUCAAGAUCCCAGCCCCAAAACUCAAAACUCAAGACUCGAGACCACAGAUCCCC-------AGA
..(((((((..((((((...(((.(((.......)))....)))...)))))).........(....)))))))).............-------... ( -23.10)
>consensus
GACUCGAGUGCUUGGGGAAUGGACGAGACUCCACCUCAAGAUCCAAGCCCCAAAACUCAAAACUCAAGACUCGAGACCACAGACCCCC_______AGA
..(((((((..((((((..((((.(((.......)))....))))..)))))).........(....))))))))....................... (-18.45 = -19.23 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:24 2006