Locus 4012

Sequence ID 2L_DroMel_CAF1
Location 11,658,257 – 11,658,352
Length 95
Max. P 0.969991
window6323 window6324

overview

Window 3

Location 11,658,257 – 11,658,352
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 98.74
Mean single sequence MFE -21.20
Consensus MFE -20.26
Energy contribution -20.10
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.96
SVM decision value 1.50
SVM RNA-class probability 0.959323
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11658257 95 + 22407834
AAACCACAAAGCAAACACAAACACAAAUAGAGAUGAGAGGGUAUGAGGAGGCUUAAAUGGGGGUUCGUGGGUGCCGCAGUGGAAACAGUGGCAAA
...((((..........((.((.....((....)).....)).))..(((.(((.....))).))))))).((((((..((....)))))))).. ( -20.50)
>DroSec_CAF1 119590 95 + 1
AAACCACAAAGCAAACACAAACACAAAUAGAGAUGAGAGGGUAUGAGGAGGCUUAAAUGGGGGUUCGUGGGUGCCGCAGUGGAAACAGUGGCAAA
...((((..........((.((.....((....)).....)).))..(((.(((.....))).))))))).((((((..((....)))))))).. ( -20.50)
>DroSim_CAF1 117396 95 + 1
AAACCACAAAGCAAACACAAACACAAAUAGAGAUGAGAGGGUAUGAGGAGGCUUAAAUGGGGGUUCGUGGGUGCCGCAGUGGAAACAGUGGCAAA
...((((..........((.((.....((....)).....)).))..(((.(((.....))).))))))).((((((..((....)))))))).. ( -20.50)
>DroEre_CAF1 141195 95 + 1
AAACCACAAAGCAAACACAAACACAAAUAGAGAUGAGAGGGUAUGAGGAGGCUUAAAUGGGGGUUCGUGGGUGCCGCAGUGGAAACAGUGGCAGA
...((((..........((.((.....((....)).....)).))..(((.(((.....))).))))))).((((((..((....)))))))).. ( -20.50)
>DroYak_CAF1 115391 95 + 1
AAACCACAAAGCAAACACAAACACAAAUAGAGAUGAGAGGGUUUGAGGAGGCUUAAAUGGGGGUUCGUGGGUGCCGCAGUGGAAACAGUGGUAAA
..(((((...(((..(((.....(((((.....(....).)))))..(((.(((.....))).))))))..))).....((....)))))))... ( -24.00)
>consensus
AAACCACAAAGCAAACACAAACACAAAUAGAGAUGAGAGGGUAUGAGGAGGCUUAAAUGGGGGUUCGUGGGUGCCGCAGUGGAAACAGUGGCAAA
...((((..........((.((.....((....)).....)).))..(((.(((.....))).))))))).((((((..((....)))))))).. (-20.26 = -20.10 +  -0.16)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 11,658,257 – 11,658,352
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 98.74
Mean single sequence MFE -16.26
Consensus MFE -16.26
Energy contribution -16.26
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 1.00
SVM decision value 1.65
SVM RNA-class probability 0.969991
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11658257 95 - 22407834
UUUGCCACUGUUUCCACUGCGGCACCCACGAACCCCCAUUUAAGCCUCCUCAUACCCUCUCAUCUCUAUUUGUGUUUGUGUUUGCUUUGUGGUUU
.............((((...((((..(((((((...((..((........................))..)).)))))))..))))..))))... ( -16.26)
>DroSec_CAF1 119590 95 - 1
UUUGCCACUGUUUCCACUGCGGCACCCACGAACCCCCAUUUAAGCCUCCUCAUACCCUCUCAUCUCUAUUUGUGUUUGUGUUUGCUUUGUGGUUU
.............((((...((((..(((((((...((..((........................))..)).)))))))..))))..))))... ( -16.26)
>DroSim_CAF1 117396 95 - 1
UUUGCCACUGUUUCCACUGCGGCACCCACGAACCCCCAUUUAAGCCUCCUCAUACCCUCUCAUCUCUAUUUGUGUUUGUGUUUGCUUUGUGGUUU
.............((((...((((..(((((((...((..((........................))..)).)))))))..))))..))))... ( -16.26)
>DroEre_CAF1 141195 95 - 1
UCUGCCACUGUUUCCACUGCGGCACCCACGAACCCCCAUUUAAGCCUCCUCAUACCCUCUCAUCUCUAUUUGUGUUUGUGUUUGCUUUGUGGUUU
.............((((...((((..(((((((...((..((........................))..)).)))))))..))))..))))... ( -16.26)
>DroYak_CAF1 115391 95 - 1
UUUACCACUGUUUCCACUGCGGCACCCACGAACCCCCAUUUAAGCCUCCUCAAACCCUCUCAUCUCUAUUUGUGUUUGUGUUUGCUUUGUGGUUU
.............((((...((((..(((((((...((..((........................))..)).)))))))..))))..))))... ( -16.26)
>consensus
UUUGCCACUGUUUCCACUGCGGCACCCACGAACCCCCAUUUAAGCCUCCUCAUACCCUCUCAUCUCUAUUUGUGUUUGUGUUUGCUUUGUGGUUU
.............((((...((((..(((((((...((..((........................))..)).)))))))..))))..))))... (-16.26 = -16.26 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:07 2006