Locus 266

Sequence ID 3R_DroMel_CAF1
Location 1,047,498 – 1,047,698
Length 200
Max. P 0.598938
window461 window462

overview

Window 1

Location 1,047,498 – 1,047,618
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.33
Mean single sequence MFE -37.00
Consensus MFE -26.51
Energy contribution -28.07
Covariance contribution 1.56
Combinations/Pair 1.15
Mean z-score -1.62
Structure conservation index 0.72
SVM decision value 0.13
SVM RNA-class probability 0.598938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1047498 120 + 27905053
CAAACAGCCAAGUAAGGUGAUUAAAAGAGAGCCGCUGGGAGGGAGAAGUGCGAUUCUGGACAUUACUUGUUGGCCAGAAUCUCAAACUUGAUGCCGUGGUCGUGCUUCUCCAACUCGCUA
.....(((.......(((..((....))..)))...(((..(((((((..((((..(((.(((((....((((........))))...))))))))..))))..)))))))..)))))). ( -40.70)
>DroSec_CAF1 19420 120 + 1
CAAACAGCCAAGAAAGGUGAUUAAAAGAGAGCCGCUGAGAGGGAGAAGUGCGAUUCUGGACCUCACUUGUUGGCCAGAAUCUCAAACUUCAUGCCGUGAUCGUGCUUCUCCAACUCGCUA
.....(((..((...(((..((....))..))).))(((..(((((((..(((((((((.((.........)))))))))).......((((...))))..)..)))))))..)))))). ( -42.10)
>DroSim_CAF1 19291 120 + 1
CAAACAGCCAAGAAAGGUGAUUAAAAGAGAGCCGCUGGGAGGGAGAAGUGCGAUUCUGGACCUCACUUGUUGGCCAGAAUCUCAAACUUCAUGCCGUGAUCGUGCUUCUCCAACUCGCUA
.....(((..((...(((..((....))..))).))(((..(((((((..(((((((((.((.........)))))))))).......((((...))))..)..)))))))..)))))). ( -41.20)
>DroEre_CAF1 19577 112 + 1
----CAGCCAAGAAAAUCGAUUAAAAGAGAGCCAUUGU----GUGAAGGUGUGUUCUGGAAUUCACUUGUUGGCCAGAAUCUCAAACUUGAUGCCGUGGUCGUGCUUCUCCAACUCGCUA
----.(((...(.....)........(((((((((.((----((.(((.((.(((((((....(....)....)))))))..))..))).)))).)))))......))))......))). ( -24.00)
>consensus
CAAACAGCCAAGAAAGGUGAUUAAAAGAGAGCCGCUGGGAGGGAGAAGUGCGAUUCUGGACCUCACUUGUUGGCCAGAAUCUCAAACUUCAUGCCGUGAUCGUGCUUCUCCAACUCGCUA
.....(((.......(((..((....))..)))...(((..((((((((((((((((((....(....)....))))))))(((..(.....)...)))..))))))))))..)))))). (-26.51 = -28.07 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,047,578 – 1,047,698
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.67
Mean single sequence MFE -41.99
Consensus MFE -37.96
Energy contribution -37.40
Covariance contribution -0.56
Combinations/Pair 1.15
Mean z-score -1.14
Structure conservation index 0.90
SVM decision value 0.06
SVM RNA-class probability 0.565543
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1047578 120 - 27905053
AUUCUUCGUGAGUCGGACAAGAUGCCCAGCACAGGCGGAGUGCUGCCUCCAGCUGCCGCCUUCUCUAAGACCGGACUAAUUAGCGAGUUGGAGAAGCACGACCACGGCAUCAAGUUUGAG
......(....)((((((..((((((..((....))((.(((((..((((((((((.......(((......))).......)).)))))))).)))))..))..))))))..)))))). ( -42.34)
>DroSec_CAF1 19500 120 - 1
AUUCUUCGUGAGUCGGACAAGAUGCCCAGCACAGGCGGAGUGCUGCCUCCAGCUGCCGCCUUCUCUAAGACCGGCCUCAUUAGCGAGUUGGAGAAGCACGAUCACGGCAUGAAGUUUGAG
...((((((..(((((((....((((.......))))..(((((..((((((((((((.(((....)))..))))..........)))))))).)))))).)).))))))))))...... ( -37.80)
>DroSim_CAF1 19371 120 - 1
AUUCUUCGUGAGUCGGACAAGAUGCCCAGCACAGGCGGAGUGCUGCCUCCAGCUGGCGCCUUCUCUAAGACCGGCCUCAUUAGCGAGUUGGAGAAGCACGAUCACGGCAUGAAGUUUGAG
...((((((..(((((((....((((.......))))..(((((..((((((((.(((((.((.....))..))).......)).)))))))).)))))).)).))))))))))...... ( -40.91)
>DroEre_CAF1 19649 120 - 1
AUUCUUCGUGAGUCAGACAAGAUGCCCAGCACAGGCGGAGUGCUGACUCCAGCUGCCGCCUUUUCUAAGACGGGCCUAAUUAGCGAGUUGGAGAAGCACGACCACGGCAUCAAGUUUGAG
......(....)((((((..((((((..((....))((.(((((..((((((((.(((.(((....))).)))((.......)).)))))))).)))))..))..))))))..)))))). ( -46.40)
>DroYak_CAF1 20408 120 - 1
AUUCUUCGUGAGUCAGACAAGAUGCCUAGCACAGGCGGAGUGCUGACUCCAGCUGCUGCCUUUUCUAAGACCGGCCUAAUUAGCGAGUUGGAGAAGCAUGACCACGGUAUCAAGUUUGAG
......(....)((((((..((((((..((....))((.(((((..((((((((((((((............)))......))).)))))))).)))))..))..))))))..)))))). ( -42.50)
>consensus
AUUCUUCGUGAGUCGGACAAGAUGCCCAGCACAGGCGGAGUGCUGCCUCCAGCUGCCGCCUUCUCUAAGACCGGCCUAAUUAGCGAGUUGGAGAAGCACGACCACGGCAUCAAGUUUGAG
......(....)((((((..((((((..((....))((.(((((..((((((((..(((.......................))))))))))).)))))..))..))))))..)))))). (-37.96 = -37.40 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:03 2006