Locus 3755

Sequence ID 3L_DroMel_CAF1
Location 10,873,288 – 10,873,431
Length 143
Max. P 0.740618
window5857 window5858 window5859

overview

Window 7

Location 10,873,288 – 10,873,391
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.44
Mean single sequence MFE -28.92
Consensus MFE -21.62
Energy contribution -21.46
Covariance contribution -0.16
Combinations/Pair 1.32
Mean z-score -0.90
Structure conservation index 0.75
SVM decision value 0.05
SVM RNA-class probability 0.558050
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10873288 103 - 23771897
GCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUGAAUGUUCGUGUGAAAAACAAAAGAGGGCGCCACUACAACA-----------------AAGGUUUGGCGAUAGCCGAGACUCCCACCC
(((((((((..((......))...)))..(((((....)))))............))))))............-----------------..((((((((....))).)))))....... ( -24.30)
>DroSec_CAF1 1246 116 - 1
GCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUAA--GGUCGUGUGAAAAGCGAAAGAGGGCGCCACAGCAACAACC-AAAAAAGCAAGUAAAAGCUCCGCUUUAGCGGAGAC-CCCACCC
((((((..((((((.(((((.........)))))--))))))((.....))....))))))((....)).......-.................((((((....))))))..-....... ( -31.10)
>DroSim_CAF1 1231 119 - 1
GCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUAAAUGUUCGCGUGAAAAGCGAAAGAGGGCGCCGCAACAACAACC-AAAAAAGCAAGUAAAAGCUCCGCAUUAGCGGAGACUCCCACCC
(((((((((..((......))...)))..........(((((.......))))).))))))...............-...............((((((((....)))))).))....... ( -32.40)
>DroEre_CAF1 615 120 - 1
ACCCUCUAGUGUCUAUCCUGCAAACUCGGUGUAAGUGUUCGUCACUUAAACGAAAGAGGGCGCCACAGCACAAACCUAGGAAAUCAGCUACAAGCUCCACAAUAGCGGAGACUCUCACCC
......((((.....((((((...(((.((.((((((.....)))))).))....))).))((....))........)))).....))))..((((((.(....).)))).))....... ( -25.20)
>DroYak_CAF1 1093 120 - 1
GCCCUCUAGUGCCUGUCAUGCAAACUUGGUGUAAAUGUUCGCGACGAAAGCGAAAGAGGGCGCCACAACAACACCCUAAAGAAGCAAGUACAAGCACCGCAAUAGGGGAGACUUCCACCC
..((((((((((.((((.(((.....((((((.....(((((.......))))).....))))))..........(....)..))).).))).)))).....))))))............ ( -31.60)
>consensus
GCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUAAAUGUUCGUGUGAAAAGCGAAAGAGGGCGCCACAACAACAACC_AAAAAAGCAAGUAAAAGCUCCGCAAUAGCGGAGACUCCCACCC
((((((............(((((.....)))))....(((((.......))))).)))))).................................((((((....)))))).......... (-21.62 = -21.46 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,873,318 – 10,873,431
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.60
Mean single sequence MFE -33.28
Consensus MFE -20.14
Energy contribution -19.26
Covariance contribution -0.88
Combinations/Pair 1.35
Mean z-score -1.58
Structure conservation index 0.61
SVM decision value 0.45
SVM RNA-class probability 0.740618
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10873318 113 + 23771897
-------UGUUGUAGUGGCGCCCUCUUUUGUUUUUCACACGAACAUUCAUAAUCAGUUUACAUAAUAGCCGCUGGAGGGCGCUCAUGUAUAUUUCCAGAUCCAGUACAAUGCGACUAAAG
-------.(((((((((((((((((...(((((.......)))))........((((.............)))))))))))).)))((((.............))))..))))))..... ( -28.74)
>DroSec_CAF1 1285 117 + 1
UUU-GGUUGUUGCUGUGGCGCCCUCUUUCGCUUUUCACACGACC--UUAUAAUCAGUUUACAUAAUAGCCGCUGGAGGGCGCUCAUGUAUAUUUCAAGAUCCAAUACUAUGGGAAUAAAA
(((-((....(((.((((((((((((..((((........(((.--.........)))........)).))..))))))))).))))))....))))).((((......))))....... ( -29.29)
>DroSim_CAF1 1271 112 + 1
UUU-GGUUGUUGUUGCGGCGCCCUCUUUCGCUUUUCACGCGAACAUUUAUAAUCAGUUUACAUAAUAGCCGCUGGAGGGCGCUCAUGUAUAUUUCAAGAUCCAGUACUA-------AAAA
.((-((.(.(((.((((((((((((.(((((.......)))))..........((((.............)))))))))))))...))).....))).).)))).....-------.... ( -30.42)
>DroEre_CAF1 655 120 + 1
CCUAGGUUUGUGCUGUGGCGCCCUCUUUCGUUUAAGUGACGAACACUUACACCGAGUUUGCAGGAUAGACACUAGAGGGUGCUCAGGUAUAUUUAAAGUUCCAUUGCCGCCAGACUGCGA
....((((((.((((.((((((((((.(((..((((((.....))))))...)))(((((.....)))))...))))))))))))((((...............)))))))))))).... ( -37.36)
>DroYak_CAF1 1133 120 + 1
UUUAGGGUGUUGUUGUGGCGCCCUCUUUCGCUUUCGUCGCGAACAUUUACACCAAGUUUGCAUGACAGGCACUAGAGGGCGCACAAGUGUAUUUAAACGUCUUGUAUUGUUAGGCUGAAA
(((((............(((((((((...((((((((.((((((...........)))))))))).))))...)))))))))((((((((......))).))))).........))))). ( -40.60)
>consensus
UUU_GGUUGUUGUUGUGGCGCCCUCUUUCGCUUUUCACACGAACAUUUAUAAUCAGUUUACAUAAUAGCCGCUGGAGGGCGCUCAUGUAUAUUUCAAGAUCCAGUACUAUGAGACUAAAA
.................((((((((((((((.......)))))............(((.....))).......)))))))))...................................... (-20.14 = -19.26 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,873,318 – 10,873,431
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.60
Mean single sequence MFE -28.48
Consensus MFE -20.62
Energy contribution -20.34
Covariance contribution -0.28
Combinations/Pair 1.25
Mean z-score -0.91
Structure conservation index 0.72
SVM decision value 0.10
SVM RNA-class probability 0.581281
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10873318 113 - 23771897
CUUUAGUCGCAUUGUACUGGAUCUGGAAAUAUACAUGAGCGCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUGAAUGUUCGUGUGAAAAACAAAAGAGGGCGCCACUACAACA-------
...........(((((.((..((((........)).))(((((((((((..((......))...)))..(((((....)))))............)))))))))).)))))..------- ( -26.10)
>DroSec_CAF1 1285 117 - 1
UUUUAUUCCCAUAGUAUUGGAUCUUGAAAUAUACAUGAGCGCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUAA--GGUCGUGUGAAAAGCGAAAGAGGGCGCCACAGCAACAACC-AAA
(((((...(((......)))....)))))......((.((((((((..((((((.(((((.........)))))--))))))((.....))....))))))))))...........-... ( -27.90)
>DroSim_CAF1 1271 112 - 1
UUUU-------UAGUACUGGAUCUUGAAAUAUACAUGAGCGCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUAAAUGUUCGCGUGAAAAGCGAAAGAGGGCGCCGCAACAACAACC-AAA
....-------......(((.((.((.......)).))(((((((((((..((......))...)))..........(((((.......))))).))))))))...........))-).. ( -28.40)
>DroEre_CAF1 655 120 - 1
UCGCAGUCUGGCGGCAAUGGAACUUUAAAUAUACCUGAGCACCCUCUAGUGUCUAUCCUGCAAACUCGGUGUAAGUGUUCGUCACUUAAACGAAAGAGGGCGCCACAGCACAAACCUAGG
..((....(((((((...((.............))...)).((((((..(((.......)))...(((...((((((.....))))))..))).)))))))))))..))........... ( -29.32)
>DroYak_CAF1 1133 120 - 1
UUUCAGCCUAACAAUACAAGACGUUUAAAUACACUUGUGCGCCCUCUAGUGCCUGUCAUGCAAACUUGGUGUAAAUGUUCGCGACGAAAGCGAAAGAGGGCGCCACAACAACACCCUAAA
...............(((((..((......)).)))))(((((((((.(..((.((.......))..))..).....(((((.......))))))))))))))................. ( -30.70)
>consensus
UUUUAGUCUCAUAGUACUGGAUCUUGAAAUAUACAUGAGCGCCCUCCAGCGGCUAUUAUGUAAACUGAUUAUAAAUGUUCGUGUGAAAAGCGAAAGAGGGCGCCACAACAACAACC_AAA
...................................((.((((((((............(((((.....)))))....(((((.......))))).))))))))))............... (-20.62 = -20.34 +  -0.28)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:54 2006