Locus 5704

Sequence ID 3R_DroMel_CAF1
Location 14,930,382 – 14,930,499
Length 117
Max. P 0.995487
window9334 window9335

overview

Window 4

Location 14,930,382 – 14,930,499
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.77
Mean single sequence MFE -27.68
Consensus MFE -11.00
Energy contribution -13.18
Covariance contribution 2.18
Combinations/Pair 1.07
Mean z-score -2.88
Structure conservation index 0.40
SVM decision value 2.58
SVM RNA-class probability 0.995487
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14930382 117 + 27905053
UGGGGUUGGGGUCAGGGUCGUCAUAGCAUUUUGAUUACAAUUCAAGCAUGUUUAAAUAUGUAUGCUUAGGCAUUAGCCAAAAUCAGAUACCCUGCUCUCCAAACUACCCAUAUU---AUU
((((.((((((.((((((.(((..(((((.((((.......))))((((((....)))))))))))..(((....))).......)))))))))..))))))....))))....---... ( -39.50)
>DroSec_CAF1 60381 93 + 1
UG------GGGUCAGGGUCGUCAUAGCAUUUUGAUUACACUUUAAGCAUGUUCAAAUAUGUAUGCUUA-------------AUCAGAUACCCUGCUCUCUAAAUUACCCA--------UU
((------(((.((((((.((((........))))......(((((((((..........))))))))-------------)......))))))..))))).........--------.. ( -22.20)
>DroSim_CAF1 59075 101 + 1
UG------GGGUCAGGGUCGUCAUAGCAUUUUGAUUACACUUAAAGCAUGUUCAAAUAUGUAUGCUUA-------------AUCAGAUACCCUGCUAACCAAACUACCCAUAUUAUUAUU
..------((((((((((.(((..((((((((((......)))))((((((....)))))))))))..-------------....)))))))))...........))))........... ( -21.40)
>DroEre_CAF1 56898 107 + 1
UG------GGGUCAGGGCCG---UAGCUUUUUGAUUACAAUUUAAGCUUGUUCAAAUGUGUAUGCUUAAGCAUUAGCCCAAAUCAGAAACGCUACUCC-CAAACUCCCCAUAUU---AUU
((------(((...(((..(---(((((((((((((.....((((((.((..(....)..)).))))))((....))...))))))))).))))).))-).....)))))....---... ( -32.30)
>DroYak_CAF1 63682 107 + 1
UG------GGGUCAGGGUCG---UAGCCUUUUGAUUACAAUUUAAGCUUGUUCAAAUAUGUAUGCUUAGGCAUUAGCCCAAAUCAAAAACCCUACUCU-UAAACUCCCUAUAUU---AUU
.(------((((..(((..(---(((..((((((((......(((((................)))))(((....)))..))))))))...)))).))-)..))))).......---... ( -22.99)
>consensus
UG______GGGUCAGGGUCGUCAUAGCAUUUUGAUUACAAUUUAAGCAUGUUCAAAUAUGUAUGCUUA_GCAUUAGCC_AAAUCAGAUACCCUGCUCUCCAAACUACCCAUAUU___AUU
........((((((((((...........(((((((.......(((((((..........))))))).(((....)))..))))))).))))))...........))))........... (-11.00 = -13.18 +   2.18)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,930,382 – 14,930,499
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.77
Mean single sequence MFE -26.48
Consensus MFE -12.10
Energy contribution -12.80
Covariance contribution 0.70
Combinations/Pair 1.15
Mean z-score -2.03
Structure conservation index 0.46
SVM decision value 0.50
SVM RNA-class probability 0.761017
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14930382 117 - 27905053
AAU---AAUAUGGGUAGUUUGGAGAGCAGGGUAUCUGAUUUUGGCUAAUGCCUAAGCAUACAUAUUUAAACAUGCUUGAAUUGUAAUCAAAAUGCUAUGACGACCCUGACCCCAACCCCA
...---....((((....((((.(..((((((.((.(((((((..((.....(((((((............))))))).....))..)))))).)...))..))))))..))))).)))) ( -29.50)
>DroSec_CAF1 60381 93 - 1
AA--------UGGGUAAUUUAGAGAGCAGGGUAUCUGAU-------------UAAGCAUACAUAUUUGAACAUGCUUAAAGUGUAAUCAAAAUGCUAUGACGACCCUGACCC------CA
..--------.((((...........((((((......(-------------(((((((.((....))...))))))))(((((.......)))))......))))))))))------.. ( -20.50)
>DroSim_CAF1 59075 101 - 1
AAUAAUAAUAUGGGUAGUUUGGUUAGCAGGGUAUCUGAU-------------UAAGCAUACAUAUUUGAACAUGCUUUAAGUGUAAUCAAAAUGCUAUGACGACCCUGACCC------CA
..........((((..(((.((((..((.(((((.((((-------------(((((((.((....))...))))).......))))))..))))).))..))))..)))))------)) ( -21.61)
>DroEre_CAF1 56898 107 - 1
AAU---AAUAUGGGGAGUUUG-GGAGUAGCGUUUCUGAUUUGGGCUAAUGCUUAAGCAUACACAUUUGAACAAGCUUAAAUUGUAAUCAAAAAGCUA---CGGCCCUGACCC------CA
...---......(((.(((.(-((.(((((.(((.((((((((((....))))))...((((.((((((......)))))))))))))).)))))))---)..))).)))))------). ( -33.10)
>DroYak_CAF1 63682 107 - 1
AAU---AAUAUAGGGAGUUUA-AGAGUAGGGUUUUUGAUUUGGGCUAAUGCCUAAGCAUACAUAUUUGAACAAGCUUAAAUUGUAAUCAAAAGGCUA---CGACCCUGACCC------CA
...---......(((.(((..-...(((.(.((((((((((((((....))))))...((((.((((((......)))))))))))))))))).)))---)......)))))------). ( -27.70)
>consensus
AAU___AAUAUGGGUAGUUUGGAGAGCAGGGUAUCUGAUUU_GGCUAAUGC_UAAGCAUACAUAUUUGAACAUGCUUAAAUUGUAAUCAAAAUGCUAUGACGACCCUGACCC______CA
...........(((............((((((..........(((....)))..(((((.....(((((((((.......))))..))))))))))......)))))).)))........ (-12.10 = -12.80 +   0.70)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:22 2006