Locus 5383

Sequence ID 2R_DroMel_CAF1
Location 17,386,739 – 17,386,830
Length 91
Max. P 0.984166
window8593 window8594

overview

Window 3

Location 17,386,739 – 17,386,830
Length 91
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 79.67
Mean single sequence MFE -23.08
Consensus MFE -15.92
Energy contribution -18.08
Covariance contribution 2.16
Combinations/Pair 1.15
Mean z-score -1.76
Structure conservation index 0.69
SVM decision value 0.54
SVM RNA-class probability 0.776608
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17386739 91 + 20766785
AGCUUUUCUUCUUUUUCUUUUUUUUUUUUGCAAGCGUCACAUUUGACGCCCCACAAAAAUGGGGGAUUAAAGGGUAUGGG---UGCGGAAAAAG
......................((((((((((..(((.((.(((((..(((((......)))))..)))))..)))))..---)))))))))). ( -22.90)
>DroSec_CAF1 102616 83 + 1
AGCUUUUCUUCUUU------UU--UUUUUGCAAGCGUCACAUUUGACGCCCCACAAAAAUGGGGGAUUAAAGGGUAUGGG---UGCGGGAAAAG
..............------((--((((((((..(((.((.(((((..(((((......)))))..)))))..)))))..---)))))))))). ( -22.50)
>DroSim_CAF1 106057 85 + 1
AGCUUUUCUUCUUU------UUUUUUUUUGCAAGCGUCACAUUUGACGCCCCACAAAAAUGGGGGAUUAAAGGGUAUGGG---UGCGGGAAAAG
..............------..((((((((((..(((.((.(((((..(((((......)))))..)))))..)))))..---)))))))))). ( -22.50)
>DroEre_CAF1 101464 69 + 1
AGCUUUUCUCCUUUUUUUUUUUUUUUGUUGCAAGCGUCACAUUUGACGCCCCACAAAAAGGGGGGUUUU-------------------------
......(((((((((((.......(((...)))((((((....)))))).....)))))))))))....------------------------- ( -16.20)
>DroYak_CAF1 84845 91 + 1
AGCUUUUCUCCUUUUUU---UUUUUUGUUGCAAGCGUCACAUUUGACGCCCCACCAAAAUGGGGGAUUAAAGGGUGUGGGGGUUGCGGCGAAAG
.................---..(((((((((((.(.((((((((((..(((((......)))))..))))...)))))).).))))))))))). ( -31.30)
>consensus
AGCUUUUCUUCUUUUU____UUUUUUUUUGCAAGCGUCACAUUUGACGCCCCACAAAAAUGGGGGAUUAAAGGGUAUGGG___UGCGGGAAAAG
......................((((((((((.((((((....))))))((((......))))....................)))))))))). (-15.92 = -18.08 +   2.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,386,739 – 17,386,830
Length 91
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 79.67
Mean single sequence MFE -19.06
Consensus MFE -14.88
Energy contribution -15.68
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.78
SVM decision value 1.97
SVM RNA-class probability 0.984166
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17386739 91 - 20766785
CUUUUUCCGCA---CCCAUACCCUUUAAUCCCCCAUUUUUGUGGGGCGUCAAAUGUGACGCUUGCAAAAAAAAAAAAGAAAAAGAAGAAAAGCU
(((((((....---.................(((((....)))))((((((....))))))................))))))).......... ( -20.90)
>DroSec_CAF1 102616 83 - 1
CUUUUCCCGCA---CCCAUACCCUUUAAUCCCCCAUUUUUGUGGGGCGUCAAAUGUGACGCUUGCAAAAA--AA------AAAGAAGAAAAGCU
((((((.....---.................(((((....)))))((((((....)))))).........--..------......)))))).. ( -19.30)
>DroSim_CAF1 106057 85 - 1
CUUUUCCCGCA---CCCAUACCCUUUAAUCCCCCAUUUUUGUGGGGCGUCAAAUGUGACGCUUGCAAAAAAAAA------AAAGAAGAAAAGCU
((((((.....---.................(((((....)))))((((((....)))))).............------......)))))).. ( -19.30)
>DroEre_CAF1 101464 69 - 1
-------------------------AAAACCCCCCUUUUUGUGGGGCGUCAAAUGUGACGCUUGCAACAAAAAAAAAAAAAAAGGAGAAAAGCU
-------------------------..........(((((((.((((((((....))))))))...)))))))..................... ( -15.10)
>DroYak_CAF1 84845 91 - 1
CUUUCGCCGCAACCCCCACACCCUUUAAUCCCCCAUUUUGGUGGGGCGUCAAAUGUGACGCUUGCAACAAAAAA---AAAAAAGGAGAAAAGCU
.((((.((.....................(((((.....)).)))((((((....)))))).............---......)).)))).... ( -20.70)
>consensus
CUUUUCCCGCA___CCCAUACCCUUUAAUCCCCCAUUUUUGUGGGGCGUCAAAUGUGACGCUUGCAAAAAAAAA____AAAAAGAAGAAAAGCU
........(((....................(((((....)))))((((((....)))))).)))............................. (-14.88 = -15.68 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:32 2006