Locus 8418

Sequence ID X_DroMel_CAF1
Location 20,901,626 – 20,901,759
Length 133
Max. P 0.872494
window13829 window13830

overview

Window 9

Location 20,901,626 – 20,901,725
Length 99
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 83.50
Mean single sequence MFE -30.40
Consensus MFE -19.75
Energy contribution -20.20
Covariance contribution 0.45
Combinations/Pair 1.13
Mean z-score -2.63
Structure conservation index 0.65
SVM decision value 0.88
SVM RNA-class probability 0.872494
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20901626 99 + 22224390
GGUAAGAAACCGAGCCUUGCUCGCCUUGCUUGCAACGGCCAACACGAGGCUGUCACAAUAGCAACAA-----CAGCUGUGAUCCAAGCCGUGUUGCAAGUAAAA
(((.....)))((((...))))...((((((((((((.....)....((((......(((((.....-----..)))))......))))..))))))))))).. ( -33.00)
>DroSec_CAF1 20896 95 + 1
GGUAAGAAACUGAGCCU---------CGCUUGCAACUUGCAACACGAGGCUGUCACAGUAGCAACAACAGAACAGCUGCGAUCCACGCCGCGUUGCAACCAAAA
(((.....(((((((((---------((.((((.....))))..)))))))....)))).(((((.........((.(((.....))).))))))).))).... ( -31.20)
>DroSim_CAF1 22784 95 + 1
GGUAAGAAACCGAGCCU---------UGCUUGCAACUUGCAACACGAGGCUGUCACAGUAGCAACAACAGAACAGCUGCGAUCCAAGCCGCGUUGCAACCAAAA
(((.......(((((..---------.))))).....((((((....((((......(((((............)))))......))))..))))))))).... ( -27.00)
>consensus
GGUAAGAAACCGAGCCU_________UGCUUGCAACUUGCAACACGAGGCUGUCACAGUAGCAACAACAGAACAGCUGCGAUCCAAGCCGCGUUGCAACCAAAA
(((.......(((((............))))).....((((((....((((......(((((............)))))......))))..))))))))).... (-19.75 = -20.20 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 20,901,663 – 20,901,759
Length 96
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 68.76
Mean single sequence MFE -26.50
Consensus MFE -9.67
Energy contribution -12.79
Covariance contribution 3.12
Combinations/Pair 1.28
Mean z-score -2.44
Structure conservation index 0.36
SVM decision value 0.12
SVM RNA-class probability 0.595314
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20901663 96 - 22224390
AACUCUAAAAAAAAUGUGAAAACAUUUUU---AAUGUUUUUACUUGCAACACGGCUUGGA-UCACAGC-UG-----UUGUUGCUAUUGUGACAGCCUCGUGUUGGC
...............((((((((((....---.))))))))))...((((((((((.(..-...))))-.(-----((((..(....)..)))))..))))))).. ( -29.00)
>DroSec_CAF1 20924 101 - 1
AAAAUUGGAAAAAAUGUGAAAAUAUUUUU---AAUGUUUUUGGUUGCAACGCGGCGUGGA-UCGCAGC-UGUUCUGUUGUUGCUACUGUGACAGCCUCGUGUUGCA
..(((..((((((((((....))))))..---....))))..)))(((((((((((....-.)))...-......(((((..(....)..)))))..)))))))). ( -31.30)
>DroSim_CAF1 22812 101 - 1
AAAAAUGGAAAAAAUGUAAAAAUAUUUUU---AAUGUUUUUGGUUGCAACGCGGCUUGGA-UCGCAGC-UGUUCUGUUGUUGCUACUGUGACAGCCUCGUGUUGCA
(((((((..((((((((....))))))))---..)))))))...((((((((((((....-....)))-......(((((..(....)..)))))..))))))))) ( -28.60)
>DroAna_CAF1 11826 92 - 1
-UGUUUUGAUAGACUGUUUAUAUUUUUUUCGCAAUGUUAUUGGAUCCGUCCUCAGUUGCACUUGCAACAUGUCCUAUUAUUUCUA-------------GUGUUGCA
-.((((....))))................((((..(((..(((....)))...(((((....)))))...............))-------------)..)))). ( -17.10)
>consensus
AAAAUUGGAAAAAAUGUGAAAAUAUUUUU___AAUGUUUUUGGUUGCAACGCGGCUUGGA_UCGCAGC_UGUUCUGUUGUUGCUACUGUGACAGCCUCGUGUUGCA
.........((((((((....))))))))................(((((((((...((..((((((..................))))))...))))))))))). ( -9.67 = -12.79 +   3.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:31 2006