Locus 757

Sequence ID 3L_DroMel_CAF1
Location 2,256,948 – 2,257,071
Length 123
Max. P 0.679909
window1167 window1168 window1169

overview

Window 7

Location 2,256,948 – 2,257,050
Length 102
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 86.57
Mean single sequence MFE -24.37
Consensus MFE -19.76
Energy contribution -20.36
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.81
SVM decision value 0.06
SVM RNA-class probability 0.562016
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2256948 102 - 23771897
CCCCCAAAAGCAAACUGAUAGCUAGCUGCAGACGGACGGACUGACAGAUGUUUUUGUCAUCCGAAAAUAGCUGGUAA---CUCGAGCCAAGAAACUGAAACUUUC
......((((....(((.(((....)))))).(((.((((.(((((((....)))))))))))......(((.(...---..).))).......)))...)))). ( -23.20)
>DroSec_CAF1 6812 94 - 1
CACCCAAAAGCAAACUGAUAG----CUGCAGGC----GGACUGACAGAUGUUUUUGUCAGCCGAAAAUAGCUGGUAA---CUCGAGCCAAGUAACUGAAACUUUC
.............(((...((----(((....(----((.((((((((....)))))))))))....)))))(((..---.....))).)))............. ( -23.50)
>DroSim_CAF1 6891 93 - 1
CCCCCAAAAGCA-ACUGAUAG----CUGCAGGC----GGGCUGACAGAUGUUUUUGUCAGCCGAAAAUAGCUGGUAA---CUCGAGCCAAGUAACUGAAACUUUC
........(((.-.......)----)).(((..----.((((((((((....)))))))))).......((((((..---.....))).)))..)))........ ( -25.10)
>DroEre_CAF1 7812 86 - 1
-------AAGCAAACUGAUAG----CUGCAGGC----GGGCUGACAGAUGUUUUUGUCAGCC-AAAAUAGCUGGUAA---CACAAGCCAAGUAACUGAAACUUUC
-------.(((.........)----)).(((..----.((((((((((....))))))))))-......((((((..---.....))).)))..)))........ ( -24.30)
>DroYak_CAF1 7480 96 - 1
ACUCCGAAAGCAAACUGAUAG----CUGCAGGC----GGGCUGACAGAUGUUUUUGUCAGCC-AAAAUAGCUGGUAACAACACAAGCCAAGUAGAUGAAACUUUC
.....(((((...........----((((.(((----.((((((((((....))))))))))-......(.((....)).)....)))..))))......))))) ( -25.73)
>consensus
CCCCCAAAAGCAAACUGAUAG____CUGCAGGC____GGGCUGACAGAUGUUUUUGUCAGCCGAAAAUAGCUGGUAA___CUCGAGCCAAGUAACUGAAACUUUC
........(((...(((.(((....)))))).......((((((((((....)))))))))).......)))(((..........)))................. (-19.76 = -20.36 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 2,256,973 – 2,257,071
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 84.19
Mean single sequence MFE -30.84
Consensus MFE -18.10
Energy contribution -20.10
Covariance contribution 2.00
Combinations/Pair 1.08
Mean z-score -2.05
Structure conservation index 0.59
SVM decision value -0.01
SVM RNA-class probability 0.529313
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2256973 98 + 23771897
--UUACCAGCUAUUUUCGGAUGACAAAAACAUCUGUCAGUCCGUCCGUCUGCAGCUAGCUAUCAGUUUGCUUUUGGGGGAGGGGGCGGGCGAAAGGAGAA
--.......((.(((((...(((((........)))))((((((((.(((.(((..(((.........))).))).)))...))))))))))))).)).. ( -30.40)
>DroSec_CAF1 6837 90 + 1
--UUACCAGCUAUUUUCGGCUGACAAAAACAUCUGUCAGUCC----GCCUGCAG----CUAUCAGUUUGCUUUUGGGUGGCGGGGCGGGCGAAAGGAGAA
--..........(((((((((((((........))))))))(----((((((.(----(((((............))))))...)))))))...))))). ( -34.50)
>DroSim_CAF1 6916 89 + 1
--UUACCAGCUAUUUUCGGCUGACAAAAACAUCUGUCAGCCC----GCCUGCAG----CUAUCAGU-UGCUUUUGGGGGCGGGGGCGGGCGAAAGGAGAA
--..........(((((((((((((........))))))))(----((((((.(----((..(((.-.....)))..)))....)))))))...))))). ( -36.30)
>DroEre_CAF1 7837 78 + 1
--UUACCAGCUAUUUU-GGCUGACAAAAACAUCUGUCAGCCC----GCCUGCAG----CUAUCAGUUUGCUU---------UGG--GGGCGAAAGCAGAA
--......(((.....-((((((((........))))))))(----((((.(((----(.........))..---------)).--)))))..))).... ( -28.00)
>DroYak_CAF1 7506 88 + 1
UGUUACCAGCUAUUUU-GGCUGACAAAAACAUCUGUCAGCCC----GCCUGCAG----CUAUCAGUUUGCUUUCGGAGU-UUGG--GCGCGAAAGGAGAA
.......((((.....-((((((((........)))))))).----......))----)).....(((.((((((..((-....--)).)))))).))). ( -25.00)
>consensus
__UUACCAGCUAUUUUCGGCUGACAAAAACAUCUGUCAGCCC____GCCUGCAG____CUAUCAGUUUGCUUUUGGGGG_GGGGGCGGGCGAAAGGAGAA
.........((.(((((((((((((........)))))))).....((((((......(((..((....))..)))........))))))))))).)).. (-18.10 = -20.10 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 2,256,973 – 2,257,071
Length 98
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 84.19
Mean single sequence MFE -26.48
Consensus MFE -18.26
Energy contribution -18.86
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.69
SVM decision value 0.30
SVM RNA-class probability 0.679909
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2256973 98 - 23771897
UUCUCCUUUCGCCCGCCCCCUCCCCCAAAAGCAAACUGAUAGCUAGCUGCAGACGGACGGACUGACAGAUGUUUUUGUCAUCCGAAAAUAGCUGGUAA--
..........(((.((...................(((.(((....)))))).....((((.(((((((....)))))))))))......)).)))..-- ( -23.30)
>DroSec_CAF1 6837 90 - 1
UUCUCCUUUCGCCCGCCCCGCCACCCAAAAGCAAACUGAUAG----CUGCAGGC----GGACUGACAGAUGUUUUUGUCAGCCGAAAAUAGCUGGUAA--
..........(((.((.(((((.......(((.........)----))...)))----)).((((((((....)))))))).........)).)))..-- ( -25.20)
>DroSim_CAF1 6916 89 - 1
UUCUCCUUUCGCCCGCCCCCGCCCCCAAAAGCA-ACUGAUAG----CUGCAGGC----GGGCUGACAGAUGUUUUUGUCAGCCGAAAAUAGCUGGUAA--
..........(((.((...((((......(((.-.......)----))...)))----)((((((((((....)))))))))).......)).)))..-- ( -31.00)
>DroEre_CAF1 7837 78 - 1
UUCUGCUUUCGCCC--CCA---------AAGCAAACUGAUAG----CUGCAGGC----GGGCUGACAGAUGUUUUUGUCAGCC-AAAAUAGCUGGUAA--
.((.(((..((((.--...---------.(((.........)----))...)))----)((((((((((....))))))))))-.....))).))...-- ( -27.00)
>DroYak_CAF1 7506 88 - 1
UUCUCCUUUCGCGC--CCAA-ACUCCGAAAGCAAACUGAUAG----CUGCAGGC----GGGCUGACAGAUGUUUUUGUCAGCC-AAAAUAGCUGGUAACA
.....((((((.(.--....-...)))))))........(((----(((.....----.((((((((((....))))))))))-....))))))...... ( -25.90)
>consensus
UUCUCCUUUCGCCCGCCCCC_CCCCCAAAAGCAAACUGAUAG____CUGCAGGC____GGGCUGACAGAUGUUUUUGUCAGCCGAAAAUAGCUGGUAA__
.............................(((...(((.(((....)))))).......((((((((((....)))))))))).......)))....... (-18.26 = -18.86 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:30 2006