Locus 8328

Sequence ID 3L_DroMel_CAF1
Location 21,810,257 – 21,810,395
Length 138
Max. P 0.982160
window13628 window13629 window13630

overview

Window 8

Location 21,810,257 – 21,810,369
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.82
Mean single sequence MFE -29.17
Consensus MFE -12.80
Energy contribution -13.97
Covariance contribution 1.17
Combinations/Pair 1.15
Mean z-score -2.02
Structure conservation index 0.44
SVM decision value 0.24
SVM RNA-class probability 0.648575
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21810257 112 + 23771897
-ACAGAUAUAUUCCAGCAAAA-UUUC------UGCCAAUCCAGAAGUAAAUUGAUUAUGGACUGGCCCAACGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGCGGAUUGUG
-.(((......((((.(((.(-((((------((......)))))))...)))....)))))))........(((((((((((((((((..((......)).))))))))))))))))). ( -33.20)
>DroSec_CAF1 30352 114 + 1
AAUGGAUAUAUUCCAGCAAAAGUUAC------UGCCAAUCCAGGAGCAAAUUGAUUAUGGACUGGCCCAGCGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGGAGCUUAUA
.....(((..((((.(((((.((..(------(((((.((((....(.....)....)))).))))..))..))..)))))((((((((..((......)).))))))))))))..))). ( -32.20)
>DroSim_CAF1 35803 114 + 1
AAUGGAUAUAUUCCAGCAAAAGUUAC------UGCCAAUCCAGGAGCAAAUUGAUUAUGGACUGGCCCAGCGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGCAGCUUAUA
..((((.....))))((....((..(------(((((.((((....(.....)....)))).))))..))..))....(((((((((((..((......)).)))))))))))))..... ( -35.30)
>DroEre_CAF1 37617 113 + 1
-AUAGAUAGAUUCGAGAAAAAAUUCC------CGUCAAUCCAGGAGCAAAUCGAUUUGGGACUCGCCCAACGACGAUUUGCAUAAUCAAAAUCGAUAAUGAGUGGAUUGUGCAGCUUAUA
-...(((.((..((.(((....))).------)))).)))...((((((((((..(((((.....)))))...))))))((((((((....((......))...)))))))).))))... ( -28.70)
>DroYak_CAF1 46206 104 + 1
GAUAGAUAGAUUCAAGAAGAAA----------------UCCAGGACCAAAUUGAUAAGGGAGUCACCCAGCGAUGAUUUGCAUAAUCCAAAACGAUAAUGAGUGGAUUGUGCAGCUUAUA
........(((((..(.(....----------------).)....((..........)))))))........((((.((((((((((((...(......)..)))))))))))).)))). ( -20.70)
>DroAna_CAF1 44917 115 + 1
-GUAGUU---UUCGAAAAAAUCGUCCGACAUUAGGCAAUAAAAAUUCAACUGGAUUAUGGAGC-GUCCAAUGCGGAUUUGCAUAAUCCGAAUCGAUAAUGAGGGAAUUGUGUGGUGGCUA
-.((((.---..(((.....))).....(((((.(((((...........(((((((((.((.-((((.....)))))).)))))))))..((......))....))))).))))))))) ( -24.90)
>consensus
_AUAGAUAUAUUCCAGAAAAAAUUAC______UGCCAAUCCAGGAGCAAAUUGAUUAUGGACUGGCCCAACGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGCAGCUUAUA
...............................................((((((....(((......)))....))))))(((((((((...((......))..)))))))))........ (-12.80 = -13.97 +   1.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,810,257 – 21,810,369
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.82
Mean single sequence MFE -27.11
Consensus MFE -10.10
Energy contribution -11.47
Covariance contribution 1.36
Combinations/Pair 1.06
Mean z-score -2.24
Structure conservation index 0.37
SVM decision value 0.29
SVM RNA-class probability 0.669647
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21810257 112 - 23771897
CACAAUCCGCACAAUCCACUCAUUAUCGAUUUGGAUUAUGCAAAUCGUCGUUGGGCCAGUCCAUAAUCAAUUUACUUCUGGAUUGGCA------GAAA-UUUUGCUGGAAUAUAUCUGU-
.....(((....((((((.((......))..))))))..(((((...((.....(((((((((...............))))))))).------))..-.))))).)))..........- ( -27.96)
>DroSec_CAF1 30352 114 - 1
UAUAAGCUCCACAAUCCACUCAUUAUCGAUUUGGAUUAUGCAAAUCGUCGCUGGGCCAGUCCAUAAUCAAUUUGCUCCUGGAUUGGCA------GUAACUUUUGCUGGAAUAUAUCCAUU
.......((((.((((((.((......))..))))))..(((((..((..((..(((((((((...............))))))))))------)..)).)))))))))........... ( -29.26)
>DroSim_CAF1 35803 114 - 1
UAUAAGCUGCACAAUCCACUCAUUAUCGAUUUGGAUUAUGCAAAUCGUCGCUGGGCCAGUCCAUAAUCAAUUUGCUCCUGGAUUGGCA------GUAACUUUUGCUGGAAUAUAUCCAUU
....(((((((.((((((.((......))..)))))).))))....((..((..(((((((((...............))))))))))------)..))....)))(((.....)))... ( -31.56)
>DroEre_CAF1 37617 113 - 1
UAUAAGCUGCACAAUCCACUCAUUAUCGAUUUUGAUUAUGCAAAUCGUCGUUGGGCGAGUCCCAAAUCGAUUUGCUCCUGGAUUGACG------GGAAUUUUUUCUCGAAUCUAUCUAU-
...........(((((((......((((....))))...((((((((...(((((.....)))))..))))))))...))))))).((------((((....))))))...........- ( -32.50)
>DroYak_CAF1 46206 104 - 1
UAUAAGCUGCACAAUCCACUCAUUAUCGUUUUGGAUUAUGCAAAUCAUCGCUGGGUGACUCCCUUAUCAAUUUGGUCCUGGA----------------UUUCUUCUUGAAUCUAUCUAUC
.(((((.((((.((((((..(......)...)))))).))))..(((((....)))))....))))).....(((...((((----------------(((......))))))).))).. ( -19.00)
>DroAna_CAF1 44917 115 - 1
UAGCCACCACACAAUUCCCUCAUUAUCGAUUCGGAUUAUGCAAAUCCGCAUUGGAC-GCUCCAUAAUCCAGUUGAAUUUUUAUUGCCUAAUGUCGGACGAUUUUUUCGAA---AACUAC-
...............(((..(((((((((((.((((((((....(((.....))).-....))))))))))))))............)))))..)))(((.....)))..---......- ( -22.40)
>consensus
UAUAAGCUGCACAAUCCACUCAUUAUCGAUUUGGAUUAUGCAAAUCGUCGCUGGGCCAGUCCAUAAUCAAUUUGCUCCUGGAUUGGCA______GGAACUUUUGCUGGAAUAUAUCUAU_
...........(((((((.........((((((.......))))))......(((....)))................)))))))................................... (-10.10 = -11.47 +   1.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,810,289 – 21,810,395
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.61
Mean single sequence MFE -36.04
Consensus MFE -22.24
Energy contribution -23.72
Covariance contribution 1.48
Combinations/Pair 1.27
Mean z-score -2.62
Structure conservation index 0.62
SVM decision value 1.91
SVM RNA-class probability 0.982160
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21810289 106 + 23771897
CAGAAGUAAAUUGAUUAUGGACUGGCCCAACGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGCGGAUUGUGAGUGGGCGGA----------GUG-GCAUGCCACUGAA---
(((..((((.....))))...)))(((((...(((((((((((((((((..((......)).)))))))))))))))))...)))))..(----------(((-(....)))))...--- ( -42.30)
>DroSec_CAF1 30386 107 + 1
CAGGAGCAAAUUGAUUAUGGACUGGCCCAGCGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGGAGCUUAUAAGUGGGCGGA----------GUGGGCAUACCACUGAA---
.....((((((((....(((......)))....))))))))((((((((..((......)).))))))))...(((((....)))))..(----------((((.....)))))...--- ( -31.20)
>DroSim_CAF1 35837 107 + 1
CAGGAGCAAAUUGAUUAUGGACUGGCCCAGCGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGCAGCUUAUAAGUGGGCGGA----------GUGGGCAUACCACUGAA---
(((..................)))(((((...(..(.((((((((((((..((......)).)))))))))))).)..)...)))))..(----------((((.....)))))...--- ( -33.27)
>DroEre_CAF1 37650 116 + 1
CAGGAGCAAAUCGAUUUGGGACUCGCCCAACGACGAUUUGCAUAAUCAAAAUCGAUAAUGAGUGGAUUGUGCAGCUUAUAAGUGGGCGGAG-UGGGCGGAGUGGGCGGACCACUGAA---
(((((.....))....(((...(((((((.((.(.((((((((((((....((......))...)))))))).(((((....))))).)))-).).))...))))))).))))))..--- ( -37.30)
>DroYak_CAF1 46230 107 + 1
CAGGACCAAAUUGAUAAGGGAGUCACCCAGCGAUGAUUUGCAUAAUCCAAAACGAUAAUGAGUGGAUUGUGCAGCUUAUAAGUGGGCGGA----------GUGGUCCGACCACUGAA---
..((((((...((((......))))((((...((((.((((((((((((...(......)..)))))))))))).))))...))))....----------.))))))..........--- ( -35.50)
>DroAna_CAF1 44953 119 + 1
AAAAUUCAACUGGAUUAUGGAGC-GUCCAAUGCGGAUUUGCAUAAUCCGAAUCGAUAAUGAGGGAAUUGUGUGGUGGCUAAGUGGGUUGCGAUUUGCGGGGGAGGCAGGUGACAGAUCCC
...........(((((.....((-.(((..((((((((.(((((((((...((......)).)).))))))).(..(((.....)))..)))))))))..))).)).(....).))))). ( -36.70)
>consensus
CAGGAGCAAAUUGAUUAUGGACUGGCCCAACGACGAUUUGCAUAAUCCAAAUCGAUAAUGAGUGGAUUGUGCAGCUUAUAAGUGGGCGGA__________GUGGGCAGACCACUGAA___
........................(((((...((((.(((((((((((...((......))..))))))))))).))))...))))).............((((.....))))....... (-22.24 = -23.72 +   1.48)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:43 2006