Locus 5570

Sequence ID	3R_DroMel_CAF1
Location	14,729,627 – 14,729,721
Length	94
Max. P	0.956255

overview

Window 8

Location	14,729,627 – 14,729,721
Length	94
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	75.05
Mean single sequence MFE	-25.07
Consensus MFE	-13.64
Energy contribution	-14.25
Covariance contribution	0.61
Combinations/Pair	1.17
Mean z-score	-1.68
Structure conservation index	0.54
SVM decision value	0.37
SVM RNA-class probability	0.707746
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14729627 94 + 27905053
AUCCAACAUCCAAUGGCC--CCUUCGUC----AUUUGGUCAUUUGGUCAUUUGUGGCCGGUCCUUGGCUCGUUAAGCCAAGCCAUUUAAUAACCACAGGU
.........((((((((.--.....)))----)))((((.(((.(((((....)))))((..(((((((.....)))))))))....))).))))..)). ( -25.20)
>DroPse_CAF1 137298 82 + 1
AUCGAUCUUCCUGCAUC------------------CUGCCAGUUGGUCAUUUGCGGCCAGUCUUUGGCUCGUUAAGCCAAGCCAUUUAGGAGCCGGAGCC
.......((((.((.((------------------(((..((((((((......)))))).))((((((.....))))))......))))))).)))).. ( -25.80)
>DroSec_CAF1 148122 86 + 1
AUCCAACAGCCAAUGGCC--CCUUCGUC----AUUUG--------GUCAUUUGUGGCCGGUCCUUGGCUCGUUAAGCCAAGCCAUUUAAUAACCACAGGU
........(((((((((.--.....)))----)))((--------((.(((.(((((......((((((.....)))))))))))..))).))))..))) ( -23.50)
>DroSim_CAF1 154044 94 + 1
AUCCAACAGCCAAUGGCC--CCUUCGUC----AUUUGGUCAUUUGGUCAUUUGUGGCCGGUCCUUGGCUCGUUAAGCCAAGCCAUUUAAUAACCACAGGG
..((....(((((((((.--.....)))----).)))))....((((.(((.(((((......((((((.....)))))))))))..))).))))..)). ( -26.70)
>DroEre_CAF1 146942 99 + 1
AUCCAACAUCCAGCAUCCAACAUCCGACAUCCAA-UGACCAUUUGGUCAUUUGUGGCCGGUCUUAGGCUCGUUAAGCCAAGCCAUUUAAUAACCACAGGU
..............................((((-(((((....)))))))(((((..((.(((.((((.....))))))))).((....))))))))). ( -21.90)
>DroYak_CAF1 156401 100 + 1
AGCCCACUUCCAACAUCCAACAACCAAUGGCCAUUUGGACAUUUGGUUAUUUGUGGCCGGCCUUAGGCUCGUUAAGCCAAGCCAUUUAAUAACCACAGGU
.(((....(((((...(((........)))....)))))....((((((((.(((((.(((.((((.....)))))))..)))))..))))))))..))) ( -27.30)
>consensus
AUCCAACAUCCAACAGCC__CCUUCGUC____AUUUGGCCAUUUGGUCAUUUGUGGCCGGUCCUUGGCUCGUUAAGCCAAGCCAUUUAAUAACCACAGGU
...........................................((((.(((.(((((......((((((.....)))))))))))..))).))))..... (-13.64 = -14.25 +   0.61)

alignment

secondary structure

dotplot

Window 9

Location	14,729,627 – 14,729,721
Length	94
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	75.05
Mean single sequence MFE	-29.76
Consensus MFE	-18.50
Energy contribution	-18.58
Covariance contribution	0.09
Combinations/Pair	1.14
Mean z-score	-1.93
Structure conservation index	0.62
SVM decision value	1.46
SVM RNA-class probability	0.956255
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14729627 94 - 27905053
ACCUGUGGUUAUUAAAUGGCUUGGCUUAACGAGCCAAGGACCGGCCACAAAUGACCAAAUGACCAAAU----GACGAAGG--GGCCAUUGGAUGUUGGAU
...(((((((......(((((((......)))))))......))))))).....((((....((((.(----(.(....)--...))))))...)))).. ( -27.80)
>DroPse_CAF1 137298 82 - 1
GGCUCCGGCUCCUAAAUGGCUUGGCUUAACGAGCCAAAGACUGGCCGCAAAUGACCAACUGGCAG------------------GAUGCAGGAAGAUCGAU
...(((((((......(((((((......)))))))......))))(((..((.((....)))).------------------..))).)))........ ( -26.80)
>DroSec_CAF1 148122 86 - 1
ACCUGUGGUUAUUAAAUGGCUUGGCUUAACGAGCCAAGGACCGGCCACAAAUGAC--------CAAAU----GACGAAGG--GGCCAUUGGCUGUUGGAU
...(((((((......(((((((......)))))))......))))))).....(--------(((..----..(....)--((((...)))).)))).. ( -27.40)
>DroSim_CAF1 154044 94 - 1
CCCUGUGGUUAUUAAAUGGCUUGGCUUAACGAGCCAAGGACCGGCCACAAAUGACCAAAUGACCAAAU----GACGAAGG--GGCCAUUGGCUGUUGGAU
.....((((((((...(((((((......))))))).((.....))...)))))))).....((((..----..(....)--((((...)))).)))).. ( -28.20)
>DroEre_CAF1 146942 99 - 1
ACCUGUGGUUAUUAAAUGGCUUGGCUUAACGAGCCUAAGACCGGCCACAAAUGACCAAAUGGUCA-UUGGAUGUCGGAUGUUGGAUGCUGGAUGUUGGAU
.(((((((((.......((((((......)))))).......)))))))(((((((....)))))-))))..(((.((((((.(....).)))))).))) ( -33.84)
>DroYak_CAF1 156401 100 - 1
ACCUGUGGUUAUUAAAUGGCUUGGCUUAACGAGCCUAAGGCCGGCCACAAAUAACCAAAUGUCCAAAUGGCCAUUGGUUGUUGGAUGUUGGAAGUGGGCU
.(((((((((.......((((((......)))))).......))))))).....((((.((((((.(..(((...)))..)))))))))))....))... ( -34.54)
>consensus
ACCUGUGGUUAUUAAAUGGCUUGGCUUAACGAGCCAAAGACCGGCCACAAAUGACCAAAUGACCAAAU____GACGAAGG__GGACAUUGGAUGUUGGAU
...(((((((......(((((((......)))))))......)))))))................................................... (-18.50 = -18.58 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:20 2006