Locus 7411

Sequence ID	3L_DroMel_CAF1
Location	19,943,240 – 19,943,439
Length	199
Max. P	0.985200

overview

Window 8

Location	19,943,240 – 19,943,359
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.93
Mean single sequence MFE	-33.99
Consensus MFE	-30.86
Energy contribution	-30.92
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-1.79
Structure conservation index	0.91
SVM decision value	0.34
SVM RNA-class probability	0.696292
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19943240 119 + 23771897
UUCCGGAGGACACGCC-CAAAUAUCAAAGUAUUUUAAAGGUCACAGCUGACGAUGCUGACCUCGGCAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUUGCUAUC
.((.(((((.(...((-((....................((((....))))(((((((....)))))))..))))(....).......)))))).))..(((((..(.....)..))))) ( -33.70)
>DroSec_CAF1 8646 120 + 1
UUCCGGAGGACACGCCCCAAAUAUCAAAGUAUUUUAAAGGUCACAGCUGACGAUGCUGACCUCGGAAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUC
.((.(((((.....((((((((((....)))))((..((((((..((.......))))))))..)).....))))).............))))).))..((((((((.....)))))))) ( -33.37)
>DroSim_CAF1 8193 119 + 1
UUCCGGAGGACACGCC-CAAAUAUCAAAGUAUUUUAAAGGUCACAGCUGACGAUGCUGACCUCGGCAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUC
.((.(((((.(...((-((....................((((....))))(((((((....)))))))..))))(....).......)))))).))..((((((((.....)))))))) ( -36.10)
>DroYak_CAF1 8777 119 + 1
UUCCGGAGGACACGCC-CAAAUAUCAAAGUAUUUUAAAGGUCACCGCAGACGAUGCUGACCUCGGCAUCAAUGGGGACAUCUACUACAGUCUCCUGAUGGAUAGUGAAUACUUUGCUAUC
....((.(....)..)-)..(((.((((((((((...((((((..(((.....)))))))))...(((((..((((((..........)))))))))))......)))))))))).))). ( -32.80)
>consensus
UUCCGGAGGACACGCC_CAAAUAUCAAAGUAUUUUAAAGGUCACAGCUGACGAUGCUGACCUCGGCAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUC
.((.(((((((.(.....((((((....))))))....))))...((((..(((((((....)))))))..((((....))))...)))))))).))..((((((((.....)))))))) (-30.86 = -30.92 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	19,943,279 – 19,943,399
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.39
Mean single sequence MFE	-38.58
Consensus MFE	-36.41
Energy contribution	-37.16
Covariance contribution	0.75
Combinations/Pair	1.03
Mean z-score	-3.40
Structure conservation index	0.94
SVM decision value	2.00
SVM RNA-class probability	0.985200
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19943279 120 + 23771897
UCACAGCUGACGAUGCUGACCUCGGCAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUUGCUAUCCAUCCAACAACUGGCGAAAUUACUCUCCUGCAGCAGCUUC
....(((((.((((((((....)))))))...(((((...........(((....(((((((((..(.....)..)))))))))........)))........)))))....)))))).. ( -40.81)
>DroSec_CAF1 8686 120 + 1
UCACAGCUGACGAUGCUGACCUCGGAAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUCCACCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUC
....(((((.((((.(((....))).)))..((((...........(((....))).((((((((((.....))))))))))))))......((.((......)).))....)))))).. ( -33.50)
>DroSim_CAF1 8232 120 + 1
UCACAGCUGACGAUGCUGACCUCGGCAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUCCACCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUC
....(((((.((((((((....)))))))..((((...........(((....))).((((((((((.....))))))))))))))......((.((......)).))....)))))).. ( -40.10)
>DroYak_CAF1 8816 120 + 1
UCACCGCAGACGAUGCUGACCUCGGCAUCAAUGGGGACAUCUACUACAGUCUCCUGAUGGAUAGUGAAUACUUUGCUAUCCAUCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUC
.....((((..(((((((....)))))))...((((((..........)))))).(((((((((..(.....)..))))))))).......................))))......... ( -39.90)
>consensus
UCACAGCUGACGAUGCUGACCUCGGCAUCAAUGGGGAAAUCUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUCCACCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUC
.....((((.((((((((....)))))))...(((((.........(((......((((((((((((.....))))))))))))......)))..........))))).)))))...... (-36.41 = -37.16 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	19,943,319 – 19,943,439
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-41.20
Consensus MFE	-40.04
Energy contribution	-39.98
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.94
Structure conservation index	0.97
SVM decision value	1.93
SVM RNA-class probability	0.982906
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19943319 120 + 23771897
CUACUACAGCCUCCUGAUGGAUAGUGAAUACUUUGCUAUCCAUCCAACAACUGGCGAAAUUACUCUCCUGCAGCAGCUUCAGUAUGCGGAGAACUCGCACUUCGAGCUCACGGUGGUGGC
(((((((.(((....(((((((((..(.....)..)))))))))........)))((......(((((.(((...((....)).)))))))).((((.....)))).))...))))))). ( -40.30)
>DroSec_CAF1 8726 120 + 1
CUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUCCACCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUCAGUAUGCGGAGAACUCGCACUUCGAGCUCACGGUGGUGGC
........(((......((((((((((.....))))))))))....(((((((..((......(((((.(((...((....)).)))))))).((((.....)))).)).)))))))))) ( -41.50)
>DroSim_CAF1 8272 120 + 1
CUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUCCACCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUCAGUAUGCGGAGAACUCGCACUUCGAGCUCACGGUGGUGGC
........(((......((((((((((.....))))))))))....(((((((..((......(((((.(((...((....)).)))))))).((((.....)))).)).)))))))))) ( -41.50)
>DroYak_CAF1 8856 120 + 1
CUACUACAGUCUCCUGAUGGAUAGUGAAUACUUUGCUAUCCAUCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUCAGUAUGCGGAGAAUUCGCACUUCGAGCUCACAGUGGUGGC
........(((....(((((((((..(.....)..)))))))))..((((((((((((.....(((((.(((...((....)).)))))))).))))).....(....).)))))))))) ( -41.50)
>consensus
CUACUACAGCCUCCUGAUGGAUAGUGAAUACUUCGCUAUCCACCCAACCACUGGCGAAAUUACUCUCCUGCAGCAGCUUCAGUAUGCGGAGAACUCGCACUUCGAGCUCACGGUGGUGGC
........(((....((((((((((((.....))))))))))))..(((((((..((......(((((.(((...((....)).)))))))).((((.....)))).)).)))))))))) (-40.04 = -39.98 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:20 2006