Locus 4757

Sequence ID	2R_DroMel_CAF1
Location	15,660,630 – 15,660,723
Length	93
Max. P	0.932992

overview

Window 3

Location	15,660,630 – 15,660,723
Length	93
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	83.01
Mean single sequence MFE	-37.27
Consensus MFE	-24.78
Energy contribution	-26.26
Covariance contribution	1.48
Combinations/Pair	1.11
Mean z-score	-3.01
Structure conservation index	0.66
SVM decision value	0.74
SVM RNA-class probability	0.837499
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15660630 93 + 20766785
CUUACCAGACA------GCCGGUGGAU--CGGCGAAAUGGUAA-------UGGGCCAAUAUGAUGGCCUCCAUGAGCUGCCUAAUGGGCCGCUCUACGGAGG-UUUUUA
.((((((....------(((((....)--))))....))))))-------..........(((..((((((..((((.(((.....))).))))...)))))-)..))) ( -38.30)
>DroSec_CAF1 537815 95 + 1
CUUACCAGACA------GCCGGUGGAUCUCGGCGAAAUGGUAA-------UGGGCCAAUAUGAUGGCCUCCAUGAGCUGCUUAAUGGGCCGCUCUAUGGAGG-UUUUUA
.((((((....------(((((......)))))....))))))-------..........(((..((((((((((((.(((.....))).)))).)))))))-)..))) ( -39.20)
>DroSim_CAF1 438513 95 + 1
CUUACCAGACA------GCCGGUGGAUCUCGGCGAAAUGGUAA-------UGGGCCAAUAUGAUGGCCUCCAUGAGCUGCCUAAUGGGCCGCUCUAUGGAGG-UUUUUA
.((((((....------(((((......)))))....))))))-------..........(((..((((((((((((.(((.....))).)))).)))))))-)..))) ( -41.60)
>DroEre_CAF1 440650 106 + 1
CUUUCCAGACAGCUGGAAUCGCUGGAU--CGGCGAAAUGGUAAUGGGUAAUGGGCCAAUAUGAUGGCCUCCAUGAGCUGCCUAAUGGGCCGCUCCAUGGCAG-UUUUUA
..((((((....))))))((((((...--)))))).......((((.....((((((......))))))))))((((((((..(((((....))))))))))-)))... ( -39.40)
>DroYak_CAF1 457210 99 + 1
CUUACCAGACUCAGACAGCCGGUGGAU--CGGCGAAAUGGUAA-------UGGGCCAAUAUGAUGGCCUCCAUGAGCUGCCUAAUGGGCCGCUCUAUGGAAG-UUUUUA
.((((((...((.....(((((....)--))))))..))))))-------..(((((......)))))(((((((((.(((.....))).)))).)))))..-...... ( -37.30)
>DroAna_CAF1 428159 88 + 1
CUUACCAGAU-----------CUGAAA--UGGUGAAAUGGUAA-------UGGGCCAAUAUGAUGGCCUUCACGAGCUGGCUAAUGG-CCAGUGUAUGAUGGCUUUUUA
.((((((...-----------......--))))))..((((..-------...)))).......((((.(((...((((((.....)-)))))...))).))))..... ( -27.80)
>consensus
CUUACCAGACA______GCCGGUGGAU__CGGCGAAAUGGUAA_______UGGGCCAAUAUGAUGGCCUCCAUGAGCUGCCUAAUGGGCCGCUCUAUGGAGG_UUUUUA
.((((((..........((((........))))....))))))........((((((......))))))((((((((.(((.....))).)))).)))).......... (-24.78 = -26.26 +   1.48)

alignment

secondary structure

dotplot

Window 4

Location	15,660,630 – 15,660,723
Length	93
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	83.01
Mean single sequence MFE	-35.03
Consensus MFE	-24.04
Energy contribution	-25.24
Covariance contribution	1.20
Combinations/Pair	1.19
Mean z-score	-3.81
Structure conservation index	0.69
SVM decision value	1.23
SVM RNA-class probability	0.932992
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15660630 93 - 20766785
UAAAAA-CCUCCGUAGAGCGGCCCAUUAGGCAGCUCAUGGAGGCCAUCAUAUUGGCCCA-------UUACCAUUUCGCCG--AUCCACCGGC------UGUCUGGUAAG
......-..(((((.((((.(((.....))).)))))))))(((((......)))))..-------((((((..(.((((--......))))------.)..)))))). ( -38.70)
>DroSec_CAF1 537815 95 - 1
UAAAAA-CCUCCAUAGAGCGGCCCAUUAAGCAGCUCAUGGAGGCCAUCAUAUUGGCCCA-------UUACCAUUUCGCCGAGAUCCACCGGC------UGUCUGGUAAG
......-..(((((.((((.((.......)).)))))))))(((((......)))))..-------((((((..(.((((........))))------.)..)))))). ( -35.30)
>DroSim_CAF1 438513 95 - 1
UAAAAA-CCUCCAUAGAGCGGCCCAUUAGGCAGCUCAUGGAGGCCAUCAUAUUGGCCCA-------UUACCAUUUCGCCGAGAUCCACCGGC------UGUCUGGUAAG
......-..(((((.((((.(((.....))).)))))))))(((((......)))))..-------((((((..(.((((........))))------.)..)))))). ( -38.90)
>DroEre_CAF1 440650 106 - 1
UAAAAA-CUGCCAUGGAGCGGCCCAUUAGGCAGCUCAUGGAGGCCAUCAUAUUGGCCCAUUACCCAUUACCAUUUCGCCG--AUCCAGCGAUUCCAGCUGUCUGGAAAG
......-...(((((.(((.(((.....))).)))))))).(((((......))))).................((((..--.....))))((((((....)))))).. ( -34.40)
>DroYak_CAF1 457210 99 - 1
UAAAAA-CUUCCAUAGAGCGGCCCAUUAGGCAGCUCAUGGAGGCCAUCAUAUUGGCCCA-------UUACCAUUUCGCCG--AUCCACCGGCUGUCUGAGUCUGGUAAG
......-..(((((.((((.(((.....))).)))))))))(((((......)))))..-------((((((.(((((((--......)))).....)))..)))))). ( -37.50)
>DroAna_CAF1 428159 88 - 1
UAAAAAGCCAUCAUACACUGG-CCAUUAGCCAGCUCGUGAAGGCCAUCAUAUUGGCCCA-------UUACCAUUUCACCA--UUUCAG-----------AUCUGGUAAG
..........((((...((((-(.....)))))...)))).(((((......)))))..-------((((((..((....--.....)-----------)..)))))). ( -25.40)
>consensus
UAAAAA_CCUCCAUAGAGCGGCCCAUUAGGCAGCUCAUGGAGGCCAUCAUAUUGGCCCA_______UUACCAUUUCGCCG__AUCCACCGGC______UGUCUGGUAAG
.........(((((.((((.(((.....))).)))))))))(((((......))))).........((((((....((((........))))..........)))))). (-24.04 = -25.24 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:37 2006