Locus 1396

Sequence ID 3L_DroMel_CAF1
Location 4,061,410 – 4,061,500
Length 90
Max. P 0.957313
window2168 window2169

overview

Window 8

Location 4,061,410 – 4,061,500
Length 90
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 73.89
Mean single sequence MFE -28.43
Consensus MFE -11.37
Energy contribution -12.15
Covariance contribution 0.78
Combinations/Pair 1.06
Mean z-score -2.44
Structure conservation index 0.40
SVM decision value 1.48
SVM RNA-class probability 0.957313
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4061410 90 + 23771897
AUG-GCAAUCAAUUUGAAAGUGUUC-------U-GUGGA-GUCG----GC-UGCUUGACCGCAA-GCUGUCGAUUCCACGACAGCUGCACUUGC---CGCAUUUGCCUA
..(-((((............((((.-------.-(((((-((((----((-.(((((....)))-)).)))))))))))))))((.((....))---.))..))))).. ( -38.50)
>DroVir_CAF1 5636 82 + 1
--G-C-AAUCAAUUUGAAAGUGUUU-------A-UGGGA-CACU-------GCCUUGACCGCAA-GCUGUCAAU---ACGACAGCUGCAGUGGC---GACAUUUGCCUA
--(-(-((..........((((((.-------.-...))-))))-------(((...((.(((.-((((((...---..))))))))).)))))---.....))))... ( -26.70)
>DroGri_CAF1 5876 85 + 1
--GGUCCAUCAAUCUGAAAGUGUUU-------A-UGGGAGCACU-------CCCUUGACCGCAA-ACUGUCAAU---ACGACAGCUGCAGUGGC---GACAUUUGCCUA
--((((..((.....))........-------.-.((((....)-------)))..))))(((.-.(((((...---..))))).)))...(((---((...))))).. ( -24.30)
>DroWil_CAF1 5667 97 + 1
UAG-CCAAUCAAUUUGAAAGUGUUUAUGGCCUUAAUGGA-GCU-CUAGG--GCCUUGACCACAA-GCUGUCAAU---ACGACAGCUGCACUUAC---GACAUUUGCCUA
(((-.(((.....(((.(((((((((.(((((((.....-...-.))))--))).))).....(-((((((...---..))))))))))))).)---))...))).))) ( -28.30)
>DroMoj_CAF1 6489 90 + 1
--G-CCCAUCAAUUUGAAAGUGUUU-------A-UGGGA-CACU----UCUCCCUUGACCGCAAAACUGUCAAU---ACGACAGCUGCAACGGCGGUGGCAUUUGCCUA
--(-((..((((...(((((((((.-------.-...))-))))----).))..))))..(((...(((((...---..))))).)))...)))...(((....))).. ( -25.80)
>DroAna_CAF1 5153 88 + 1
AAG-GCCAUCAAUUUGAAACUGUU--------U-AUGGA-GUCU----GG-AG-UUGACCGCAG-GCUGUCAAUACGACGACAGCUGCAAUAGC---CACAUUUGCCUA
.((-((..(((((((.(.(((.(.--------.-..).)-)).)----.)-))-))))..((((-.(((((........)))))))))......---.......)))). ( -27.00)
>consensus
__G_CCAAUCAAUUUGAAAGUGUUU_______A_UGGGA_CACU____G__CCCUUGACCGCAA_GCUGUCAAU___ACGACAGCUGCAAUGGC___GACAUUUGCCUA
.................(((((((............((....................))(((..((((((........))))))))).........)))))))..... (-11.37 = -12.15 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 4,061,410 – 4,061,500
Length 90
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 73.89
Mean single sequence MFE -27.80
Consensus MFE -14.65
Energy contribution -14.35
Covariance contribution -0.30
Combinations/Pair 1.44
Mean z-score -2.03
Structure conservation index 0.53
SVM decision value 1.27
SVM RNA-class probability 0.938979
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4061410 90 - 23771897
UAGGCAAAUGCG---GCAAGUGCAGCUGUCGUGGAAUCGACAGC-UUGCGGUCAAGCA-GC----CGAC-UCCAC-A-------GAACACUUUCAAAUUGAUUGC-CAU
..(((((...((---((......((((((((......)))))))-)(((......)))-))----))..-.....-.-------(((....))).......))))-).. ( -30.60)
>DroVir_CAF1 5636 82 - 1
UAGGCAAAUGUC---GCCACUGCAGCUGUCGU---AUUGACAGC-UUGCGGUCAAGGC-------AGUG-UCCCA-U-------AAACACUUUCAAAUUGAUU-G-C--
...((((.....---(((((((((((((((..---...))))))-.))))))...)))-------((((-(....-.-------..)))))..........))-)-)-- ( -27.40)
>DroGri_CAF1 5876 85 - 1
UAGGCAAAUGUC---GCCACUGCAGCUGUCGU---AUUGACAGU-UUGCGGUCAAGGG-------AGUGCUCCCA-U-------AAACACUUUCAGAUUGAUGGACC--
..(((.......---)))((((((((((((..---...))))).-)))))))...(((-------(....)))).-.-------.......((((......))))..-- ( -26.20)
>DroWil_CAF1 5667 97 - 1
UAGGCAAAUGUC---GUAAGUGCAGCUGUCGU---AUUGACAGC-UUGUGGUCAAGGC--CCUAG-AGC-UCCAUUAAGGCCAUAAACACUUUCAAAUUGAUUGG-CUA
..(((....(((---(.(((((..((((((..---...))))))-((((((((..(((--.....-.))-).......)))))))).)))))......))))..)-)). ( -25.90)
>DroMoj_CAF1 6489 90 - 1
UAGGCAAAUGCCACCGCCGUUGCAGCUGUCGU---AUUGACAGUUUUGCGGUCAAGGGAGA----AGUG-UCCCA-U-------AAACACUUUCAAAUUGAUGGG-C--
..(((....)))...(((..((((((((((..---...))))))..))))(((((..((((----.(((-(....-.-------..))))))))...))))).))-)-- ( -29.30)
>DroAna_CAF1 5153 88 - 1
UAGGCAAAUGUG---GCUAUUGCAGCUGUCGUCGUAUUGACAGC-CUGCGGUCAA-CU-CC----AGAC-UCCAU-A--------AACAGUUUCAAAUUGAUGGC-CUU
.((((...((((---(.....((((((((((......)))))).-))))((((..-..-..----.)))-)))))-)--------..((((.....))))...))-)). ( -27.40)
>consensus
UAGGCAAAUGUC___GCCACUGCAGCUGUCGU___AUUGACAGC_UUGCGGUCAAGGC__C____AGUC_UCCAA_A_______AAACACUUUCAAAUUGAUGGG_C__
..(((..........)))(((((((((((((......)))))))..))))))......................................................... (-14.65 = -14.35 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:26 2006