Locus 6654

Sequence ID	X_DroMel_CAF1
Location	16,609,323 – 16,609,414
Length	91
Max. P	0.962362

overview

Window 7

Location	16,609,323 – 16,609,414
Length	91
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	77.68
Mean single sequence MFE	-12.53
Consensus MFE	-9.88
Energy contribution	-9.92
Covariance contribution	0.04
Combinations/Pair	1.09
Mean z-score	-1.91
Structure conservation index	0.79
SVM decision value	1.54
SVM RNA-class probability	0.962362
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16609323 91 + 22224390
CAAUUUACCAUU------UUACCAU-------------------UUUCCCAUUUUCCAUUUCCCCCGUACCCAAGUGCGUGUGUGUGUGCGGUUUCCCAGCACCUUUUUUACACAU
............------.......-------------------.....................(((((....)))))((((((.((((((....)).))))......)))))). ( -14.60)
>DroSec_CAF1 21824 86 + 1
CCAUUUUCCAUU------UUACCAU-------------------UUUCCCAUUUUCCAUUUCC-CCGUACCCAAGUGCGUG----UGUGCGGUUUCCCAGCACCUUUUUUACACAU
............------.......-------------------...................-..((((....))))(((----(((((((....)).)))).......)))).. ( -11.51)
>DroSim_CAF1 19751 92 + 1
CCAUUUCCCAUUUUCGAUUUACCAU-------------------UUUCCCAUUUUCCAUUUCC-CCGUACCCAAGUGCGUG----UGUGCGGUUUCCCAGCACCUUUUUUACACAU
.........................-------------------...................-..((((....))))(((----(((((((....)).)))).......)))).. ( -11.51)
>DroEre_CAF1 21832 86 + 1
CAAUUUACCAUU------UUCCCUAUCCAAU---------------------UUUCCAUUUCU-CCGUACCCAACUGCGCGU--GUGUGCGGUUUCCCAGCACCUUUUUUACACAU
............------.............---------------------...........-.((((......)))).((--((((((((....)).)))).......)))).. (  -9.81)
>DroYak_CAF1 23302 107 + 1
CAGUUUAGCAUU------UUCCCUUUUCAAUUUCCCAUUUACAAUUUACCAUUUUCCAUUUCC-CCGCACCCAAGUGCGUGU--GUGUGCGGUUUCCCAGCACCUUUUUUACACAU
............------.............................................-.(((((....)))))(((--((((((((....)).)))).......))))). ( -15.21)
>consensus
CAAUUUACCAUU______UUACCAU___________________UUUCCCAUUUUCCAUUUCC_CCGUACCCAAGUGCGUGU__GUGUGCGGUUUCCCAGCACCUUUUUUACACAU
.................................................................(((((....))))).......((((((....)).))))............. ( -9.88 =  -9.92 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	16,609,323 – 16,609,414
Length	91
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	77.68
Mean single sequence MFE	-17.15
Consensus MFE	-15.30
Energy contribution	-15.14
Covariance contribution	-0.16
Combinations/Pair	1.09
Mean z-score	-1.34
Structure conservation index	0.89
SVM decision value	0.97
SVM RNA-class probability	0.892535
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16609323 91 - 22224390
AUGUGUAAAAAAGGUGCUGGGAAACCGCACACACACACGCACUUGGGUACGGGGGAAAUGGAAAAUGGGAAA-------------------AUGGUAA------AAUGGUAAAUUG
.(((((.......((((.((....))))))......)))))((((....))))...................-------------------.......------............ ( -17.62)
>DroSec_CAF1 21824 86 - 1
AUGUGUAAAAAAGGUGCUGGGAAACCGCACA----CACGCACUUGGGUACGG-GGAAAUGGAAAAUGGGAAA-------------------AUGGUAA------AAUGGAAAAUGG
.(((((.......((((.((....)))))).----.)))))((((....)))-)..................-------------------.......------............ ( -16.00)
>DroSim_CAF1 19751 92 - 1
AUGUGUAAAAAAGGUGCUGGGAAACCGCACA----CACGCACUUGGGUACGG-GGAAAUGGAAAAUGGGAAA-------------------AUGGUAAAUCGAAAAUGGGAAAUGG
.(((((.......((((.((....)))))).----.)))))((((....)))-)..................-------------------......................... ( -16.00)
>DroEre_CAF1 21832 86 - 1
AUGUGUAAAAAAGGUGCUGGGAAACCGCACAC--ACGCGCAGUUGGGUACGG-AGAAAUGGAAA---------------------AUUGGAUAGGGAA------AAUGGUAAAUUG
.(((((.......((((.((....))))))..--..)))))...........-...........---------------------.............------............ ( -14.80)
>DroYak_CAF1 23302 107 - 1
AUGUGUAAAAAAGGUGCUGGGAAACCGCACAC--ACACGCACUUGGGUGCGG-GGAAAUGGAAAAUGGUAAAUUGUAAAUGGGAAAUUGAAAAGGGAA------AAUGCUAAACUG
.(((((.......((((.((....))))))))--)))(((((....))))).-.............................................------............ ( -21.31)
>consensus
AUGUGUAAAAAAGGUGCUGGGAAACCGCACAC__ACACGCACUUGGGUACGG_GGAAAUGGAAAAUGGGAAA___________________AUGGUAA______AAUGGUAAAUUG
.(((((.......((((.((....))))))......)))))........................................................................... (-15.30 = -15.14 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:17 2006