Locus 1499

Sequence ID	X_DroMel_CAF1
Location	4,426,474 – 4,426,674
Length	200
Max. P	0.942429

overview

Window 5

Location	4,426,474 – 4,426,594
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.64
Mean single sequence MFE	-32.16
Consensus MFE	-21.86
Energy contribution	-23.34
Covariance contribution	1.48
Combinations/Pair	1.21
Mean z-score	-2.05
Structure conservation index	0.68
SVM decision value	0.05
SVM RNA-class probability	0.559561
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4426474 120 - 22224390
GUUGUUGCUCUUCCUCUGUUGUGACAUUUAUUUGCUCCUAAUUCCUGCGGUUAUCUCCGCCAGAAGGUUAGCCAGAGAUAGUCCAAUUAUGCAUGGAUUGUCCAGGAAGAGUCAUCAUCC
..((.(((((((((((((..(..(.......)..)..((((((.((((((......))).)))..)))))).))))(((((((((........)))))))))..))))))).)).))... ( -35.50)
>DroSec_CAF1 28856 120 - 1
GUUCUUGCUCUUCCUCUGUUGUGACAUUUAUUUGCUCCUAAUUCCCGUGGUUAUCUUCGCCAGAAGGUUAGCCAGAGAUAGUCCAAUUAUGCAUGGAUUGUCCAGGAGGAGUCAUCAUCC
......(((((((((..((((.((((......)).)).)))).....(((((((((((....))))).))))))(.(((((((((........)))))))))))))))))))........ ( -34.90)
>DroSim_CAF1 30174 108 - 1
GUUCUUGCUCUUCCUCUGUUGUGACAUUUAUUUGCUCCUAAUUCCUGCGGUUAUCUCCGCC------------AGAGAUAGUCCAAUUAUGCAUGGAUUGUCCAGGAGGAGUCAUCAUCC
......(((((((((((((((.((((......)).)).))).....((((......)))))------------)))(((((((((........)))))))))..))))))))........ ( -31.30)
>DroEre_CAF1 29802 117 - 1
GUUAUU---UUUCCUCUGUUGUGACAUUUAUUUGCUCCUAAUUCCUGUGGUUAUCUCCGCCAGAAGGUUAGCCAAAGAUAGUCCAAUUAUGCAUGGAUUGUCCAGGAAGAGUCAUCAUCC
(((((.---.(......)..)))))........((((....((((((((((((...((.......)).))))))..(((((((((........)))))))))))))))))))........ ( -30.20)
>DroYak_CAF1 29414 117 - 1
GUUAUU---UGUCCUCUGUUAUGACAAAUAUUUCCUCCUAAUUCCUGUGGUUAUCUCCGUCAGAAGGUUAGCCAGAGAUUGUCCAAUUAUGUAUGGAUUGUCCAGGAAGAGUCAUCAUCC
..((((---((((.........))))))))....(((....((((((((((((...((.......)).))))))..(((.(((((........))))).))))))))))))......... ( -28.90)
>consensus
GUUAUUGCUCUUCCUCUGUUGUGACAUUUAUUUGCUCCUAAUUCCUGUGGUUAUCUCCGCCAGAAGGUUAGCCAGAGAUAGUCCAAUUAUGCAUGGAUUGUCCAGGAAGAGUCAUCAUCC
......(((((((((...............((((.......(((..((((......))))..))).......))))(((((((((........))))))))).)))))))))........ (-21.86 = -23.34 +   1.48)

alignment

secondary structure

dotplot

Window 6

Location	4,426,554 – 4,426,674
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.97
Mean single sequence MFE	-29.04
Consensus MFE	-25.08
Energy contribution	-26.64
Covariance contribution	1.56
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.86
SVM decision value	1.33
SVM RNA-class probability	0.942429
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4426554 120 + 22224390
UAGGAGCAAAUAAAUGUCACAACAGAGGAAGAGCAACAACUGCCUGCAAAGAGGGAACUCAUUAGUCAGUCGGAAUUGCAGCGGUUCCACUUCAAUUUCAUUACUUCCACAUCUUCGAUU
..((((........(((....)))..(((((.......((((.(((....(((....)))..))).)))).(((((((.((.(....).)).)))))))....)))))....)))).... ( -26.40)
>DroSec_CAF1 28936 120 + 1
UAGGAGCAAAUAAAUGUCACAACAGAGGAAGAGCAAGAACUGCCAGCAAAGAGGGAACUCAUUAGGCAGUCGAAAUUGCAGCGGUUCCACUUCAAUUUCAUUACUUCCACAUCUUCGAUU
..((((........(((....)))..(((((.....((.(((((......(((....)))....)))))))(((((((.((.(....).)).)))))))....)))))....)))).... ( -31.70)
>DroSim_CAF1 30242 120 + 1
UAGGAGCAAAUAAAUGUCACAACAGAGGAAGAGCAAGAACUGCCAGCAAAGAGGGAACUCAUUAGGCAGUCGAAAUUGCAGCGGUUCCACUUCAAUUUCAUUACUUCCACAUCUUCGAUU
..((((........(((....)))..(((((.....((.(((((......(((....)))....)))))))(((((((.((.(....).)).)))))))....)))))....)))).... ( -31.70)
>DroEre_CAF1 29882 116 + 1
UAGGAGCAAAUAAAUGUCACAACAGAGGAAA---AAUAACUGCCUGCAAGGAGG-CACUCAUUAGGCAAUCGGAAUUGCAGCAGUUCCACUUCAAUUUCAUUACUUCCACAUCUUCGAUU
..((((........(((....)))((((...---......((((((....(((.-..)))..))))))...(((((((...))))))).))))...........))))............ ( -22.70)
>DroYak_CAF1 29494 116 + 1
UAGGAGGAAAUAUUUGUCAUAACAGAGGACA---AAUAACUGCCUGCAAGGAGG-CACUCAUUAGGCAGUCGGAAUUGCAGCAGUUCCACUUCAAUUUCAUUACUUCCACAUCUUCGAUU
..(((((...((((((((.........))))---))))((((((((....(((.-..)))..)))))))).(((((((...)))))))...............)))))............ ( -32.70)
>consensus
UAGGAGCAAAUAAAUGUCACAACAGAGGAAGAGCAAGAACUGCCUGCAAAGAGGGAACUCAUUAGGCAGUCGGAAUUGCAGCGGUUCCACUUCAAUUUCAUUACUUCCACAUCUUCGAUU
..((((........(((....)))..(((((.......((((((((....(((....)))..)))))))).(((((((.((.(....).)).)))))))....)))))....)))).... (-25.08 = -26.64 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:15 2006