Locus 6073

Sequence ID	3R_DroMel_CAF1
Location	15,949,531 – 15,949,621
Length	90
Max. P	0.989494

overview

Window 6

Location	15,949,531 – 15,949,621
Length	90
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	88.94
Mean single sequence MFE	-29.80
Consensus MFE	-23.66
Energy contribution	-24.70
Covariance contribution	1.04
Combinations/Pair	1.07
Mean z-score	-2.63
Structure conservation index	0.79
SVM decision value	2.17
SVM RNA-class probability	0.989494
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15949531 90 + 27905053
GACC------C-AAAUGGGAUAUUCUUGAGCGCUUUUUAAGGCUCAAUCUGUGUCCUUCCAGCCAGCCCAUCAAUGGGUUCCGGCUGUCGGUUCCCU
((((------.-....(((((((..((((((.((.....))))))))...)))))))..(((((((((((....))))))..)))))..)))).... ( -33.50)
>DroSec_CAF1 75891 90 + 1
GACC------C-AAAUGGGAUAUUCUUGAGCUCUUUUUAAGGCUCAAUCUGUGUCCUUGCAGCCAACCCAUCAAUGGGUUCCGGCUGUCGGUGCCCU
.(((------.-....(((((((..(((((((........)))))))...))))))).((((((((((((....))))))..)))))).)))..... ( -35.00)
>DroSim_CAF1 51234 90 + 1
GACC------C-AAAUGGGAUAUUCUUGAGCUCUUUUUAAGGCUCAAUCUGUGUCCUUGCAGCCAACCCAUCAAUGGGUUCCGGCUGUCGGUGCCCU
.(((------.-....(((((((..(((((((........)))))))...))))))).((((((((((((....))))))..)))))).)))..... ( -35.00)
>DroEre_CAF1 50877 91 + 1
GACC------CAAAAUGGGAUAUUCUUGAGCGCUUUUUAAGGCUCAAUCUGCCUCCUGCCAUCCAGCCCAUCAAUGCGUUCCGGCUGUCGGUGCCCA
....------.....((((......((((((.((.....))))))))...(((..(.(((.....((........)).....))).)..))).)))) ( -22.10)
>DroYak_CAF1 79603 97 + 1
GACCUAUGCACAAAAUGGGAUAUUCUUGAGCGCUUUUUAAGGCUCAAUCUGUGUCCACCCAUCCAGCUCAUCAAUGGGUUCCGACUGUCACUGCCCA
(((..............((((((..((((((.((.....))))))))...))))))((((((...........)))))).......)))........ ( -23.40)
>consensus
GACC______C_AAAUGGGAUAUUCUUGAGCGCUUUUUAAGGCUCAAUCUGUGUCCUUCCAGCCAGCCCAUCAAUGGGUUCCGGCUGUCGGUGCCCU
(((.............(((((((..((((((.((.....))))))))...)))))))...((((((((((....))))))..)))))))........ (-23.66 = -24.70 +   1.04)

alignment

secondary structure

dotplot

Window 7

Location	15,949,531 – 15,949,621
Length	90
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	88.94
Mean single sequence MFE	-29.84
Consensus MFE	-23.70
Energy contribution	-24.14
Covariance contribution	0.44
Combinations/Pair	1.12
Mean z-score	-1.87
Structure conservation index	0.79
SVM decision value	0.90
SVM RNA-class probability	0.876864
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15949531 90 - 27905053
AGGGAACCGACAGCCGGAACCCAUUGAUGGGCUGGCUGGAAGGACACAGAUUGAGCCUUAAAAAGCGCUCAAGAAUAUCCCAUUU-G------GGUC
.((((.((..(((((((..((((....)))))))))))...)).......((((((((.....)).)))))).....))))....-.------.... ( -34.50)
>DroSec_CAF1 75891 90 - 1
AGGGCACCGACAGCCGGAACCCAUUGAUGGGUUGGCUGCAAGGACACAGAUUGAGCCUUAAAAAGAGCUCAAGAAUAUCCCAUUU-G------GGUC
..(((.((((((((((..(((((....)))))))))))...(((......((((((((.....)).)))))).....)))...))-)------)))) ( -30.60)
>DroSim_CAF1 51234 90 - 1
AGGGCACCGACAGCCGGAACCCAUUGAUGGGUUGGCUGCAAGGACACAGAUUGAGCCUUAAAAAGAGCUCAAGAAUAUCCCAUUU-G------GGUC
..(((.((((((((((..(((((....)))))))))))...(((......((((((((.....)).)))))).....)))...))-)------)))) ( -30.60)
>DroEre_CAF1 50877 91 - 1
UGGGCACCGACAGCCGGAACGCAUUGAUGGGCUGGAUGGCAGGAGGCAGAUUGAGCCUUAAAAAGCGCUCAAGAAUAUCCCAUUUUG------GGUC
(((((.(((.....)))...((.((...(((((.(((.((.....))..))).)))))...)).))))))).......(((.....)------)).. ( -28.40)
>DroYak_CAF1 79603 97 - 1
UGGGCAGUGACAGUCGGAACCCAUUGAUGAGCUGGAUGGGUGGACACAGAUUGAGCCUUAAAAAGCGCUCAAGAAUAUCCCAUUUUGUGCAUAGGUC
((((........(((...(((((((.(.....).))))))).))).....((((((((.....)).))))))......))))............... ( -25.10)
>consensus
AGGGCACCGACAGCCGGAACCCAUUGAUGGGCUGGCUGGAAGGACACAGAUUGAGCCUUAAAAAGCGCUCAAGAAUAUCCCAUUU_G______GGUC
.(((..((..(((((((..((((....)))))))))))...)).......((((((((.....)).))))))......)))................ (-23.70 = -24.14 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:59 2006