Locus 6464

Sequence ID	3R_DroMel_CAF1
Location	16,997,228 – 16,997,339
Length	111
Max. P	0.781320

overview

Window 7

Location	16,997,228 – 16,997,339
Length	111
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	88.42
Mean single sequence MFE	-28.08
Consensus MFE	-22.02
Energy contribution	-22.46
Covariance contribution	0.44
Combinations/Pair	1.18
Mean z-score	-1.60
Structure conservation index	0.78
SVM decision value	0.29
SVM RNA-class probability	0.670719
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16997228 111 + 27905053
UUGUGCACCAACCUAAUAUCAAGUGCCAAAGUGAGCGCAGCAAAUGCAUUUAGCAUAUUAUUUAAAUGCAUUUAUUCAGUGGUACUGUGCAUUUCAGA----AGCCUGUUAUGGU
..((((((.............(((((((...(((((...))((((((((((((........))))))))))))..))).)))))))))))))......----.(((......))) ( -28.11)
>DroSec_CAF1 16320 112 + 1
UUGUGCACCAGCCUAAUAUCAAGUGCCAAAGUCAGCACAGCAAAUGCAUUUAGCAUA---UUUAAAUGCAUUUAUUCAGUGGUACUGUGUAUUUCAGAGAUAGGCCUUAUAUGGU
......(((((((((.(((((.((((........))))...((((((((((((....---.))))))))))))......)))))((.((.....)).)).)))))......)))) ( -28.60)
>DroSim_CAF1 16306 112 + 1
UUGUGCACCAGCCUAAUAUCAAGUGCCAAAGUCAGCACAGCAAAUGCAUUUAGUAUA---UUUAAAUGCAUUUAUUCAGUGGUACUGUGUAUUUCAGAGAUAGGCCUGAUAUGGU
......(((((((((.(((((.((((........))))...((((((((((((....---.))))))))))))......)))))((.((.....)).)).)))))......)))) ( -29.50)
>DroEre_CAF1 16437 111 + 1
UUGUGCGCCAACCUAAUAUCAAGUGCCAAAGUCACCACGGCA-AUGCAUUUAGCAUA---UUCAAAUGCAUUUAUUCAGUGGUACCGUGUAUUUCAGAGAUGUGCCUGGUAUGGU
......(((((((..(((((((((((.(..((.(((((...(-((((((((......---...)))))))))......)))))))..)))))))....)))))....))).)))) ( -26.60)
>DroYak_CAF1 19658 111 + 1
UUGUGCACCAACCUAAUUUCAAGUGCCAAAGUCAGCACGGCA-AGGCACUUGGCAUA---UUCAAAUGCAUUUAUUCACUGCUACCGUGUAUUUCAGAGAAAUGCCUGAUAUGGU
....(((............((((((((...(((.....))).-.))))))))((((.---.....))))..........))).((((((....((((........)))))))))) ( -27.60)
>consensus
UUGUGCACCAACCUAAUAUCAAGUGCCAAAGUCAGCACAGCAAAUGCAUUUAGCAUA___UUUAAAUGCAUUUAUUCAGUGGUACUGUGUAUUUCAGAGAUAGGCCUGAUAUGGU
..((((((..(((.........((((........))))...((((((((((((........)))))))))))).......)))...))))))...........(((......))) (-22.02 = -22.46 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	16,997,228 – 16,997,339
Length	111
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	88.42
Mean single sequence MFE	-27.82
Consensus MFE	-20.80
Energy contribution	-22.04
Covariance contribution	1.24
Combinations/Pair	1.10
Mean z-score	-1.92
Structure conservation index	0.75
SVM decision value	0.56
SVM RNA-class probability	0.781320
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16997228 111 - 27905053
ACCAUAACAGGCU----UCUGAAAUGCACAGUACCACUGAAUAAAUGCAUUUAAAUAAUAUGCUAAAUGCAUUUGCUGCGCUCACUUUGGCACUUGAUAUUAGGUUGGUGCACAA
.......(((...----.)))...(((((...(((......((((((((((((..........))))))))))))....(((......)))...........)))..)))))... ( -25.20)
>DroSec_CAF1 16320 112 - 1
ACCAUAUAAGGCCUAUCUCUGAAAUACACAGUACCACUGAAUAAAUGCAUUUAAA---UAUGCUAAAUGCAUUUGCUGUGCUGACUUUGGCACUUGAUAUUAGGCUGGUGCACAA
..(((....((((((..((.........(((.....)))..((((((((((((..---.....))))))))))))..(((((......)))))..))...)))))).)))..... ( -28.50)
>DroSim_CAF1 16306 112 - 1
ACCAUAUCAGGCCUAUCUCUGAAAUACACAGUACCACUGAAUAAAUGCAUUUAAA---UAUACUAAAUGCAUUUGCUGUGCUGACUUUGGCACUUGAUAUUAGGCUGGUGCACAA
......(((((......)))))........((((((((((.((((((((((((..---.....))))))))))))..(((((......)))))......))))..)))))).... ( -30.50)
>DroEre_CAF1 16437 111 - 1
ACCAUACCAGGCACAUCUCUGAAAUACACGGUACCACUGAAUAAAUGCAUUUGAA---UAUGCUAAAUGCAU-UGCCGUGGUGACUUUGGCACUUGAUAUUAGGUUGGCGCACAA
.......((((......)))).........(..(((((.((((((((((((((..---.....)))))))))-)((((.(....)..))))......)))).)).)))..).... ( -25.20)
>DroYak_CAF1 19658 111 - 1
ACCAUAUCAGGCAUUUCUCUGAAAUACACGGUAGCAGUGAAUAAAUGCAUUUGAA---UAUGCCAAGUGCCU-UGCCGUGCUGACUUUGGCACUUGAAAUUAGGUUGGUGCACAA
((((.(((.((((.(((.(((...(((...))).))).))).....(((((((..---.....)))))))..-))))(((((......))))).........)))))))...... ( -29.70)
>consensus
ACCAUAUCAGGCAUAUCUCUGAAAUACACAGUACCACUGAAUAAAUGCAUUUAAA___UAUGCUAAAUGCAUUUGCUGUGCUGACUUUGGCACUUGAUAUUAGGUUGGUGCACAA
.......((((......)))).........((((((((((.((((((((((((..........))))))))))))..(((((......)))))......))))..)))))).... (-20.80 = -22.04 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:07 2006