Locus 3728

Sequence ID	3R_DroMel_CAF1
Location	10,122,054 – 10,122,155
Length	101
Max. P	0.768249

overview

Window 5

Location	10,122,054 – 10,122,155
Length	101
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.96
Mean single sequence MFE	-32.18
Consensus MFE	-20.67
Energy contribution	-21.15
Covariance contribution	0.48
Combinations/Pair	1.10
Mean z-score	-2.08
Structure conservation index	0.64
SVM decision value	-0.02
SVM RNA-class probability	0.521953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10122054 101 + 27905053
AAUUUAUGAGUGACUGAACC--GCAUUAGCCGCAUAAUUUAUGGCUCUGAUUAUGGGCCAUUCG-GCCAAUG----------------AAAAGUGGACCAACGUGGCUCAAAGUCUUGAC
...........((((.....--.....((((((.......(((((((.......)))))))..(-((((.(.----------------...).))).))...))))))...))))..... ( -27.22)
>DroSec_CAF1 31320 102 + 1
AAUUUAUGAGUGACUGAGCC--GCAUUAGCCGCAUAAUUUAUGGCUCUGAUUAUGGGCCAUUCGGGCCCACG----------------AAAAGUGGACCAACGUGGCUCAAAGUCUUGAC
...........(((((((((--((....(((.(((((((.........)))))))))).....((..((((.----------------....)))).))...)))))))..))))..... ( -35.40)
>DroSim_CAF1 27729 102 + 1
AAUUUAUGAGUGACUGAGCC--GCAUUAGCCGCAUAAUUUAUGGCUCUGAUUAUGGGCCAUUCGGGCCAACG----------------AAAAGUGGACCAACUUGGCUCAAAGUCUUGAC
...........(((((((((--(..((.(((((........((((((.......))))))((((......))----------------))..)))).).))..))))))..))))..... ( -31.10)
>DroEre_CAF1 31064 101 + 1
AAUUUAUGAGUGCCUGAGCC--ACAUUAGCCGCAUAAUUUAUGGCUCUGAUUAUGGGCCAAUCG-GCCAACG----------------AGAAGUGGACUAACGUGGCUCCGAGUCUUGAC
.......(((.(((.(((((--((.((((((((........((((((.......)))))).(((-.....))----------------)...)))).)))).))))))).).)))))... ( -37.20)
>DroYak_CAF1 31820 119 + 1
AAUUUAUUAUUGCCUGAGCCGCACAUUAGCCGCAUAAUUUAUGGCUCUGAUUAUGGGCCAUUCG-GCCAACGAAAUAACGACAAAACGAAAAGCUGACCAACGUGGCUCAAAGUCUUGAC
......(((..((.((((((((...(((((...........((((((.......))))))((((-.....))))..................))))).....))))))))..))..))). ( -30.00)
>consensus
AAUUUAUGAGUGACUGAGCC__GCAUUAGCCGCAUAAUUUAUGGCUCUGAUUAUGGGCCAUUCG_GCCAACG________________AAAAGUGGACCAACGUGGCUCAAAGUCUUGAC
...........(((((((((.........((((........((((((.......))))))..((......))....................))))........)))))..))))..... (-20.67 = -21.15 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	10,122,054 – 10,122,155
Length	101
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.96
Mean single sequence MFE	-32.35
Consensus MFE	-21.84
Energy contribution	-22.12
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.34
Structure conservation index	0.68
SVM decision value	0.52
SVM RNA-class probability	0.768249
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10122054 101 - 27905053
GUCAAGACUUUGAGCCACGUUGGUCCACUUUU----------------CAUUGGC-CGAAUGGCCCAUAAUCAGAGCCAUAAAUUAUGCGGCUAAUGC--GGUUCAGUCACUCAUAAAUU
.....((((..(((((.((((((((.......----------------....(((-(....))))((((((...........)))))).)))))))).--)))))))))........... ( -28.90)
>DroSec_CAF1 31320 102 - 1
GUCAAGACUUUGAGCCACGUUGGUCCACUUUU----------------CGUGGGCCCGAAUGGCCCAUAAUCAGAGCCAUAAAUUAUGCGGCUAAUGC--GGCUCAGUCACUCAUAAAUU
.....((((..(((((.((((((((..((..(----------------..((((((.....))))))..)..)).((.(((...))))))))))))).--)))))))))........... ( -36.70)
>DroSim_CAF1 27729 102 - 1
GUCAAGACUUUGAGCCAAGUUGGUCCACUUUU----------------CGUUGGCCCGAAUGGCCCAUAAUCAGAGCCAUAAAUUAUGCGGCUAAUGC--GGCUCAGUCACUCAUAAAUU
.....((((..(((((...((((.(((.....----------------...))).)))).(((((((((((...........)))))).)))))....--)))))))))........... ( -30.00)
>DroEre_CAF1 31064 101 - 1
GUCAAGACUCGGAGCCACGUUAGUCCACUUCU----------------CGUUGGC-CGAUUGGCCCAUAAUCAGAGCCAUAAAUUAUGCGGCUAAUGU--GGCUCAGGCACUCAUAAAUU
...........((((((((((((((((.....----------------...((((-((((((.....))))).).)))).......)).)))))))))--)))))............... ( -33.36)
>DroYak_CAF1 31820 119 - 1
GUCAAGACUUUGAGCCACGUUGGUCAGCUUUUCGUUUUGUCGUUAUUUCGUUGGC-CGAAUGGCCCAUAAUCAGAGCCAUAAAUUAUGCGGCUAAUGUGCGGCUCAGGCAAUAAUAAAUU
........((((((((.(((((((((((....((......)).......))))))-))).(((((((((((...........)))))).)))))...)).))))))))............ ( -32.80)
>consensus
GUCAAGACUUUGAGCCACGUUGGUCCACUUUU________________CGUUGGC_CGAAUGGCCCAUAAUCAGAGCCAUAAAUUAUGCGGCUAAUGC__GGCUCAGUCACUCAUAAAUU
.....((((..(((((.((((((((...........................(((.......)))((((((...........)))))).))))))))...)))))))))........... (-21.84 = -22.12 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:35 2006