Locus 6653

Sequence ID	3L_DroMel_CAF1
Location	17,716,093 – 17,716,238
Length	145
Max. P	0.781560

overview

Window 8

Location	17,716,093 – 17,716,200
Length	107
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	83.64
Mean single sequence MFE	-30.18
Consensus MFE	-19.96
Energy contribution	-23.27
Covariance contribution	3.31
Combinations/Pair	1.04
Mean z-score	-1.52
Structure conservation index	0.66
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17716093 107 + 23771897
CAACACCGCAUUAAAUGUGCACGACAUCAAAUUGAUGAGGCUGCCACGGCCGGCGGCAGAUAGAGCACCAUGUAUGCCGAUUUGGCUUUAUUUAGACCAAACUGGCU
.......((((.....((((....((((.....))))..((((((......)))))).......)))).))))..((((.(((((((......)).))))).)))). ( -33.20)
>DroSec_CAF1 93846 107 + 1
CAACACCACAUUAAAUGUGCACGACAUCAAAUUGAUGAGGCUGCCACGGCCGGCGGCAGAUAGAGCACCAUGGAUGCCGAUUUGGCUUUAUUUAGACCAAACUGGCU
.........(((....((((....((((.....))))..((((((......)))))).......))))....)))((((.(((((((......)).))))).)))). ( -32.70)
>DroSim_CAF1 87942 107 + 1
CAACACCACAUUAAAUGUGCACGACAUCAAAUUGAUGAGGCUGCCACGGCCGGCGGCAGAUAGAGCACCAUGGAUGCCGAUUUGGCUUUAUUUAGACCAAACUGGCU
.........(((....((((....((((.....))))..((((((......)))))).......))))....)))((((.(((((((......)).))))).)))). ( -32.70)
>DroAna_CAF1 83065 92 + 1
CAACACCACAUUAAAUGUGCACGACAUCAAAUUGAUGAGGCUGCCACUGGUUCUGGCAGAUAUGGCAAUAGUGCUGGCUAUUUAGCUAAAUU---------------
..................((((..((((.....))))...((((((.......))))))...........))))(((((....)))))....--------------- ( -22.10)
>consensus
CAACACCACAUUAAAUGUGCACGACAUCAAAUUGAUGAGGCUGCCACGGCCGGCGGCAGAUAGAGCACCAUGGAUGCCGAUUUGGCUUUAUUUAGACCAAACUGGCU
................((((....((((.....))))..((((((......)))))).......)))).......((((.(((((((......)).))))).)))). (-19.96 = -23.27 +   3.31)

alignment

secondary structure

dotplot

Window 9

Location	17,716,127 – 17,716,238
Length	111
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	68.96
Mean single sequence MFE	-29.38
Consensus MFE	-17.67
Energy contribution	-20.55
Covariance contribution	2.88
Combinations/Pair	1.16
Mean z-score	-1.46
Structure conservation index	0.60
SVM decision value	0.56
SVM RNA-class probability	0.781560
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17716127 111 - 23771897
CGACUUCUUAGAA--AAUAUGUAAGAGGACCUGGCUAACUAGCCAGUUUGGUCUAAAUAAAGCCAAAUCGGCAUACAUGGUGCUCUAUCUGCCGCCGGCCGUGGCAGCCUCAU
((((((((((.(.--....).)))))))..((((((....))))))(((((.((......))))))))))((((.....)))).....(((((((.....)))))))...... ( -34.30)
>DroSec_CAF1 93880 104 - 1
--------CAGAAAGAGGUUGUAAGAGGUCC-GACUAACUAGCCAGUUUGGUCUAAAUAAAGCCAAAUCGGCAUCCAUGGUGCUCUAUCUGCCGCCGGCCGUGGCAGCCUCAU
--------......((((((((....((((.-.........(((.((((((.((......)))))))).)))......(((((.......).))))))))...)))))))).. ( -37.50)
>DroSim_CAF1 87976 111 - 1
CAACUUCUCAGAA--AAUUUGUAAGAGAACCUGGCUAGCUAGCCAGUUUGGUCUAAAUAAAGCCAAAUCGGCAUCCAUGGUGCUCUAUCUGCCGCCGGCCGUGGCAGCCUCAU
..........((.--........((((.((((((.......(((.((((((.((......)))))))).)))..))).))).))))..(((((((.....)))))))..)).. ( -32.00)
>DroAna_CAF1 83099 90 - 1
CUAUU--CUAUAA--GAUCUUUGAGAAGAACUCUAU-------------------AAUUUAGCUAAAUAGCCAGCACUAUUGCCAUAUCUGCCAGAACCAGUGGCAGCCUCAU
.....--......--......((((...........-------------------......((..(((((......))))))).....((((((.......)))))).)))). ( -13.70)
>consensus
C_ACU__UCAGAA__AAUUUGUAAGAGGACCUGGCUAACUAGCCAGUUUGGUCUAAAUAAAGCCAAAUCGGCAUCCAUGGUGCUCUAUCUGCCGCCGGCCGUGGCAGCCUCAU
........................((((.....((((....(((.(((((((.........))))))).))).....)))).......(((((((.....))))))))))).. (-17.67 = -20.55 +   2.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:35 2006