Locus 6193

Sequence ID	2R_DroMel_CAF1
Location	19,490,801 – 19,490,946
Length	145
Max. P	0.976805

overview

Window 6

Location	19,490,801 – 19,490,909
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.56
Mean single sequence MFE	-31.68
Consensus MFE	-27.30
Energy contribution	-27.93
Covariance contribution	0.63
Combinations/Pair	1.06
Mean z-score	-1.77
Structure conservation index	0.86
SVM decision value	0.78
SVM RNA-class probability	0.847720
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19490801 108 + 20766785
UAAAUGUGUUUUUCGCAUGAACGAAUUAACGGAGCGUAUCU------------GCGGUUGCCGAAAGGUAAAGCAAAUUUCGUUGUUCCAUAAGUUGGUGGAAACAAGGGAGUGCAUUAA
....(.((((.((((......))))..)))).)((.....(------------((..(((((....))))).))).(((((.(((((((((......)))).))))).)))))))..... ( -31.60)
>DroSec_CAF1 2664 108 + 1
UAAAUGUGUUUUUCGCAUGAACGAAUUAACGGAGCGUAUCU------------GCGGUUGCCGAAAGGUGAAGCCAAUUUCGUUGUUCCAUAAGUUGGUGGAAACAAGGGAGCGCAUUAA
..(((((((((((......((((((....((((.....)))------------).(((((((....)))..))))...)))))).((((((......))))))....))))))))))).. ( -32.40)
>DroEre_CAF1 3073 120 + 1
UAAAUGUGUUUUUCGCAUGAACGAAUUAACGGAGCGUAUCUGCCUAUACAUUUGCGGUUUCCGAAAGGUGAAGCAAAUUUCGUUGUUCCACAACUUUGUGGAAACAAGGGAGUGCAGUAA
....(.((((.((((......))))..)))).)......((((........((((..((.((....)).)).))))(((((.((((((((((....))))).))))).)))))))))... ( -32.90)
>DroYak_CAF1 2777 120 + 1
UAAAUGUGUUUUUCGCAUGAACGAAUUAACGGAGCGUAUCUGCCUACAUAUUUGCGGUUUCCGAAAGCUGAAGCAAAUUUCGUUGUUCCAUAACUUUGUGGAAACAAGGGAGUGCAGUAA
.((((((((..((((......))))....((((.....))))...))))))))((.((((((....)..)))))..(((((.((((((((((....))))).))))).)))))))..... ( -29.80)
>consensus
UAAAUGUGUUUUUCGCAUGAACGAAUUAACGGAGCGUAUCU____________GCGGUUGCCGAAAGGUGAAGCAAAUUUCGUUGUUCCAUAACUUGGUGGAAACAAGGGAGUGCAGUAA
....(.((((.((((......))))..)))).)((..................((..(((((....))))).))..(((((.(((((((((......)))).))))).)))))))..... (-27.30 = -27.93 +   0.63)

alignment

secondary structure

dotplot

Window 7

Location	19,490,841 – 19,490,946
Length	105
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	85.36
Mean single sequence MFE	-33.50
Consensus MFE	-27.08
Energy contribution	-27.20
Covariance contribution	0.12
Combinations/Pair	1.19
Mean z-score	-2.50
Structure conservation index	0.81
SVM decision value	1.78
SVM RNA-class probability	0.976805
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19490841 105 + 20766785
U------------GCGGUUGCCGAAAGGUAAAGCAAAUUUCGUUGUUCCAUAAGUUGGUGGAAACAAGGGAGUGCAUUAAUUUACGGGCUCUGAAAUGCCGGAAGUGAAUUUAAUAU
(------------((..(((((....))))).))).(((((.(((((((((......)))).))))).)))))..((((((((((.(((........)))....))))).))))).. ( -33.20)
>DroSec_CAF1 2704 105 + 1
U------------GCGGUUGCCGAAAGGUGAAGCCAAUUUCGUUGUUCCAUAAGUUGGUGGAAACAAGGGAGCGCAUUAAUUUACGGGCUCUGAGAUGCCGGAAGUGUAUUCAAUAU
(------------(((((((((....)))..))))..((((.(((((((((......)))).))))).)))).)))...((((.(.(((........))).)))))........... ( -30.90)
>DroEre_CAF1 3113 117 + 1
UGCCUAUACAUUUGCGGUUUCCGAAAGGUGAAGCAAAUUUCGUUGUUCCACAACUUUGUGGAAACAAGGGAGUGCAGUAAUUUAUGGGCUCCGAAAUGCCGGAAGUAUAUUCAAUAU
.(((((((...(((((.(((((....)).))).)..(((((.((((((((((....))))).))))).))))))))).....)))))))((((......)))).............. ( -38.40)
>DroYak_CAF1 2817 117 + 1
UGCCUACAUAUUUGCGGUUUCCGAAAGCUGAAGCAAAUUUCGUUGUUCCAUAACUUUGUGGAAACAAGGGAGUGCAGUAAUUUAUGGGCUCUGAAAUGCCGGAAGUAUAUUCAAUAU
.(((((.....((((.((((((....)..)))))..(((((.((((((((((....))))).))))).))))))))).......)))))..(((((((.(....)))).)))).... ( -31.50)
>consensus
U____________GCGGUUGCCGAAAGGUGAAGCAAAUUUCGUUGUUCCAUAACUUGGUGGAAACAAGGGAGUGCAGUAAUUUACGGGCUCUGAAAUGCCGGAAGUAUAUUCAAUAU
..............((((((((....))))......(((((.(((((((((......)))).))))).(((((.((........)).))))))))))))))(((.....)))..... (-27.08 = -27.20 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:08 2006