Locus 4190

Sequence ID	2L_DroMel_CAF1
Location	12,004,980 – 12,005,072
Length	92
Max. P	0.999947

overview

Window 4

Location	12,004,980 – 12,005,072
Length	92
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	90.20
Mean single sequence MFE	-44.66
Consensus MFE	-39.88
Energy contribution	-40.32
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-4.20
Structure conservation index	0.89
SVM decision value	4.76
SVM RNA-class probability	0.999947
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12004980 92 + 22407834
GCUCCAAGAUUCCGCCGGCAAUUCUGCCGGCGAUGGCCCCCAAAUGGCCAGUGGAGC--CGUUGACCAGCGAGCGUAUGGUCAGCUAUUGAUGU
((((((......((((((((....)))))))).(((((.......))))).))))))--.((((((((((....)).))))))))......... ( -46.60)
>DroSec_CAF1 5760 94 + 1
GCUCCAAGAUUCCGCUGGCAAUUCUGCCGGCGAUGGCCCCCAAAUGGCCAGUGGAGCCCCGUUGACCAGCGAGCGUAUGGUCAGCUAUUGAUGU
((((((......((((((((....)))))))).(((((.......))))).))))))...((((((((((....)).))))))))......... ( -44.40)
>DroSim_CAF1 4964 94 + 1
GCUCCAAGAUUCCGCCGGCGAUUCUGCCGGCGAUGGCCCCCAAAUGGCCAGUGGAGCCCCAUUGACCAGCGAGCGUAUGGUCAGCUAUUGAUGU
((((((......((((((((....)))))))).(((((.......))))).))))))....(((((((((....)).))))))).......... ( -42.20)
>DroEre_CAF1 4962 87 + 1
GCUCCAAGAGUCCGCCGGCUAUUCUGCCGGCGUUGGCC-CCAAAUGGCCAGUGGAGC--UGUUGACCAG----CGUAUGGUCAGCCAUUGAUGU
((((((......(((((((......)))))))((((((-......))))))))))))--.((((((((.----....))))))))......... ( -46.00)
>DroYak_CAF1 5080 87 + 1
GCUCCAAGAGUCCGCCGGCUAUUCUGCCGGCAAUGGGC-UCAAAUGGCCAGUGGAGC--AGUUGACCAG----CGUAUGGUCAGCUAUUGAUGU
((((((.((((((((((((......))))))...))))-))..........))))))--(((((((((.----....)))))))))........ ( -44.10)
>consensus
GCUCCAAGAUUCCGCCGGCAAUUCUGCCGGCGAUGGCCCCCAAAUGGCCAGUGGAGC__CGUUGACCAGCGAGCGUAUGGUCAGCUAUUGAUGU
((((((......(((((((......))))))).(((((.......))))).))))))...((((((((.........))))))))......... (-39.88 = -40.32 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	12,004,980 – 12,005,072
Length	92
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	90.20
Mean single sequence MFE	-38.06
Consensus MFE	-35.76
Energy contribution	-35.84
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-2.71
Structure conservation index	0.94
SVM decision value	4.54
SVM RNA-class probability	0.999918
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12004980 92 - 22407834
ACAUCAAUAGCUGACCAUACGCUCGCUGGUCAACG--GCUCCACUGGCCAUUUGGGGGCCAUCGCCGGCAGAAUUGCCGGCGGAAUCUUGGAGC
.........(.((((((.........)))))).).--((((((.(((((.......)))))((((((((......)))))))).....)))))) ( -40.20)
>DroSec_CAF1 5760 94 - 1
ACAUCAAUAGCUGACCAUACGCUCGCUGGUCAACGGGGCUCCACUGGCCAUUUGGGGGCCAUCGCCGGCAGAAUUGCCAGCGGAAUCUUGGAGC
.........(.((((((.........)))))).)...((((((.(((((.......)))))((((.(((......))).)))).....)))))) ( -34.10)
>DroSim_CAF1 4964 94 - 1
ACAUCAAUAGCUGACCAUACGCUCGCUGGUCAAUGGGGCUCCACUGGCCAUUUGGGGGCCAUCGCCGGCAGAAUCGCCGGCGGAAUCUUGGAGC
...........((((((.........)))))).....((((((.(((((.......)))))((((((((......)))))))).....)))))) ( -39.50)
>DroEre_CAF1 4962 87 - 1
ACAUCAAUGGCUGACCAUACG----CUGGUCAACA--GCUCCACUGGCCAUUUGG-GGCCAACGCCGGCAGAAUAGCCGGCGGACUCUUGGAGC
.......((..((((((....----.)))))).))--((((((.(((((......-))))).(((((((......)))))))......)))))) ( -41.80)
>DroYak_CAF1 5080 87 - 1
ACAUCAAUAGCUGACCAUACG----CUGGUCAACU--GCUCCACUGGCCAUUUGA-GCCCAUUGCCGGCAGAAUAGCCGGCGGACUCUUGGAGC
........((.((((((....----.)))))).))--((((((..((((....).-)))..((((((((......)))))))).....)))))) ( -34.70)
>consensus
ACAUCAAUAGCUGACCAUACGCUCGCUGGUCAACG__GCUCCACUGGCCAUUUGGGGGCCAUCGCCGGCAGAAUAGCCGGCGGAAUCUUGGAGC
.........(.((((((.........)))))).)...((((((.(((((.......))))).(((((((......)))))))......)))))) (-35.76 = -35.84 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:02 2006