Locus 6363

Sequence ID	2R_DroMel_CAF1
Location	19,945,798 – 19,945,892
Length	94
Max. P	0.688420

overview

Window 3

Location	19,945,798 – 19,945,892
Length	94
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	87.24
Mean single sequence MFE	-28.52
Consensus MFE	-21.94
Energy contribution	-21.90
Covariance contribution	-0.04
Combinations/Pair	1.31
Mean z-score	-1.68
Structure conservation index	0.77
SVM decision value	0.32
SVM RNA-class probability	0.688420
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19945798 94 + 20766785
AGCGUUUUCGCUUAGGAGUCAUCAGCAUUAUCAGCUGGCGAACUGGAUA-----UAUAUGAGGAUGGCAAAGGGUGAUCCUUUAUUUAGUGGUCCUAUU-
((((....))))(((((.((..((((.......))))..))((((((((-----.....((((((.((.....)).))))))))))))))..)))))..- ( -29.30)
>DroSec_CAF1 28840 94 + 1
AGCGUUUUCGCUUAGGAGUCAUCAGCAUUAUCAGCUGGCGAACUGGAUA-----UAUAUAGGGAUGGCAUAGGGUGAUCCCUAAUUUUGUGGUCCUAUU-
((((....))))(((((.((..((((.......))))..))........-----....(((((((.((.....)).))))))).........)))))..- ( -28.20)
>DroSim_CAF1 31095 99 + 1
AGCGUUUUCGCUUAGGAGUCAUCAGCAUUAUCAGCUGGCGAACUGGAUAUACUAUAUAUGAGGAUGGCAUAGGGUGAUCCUUAAUUUUGUGGUCCUAUU-
((((....))))(((((.((..((((.......))))..))..........(((((..(((((((.((.....)).)))))))....))))))))))..- ( -28.20)
>DroEre_CAF1 27912 94 + 1
AGCGCUUUCGCUUAGGAGUCAUCAGCAUUAUCAGCUGGCGAACUGGAUA-----UAUAUGUUGCUGGCGUAGGGUGACCCCUGAUUUUGUGACCCUAAU-
.(((....)))(((((.(((....(((..((((((..((((..((....-----..))..))))..))...((....))..))))..))))))))))).- ( -29.10)
>DroYak_CAF1 26455 95 + 1
AGCGUUUUCGCUUAGGAGUCAUCAGCAUUAUCAGCUGGCGAACUAGAUA-----UAUAUGGAGCUGGCAUAGGGUGACCCCUGAUCUAGUGGCCUGUAUU
.(((....)))((((...((..((((.......))))..)).))))..(-----((((.((.(((((..(((((....)))))..)))))..))))))). ( -27.80)
>consensus
AGCGUUUUCGCUUAGGAGUCAUCAGCAUUAUCAGCUGGCGAACUGGAUA_____UAUAUGAGGAUGGCAUAGGGUGAUCCCUAAUUUUGUGGUCCUAUU_
.(((....)))((((...((..((((.......))))..)).))))..............(((((.((((((((....)))))....))).))))).... (-21.94 = -21.90 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	19,945,798 – 19,945,892
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	87.24
Mean single sequence MFE	-22.60
Consensus MFE	-15.26
Energy contribution	-16.02
Covariance contribution	0.76
Combinations/Pair	1.05
Mean z-score	-1.97
Structure conservation index	0.68
SVM decision value	0.11
SVM RNA-class probability	0.585975
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19945798 94 - 20766785
-AAUAGGACCACUAAAUAAAGGAUCACCCUUUGCCAUCCUCAUAUA-----UAUCCAGUUCGCCAGCUGAUAAUGCUGAUGACUCCUAAGCGAAAACGCU
-..(((((........((((((.....)))))).((((..(((...-----((((.(((......))))))))))..))))..)))))((((....)))) ( -20.50)
>DroSec_CAF1 28840 94 - 1
-AAUAGGACCACAAAAUUAGGGAUCACCCUAUGCCAUCCCUAUAUA-----UAUCCAGUUCGCCAGCUGAUAAUGCUGAUGACUCCUAAGCGAAAACGCU
-..(((((.........(((((((...........)))))))....-----........(((.((((.......)))).))).)))))((((....)))) ( -22.30)
>DroSim_CAF1 31095 99 - 1
-AAUAGGACCACAAAAUUAAGGAUCACCCUAUGCCAUCCUCAUAUAUAGUAUAUCCAGUUCGCCAGCUGAUAAUGCUGAUGACUCCUAAGCGAAAACGCU
-..(((((............((((.(..(((((...........)))))..)))))...(((.((((.......)))).))).)))))((((....)))) ( -19.60)
>DroEre_CAF1 27912 94 - 1
-AUUAGGGUCACAAAAUCAGGGGUCACCCUACGCCAGCAACAUAUA-----UAUCCAGUUCGCCAGCUGAUAAUGCUGAUGACUCCUAAGCGAAAGCGCU
-.(((((((((.......((((....))))....(((((.......-----((((.(((......))))))).))))).)))).)))))((....))... ( -28.30)
>DroYak_CAF1 26455 95 - 1
AAUACAGGCCACUAGAUCAGGGGUCACCCUAUGCCAGCUCCAUAUA-----UAUCUAGUUCGCCAGCUGAUAAUGCUGAUGACUCCUAAGCGAAAACGCU
.....(((..(((((((.((((....))))(((.......)))...-----.)))))))(((.((((.......)))).)))..))).((((....)))) ( -22.30)
>consensus
_AAUAGGACCACAAAAUCAGGGAUCACCCUAUGCCAUCCCCAUAUA_____UAUCCAGUUCGCCAGCUGAUAAUGCUGAUGACUCCUAAGCGAAAACGCU
...(((((..........((((....)))).............................(((.((((.......)))).))).)))))((((....)))) (-15.26 = -16.02 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:14 2006