Locus 4960

Sequence ID	2L_DroMel_CAF1
Location	14,237,596 – 14,237,700
Length	104
Max. P	0.994069

overview

Window 6

Location	14,237,596 – 14,237,700
Length	104
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	72.17
Mean single sequence MFE	-21.05
Consensus MFE	-14.26
Energy contribution	-15.32
Covariance contribution	1.06
Combinations/Pair	1.21
Mean z-score	-1.83
Structure conservation index	0.68
SVM decision value	1.69
SVM RNA-class probability	0.972259
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14237596 104 + 22407834
UCUGGAAUGCCCAAUAACCAAGUACUUGAUUAUAGGGGUAAACAAUUUACUAGCUAAUUGGAUUUAAUAAGUGUGCUUAUAUUGCUUAUAUGUGGAAUA------------AAUUA----
.......(((((.((((.(((....))).))))..)))))..(((((........)))))(((((((((((....))))).(..(......)..)..))------------)))).---- ( -16.80)
>DroSec_CAF1 70284 98 + 1
--UGGAAUGCCCUAUACCCAAGUACUUGAUUAUAGGGGUA-ACAAUUUAUUAGGUAAUUGAAUUUAAUAAGUGUGUAAAUAUU-----UAUG-GGAAUA------------AAUAAAU-A
--.......(((((((..(((....)))..)))))))...-((((((((((((((......))))))))))).)))...((((-----(((.-...)))------------))))...-. ( -21.00)
>DroSim_CAF1 62534 98 + 1
--UGGAAUGCCCUAUACCCAAGUACUUGAUUAUAGGGGUA-ACAAUUUAUUAGCUAUUUGAGUUUAAUAAGUGUGUAAAUAUU-----UAUG-GGAAUA------------AAUAAAU-A
--.......(((((((..(((....)))..)))))))...-((((((((((((((.....)).))))))))).)))...((((-----(((.-...)))------------))))...-. ( -19.80)
>DroEre_CAF1 71293 107 + 1
------AUGCCCCAUAGCCAAGUACUUGAUCAUAGGGGUA-ACUAUUAAUUAGCUAUUAUUAGCUAAUUAGUGUGUCUUUAUU-----UCUA-UGUCUUACUUUCCAUCUUAAGAAACCG
------..........(..(((((...((.(((((..(((-(((((((((((((((....))))))))))))).))...))).-----.)))-)))).)))))..).............. ( -26.60)
>consensus
__UGGAAUGCCCUAUACCCAAGUACUUGAUUAUAGGGGUA_ACAAUUUAUUAGCUAAUUGAAUUUAAUAAGUGUGUAAAUAUU_____UAUG_GGAAUA____________AAUAAAU_A
.........((((((((.(((....))).))))))))....((.(((((((((((......))))))))))))).............................................. (-14.26 = -15.32 +   1.06)

alignment

secondary structure

dotplot

Window 7

Location	14,237,596 – 14,237,700
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	72.17
Mean single sequence MFE	-17.34
Consensus MFE	-11.00
Energy contribution	-10.38
Covariance contribution	-0.62
Combinations/Pair	1.24
Mean z-score	-2.16
Structure conservation index	0.63
SVM decision value	2.45
SVM RNA-class probability	0.994069
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14237596 104 - 22407834
----UAAUU------------UAUUCCACAUAUAAGCAAUAUAAGCACACUUAUUAAAUCCAAUUAGCUAGUAAAUUGUUUACCCCUAUAAUCAAGUACUUGGUUAUUGGGCAUUCCAGA
----.....------------...........((((((((((.(((....................))).)))..))))))).(((.((((((((....)))))))).)))......... ( -16.55)
>DroSec_CAF1 70284 98 - 1
U-AUUUAUU------------UAUUCC-CAUA-----AAUAUUUACACACUUAUUAAAUUCAAUUACCUAAUAAAUUGU-UACCCCUAUAAUCAAGUACUUGGGUAUAGGGCAUUCCA--
(-(..((((------------(((...-.)))-----))))..))...............(((((........))))).-...(((((((..(((....)))..))))))).......-- ( -14.20)
>DroSim_CAF1 62534 98 - 1
U-AUUUAUU------------UAUUCC-CAUA-----AAUAUUUACACACUUAUUAAACUCAAAUAGCUAAUAAAUUGU-UACCCCUAUAAUCAAGUACUUGGGUAUAGGGCAUUCCA--
(-(..((((------------(((...-.)))-----))))..))...................((((.........))-)).(((((((..(((....)))..))))))).......-- ( -13.90)
>DroEre_CAF1 71293 107 - 1
CGGUUUCUUAAGAUGGAAAGUAAGACA-UAGA-----AAUAAAGACACACUAAUUAGCUAAUAAUAGCUAAUUAAUAGU-UACCCCUAUGAUCAAGUACUUGGCUAUGGGGCAU------
.(.(((((......))))).)..(((.-((..-----..)).........((((((((((....))))))))))...))-)..(((((((..(((....)))..)))))))...------ ( -24.70)
>consensus
U_AUUUAUU____________UAUUCC_CAUA_____AAUAUAUACACACUUAUUAAAUUCAAAUAGCUAAUAAAUUGU_UACCCCUAUAAUCAAGUACUUGGGUAUAGGGCAUUCCA__
..................................................((((((............)))))).........(((((((.((((....)))).)))))))......... (-11.00 = -10.38 +  -0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:01 2006