Locus 4175

Sequence ID	2R_DroMel_CAF1
Location	13,739,305 – 13,739,431
Length	126
Max. P	0.734549

overview

Window 2

Location	13,739,305 – 13,739,411
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.62
Mean single sequence MFE	-31.78
Consensus MFE	-22.28
Energy contribution	-22.62
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.70
SVM decision value	-0.01
SVM RNA-class probability	0.527497
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13739305 106 - 20766785
UCGGGGCAUGUGUUGGAUCCGUUCGAGCCGCUCGCAGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUGAUGCCGAUUGCAAC--------UGCAUC------
((((.(((.((((((((.....))(((.((.(..(((((((((.........)))))))))..).)).)))....))))))...)).).)))).(((...--------.)))..------ ( -29.60)
>DroVir_CAF1 45580 95 - 1
UCGAGGCAUGUGUUG----------AGCCGC-CGUCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUGAUGCCGAUUGCUGC--------UGCUGC------
..(((((..(.((((----------((((((-....)))))..))))).)((((((....)))))))))))...(((.(((..(((....)))..).)).--------)))...------ ( -27.10)
>DroPse_CAF1 37437 106 - 1
UUGGGGCAUGUGUUUGAGCGGCUGGAGCCGCUCGCAGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUGAUGCCGAUUGCAGC--------UGCAGC------
.((((((((......(((((((....)))))))((((((((((.........))))))))))..))))))))..(((.((....)).)))...((((...--------.)))).------ ( -40.40)
>DroGri_CAF1 44549 95 - 1
UCGAGGCAUGUGUUG----------AGCCGC-CGUCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUGAUGCCGAUUGCUGC--------UGCUGC------
..(((((..(.((((----------((((((-....)))))..))))).)((((((....)))))))))))...(((.(((..(((....)))..).)).--------)))...------ ( -27.10)
>DroWil_CAF1 41577 100 - 1
UCGAGGCAUGUGUUGGAGCU------GCCGCGCACAGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUGAUGCCGUUUGCAGC--------CACAGC------
..(((((((((((.((....------.))))))((((((((((.........))))))))))..))))))).((((((.((..........)))))))).--------......------ ( -29.60)
>DroAna_CAF1 42689 111 - 1
UCGAGGCAUGUGUUGAU---------GCCGCUCGCCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUCAAGCCGAUUGCUGCUUGCAAGUUGCAACUGGAAG
..(((((..(.((((((---------(((((.....))))).)))))).)((((((....))))))))))).(((((((...((.(((((.(....).))))).)))))))))....... ( -36.90)
>consensus
UCGAGGCAUGUGUUGGA________AGCCGCUCGCAGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACACUUUUGAUGCCGAUUGCAGC________UGCAGC______
....(((((((((((...........(((((.....)))))........(((((((....)))))))........)))))).....)))))............................. (-22.28 = -22.62 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	13,739,331 – 13,739,431
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.50
Mean single sequence MFE	-29.67
Consensus MFE	-18.69
Energy contribution	-18.72
Covariance contribution	0.03
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.63
SVM decision value	0.43
SVM RNA-class probability	0.734549
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13739331 100 - 20766785
------------GC--UGG-GC-----CUCCUCUAUAAGGUCGGGGCAUGUGUUGGAUCCGUUCGAGCCGCUCGCAGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
------------((--..(-((-----((........)))))((((((((((((.((.....)).)).)))..((((((((((.........))))))))))..)))))))...)).... ( -31.40)
>DroVir_CAF1 45606 86 - 1
------------GC--AGU-G--------GCUCUAUAAGGUCGAGGCAUGUGUUG----------AGCCGC-CGUCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
------------((--(((-(--------(((......))))(((((..(.((((----------((((((-....)))))..))))).)((((((....)))))))))))))))).... ( -30.20)
>DroGri_CAF1 44575 86 - 1
------------AC--UGU-G--------GCUCUAUAAGGUCGAGGCAUGUGUUG----------AGCCGC-CGUCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
------------..--(((-(--------(((......))))(((((..(.((((----------((((((-....)))))..))))).)((((((....)))))))))))...)))... ( -25.90)
>DroWil_CAF1 41603 106 - 1
AGCAGCAACAACGA--AGA-GC-----CUUCUCUAUAAGGUCGAGGCAUGUGUUGGAGCU------GCCGCGCACAGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
....((((......--.((-.(-----(((......))))))(((((((((((.((....------.))))))((((((((((.........))))))))))..))))))).)))).... ( -33.60)
>DroMoj_CAF1 50593 87 - 1
------------GC--AGUUG--------CCUCUAUAAGGUCGAGGCAUGUGUUG----------AGCCGA-CGUCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
------------((--(((.(--------(((.....)))).(((((((......----------(((.((-((..((........)).)))).))).......)))))))))))).... ( -27.32)
>DroAna_CAF1 42729 98 - 1
------------ACAUUGG-GCAUUGGCUCCUCUAUAAGGUCGAGGCAUGUGUUGAU---------GCCGCUCGCCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
------------.......-(((..((((.........))))(((((..(.((((((---------(((((.....))))).)))))).)((((((....)))))))))))..))).... ( -29.60)
>consensus
____________GC__AGU_G________CCUCUAUAAGGUCGAGGCAUGUGUUG__________AGCCGC_CGCCGUGGUAAUUAACUCGUUUGCUAUUGUAAAUGCCUCAUUGCAACA
..........................................(((((...................(((((.....))))).........((((((....)))))))))))......... (-18.69 = -18.72 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:32 2006