Locus 5240

Sequence ID	2L_DroMel_CAF1
Location	14,789,496 – 14,789,608
Length	112
Max. P	0.846967

overview

Window 2

Location	14,789,496 – 14,789,608
Length	112
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	80.12
Mean single sequence MFE	-23.86
Consensus MFE	-11.71
Energy contribution	-14.06
Covariance contribution	2.35
Combinations/Pair	1.15
Mean z-score	-2.30
Structure conservation index	0.49
SVM decision value	0.77
SVM RNA-class probability	0.846967
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14789496 112 + 22407834
CCUAACAUUGGGACGCCGAGCACAAGCUCAGCGGCAGGACUCAAAGCCCUUCUA--GUUAAGCCUGGA-AAUACAUUUGAAAUUUAUCAAAAAUAAAUUCCUCGUCUGCCAUUUU
((((....))))..((.((((....)))).))(((((.(((((((....(((((--(......)))))-).....)))))(((((((.....)))))))....)))))))..... ( -29.90)
>DroSec_CAF1 35984 112 + 1
CCUUACAUCGGGACGCAGAGCACAAGCUCAGCGGCAGGACUCAAAGCUCUUCUA--GUUAAGCUUUGA-AAUACAUUUGAAAUUUAUUAAAAAUAUAUUCCUCGUCUGCCAUUUU
(((......)))..((.((((....)))).))(((((.((((((((((......--....))))))))-......(((((......)))))............)))))))..... ( -27.50)
>DroSim_CAF1 36580 112 + 1
CCUUACAUCGGGACGCAGAGCACAAGCUCAGCGGUAUGACUCAAAGCUCUUCUA--GUUAAGCUUUGA-AAUACAUUUGAAAUUUAUUAAAAAUAUAUUCCUCGUCUGCCAUUUU
(((......)))..((.((((....)))).))((((.(((((((((((......--....))))))))-......(((((......)))))............)))))))..... ( -25.50)
>DroEre_CAF1 28939 112 + 1
CCUUACAUAGGAACACACAUCACAAGCUCAACGGCAGGACUCAAAGCUCUCCUA--GUUAAGCUUUGA-AAUACAUUUAAAAUUUAUUAAAAGUAAAUUCCUCGUCUGCCAUUUU
(((.....))).....................(((((.((((((((((......--....))))))))-..(((.(((((......))))).)))........)))))))..... ( -22.20)
>DroAna_CAF1 25536 97 + 1
CCUUACAUAGU-----------------GAGCAACAGGACUCGAAACUCUUCUUUCCUCAAGCUUUGAAAAUUCAUUUGAAAUUUAUUAAAAAACAAAGCCGC-UCUGCCUUUUC
...........-----------------((((...((((...(((....)))..))))...((((((....(((....))).(((....)))..)))))).))-))......... ( -14.20)
>consensus
CCUUACAUAGGGACGCAGAGCACAAGCUCAGCGGCAGGACUCAAAGCUCUUCUA__GUUAAGCUUUGA_AAUACAUUUGAAAUUUAUUAAAAAUAAAUUCCUCGUCUGCCAUUUU
..............((.((((....)))).))((((.(((((((((((............)))))))).......(((((......)))))............)))))))..... (-11.71 = -14.06 +   2.35)

alignment

secondary structure

dotplot

Window 3

Location	14,789,496 – 14,789,608
Length	112
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	80.12
Mean single sequence MFE	-29.06
Consensus MFE	-18.99
Energy contribution	-20.98
Covariance contribution	1.99
Combinations/Pair	1.28
Mean z-score	-1.87
Structure conservation index	0.65
SVM decision value	0.57
SVM RNA-class probability	0.784037
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14789496 112 - 22407834
AAAAUGGCAGACGAGGAAUUUAUUUUUGAUAAAUUUCAAAUGUAUU-UCCAGGCUUAAC--UAGAAGGGCUUUGAGUCCUGCCGCUGAGCUUGUGCUCGGCGUCCCAAUGUUAGG
.....(((((((..((((..(((.(((((......))))).))).)-)))((((((...--.....))))))...)).)))))(((((((....))))))).............. ( -36.20)
>DroSec_CAF1 35984 112 - 1
AAAAUGGCAGACGAGGAAUAUAUUUUUAAUAAAUUUCAAAUGUAUU-UCAAAGCUUAAC--UAGAAGAGCUUUGAGUCCUGCCGCUGAGCUUGUGCUCUGCGUCCCGAUGUAAGG
.....(((((((..(((((((((((..((....))..)))))))))-))(((((((...--.....)))))))..)).)))))((.((((....)))).)).............. ( -33.10)
>DroSim_CAF1 36580 112 - 1
AAAAUGGCAGACGAGGAAUAUAUUUUUAAUAAAUUUCAAAUGUAUU-UCAAAGCUUAAC--UAGAAGAGCUUUGAGUCAUACCGCUGAGCUUGUGCUCUGCGUCCCGAUGUAAGG
......(((..((.(((......................(((...(-(((((((((...--.....)))))))))).)))..(((.((((....)))).)))))))).))).... ( -29.90)
>DroEre_CAF1 28939 112 - 1
AAAAUGGCAGACGAGGAAUUUACUUUUAAUAAAUUUUAAAUGUAUU-UCAAAGCUUAAC--UAGGAGAGCUUUGAGUCCUGCCGUUGAGCUUGUGAUGUGUGUUCCUAUGUAAGG
..((((((((((........(((.(((((......))))).)))..-(((((((((...--.....))))))))))).))))))))((((...........)))).......... ( -27.90)
>DroAna_CAF1 25536 97 - 1
GAAAAGGCAGA-GCGGCUUUGUUUUUUAAUAAAUUUCAAAUGAAUUUUCAAAGCUUGAGGAAAGAAGAGUUUCGAGUCCUGUUGCUC-----------------ACUAUGUAAGG
.........((-(((((((((...((((............))))....)))))))..((((..(((....)))...))))...))))-----------------........... ( -18.20)
>consensus
AAAAUGGCAGACGAGGAAUUUAUUUUUAAUAAAUUUCAAAUGUAUU_UCAAAGCUUAAC__UAGAAGAGCUUUGAGUCCUGCCGCUGAGCUUGUGCUCUGCGUCCCGAUGUAAGG
.....(((((((..((((((((((...))))))))))..........(((((((((..........)))))))))))).))))((.((((....)))).)).............. (-18.99 = -20.98 +   1.99)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:30 2006