Locus 5013

Sequence ID	3L_DroMel_CAF1
Location	13,765,278 – 13,765,450
Length	172
Max. P	0.729855

overview

Window 1

Location	13,765,278 – 13,765,391
Length	113
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	75.07
Mean single sequence MFE	-28.04
Consensus MFE	-10.29
Energy contribution	-10.35
Covariance contribution	0.06
Combinations/Pair	1.26
Mean z-score	-2.24
Structure conservation index	0.37
SVM decision value	0.42
SVM RNA-class probability	0.729855
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13765278 113 + 23771897
UCAGGUCUGUUCAAGACAGUCCCGAAAAUAAUUUAUUAUUAAUCAUGCUGUAAUUUGCUUUCUUGGCAGGGCAGACAUUA---UGGCCAAAU--GACCUUUUGGUCAUUUACGCUUCA
....((((((((...(((((......(((((....)))))......)))))....((((.....))))))))))))....---.(((.((((--((((....))))))))..)))... ( -31.50)
>DroVir_CAF1 8028 96 + 1
-------------GGUCAGUCC-GCA----AUCAUUAAUUCAUAAAGCUGUAAUUUGCUUU--UGGCCAAGCCAACAGCCGAGCAGCCAGAC--AACCUUUCGGUCAUUUGCGCUGCA
-------------......((.-((.----.............(((((........)))))--((((...))))...)).))(((((((((.--.(((....)))..)))).))))). ( -25.90)
>DroSec_CAF1 11898 113 + 1
UCAGGUCUGUUCAAGACAGUCCCAAAAAUAAUUAAUAAUUAAUCAUGCUGUAAUUUGCUUUCUUGGCAGGGCAGACAUUA---UGGCCAAAU--GACCUUUUGGUCAUUUACGCUUCA
....((((((((...(((((......(((........)))......)))))....((((.....))))))))))))....---.(((.((((--((((....))))))))..)))... ( -29.50)
>DroEre_CAF1 11143 113 + 1
UCAGGUCUGUUCAAGACAGUCCCGAAAAUAAUUAAUAAUUAAUCAUGCUGUAAUUUGCUUUCUUGGCAGGGCAGACAUUA---UAGCCAAAU--GACCUUUUGGUCAUUUACGCUUCA
((.((.(((((...))))).)).)).....................(((((((((((((((......))))))))..)))---)))).((((--((((....))))))))........ ( -30.00)
>DroYak_CAF1 9159 113 + 1
UCAGGUCUGUUCAAGACAGUCCCGAAAAUAAUUAAUAAUUAAUCAAGUUGUAAUUUGCUUUCUUGGCAGGGCAGACAUUA---UAGCCAAAU--GACCUUUUGGUCAUUUACUCCGCA
((.((.(((((...))))).)).)).....................(((((((((((((((......))))))))..)))---)))).((((--((((....))))))))........ ( -27.80)
>DroMoj_CAF1 33955 94 + 1
-------------GGUCAGUCC-GCAA---AUCAUUAAUUCAUAAAGCUGUAAUUUGCUUU--UGACCGAGCCG--AGCCA---AGCCAGACAUAAGCUUUCGGUCAUUUGCGCUGCA
-------------.(.(((..(-((((---(............(((((........)))))--(((((((...(--(((..---............))))))))))))))))))))). ( -23.54)
>consensus
UCAGGUCUGUUCAAGACAGUCCCGAAAAUAAUUAAUAAUUAAUCAAGCUGUAAUUUGCUUUCUUGGCAGGGCAGACAUUA___UAGCCAAAU__GACCUUUUGGUCAUUUACGCUGCA
..............................................((.(((((((((((........)))))))..........((((((........))))))...)))))).... (-10.29 = -10.35 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	13,765,356 – 13,765,450
Length	94
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	70.94
Mean single sequence MFE	-25.73
Consensus MFE	-12.35
Energy contribution	-13.18
Covariance contribution	0.84
Combinations/Pair	1.41
Mean z-score	-1.68
Structure conservation index	0.48
SVM decision value	0.36
SVM RNA-class probability	0.703602
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13765356 94 - 23771897
GUACGUCAUCAUCAUCUUCCCUUUGGCGUUGACUGUCUGGGAUUCGUCUGCUUUUCGCUUGAAGCGUAAAUGACCAAAAGGUCAUUUGGCCA---UA
....(((..........((((...((((.....)))).)))).......(((((......)))))..((((((((....)))))))))))..---.. ( -23.90)
>DroVir_CAF1 8086 77 - 1
GUGUG-----------------CAUGUG-UG--UGUGGACUAUUUGUCUGCUUAUAAUUUGCAGCGCAAAUGACCGAAAGGUUGUCUGGCUGCUCGG
.....-----------------....((-((--.(..(((.....)))..).))))....(((((.((.(..(((....)))..).))))))).... ( -27.90)
>DroGri_CAF1 30427 78 - 1
GUGUG-----------------UUUGUGUUG--UGUGUACUAUUUGUCUGCUUAUAAAUUGCAGCGCAAAUGACCGAAAGGUUGUCUGCCUGCUCGA
....(-----------------((((((...--.((..((.....))..)).))))))).((((.(((.(..(((....)))..).))))))).... ( -22.70)
>DroSec_CAF1 11976 94 - 1
GUACGCCAUCAUCAUCUUCCCUUUGGCGUUGACUGUCUGGGAUUCGUCUGCUUUUCGGUUGAAGCGUAAAUGACCAAAAGGUCAUUUGGCCA---UA
....(((..........((((...((((.....)))).)))).......(((((......)))))..((((((((....)))))))))))..---.. ( -26.60)
>DroEre_CAF1 11221 94 - 1
GUACGCCAUCAUCAUCAUCCCUUUGGCGUUGACUGUCUGGGAUUCGUCUGCUUUUCGGUUGAAGCGUAAAUGACCAAAAGGUCAUUUGGCUA---UA
....(((.........(((((...((((.....)))).)))))......(((((......)))))..((((((((....)))))))))))..---.. ( -27.70)
>DroYak_CAF1 9237 94 - 1
GUUCGCCAUCAUCAUCAUCCCUUUGGCGUUGACUGUCUGGGUUUCGUCUGCUUUUCGGUUGCGGAGUAAAUGACCAAAAGGUCAUUUGGCUA---UA
....(((...........(((...((((.....)))).))).....(((((.........)))))..((((((((....)))))))))))..---.. ( -25.60)
>consensus
GUACGCCAUCAUCAUC_UCCCUUUGGCGUUGACUGUCUGGGAUUCGUCUGCUUUUCGGUUGAAGCGUAAAUGACCAAAAGGUCAUUUGGCUA___UA
....(((..................(((((......((((((..........))))))....)))))((((((((....)))))))))))....... (-12.35 = -13.18 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:36 2006