Locus 2274

Sequence ID	2L_DroMel_CAF1
Location	6,169,378 – 6,169,509
Length	131
Max. P	0.660698

overview

Window 2

Location	6,169,378 – 6,169,479
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.91
Mean single sequence MFE	-20.10
Consensus MFE	-10.35
Energy contribution	-10.38
Covariance contribution	0.03
Combinations/Pair	1.29
Mean z-score	-1.85
Structure conservation index	0.52
SVM decision value	0.27
SVM RNA-class probability	0.660698
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6169378 101 - 22407834
UCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUUUCUGCCA---UCC--CCACCAUCU--GC-ACUCCCCACCAUCUACAACUCUUGACUG---
......((((((((..(--------((((.....)))))((((((..((..((((..........))---)).--.))..)).)--))-)..................)))))))).--- ( -18.50)
>DroPse_CAF1 21899 115 - 1
UCAACGACGAGAGGCCGGAGUCGAGUGUGUCUUUGGCUUUGUAAUCAUGAUGAUGAUCUCUCUCUCU---CCCUGUCUCUGUCUCUCC-GUGCCAUCCCAUCCCCCACUCU-GUCUGGGG
.....(((.((((((.((((..(((...((.....))...(..(((((....)))))..).))).))---))..))))))))).....-.............(((((....-...))))) ( -28.20)
>DroSec_CAF1 5665 99 - 1
UCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAGUCUUGAUGAUGAUCUUUCUGCC---------UCACCAUCCCCCC-ACUCCCCUCCAUCCACAACUCUUGACUG---
......((((((((..(--------((((.....))))).((((....(((....)))...)))).---------.............-...................)))))))).--- ( -19.10)
>DroSim_CAF1 15050 100 - 1
UCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUUUCUGCC---------UCACUAUCCCCCCUACUCCCCUCCAUCCACAACUCUUGACUG---
......((((((((..(--------((((.....))))).(((.....(((....)))....))).---------.................................)))))))).--- ( -15.40)
>DroEre_CAF1 4919 101 - 1
UCAACAAGUCGAGACCG--------AGUGUCUUUCACUUGGCAAUCUUGAUGAUUAUCUUUCUGCCU---CCC--CCUCCCCCU--CC-ACUCCCCGCCAUCCACCACUCUCGACUG---
......(((((((((((--------((((.....))))))).((((.....))))............---...--.........--..-...................)))))))).--- ( -22.50)
>DroYak_CAF1 15295 103 - 1
UCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUGCCUGCCUUUACCC--CCACUGCCU--CC-ACUCUUCUCCAUCCACCA-UCUUGACUG---
......((((((((..(--------((((.....))))).((((((........))).)))............--.........--..-..................-)))))))).--- ( -16.90)
>consensus
UCAACAAGUCGAGACCG________AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUUUCUGCCU___CCC__CCACCAUCU__CC_ACUCCCCUCCAUCCACAACUCUUGACUG___
......((((((((............(((.....)))...(((.....(((....)))....)))...........................................)))))))).... (-10.35 = -10.38 +   0.03)

alignment

secondary structure

dotplot

Window 3

Location	6,169,412 – 6,169,509
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.97
Mean single sequence MFE	-21.49
Consensus MFE	-13.58
Energy contribution	-14.13
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.51
Structure conservation index	0.63
SVM decision value	-0.01
SVM RNA-class probability	0.527575
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6169412 97 - 22407834
----------GGCCAUACUUCGCCCCAAUAAAACGCAUCAUCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUUUCUGCCA---UCC--CCACC
----------(((........((...........))(((((((.((((....(.(.(--------((((.....))))).))...)))).)))))))......))).---...--..... ( -19.50)
>DroPse_CAF1 21937 117 - 1
CUUGGCCCCUUGCCACACCGCGCCUCAAUCAAACGCAUCAUCAACGACGAGAGGCCGGAGUCGAGUGUGUCUUUGGCUUUGUAAUCAUGAUGAUGAUCUCUCUCUCU---CCCUGUCUCU
..((((.....))))....................((((((((.......((((((((((.((....)).)))))))))).......))))))))............---.......... ( -28.44)
>DroSec_CAF1 5701 93 - 1
----------GGCCAUACUUCGCCCCAAUAAAACGCAUCAUCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAGUCUUGAUGAUGAUCUUUCUGCC---------UCACC
----------(((........((...........))(((((((.....(((((((.(--------((((.....)))))....))))))))))))))......)))---------..... ( -21.30)
>DroSim_CAF1 15087 93 - 1
----------GGCCAUACUUCGCCCCAAUAAAACGCAUCAUCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUUUCUGCC---------UCACU
----------(((........((...........))(((((((.((((....(.(.(--------((((.....))))).))...)))).)))))))......)))---------..... ( -19.00)
>DroEre_CAF1 4953 97 - 1
----------GGCCAUACUUCGCCCCAAUAAAACGCAUCAUCAACAAGUCGAGACCG--------AGUGUCUUUCACUUGGCAAUCUUGAUGAUUAUCUUUCUGCCU---CCC--CCUCC
----------(((........)))..........(((..........((((((((((--------((((.....)))))))...)))))))...........)))..---...--..... ( -20.90)
>DroYak_CAF1 15328 100 - 1
----------GGCCAUACUUCGCCCCAAUAAAACGCAUCAUCAACAAGUCGAGACCG--------AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUGCCUGCCUUUACCC--CCACU
----------(((........)))..........(((((((((.((((....(.(.(--------((((.....))))).))...)))).))))))..)))............--..... ( -19.80)
>consensus
__________GGCCAUACUUCGCCCCAAUAAAACGCAUCAUCAACAAGUCGAGACCG________AGUGUCUUUCACUUUGCAAUCUUGAUGAUGAUCUUUCUGCCU___CCC__CCACC
..........(((........)))...........((((((((((((((.((((((..........).)))))..)))).).....)))))))))......................... (-13.58 = -14.13 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:47 2006