Locus 3397

Sequence ID	3R_DroMel_CAF1
Location	9,197,358 – 9,197,448
Length	90
Max. P	0.964912

overview

Window 0

Location	9,197,358 – 9,197,448
Length	90
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	71.15
Mean single sequence MFE	-20.92
Consensus MFE	-8.53
Energy contribution	-8.95
Covariance contribution	0.42
Combinations/Pair	1.22
Mean z-score	-1.77
Structure conservation index	0.41
SVM decision value	0.07
SVM RNA-class probability	0.569687
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9197358 90 + 27905053
UUUCAAACUCUUAAA-------U------UUUUACUUACGCAAUCAGAAAUAGGCCGAGAUCCGGCCAAAACCAGGCCCAAUCCGACCAGUAAAAUGGUCACU
...............-------.------.......................(((((.....))))).......((......))(((((......)))))... ( -18.20)
>DroSec_CAF1 34488 97 + 1
UCUCAAAUACUUAACUAAAUGAG------UGUUACUUACGCAAUCAGAAAUAGGUCGAGAUCCUGCCAAAACCAGGCCCAAUCCGACCAUUAUGAUGGUCACU
.....((((((((......))))------))))......((.((((..(((.(((((.(((...(((.......)))...))))))))))).)))).)).... ( -22.90)
>DroSim_CAF1 33304 97 + 1
UCUCAAAUACUUAACUAAAUGAG------UGUUACUUACGCAAUCAGAAAUAGGCCGAGAUCCGGCCAAAACCAGGCCCAAUCCGACCAGUAAAAUGGUCACU
((((.((((((((......))))------))))......((....(....)..)).))))...((((.......))))......(((((......)))))... ( -23.50)
>DroEre_CAF1 40041 95 + 1
-------UACUUGAAUAAGUGUAUAACU-UUAUACUUACGCAAUCGGAAAUAGGCCGAGACCCGGCCAAAACCAGACCCAAUCCGACCAGUAAAAUGGCCGCU
-------...(((..((((((((.....-.))))))))..)))(((((....(((((.....))))).......(...)..)))))(((......)))..... ( -23.80)
>DroYak_CAF1 33308 101 + 1
ACGCC--AGCUUGAAUAAGUGUAUAGCUUUUAUACGUACGCAAUCGGAAAUAGGCCGAGACCCGGCCAAAACCAGGCCCAAUCCGACCAAUAAAAUGGCCACU
..(((--(..(((.....((((((...........))))))..(((((....(((((.....)((......)).))))...)))))....)))..)))).... ( -24.40)
>DroAna_CAF1 36409 71 + 1
--------------------------------GACUUACGCAAUCCGAGAUGGGGCGGCUGCCAGCCAAAACCAGGCCUAAACCGACCAGAAAAAUAGAUGCU
--------------------------------.......(((.((.....(((..(((......(((.......))).....))).)))........))))). ( -12.72)
>consensus
UCUCA__UACUUAAAUAA_UG_A______UUUUACUUACGCAAUCAGAAAUAGGCCGAGAUCCGGCCAAAACCAGGCCCAAUCCGACCAGUAAAAUGGUCACU
....................................................(((((.....))))).................(.(((......))).)... ( -8.53 =  -8.95 +   0.42)

alignment

secondary structure

dotplot

Window 1

Location	9,197,358 – 9,197,448
Length	90
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	71.15
Mean single sequence MFE	-26.76
Consensus MFE	-19.85
Energy contribution	-19.88
Covariance contribution	0.03
Combinations/Pair	1.31
Mean z-score	-1.40
Structure conservation index	0.74
SVM decision value	1.57
SVM RNA-class probability	0.964912
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9197358 90 - 27905053
AGUGACCAUUUUACUGGUCGGAUUGGGCCUGGUUUUGGCCGGAUCUCGGCCUAUUUCUGAUUGCGUAAGUAAAA------A-------UUUAAGAGUUUGAAA
(((((.....)))))(((((((((.((((.......)))).)))).))))).........((((....))))..------.-------............... ( -27.30)
>DroSec_CAF1 34488 97 - 1
AGUGACCAUCAUAAUGGUCGGAUUGGGCCUGGUUUUGGCAGGAUCUCGACCUAUUUCUGAUUGCGUAAGUAACA------CUCAUUUAGUUAAGUAUUUGAGA
........(((.((.(((((((((..(((.......)))..)))).)))))...)).)))((((....))))..------((((..((......))..)))). ( -26.10)
>DroSim_CAF1 33304 97 - 1
AGUGACCAUUUUACUGGUCGGAUUGGGCCUGGUUUUGGCCGGAUCUCGGCCUAUUUCUGAUUGCGUAAGUAACA------CUCAUUUAGUUAAGUAUUUGAGA
(((((.....)))))(((((((((.((((.......)))).)))).)))))......((.((((....))))))------((((..((......))..)))). ( -31.00)
>DroEre_CAF1 40041 95 - 1
AGCGGCCAUUUUACUGGUCGGAUUGGGUCUGGUUUUGGCCGGGUCUCGGCCUAUUUCCGAUUGCGUAAGUAUAA-AGUUAUACACUUAUUCAAGUA-------
..((((((......))))))((.(((((.(((....(((((.....))))).....))).........(((((.-...)))))))))).)).....------- ( -26.30)
>DroYak_CAF1 33308 101 - 1
AGUGGCCAUUUUAUUGGUCGGAUUGGGCCUGGUUUUGGCCGGGUCUCGGCCUAUUUCCGAUUGCGUACGUAUAAAAGCUAUACACUUAUUCAAGCU--GGCGU
....((((.(((...(((((((((.((((.......)))).)))).))))).................(((((.....)))))........))).)--))).. ( -30.80)
>DroAna_CAF1 36409 71 - 1
AGCAUCUAUUUUUCUGGUCGGUUUAGGCCUGGUUUUGGCUGGCAGCCGCCCCAUCUCGGAUUGCGUAAGUC--------------------------------
.((((((........((.(((((..((((.......))))...))))))).......))).))).......-------------------------------- ( -19.06)
>consensus
AGUGACCAUUUUACUGGUCGGAUUGGGCCUGGUUUUGGCCGGAUCUCGGCCUAUUUCUGAUUGCGUAAGUAAAA______C_CA_UUAUUUAAGUA__UGAGA
...............(((((((((.((((.......)))).)))).)))))..........(((....)))................................ (-19.85 = -19.88 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:56 2006