Locus 8488

Sequence ID	3L_DroMel_CAF1
Location	22,282,811 – 22,282,998
Length	187
Max. P	0.984748

overview

Window 0

Location	22,282,811 – 22,282,918
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	75.94
Mean single sequence MFE	-24.50
Consensus MFE	-13.93
Energy contribution	-13.42
Covariance contribution	-0.50
Combinations/Pair	1.16
Mean z-score	-2.48
Structure conservation index	0.57
SVM decision value	1.98
SVM RNA-class probability	0.984748
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22282811 107 + 23771897
----AUGACCAGCCUCAGCCGGCUUUGAUUGCAUUUUUUUUCAAAUUAAUUUAGCCAUUUGGCUGUGCCGCACUUUUAGUGC---------CAGCACACAUGGCUGCACAAACAAUUAAA
----.((..(((((..((((((((..(((((.((((......))))))))).))))....))))((((.((((.....))))---------..))))....)))))..)).......... ( -30.60)
>DroSec_CAF1 41181 93 + 1
----AUG-----CCUCAG----CUUUGAUUGCAUUUCUUUCCAAAUUAAUUUAGCCAUUUGGCUGUGC-----CUUUAGUGC---------CAGCACACAUGGCUGCACAAACAAUUAAA
----.((-----(....(----(.......))....................((((((.((((((.((-----(....).))---------)))).)).)))))))))............ ( -21.80)
>DroSim_CAF1 33208 93 + 1
----AUG-----CCUCAG----CUUUGAUUGCAUUUCUUUCCAAAUUAAUUUAGCCAUUUGGCUGUGC-----UUUUAGUGC---------CAGCACACAUGGCUGCACAAACAAUUAAA
----.((-----(....(----(.......))....................((((((.((((((.((-----.......))---------)))).)).)))))))))............ ( -22.30)
>DroYak_CAF1 5840 119 + 1
CAUACUGCUAAGCCUCUACC-GCUUUGAUUGCAUUUCUUUCGAAAUGAAUUUAGUCAUAGGGCUGUCCCGAAUCUCUAGUGUUUUUUUUAAUUGUUUACAUGACUGCACAAACAAUUAAA
.((((((...((((.(((..-(((..((((.((((((....)))))))))).)))..))))))).....(.....)))))))....(((((((((((...((....)).))))))))))) ( -23.30)
>consensus
____AUG_____CCUCAG____CUUUGAUUGCAUUUCUUUCCAAAUUAAUUUAGCCAUUUGGCUGUGC_____CUUUAGUGC_________CAGCACACAUGGCUGCACAAACAAUUAAA
........................(((((((....................(((((....))))).............((((..........(((.......)))))))...))))))). (-13.93 = -13.42 +  -0.50)

alignment

secondary structure

dotplot

Window 1

Location	22,282,847 – 22,282,958
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.52
Mean single sequence MFE	-23.23
Consensus MFE	-13.35
Energy contribution	-12.60
Covariance contribution	-0.75
Combinations/Pair	1.30
Mean z-score	-2.00
Structure conservation index	0.57
SVM decision value	0.17
SVM RNA-class probability	0.614657
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22282847 111 + 23771897
UCAAAUUAAUUUAGCCAUUUGGCUGUGCCGCACUUUUAGUGC---------CAGCACACAUGGCUGCACAAACAAUUAAAAAUAAUGAAAAACUGCAAAAGAGCAAUAUUAAAGAAGGCA
.............(((..(((..(((((.((((.....))))---------.(((.(....)))))))))..)))..................(((......)))...........))). ( -23.80)
>DroSec_CAF1 41208 106 + 1
CCAAAUUAAUUUAGCCAUUUGGCUGUGC-----CUUUAGUGC---------CAGCACACAUGGCUGCACAAACAAUUAAAAAUAAUGAAAAACUGCAGAGCAGCAAUAUUAAAGAAGCCA
...........(((((((.((((((.((-----(....).))---------)))).)).)))))))..........................((((...))))................. ( -22.00)
>DroSim_CAF1 33235 106 + 1
CCAAAUUAAUUUAGCCAUUUGGCUGUGC-----UUUUAGUGC---------CAGCACACAUGGCUGCACAAACAAUUAAAAAUAAUGAAAAACUGCAGAGCAGCAAUAUUAAAGAAGCCA
...........(((((....))))).((-----((((.((((---------.(((.(....)))))))).......................((((...)))).........)))))).. ( -23.20)
>DroYak_CAF1 5879 120 + 1
CGAAAUGAAUUUAGUCAUAGGGCUGUCCCGAAUCUCUAGUGUUUUUUUUAAUUGUUUACAUGACUGCACAAACAAUUAAAAGUAAUGCAAAACUGCAGUACCGCAAUAGUAAAGGAGAAA
....((((......)))).(((....)))...(((((.(((((.(((((((((((((...((....)).))))))))))))).))))).....(((......)))........))))).. ( -23.90)
>consensus
CCAAAUUAAUUUAGCCAUUUGGCUGUGC_____CUUUAGUGC_________CAGCACACAUGGCUGCACAAACAAUUAAAAAUAAUGAAAAACUGCAGAACAGCAAUAUUAAAGAAGCCA
...........(((((....))))).......(((((.((((..........(((.......)))))))........................(((......)))........))))).. (-13.35 = -12.60 +  -0.75)

alignment

secondary structure

dotplot

Window 2

Location	22,282,887 – 22,282,998
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.10
Mean single sequence MFE	-29.66
Consensus MFE	-9.29
Energy contribution	-8.97
Covariance contribution	-0.32
Combinations/Pair	1.27
Mean z-score	-2.07
Structure conservation index	0.31
SVM decision value	1.32
SVM RNA-class probability	0.941565
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22282887 111 - 23771897
CACCAGCAUGGCUAUGCAUAAGCGGGAGGUUGGUCAAUGGUGCCUUCUUUAAUAUUGCUCUUUUGCAGUUUUUCAUUAUUUUUAAUUGUUUGUGCAGCCAUGUGUGCUG---------GC
..(((((((((((..(((((((((((((((...........))))))).....(((((......)))))..................)))))))))))))....)))))---------). ( -36.70)
>DroSec_CAF1 41243 107 - 1
CAGCAGCAUAGCUAUGCAUA----GGAGGUUGGUCAGUGGUGGCUUCUUUAAUAUUGCUGCUCUGCAGUUUUUCAUUAUUUUUAAUUGUUUGUGCAGCCAUGUGUGCUG---------GC
(((((((((.(((..(((((----((..(((((..((((((((.......((.(((((......))))).)))))))))).)))))..)))))))))).)))).)))))---------.. ( -30.11)
>DroSim_CAF1 33270 107 - 1
CAGCAGCAUAGCUAUGCAUA----GGAGGUUGGUCAGUGGUGGCUUCUUUAAUAUUGCUGCUCUGCAGUUUUUCAUUAUUUUUAAUUGUUUGUGCAGCCAUGUGUGCUG---------GC
(((((((((.(((..(((((----((..(((((..((((((((.......((.(((((......))))).)))))))))).)))))..)))))))))).)))).)))))---------.. ( -30.11)
>DroEre_CAF1 39862 86 - 1
CAG-------------CAUAGGCUCCAGGUUGGCCAGUGGUGCCUUCUUUACCAUUGCUGCACUGCAGCUUAACAUUACUUUUCAUUUUUUGUGCAGCC---------------------
..(-------------(((((((.(((((....))..))).)))............(((((...))))).....................)))))....--------------------- ( -22.60)
>DroYak_CAF1 5919 107 - 1
CAG-------------CAUAGGCUGGAGGUUGGCCAGUGGUUUCUCCUUUACUAUUGCGGUACUGCAGUUUUGCAUUACUUUUAAUUGUUUGUGCAGUCAUGUAAACAAUUAAAAAAAAC
..(-------------((.((((((.((..(.((.((((((.........)))))))).)..)).))))))))).....(((((((((((..((((....)))))))))))))))..... ( -28.80)
>consensus
CAGCAGCAU_GCUAUGCAUA_GC_GGAGGUUGGUCAGUGGUGCCUUCUUUAAUAUUGCUGCUCUGCAGUUUUUCAUUAUUUUUAAUUGUUUGUGCAGCCAUGUGUGCUG_________GC
...........................(((((..(((..((...............(((((...)))))...............))..).))..)))))..................... ( -9.29 =  -8.97 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:52 2006