Locus 1209

Sequence ID	2L_DroMel_CAF1
Location	3,244,940 – 3,245,170
Length	230
Max. P	0.974521

overview

Window 2

Location	3,244,940 – 3,245,054
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.07
Mean single sequence MFE	-32.08
Consensus MFE	-20.11
Energy contribution	-21.23
Covariance contribution	1.12
Combinations/Pair	1.12
Mean z-score	-2.37
Structure conservation index	0.63
SVM decision value	1.08
SVM RNA-class probability	0.911886
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3244940 114 + 22407834
UAUAUCUAUAUCUACAUGAGCUCUCUCUCUCUACAUAUAUAU------AUGUUAAGCCUGCGGACAGACGACCUGAAGUAGAUGCAAUGAACAGGGGAGCUUUAUGGGUAUUGUAGGUAA
..((((((((....((((((((((((...((.(((((....)------))))...((((((...(((.....)))..))))..))...))...))))))).))))).....)))))))). ( -30.00)
>DroSec_CAF1 78999 120 + 1
UAUAUCUAUAUCUACAUGAGCUCUCACUACAUAUAUAUGUAUAUGUAUGUGUAAAGCCUGCGGACAGACGACCUGACGUAGAUGCAAUGAACAGGGGAGCUUUAUAGGUAUUGUAGGUAA
..((((((((((((...((((((((..(((((((((((....)))))))))))..(((((((..(((.....))).)))))..)).........))))))))..)))))...))))))). ( -39.20)
>DroSim_CAF1 82129 116 + 1
UAUAUCUAUAUCUACAUGAGCUCUCACUACAU----AUGUAUAUCUAUGUGUAAAGCCUGCGGACAGACGACCUGGAGUAGAUGCAAUGAACAGGGGAGCUUUAUGGGUAUUGUAGGUAA
..((((((((....(((((((((((..(((((----(((......))))))))..((((((...(((.....)))..))))..)).........)))))).))))).....)))))))). ( -34.70)
>DroEre_CAF1 75875 106 + 1
UAUAUCUAUAUCUACAUGAGCUCUCACAAUAU--------------AUGUGUAAAGCCUGCGGACAGACGAGCUGAAGUGGAUGCAAUGAACAGGGGAGCUUUAUGGGUAUUGUAGGUAA
..(((((((((((((.(.(((((.((((....--------------.))))....(.(((....))).)))))).).)))))))(((((..((((....))...))..))))))))))). ( -27.50)
>DroYak_CAF1 75045 102 + 1
UAUAUCUAUAUCUACACGAGCUCUCACAAUAUACAU----ACUCGUAUGUGUAAAGCCGGCGGACAG--------------AUGCAAUGAACAGGGGAGCUUUAUGGGUAUUGUAGGUAA
..((((((((.((....((((((((....(((((((----(....))))))))......(((.....--------------.))).........))))))))....))...)))))))). ( -29.00)
>consensus
UAUAUCUAUAUCUACAUGAGCUCUCACUAUAUA_AUAU_UAU___UAUGUGUAAAGCCUGCGGACAGACGACCUGAAGUAGAUGCAAUGAACAGGGGAGCUUUAUGGGUAUUGUAGGUAA
..((((((((((((...((((((((...((((................))))...((((((...(((.....)))..))))..)).........))))))))..)))))...))))))). (-20.11 = -21.23 +   1.12)

alignment

secondary structure

dotplot

Window 3

Location	3,245,054 – 3,245,170
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.79
Mean single sequence MFE	-33.92
Consensus MFE	-28.78
Energy contribution	-28.46
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-1.67
Structure conservation index	0.85
SVM decision value	1.06
SVM RNA-class probability	0.908203
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3245054 116 + 22407834
UUUAUGGGGUUUUUCCCGAGUGUGUCGAUUGAAUAUUGAUCAUGUACCGCAUCACGUAUACGAGCGGUGGACGUGGGUGAAAUCGAUUCACCUACCUA----CAUAUAAGAUGUAUGAUG
....(((((....))))).....((((((..(...)..)))...((((((.((........)))))))))))(((((((((.....)))))))))...----(((((.....)))))... ( -35.00)
>DroSec_CAF1 79119 112 + 1
UUUAUGGGGUUUUUCCCGAGUGUGUCGAUUGAAUAUUGAUCAUGUACCGCAUCACGUAUACGAGCGGUGGACGUGGGUGAAAUCGAUUCACC----UA----CAUAUAAGAUGUAUGAUG
....(((((....))))).(((..(((((..(...)..))).(.((((((.((........)))))))).).(((((((((.....))))))----))----)......))..))).... ( -34.60)
>DroSim_CAF1 82245 112 + 1
UUUAUGGGGUUUUUCCCGAGUGUGUCGAUUGAAUAUUGAUCAUGUACCGCAUCACGUAUACGAGCGGUGGACGUGGGUGAAAUCGAUUCGCC----UA----CAUAUAAGAUGUAUGAUG
....(((((....))))).(((..(((((..(...)..))).(.((((((.((........)))))))).).(((((((((.....))))))----))----)......))..))).... ( -34.20)
>DroEre_CAF1 75981 115 + 1
UUUAUGGGGUUU-UCCCCAGUGUGUCGAUUGAAUAUUGAUCAUGUACCGCAUCACGUAUACGAGCGGUGGACGUGGGCGAAAUCGAUUCACC----UAGGAGUAUAUAAGAUGUAUGAUG
....(((((...-.)))))(((.(((((((.....(((..((((((((((.((........)))))))..)))))..)))))))))).))).----.....((((((...)))))).... ( -33.60)
>DroYak_CAF1 75147 112 + 1
UUUAUGGGGUUUUUCCCGAGUGUGUCGAUUGAAUAUUGAUCAUGUACCGCAUCACGUAUACGACCGGUGGACGUGGGUGAAAUCGAUUCACC----UA----CAUAUAAGAUGUAUGCUG
....(((((....))))).(((..(((((..(...)..)))..((.((((....((....))....))))))(((((((((.....))))))----))----)......))..))).... ( -32.20)
>consensus
UUUAUGGGGUUUUUCCCGAGUGUGUCGAUUGAAUAUUGAUCAUGUACCGCAUCACGUAUACGAGCGGUGGACGUGGGUGAAAUCGAUUCACC____UA____CAUAUAAGAUGUAUGAUG
.....((((....))))..(((.(((((((.........((((((.((((....((....))....))))))))))....))))))).)))...........(((((.....)))))... (-28.78 = -28.46 +  -0.32)

alignment

secondary structure

dotplot

Window 4

Location	3,245,054 – 3,245,170
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.79
Mean single sequence MFE	-25.62
Consensus MFE	-21.86
Energy contribution	-22.14
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.85
SVM decision value	1.73
SVM RNA-class probability	0.974521
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3245054 116 - 22407834
CAUCAUACAUCUUAUAUG----UAGGUAGGUGAAUCGAUUUCACCCACGUCCACCGCUCGUAUACGUGAUGCGGUACAUGAUCAAUAUUCAAUCGACACACUCGGGAAAAACCCCAUAAA
.....(((((.....)))----)).((.((((((.....)))))).))(((.((((((((......))).)))))...(((.......)))...)))......(((......)))..... ( -27.90)
>DroSec_CAF1 79119 112 - 1
CAUCAUACAUCUUAUAUG----UA----GGUGAAUCGAUUUCACCCACGUCCACCGCUCGUAUACGUGAUGCGGUACAUGAUCAAUAUUCAAUCGACACACUCGGGAAAAACCCCAUAAA
.(((((.........(((----(.----((((((.....)))))).))))..((((((((......))).)))))..))))).....................(((......)))..... ( -26.20)
>DroSim_CAF1 82245 112 - 1
CAUCAUACAUCUUAUAUG----UA----GGCGAAUCGAUUUCACCCACGUCCACCGCUCGUAUACGUGAUGCGGUACAUGAUCAAUAUUCAAUCGACACACUCGGGAAAAACCCCAUAAA
.(((((.........(((----(.----((.(((.....))).)).))))..((((((((......))).)))))..))))).....................(((......)))..... ( -22.30)
>DroEre_CAF1 75981 115 - 1
CAUCAUACAUCUUAUAUACUCCUA----GGUGAAUCGAUUUCGCCCACGUCCACCGCUCGUAUACGUGAUGCGGUACAUGAUCAAUAUUCAAUCGACACACUGGGGA-AAACCCCAUAAA
........................----((((((.....))))))...(((.((((((((......))).)))))...(((.......)))...)))....(((((.-...))))).... ( -27.00)
>DroYak_CAF1 75147 112 - 1
CAGCAUACAUCUUAUAUG----UA----GGUGAAUCGAUUUCACCCACGUCCACCGGUCGUAUACGUGAUGCGGUACAUGAUCAAUAUUCAAUCGACACACUCGGGAAAAACCCCAUAAA
..(.(((((((....(((----(.----((((((.....)))))).)))).....))).)))).)(((.((((((...(((.......))))))).)))))..(((......)))..... ( -24.70)
>consensus
CAUCAUACAUCUUAUAUG____UA____GGUGAAUCGAUUUCACCCACGUCCACCGCUCGUAUACGUGAUGCGGUACAUGAUCAAUAUUCAAUCGACACACUCGGGAAAAACCCCAUAAA
............................((((((.....))))))...(((.((((((((......))).)))))...(((.......)))...)))......(((......)))..... (-21.86 = -22.14 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:35 2006