Locus 558

Sequence ID	2L_DroMel_CAF1
Location	1,740,519 – 1,740,706
Length	187
Max. P	0.986284

overview

Window 2

Location	1,740,519 – 1,740,626
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	70.48
Mean single sequence MFE	-20.41
Consensus MFE	-7.44
Energy contribution	-8.62
Covariance contribution	1.19
Combinations/Pair	1.13
Mean z-score	-2.89
Structure conservation index	0.36
SVM decision value	0.89
SVM RNA-class probability	0.876361
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1740519 107 + 22407834
AUUUUAAUAACUAUUUCCCAA----UAGUUACACACCUUUCCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCUCC---------CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCC
.......((((((((....))----))))))................((((((((((.....(((((.........---------..))))).))))))))))................. ( -18.70)
>DroSim_CAF1 4119 107 + 1
AUUUCAAUAACUAUUUCCCAA----UAGUUACACACCUUUCCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCUCC---------CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCC
.......((((((((....))----))))))................((((((((((.....(((((.........---------..))))).))))))))))................. ( -18.70)
>DroWil_CAF1 13312 112 + 1
A-UUUGAUGAUUUUAUGGCUAUAUUUAGUUACCUACUGU-----UAG--GUAAACAAAAUUGUUUAGCAUUCCAACACUAUUACUUAAAAUCUUAGUUUGCUUAAAUUGUUAGACCGUCC
.-(((((..((((...(((((.((((..(((((((....-----)))--))))...))))....))))....(((.((((.............))))))))..))))..)))))...... ( -17.12)
>DroYak_CAF1 4136 107 + 1
UGUUAAUAAACUAUUUCCCAA----UAGUUACACACCUGUCCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCGCC---------CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCC
(((((((.(((((((....))----))))).................((((((((((....((.((((....))))---------.)).....)))))))))).....)))))))..... ( -27.10)
>consensus
AUUUUAAUAACUAUUUCCCAA____UAGUUACACACCUUUCCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCUCC_________CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCC
...............................................((((((((((.....(((((....................))))).))))))))))................. ( -7.44 =  -8.62 +   1.19)

alignment

secondary structure

dotplot

Window 3

Location	1,740,555 – 1,740,666
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	73.74
Mean single sequence MFE	-24.72
Consensus MFE	-12.79
Energy contribution	-15.10
Covariance contribution	2.31
Combinations/Pair	1.15
Mean z-score	-2.16
Structure conservation index	0.52
SVM decision value	0.95
SVM RNA-class probability	0.888646
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1740555 111 + 22407834
CCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCUCC---------CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACA
((.....((((((((((.....(((((.........---------..))))).)))))))))).(((((((..(...(((......)))..)..)))))))(((....)))..))..... ( -25.90)
>DroSim_CAF1 4155 111 + 1
CCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCUCC---------CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACA
((.....((((((((((.....(((((.........---------..))))).)))))))))).(((((((..(...(((......)))..)..)))))))(((....)))..))..... ( -25.90)
>DroWil_CAF1 13350 106 + 1
----UAG--GUAAACAAAAUUGUUUAGCAUUCCAACACUAUUACUUAAAAUCUUAGUUUGCUUAAAUUGUUAGACCGUCCAAAAACAGGA--------ACUGACCUAACCCAAUGGGCAA
----..(--.((((((....)))))).).............................(((((((....(((((....(((.......)))--------......)))))....))))))) ( -16.40)
>DroYak_CAF1 4172 111 + 1
CCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCGCC---------CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACA
((.....((((((((((....((.((((....))))---------.)).....)))))))))).(((((((..(...(((......)))..)..)))))))(((....)))..))..... ( -30.70)
>consensus
CCAUCAAGUGCAAACAACAUUCUAGGCGAUUCCUCC_________CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACA
.......((((((((((.....(((((....................))))).)))))))))).............(((((.....((((((.......))).)))......)))))... (-12.79 = -15.10 +   2.31)

alignment

secondary structure

dotplot

Window 4

Location	1,740,591 – 1,740,706
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	74.04
Mean single sequence MFE	-22.58
Consensus MFE	-14.96
Energy contribution	-15.65
Covariance contribution	0.69
Combinations/Pair	1.19
Mean z-score	-2.09
Structure conservation index	0.66
SVM decision value	2.04
SVM RNA-class probability	0.986284
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1740591 115 + 22407834
-----CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACAUAAAAUUAGCAAACAUUAGCUAACUGCGGAAUAAUCAACU
-----.((((....(((((((.(((....)))....(((((...(..(((((.......))).))..)....)))))...........)))))))..))))................... ( -25.60)
>DroSim_CAF1 4191 115 + 1
-----CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACAUAAAAUUAGCAAACAUUAGCGAACUGCGGAAUAAUCAACU
-----..(((....(((((((.(((....)))....(((((...(..(((((.......))).))..)....)))))...........)))))))..))).................... ( -24.90)
>DroWil_CAF1 13384 98 + 1
UUACUUAAAAUCUUAGUUUGCUUAAAUUGUUAGACCGUCCAAAAACAGGA--------ACUGACCUAACCCAAUGGGCAAUAAAAUUAGCAAAUUCUAGUCAAUUC--------------
...........((.((((((((......(((((....(((.......)))--------.)))))....(((...)))..........))))))))..)).......-------------- ( -14.20)
>DroYak_CAF1 4208 115 + 1
-----CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACAUAAAAUUAGCAAACAUUAGCUAACUGGAGAAUAAUCAACU
-----.((((....(((((((.(((....)))....(((((...(..(((((.......))).))..)....)))))...........)))))))..))))................... ( -25.60)
>consensus
_____CAGCUUAUUUGUUUGCAUAAGUAAUUAGCAAACCCUAAAUCGGGCAGAAAAUUACUGACCUAAGUCAAGGGUACAUAAAAUUAGCAAACAUUAGCUAACUGCGGAAUAAUCAACU
.......(((....(((((((.(((....(((....(((((.....((((((.......))).)))......)))))...)))..))))))))))..))).................... (-14.96 = -15.65 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	1,740,591 – 1,740,706
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	74.04
Mean single sequence MFE	-24.79
Consensus MFE	-16.80
Energy contribution	-17.93
Covariance contribution	1.13
Combinations/Pair	1.27
Mean z-score	-1.51
Structure conservation index	0.68
SVM decision value	0.32
SVM RNA-class probability	0.687159
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1740591 115 - 22407834
AGUUGAUUAUUCCGCAGUUAGCUAAUGUUUGCUAAUUUUAUGUACCCUUGACUUAGGUCAGUAAUUUUCUGCCCGAUUUAGGGUUUGCUAAUUACUUAUGCAAACAAAUAAGCUG-----
.((.((....)).))...(((((..(((((((................((((....))))((((((....((((......)))).....))))))....)))))))....)))))----- ( -27.50)
>DroSim_CAF1 4191 115 - 1
AGUUGAUUAUUCCGCAGUUCGCUAAUGUUUGCUAAUUUUAUGUACCCUUGACUUAGGUCAGUAAUUUUCUGCCCGAUUUAGGGUUUGCUAAUUACUUAUGCAAACAAAUAAGCUG-----
.((.((....)).)).....(((..(((((((................((((....))))((((((....((((......)))).....))))))....)))))))....)))..----- ( -26.20)
>DroWil_CAF1 13384 98 - 1
--------------GAAUUGACUAGAAUUUGCUAAUUUUAUUGCCCAUUGGGUUAGGUCAGU--------UCCUGUUUUUGGACGGUCUAACAAUUUAAGCAAACUAAGAUUUUAAGUAA
--------------..............((((((((((((((((.......(((((..(.((--------((........)))))..))))).......))))..)))))))...))))) ( -18.34)
>DroYak_CAF1 4208 115 - 1
AGUUGAUUAUUCUCCAGUUAGCUAAUGUUUGCUAAUUUUAUGUACCCUUGACUUAGGUCAGUAAUUUUCUGCCCGAUUUAGGGUUUGCUAAUUACUUAUGCAAACAAAUAAGCUG-----
((((((((.......))))))))..(((((((................((((....))))((((((....((((......)))).....))))))....))))))).........----- ( -27.10)
>consensus
AGUUGAUUAUUCCGCAGUUAGCUAAUGUUUGCUAAUUUUAUGUACCCUUGACUUAGGUCAGUAAUUUUCUGCCCGAUUUAGGGUUUGCUAAUUACUUAUGCAAACAAAUAAGCUG_____
..................(((((..(((((((................((((....))))((((((....((((......)))).....))))))....)))))))....)))))..... (-16.80 = -17.93 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:41 2006