Locus 2210

Sequence ID	3L_DroMel_CAF1
Location	6,090,840 – 6,091,080
Length	240
Max. P	0.974331

overview

Window 5

Location	6,090,840 – 6,090,960
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-33.53
Consensus MFE	-32.22
Energy contribution	-32.00
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.68
Structure conservation index	0.96
SVM decision value	1.63
SVM RNA-class probability	0.968672
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6090840 120 + 23771897
UUUACUAAAUUUUCGCUGAAACGAAAGUCACUUUCAAAAUGGUCGGAUUCAAUGCCUCUGACCAGUUGCCAAGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGAC
........(((((((......))))))).....((((((((((((((.........)))))))).(((((..(((..(((((((.....)))))))..))).....)))))..)))))). ( -33.40)
>DroSec_CAF1 39189 120 + 1
UUUACUACAUUUUCGCUGAAACGAAAGUCACUUUCAAAAUGGUCGGAUUCAAUGCCUCUGACCAGUUGCCAGGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGAC
........(((((((......))))))).....((((((((((((((.........))))))))(((.(((((((..(((((((.....)))))))..))).)))))))....)))))). ( -34.30)
>DroSim_CAF1 40509 120 + 1
UUUACUACAUUUUCGCUGAAAUGAAAGUCACUUUCAAAAUGGUCGGAUUCAAUGCCUCUGACCAGUUGCCAGGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGAC
..............(((....((((((...))))))...((((((((.........))))))))(((.(((((((..(((((((.....)))))))..))).))))))).)))....... ( -32.90)
>consensus
UUUACUACAUUUUCGCUGAAACGAAAGUCACUUUCAAAAUGGUCGGAUUCAAUGCCUCUGACCAGUUGCCAGGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGAC
........(((((((......))))))).....((((((((((((((.........)))))))).(((((..(((..(((((((.....)))))))..))).....)))))..)))))). (-32.22 = -32.00 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	6,090,840 – 6,090,960
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-33.50
Consensus MFE	-32.25
Energy contribution	-32.37
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.56
Structure conservation index	0.96
SVM decision value	0.14
SVM RNA-class probability	0.600950
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6090840 120 - 23771897
GUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCUUGGCAACUGGUCAGAGGCAUUGAAUCCGACCAUUUUGAAAGUGACUUUCGUUUCAGCGAAAAUUUAGUAAA
((((..((.(((((.....(((((((((((((...)))))))))))))..)))))))((((.((..(...)..)).))))..........))))((((((....)))))).......... ( -32.90)
>DroSec_CAF1 39189 120 - 1
GUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCCUGGCAACUGGUCAGAGGCAUUGAAUCCGACCAUUUUGAAAGUGACUUUCGUUUCAGCGAAAAUGUAGUAAA
((((..((.(((((..((.(((((((((((((...))))))))))))))))))))))((((.((..(...)..)).))))..........))))((((((....)))))).......... ( -34.90)
>DroSim_CAF1 40509 120 - 1
GUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCCUGGCAACUGGUCAGAGGCAUUGAAUCCGACCAUUUUGAAAGUGACUUUCAUUUCAGCGAAAAUGUAGUAAA
.((((((..(((((..((.(((((((((((((...)))))))))))))))))))).(((((.((..(...)..)).))))))))))).....(((..(((((......))))).)))... ( -32.70)
>consensus
GUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCCUGGCAACUGGUCAGAGGCAUUGAAUCCGACCAUUUUGAAAGUGACUUUCGUUUCAGCGAAAAUGUAGUAAA
((((..((.(((((..((.(((((((((((((...))))))))))))))))))))))((((.((..(...)..)).))))..........))))((((((....)))))).......... (-32.25 = -32.37 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	6,090,880 – 6,091,000
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-41.40
Consensus MFE	-40.27
Energy contribution	-40.60
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.66
Structure conservation index	0.97
SVM decision value	1.68
SVM RNA-class probability	0.971625
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6090880 120 + 23771897
GGUCGGAUUCAAUGCCUCUGACCAGUUGCCAAGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCC
(((((((.........))))))).....(((.(((..(((((((.....)))))))..)))..)))(((((.....((..((((((.....))))))..)).......)))))....... ( -39.40)
>DroSec_CAF1 39229 120 + 1
GGUCGGAUUCAAUGCCUCUGACCAGUUGCCAGGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUAUCC
(((((((.........))))))).....(((((((..(((((((.....)))))))..))).))))(((((.....((..((((((.....))))))..)).......)))))....... ( -42.40)
>DroSim_CAF1 40549 120 + 1
GGUCGGAUUCAAUGCCUCUGACCAGUUGCCAGGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCC
(((((((.........))))))).....(((((((..(((((((.....)))))))..))).))))(((((.....((..((((((.....))))))..)).......)))))....... ( -42.40)
>consensus
GGUCGGAUUCAAUGCCUCUGACCAGUUGCCAGGCAAAAUCAAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCC
(((((((.........))))))).....(((((((..(((((((.....)))))))..))).))))(((((.....((..((((((.....))))))..)).......)))))....... (-40.27 = -40.60 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	6,090,880 – 6,091,000
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-45.60
Consensus MFE	-46.01
Energy contribution	-45.57
Covariance contribution	-0.44
Combinations/Pair	1.05
Mean z-score	-2.42
Structure conservation index	1.01
SVM decision value	1.73
SVM RNA-class probability	0.974331
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6090880 120 - 23771897
GGACAAUGGCAACGGUGGGUGGAGCCACCAUAAUGGCGGCGUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCUUGGCAACUGGUCAGAGGCAUUGAAUCCGACC
((((((((.(...((..(((.(((((.((.....)).))).))....)))..))((((.(((((((((((((...)))))))))))))))))............).)))))..))).... ( -44.30)
>DroSec_CAF1 39229 120 - 1
GGAUAAUGGCAACGGUGGGUGGAGCCACCAUAAUGGCGGCGUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCCUGGCAACUGGUCAGAGGCAUUGAAUCCGACC
((((((((.(...((..(((.(((((.((.....)).))).))....)))..))((((.(((((((((((((...)))))))))))))))))............).))))..)))).... ( -45.50)
>DroSim_CAF1 40549 120 - 1
GGACAAUGGCAACGGUGGGUGGAGCCACCAUAAUGGCGGCGUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCCUGGCAACUGGUCAGAGGCAUUGAAUCCGACC
((((((((.(...((..(((.(((((.((.....)).))).))....)))..))((((.(((((((((((((...)))))))))))))))))............).)))))..))).... ( -47.00)
>consensus
GGACAAUGGCAACGGUGGGUGGAGCCACCAUAAUGGCGGCGUCAAAAGCUUGCCCCAGCGCAGGAUCAAUAGGAGUUAUUGAUUUUGCCUGGCAACUGGUCAGAGGCAUUGAAUCCGACC
((((((((.(...((..(((.(((((.((.....)).))).))....)))..))((((.(((((((((((((...)))))))))))))))))............).)))))..))).... (-46.01 = -45.57 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	6,090,920 – 6,091,040
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.61
Mean single sequence MFE	-32.57
Consensus MFE	-31.37
Energy contribution	-31.37
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.96
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6090920 120 + 23771897
AAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCCCCAGUGUGCUGGCACCACCACCGCACCGCACCACCUCCAC
..................(((((((((((((((.......)).((....(((((((......))))))).))..))).)))))))(((((((.....)))..)))).))).......... ( -34.90)
>DroSec_CAF1 39269 120 + 1
AAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUAUCCCCAGUGUACUGGCACCACCACCGCACCGCACCACCUCCAC
..................((((.((((((((.....((..((((((.....))))))..)).......))))).......((((....)))).....))).))))............... ( -31.40)
>DroSim_CAF1 40589 120 + 1
AAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCCCCAGUGUUCUGGCACCACCACCGCACCGCACCACCUCCAC
..................((((.((((((((((.......)).((....(((((((......))))))).))..))).)))))((((..(((.....)))..)))))))).......... ( -31.40)
>consensus
AAUAACUCCUAUUGAUCCUGCGCUGGGGCAAGCUUUUGACGCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCCCCAGUGUACUGGCACCACCACCGCACCGCACCACCUCCAC
..................((((.((((((((.....((..((((((.....))))))..)).......))))).......((((....)))).....))).))))............... (-31.37 = -31.37 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	6,090,960 – 6,091,080
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.06
Mean single sequence MFE	-31.09
Consensus MFE	-30.04
Energy contribution	-30.04
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.97
SVM decision value	0.95
SVM RNA-class probability	0.888272
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6090960 120 + 23771897
GCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCCCCAGUGUGCUGGCACCACCACCGCACCGCACCACCUCCACCUCUACCCACUUUUGCGCCAUCGAAACAUGGCGCUCGAAC
((((((.....))))))..........(.(((...((....))(((((.(((.....))).))))).))).)......................(((((((......)))))))...... ( -32.80)
>DroSec_CAF1 39309 120 + 1
GCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUAUCCCCAGUGUACUGGCACCACCACCGCACCGCACCACCUCCACCUCCACCCACUUUUGCGCCAUCGAAACAUGGCGCUCGAAC
((((((.....)))))).........((.(((........((((....))))..........))).))..........................(((((((......)))))))...... ( -30.07)
>DroSim_CAF1 40629 120 + 1
GCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCCCCAGUGUUCUGGCACCACCACCGCACCGCACCACCUCCACCUCCACCCACUUUUGCGCCAUCGAAACAUGGCGCUCGAAC
((((((.....)))))).........((.((((((((....)))))...(((.....)))..))).))..........................(((((((......)))))))...... ( -30.40)
>consensus
GCCGCCAUUAUGGUGGCUCCACCCACCGUUGCCAUUGUCCCCAGUGUACUGGCACCACCACCGCACCGCACCACCUCCACCUCCACCCACUUUUGCGCCAUCGAAACAUGGCGCUCGAAC
((((((.....)))))).........((.(((........((((....))))..........))).))..........................(((((((......)))))))...... (-30.04 = -30.04 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:59 2006