Locus 5637

Sequence ID	3L_DroMel_CAF1
Location	15,489,953 – 15,490,153
Length	200
Max. P	0.940506

overview

Window 3

Location	15,489,953 – 15,490,073
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-40.24
Consensus MFE	-31.95
Energy contribution	-34.64
Covariance contribution	2.69
Combinations/Pair	1.09
Mean z-score	-3.00
Structure conservation index	0.79
SVM decision value	1.31
SVM RNA-class probability	0.940506
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15489953 120 + 23771897
UCCAUAGUAGCAAAUAUAGUACUUUCUGCAACUACUCGAGCUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACCAACGUGGAGCAAUAAGUGGCGGCAUCCGUGACCAU
....((((.(((..............))).)))).....((((((.((.....((((((.......))))))((((((((((((....))))))))))))))))))))............ ( -41.84)
>DroSec_CAF1 31157 120 + 1
UCCAUAGUAGCAAAUAUAGUAAUUUCUGCAACUGCUCGAGCUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAU
..(((.((((.((((......))))))))..........(((((((.(....(((((((.......)))))))(((((((((((....)))))))))))).)))))))....)))..... ( -45.10)
>DroSim_CAF1 33183 120 + 1
UCCAUAGUAGCAAAUAUAGUACUUUCUGCAACUACUCGAGCUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAU
....((((.(((..............))).)))).....(((((((.(....(((((((.......)))))))(((((((((((....)))))))))))).)))))))............ ( -44.14)
>DroYak_CAF1 113537 120 + 1
UCCAUAGUAGCAAAUAUAGUAUUGUCUGCAACUACUAGAACUACCGACAUAAACCAGUCUGUCGCUGGAUUGUGGUUGGCCCAUUAACGUGGAGCAAAACGUGGCUGCAUCCGUGACCAU
......(((((.....((((((((....))).)))))....(((((((((((.(((((.....))))).)))).))))((((((....)))).)).....))))))))............ ( -29.90)
>consensus
UCCAUAGUAGCAAAUAUAGUACUUUCUGCAACUACUCGAGCUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAU
....((((.(((..............))).)))).....((((((.((....(((((((.......)))))))(((((((((((....))))))))))).))))))))............ (-31.95 = -34.64 +   2.69)

alignment

secondary structure

dotplot

Window 4

Location	15,489,953 – 15,490,073
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-39.05
Consensus MFE	-32.34
Energy contribution	-33.27
Covariance contribution	0.94
Combinations/Pair	1.09
Mean z-score	-2.24
Structure conservation index	0.83
SVM decision value	1.13
SVM RNA-class probability	0.919791
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15489953 120 - 23771897
AUGGUCACGGAUGCCGCCACUUAUUGCUCCACGUUGGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAGCUCGAGUAGUUGCAGAAAGUACUAUAUUUGCUACUAUGGA
.......(((.(((((.((....(((((((((....)))))))))..(((((((.......)))))))...)).)))))..))).(((((.(((((.(......).))))).)))))... ( -42.70)
>DroSec_CAF1 31157 120 - 1
AUGGUCACGGAUGCCGCCACCUAUUGCUCCACGUUAGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAGCUCGAGCAGUUGCAGAAAUUACUAUAUUUGCUACUAUGGA
(((((..(((.(((((.((....(((((((((....)))))))))..(((((((.......)))))))...)).)))))..)))(((((.((.((......)).)).))))))))))... ( -41.50)
>DroSim_CAF1 33183 120 - 1
AUGGUCACGGAUGCCGCCACCUAUUGCUCCACGUUAGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAGCUCGAGUAGUUGCAGAAAGUACUAUAUUUGCUACUAUGGA
.......(((.(((((.((....(((((((((....)))))))))..(((((((.......)))))))...)).)))))..))).(((((.(((((.(......).))))).)))))... ( -43.30)
>DroYak_CAF1 113537 120 - 1
AUGGUCACGGAUGCAGCCACGUUUUGCUCCACGUUAAUGGGCCAACCACAAUCCAGCGACAGACUGGUUUAUGUCGGUAGUUCUAGUAGUUGCAGACAAUACUAUAUUUGCUACUAUGGA
.(((((..(((.((((.......))))))).((....)))))))((((((..(((((....).))))....))).)))...((((.((((.(((((..........))))).)))))))) ( -28.70)
>consensus
AUGGUCACGGAUGCCGCCACCUAUUGCUCCACGUUAGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAGCUCGAGUAGUUGCAGAAAGUACUAUAUUUGCUACUAUGGA
.........((.((.(((.....(((((((((....)))))))))..(((((((.......))))))).......))).))))..(((((.(((((..........))))).)))))... (-32.34 = -33.27 +   0.94)

alignment

secondary structure

dotplot

Window 5

Location	15,489,993 – 15,490,113
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-43.97
Consensus MFE	-34.46
Energy contribution	-36.52
Covariance contribution	2.06
Combinations/Pair	1.12
Mean z-score	-3.54
Structure conservation index	0.78
SVM decision value	1.21
SVM RNA-class probability	0.931540
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15489993 120 + 23771897
CUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACCAACGUGGAGCAAUAAGUGGCGGCAUCCGUGACCAUGUUAUUCGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGA
.(((((.(((...((((((.......))))))((((((((((((....))))))))))))))).)))))((((((((...))))..)))).........((((((........)))))). ( -43.80)
>DroSec_CAF1 31197 120 + 1
CUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAUGUUAUUUGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGA
...(((......(((((((.......)))))))(((((((((((....)))))))))))((((((((.....((((..........(((....))))))).....))))))))...))). ( -48.20)
>DroSim_CAF1 33223 120 + 1
CUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAUGUUAUUUGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGA
...(((......(((((((.......)))))))(((((((((((....)))))))))))((((((((.....((((..........(((....))))))).....))))))))...))). ( -48.20)
>DroYak_CAF1 113577 120 + 1
CUACCGACAUAAACCAGUCUGUCGCUGGAUUGUGGUUGGCCCAUUAACGUGGAGCAAAACGUGGCUGCAUCCGUGACCAUGUCAUUAGGAUCUCCAUCACCGUUUCCACCAUCAAAUGGA
...(((((((((.(((((.....))))).)))).))))).(((((...(((((((...((((((..((....))..)))))).....((....))......).)))))).....))))). ( -35.70)
>consensus
CUGCCGACAUAUACAAUCCUGUCGCUGGAUUGUUGUUGCUCCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAUGUUAUUUGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGA
.(((((.(((..(((((((.......)))))))(((((((((((....))))))))))).))).)))))((((((((...)))))..))).........((((((........)))))). (-34.46 = -36.52 +   2.06)

alignment

secondary structure

dotplot

Window 6

Location	15,489,993 – 15,490,113
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-39.80
Consensus MFE	-34.72
Energy contribution	-35.48
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-1.72
Structure conservation index	0.87
SVM decision value	0.66
SVM RNA-class probability	0.815708
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15489993 120 - 23771897
UCCAUUCGAUGGCGGAAAUGGUGAUGGAGAUCCGAAUAACAUGGUCACGGAUGCCGCCACUUAUUGCUCCACGUUGGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAG
.....((((((((((...(.(((((((....))(.....)...))))).)...))))).....(((((((((....)))))))))..(((((((.......)))))))....)))))... ( -42.80)
>DroSec_CAF1 31197 120 - 1
UCCAUUCGAUGGCGGAAAUGGUGAUGGAGAUCCAAAUAACAUGGUCACGGAUGCCGCCACCUAUUGCUCCACGUUAGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAG
.....((((((((((...(.(((((((....)))..........)))).)...))))).....(((((((((....)))))))))..(((((((.......)))))))....)))))... ( -43.00)
>DroSim_CAF1 33223 120 - 1
UCCAUUCGAUGGCGGAAAUGGUGAUGGAGAUCCAAAUAACAUGGUCACGGAUGCCGCCACCUAUUGCUCCACGUUAGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAG
.....((((((((((...(.(((((((....)))..........)))).)...))))).....(((((((((....)))))))))..(((((((.......)))))))....)))))... ( -43.00)
>DroYak_CAF1 113577 120 - 1
UCCAUUUGAUGGUGGAAACGGUGAUGGAGAUCCUAAUGACAUGGUCACGGAUGCAGCCACGUUUUGCUCCACGUUAAUGGGCCAACCACAAUCCAGCGACAGACUGGUUUAUGUCGGUAG
((((((..((.((....)).))))))))....(((.((((((((....((.((..(((.((((..((.....)).))))))))).)).....(((((....).)))).)))))))).))) ( -30.40)
>consensus
UCCAUUCGAUGGCGGAAAUGGUGAUGGAGAUCCAAAUAACAUGGUCACGGAUGCCGCCACCUAUUGCUCCACGUUAGUGGAGCAACAACAAUCCAGCGACAGGAUUGUAUAUGUCGGCAG
.....((((((((((...(.(((((((....))..........))))).)...))))).....(((((((((....)))))))))..(((((((.......)))))))....)))))... (-34.72 = -35.48 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	15,490,033 – 15,490,153
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-36.75
Consensus MFE	-32.66
Energy contribution	-33.73
Covariance contribution	1.06
Combinations/Pair	1.13
Mean z-score	-1.93
Structure conservation index	0.89
SVM decision value	1.09
SVM RNA-class probability	0.914288
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15490033 120 + 23771897
CCACCAACGUGGAGCAAUAAGUGGCGGCAUCCGUGACCAUGUUAUUCGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGAGGAGUCUCUAUGGGAUCCGUUUCAUUUCUGCACUUUACAU
((((....)))).(((....((.((((...)))).)).(((.....((((((.((((......((((.((((...)))).)))).....))))))))))...)))...)))......... ( -35.00)
>DroSec_CAF1 31237 120 + 1
CCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAUGUUAUUUGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGAGGAGUCUCUAUGGGAUCCGUGUCAUUUCUGCACUUUACAU
((((....)))).(((...(((.((((...)))).)))(((.....((((((.((((......((((.((((...)))).)))).....))))))))))...)))...)))......... ( -40.00)
>DroSim_CAF1 33263 120 + 1
CCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAUGUUAUUUGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGAGGAGUCUCUGUGGGAUCCGUGCCAUUUCUGCACUUUACAU
((((....))))((((...(((.((((...)))).))).))))....(((((.((((......((((.((((...)))).)))).....)))))))))((((.......))))....... ( -41.50)
>DroYak_CAF1 113617 120 + 1
CCAUUAACGUGGAGCAAAACGUGGCUGCAUCCGUGACCAUGUCAUUAGGAUCUCCAUCACCGUUUCCACCAUCAAAUGGAGGAUUCUCCAUGGCAUCCGUGCCAUUUCUGCACUUUACAU
........(((((((...((((((..((....))..)))))).....((....))......).))))))......((((((....))))))((((....))))................. ( -30.50)
>consensus
CCACUAACGUGGAGCAAUAGGUGGCGGCAUCCGUGACCAUGUUAUUUGGAUCUCCAUCACCAUUUCCGCCAUCGAAUGGAGGAGUCUCUAUGGGAUCCGUGCCAUUUCUGCACUUUACAU
((((....)))).(((..(((((((.((....(((((...)))))..(((((.((((......((((.((((...)))).)))).....)))))))))))))))))).)))......... (-32.66 = -33.73 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:14 2006