Locus 7550

Sequence ID 2L_DroMel_CAF1
Location 20,931,629 – 20,931,821
Length 192
Max. P 0.992512
window12136 window12137 window12138 window12139

overview

Window 6

Location 20,931,629 – 20,931,741
Length 112
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 80.29
Mean single sequence MFE -29.73
Consensus MFE -21.55
Energy contribution -22.67
Covariance contribution 1.11
Combinations/Pair 1.05
Mean z-score -2.76
Structure conservation index 0.72
SVM decision value 2.33
SVM RNA-class probability 0.992512
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20931629 112 + 22407834
CCACCGCUCACAUUUUCCUCAUUUUCCCCAUCGCCUGAUGGCGGAGGCGGCUUUCCACC-------GGAUUCUUUUCGCUUUUCUGCGCCGCGAACGCUGCUGCUGAUUUUCACUUCUU
.....((.................((((((((....))))).)))((((((.(((...(-------((........(((......)))))).))).))))))))............... ( -27.40)
>DroSec_CAF1 18050 110 + 1
CCACCGCUCACAUUUUCCUCAUUUUCCCCAUCGCCUGAUGGUGGAGGCAGCU--CCACC-------GGCUUCUUUUCGCUUUUAUGCGCCGCCACCGCUUCUGCUGAUUUUCACUUCUU
.............................(((((..((((((((.(((((((--.....-------)))).......((......))))).))))))..)).)).)))........... ( -23.20)
>DroEre_CAF1 15556 108 + 1
-----------AUUUUCCUUAUUUUCCCCAUCGCUUGAUGGCGGAGGCGGCUUUCCACCGAAAGGCGGAUUUCUUCCGCUUUUCCACGCCGCCAGCGCUGCUGCUGAUUUUCACUUCUU
-----------.............((((((((....))))).)))((((((........((((((((((.....))))))))))...))))))((((....)))).............. ( -38.60)
>consensus
CCACCGCUCACAUUUUCCUCAUUUUCCCCAUCGCCUGAUGGCGGAGGCGGCUUUCCACC_______GGAUUCUUUUCGCUUUUCUGCGCCGCCAACGCUGCUGCUGAUUUUCACUUCUU
........................((((((((....))))).)))((((((...............(((.....)))((......))))))))...((....))............... (-21.55 = -22.67 +   1.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,931,629 – 20,931,741
Length 112
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 80.29
Mean single sequence MFE -34.87
Consensus MFE -23.81
Energy contribution -23.87
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.75
Structure conservation index 0.68
SVM decision value 2.13
SVM RNA-class probability 0.988771
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20931629 112 - 22407834
AAGAAGUGAAAAUCAGCAGCAGCGUUCGCGGCGCAGAAAAGCGAAAAGAAUCC-------GGUGGAAAGCCGCCUCCGCCAUCAGGCGAUGGGGAAAAUGAGGAAAAUGUGAGCGGUGG
...................((.((((((((.(((......))).......(((-------(((((....)))))(((.(((((....))))))))......)))...)))))))).)). ( -38.70)
>DroSec_CAF1 18050 110 - 1
AAGAAGUGAAAAUCAGCAGAAGCGGUGGCGGCGCAUAAAAGCGAAAAGAAGCC-------GGUGG--AGCUGCCUCCACCAUCAGGCGAUGGGGAAAAUGAGGAAAAUGUGAGCGGUGG
............(((((((.(.((((..(..(((......)))....)..)))-------).)..--..)))).(((.(((((....))))))))...))).................. ( -28.90)
>DroEre_CAF1 15556 108 - 1
AAGAAGUGAAAAUCAGCAGCAGCGCUGGCGGCGUGGAAAAGCGGAAGAAAUCCGCCUUUCGGUGGAAAGCCGCCUCCGCCAUCAAGCGAUGGGGAAAAUAAGGAAAAU-----------
..............(((......)))((((((.........(....)...((((((....))))))..))))))(((.(((((....)))))))).............----------- ( -37.00)
>consensus
AAGAAGUGAAAAUCAGCAGCAGCGCUGGCGGCGCAGAAAAGCGAAAAGAAUCC_______GGUGGAAAGCCGCCUCCGCCAUCAGGCGAUGGGGAAAAUGAGGAAAAUGUGAGCGGUGG
...............((....))...((((((((......)).........(((.....)))......))))))(((.(((((....))))))))........................ (-23.81 = -23.87 +   0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,931,668 – 20,931,781
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.74
Mean single sequence MFE -36.13
Consensus MFE -25.46
Energy contribution -26.16
Covariance contribution 0.70
Combinations/Pair 1.09
Mean z-score -1.64
Structure conservation index 0.70
SVM decision value 0.06
SVM RNA-class probability 0.565187
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20931668 113 - 22407834
UUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUCGCGGCGCAGAAAAGCGAAAAGAAUCC-------GGUGGAAAGCCGCCUCCGCC
.....(((((((((.(((.(((((..(((((((....))))))).(((((.....((....)).))))).)))))...)))))))).......-------(((((....))))).)))). ( -37.20)
>DroSec_CAF1 18089 111 - 1
UUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGAAGCGGUGGCGGCGCAUAAAAGCGAAAAGAAGCC-------GGUGG--AGCUGCCUCCACC
..((..(.(((((..((.((...((((((((((....)))))).))))...)).))..))))).)..))(((..................)))-------(((((--((....))))))) ( -35.97)
>DroSim_CAF1 16301 113 - 1
UUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUGGCGGCGCAGAAAAGCGAAAAGAAGCC-------GGUGGAAAGCCGCCUCCACC
(((((((((((((.(((.........(((((((....)))))))))).)))))).)))))))....(((..(((......))).......)))-------((((((........)))))) ( -34.70)
>DroEre_CAF1 15584 120 - 1
UUGUUGCGGUUUUGACUUAUGUGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGCUGGCGGCGUGGAAAAGCGGAAGAAAUCCGCCUUUCGGUGGAAAGCCGCCUCCGCC
.((((((((((((.(((.........(((((((....)))))))))).)))))).))))))(((..((((((.........(....)...((((((....))))))..))))))..))). ( -48.30)
>DroYak_CAF1 16286 93 - 1
UUGUUGCGGUUUUGACUUAUGUGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUGGCGUCGCACAAAAACGCAAAGAAUAC---------------------------
.((((((((((((.(((.........(((((((....)))))))))).)))))).))))))(((((.((...)).....))))).........--------------------------- ( -24.50)
>consensus
UUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUGGCGGCGCAGAAAAGCGAAAAGAAUCC_______GGUGGAAAGCCGCCUCCACC
.((((((((((((.(((.........(((((((....)))))))))).)))))).))))))((((.....))))..........................((((((........)))))) (-25.46 = -26.16 +   0.70)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,931,701 – 20,931,821
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -37.08
Consensus MFE -33.40
Energy contribution -33.16
Covariance contribution -0.24
Combinations/Pair 1.11
Mean z-score -1.78
Structure conservation index 0.90
SVM decision value 2.14
SVM RNA-class probability 0.988900
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20931701 120 - 22407834
UUGUUGCUGUAUUCACAUUGGUUGCUCCAUUUCGCCGUUGUUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUCGCGGCGCAGAAAA
......((((........(((.....)))....((((((((((((((((((((.(((.........(((((((....)))))))))).)))))).)))))))))...))))))))).... ( -37.40)
>DroSec_CAF1 18120 120 - 1
UUGUUGCUGUAUUCACAUUGGUUGCUCCAUUUCGCCGGUGUUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGAAGCGGUGGCGGCGCAUAAAA
..(((((((((...((((((((...........))))))))...))))))...)))(((((((((((((((((....))))))).......(((.((....))))).)).)))))))).. ( -33.70)
>DroSim_CAF1 16334 120 - 1
UUGUUGCCGUAUUCACAUUGGUUGCUCCAUUUCGCCGUUGUUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUGGCGGCGCAGAAAA
((((.(((..........(((.....)))....((((.(((((((((((((((.(((.........(((((((....)))))))))).)))))).))))))))).))))))))))).... ( -39.70)
>DroEre_CAF1 15624 120 - 1
UUGUUGCUGUGUUCACAUUGGUUGCUCCAUUUCGCUGUUGUUGUUGCGGUUUUGACUUAUGUGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGCUGGCGGCGUGGAAAA
..((.((((((....)).)))).))(((((.(((((..(((((((((((((((.(((.........(((((((....)))))))))).)))))).)))))))))..))))).)))))... ( -40.20)
>DroYak_CAF1 16299 120 - 1
UUGUUGCUGCGUUCACAUUGGUUUCUCUAUUUCGCUGUUGUUGUUGCGGUUUUGACUUAUGUGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUGGCGUCGCACAAAA
...(((.((((.......(((.....)))...((((..(((((((((((((((.(((.........(((((((....)))))))))).)))))).)))))))))..)))).))))))).. ( -34.40)
>consensus
UUGUUGCUGUAUUCACAUUGGUUGCUCCAUUUCGCCGUUGUUGUUGCGGUUUUGACUUAUGCGCGCUCUUAAUUGUUGUUAAGAAGUGAAAAUCAGCAGCAGCGUUGGCGGCGCAGAAAA
....(((...........(((.....)))...(((((.(((((((((((((((.(((.........(((((((....)))))))))).)))))).))))))))).)))))..)))..... (-33.40 = -33.16 +  -0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:38 2006