Locus 5349

Sequence ID 2R_DroMel_CAF1
Location 17,289,606 – 17,289,732
Length 126
Max. P 0.980429
window8547 window8548 window8549 window8550

overview

Window 7

Location 17,289,606 – 17,289,706
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.19
Mean single sequence MFE -30.25
Consensus MFE -18.21
Energy contribution -18.27
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -3.66
Structure conservation index 0.60
SVM decision value 1.86
SVM RNA-class probability 0.980429
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289606 100 + 20766785
AGGAGUCCUUUUUAUUUGACGCUGCCACUGCUGC-----------------AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGU---
.((((.............((((.((...((((((-----------------...))))))..))))))(((((((((((.....)))))))))))........))))..........--- ( -29.70)
>DroPse_CAF1 15948 85 + 1
GGAAGUCCC-UUUAUUUGGGGCUG-------------------------------CAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUCCAUU---
(((((((((-.......))))))(-------------------------------((....)))(((.(((((((((((.....)))))))))))....)))..)))..........--- ( -30.10)
>DroSim_CAF1 15680 100 + 1
AGGAGUCCUUUUUAUUUGGCGCUGCCACUGCUGC-----------------AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAUUUGUUUUUCAUUUUCCAUUUUUCAGU---
.((((.............(((((((.......))-----------------)))))...((((.....((((.((((((.....)))))).))))....))))))))..........--- ( -28.10)
>DroEre_CAF1 9713 100 + 1
UGGAGUCCUUUUUAUUUGGCGCUGCCACUGCUGC-----------------AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGU---
(((((.............(((((((.......))-----------------)))))...((((.....(((((((((((.....)))))))))))....))))))))).........--- ( -31.60)
>DroAna_CAF1 1158 117 + 1
---AGUCCCUUUUAUUUGGCUCUGCUACUGCCACUGCCACUGCCACCGCCUGGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGCGAU
---.............((((...((....))....)))).......(((.(((((((....)))))..(((((((((((.....)))))))))))..................))))).. ( -31.90)
>DroPer_CAF1 15853 85 + 1
GGAAGUCCC-UUUAUUUGGGGCUG-------------------------------CAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUCCAUU---
(((((((((-.......))))))(-------------------------------((....)))(((.(((((((((((.....)))))))))))....)))..)))..........--- ( -30.10)
>consensus
AGGAGUCCCUUUUAUUUGGCGCUGCCACUGCUGC_________________AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGU___
................(((.(((((.............................)))))((((.....(((((((((((.....)))))))))))....)))).........)))..... (-18.21 = -18.27 +   0.06)

alignment

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secondary structure

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Window 8

Location 17,289,606 – 17,289,706
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.19
Mean single sequence MFE -25.43
Consensus MFE -16.96
Energy contribution -17.24
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -2.52
Structure conservation index 0.67
SVM decision value 1.25
SVM RNA-class probability 0.936540
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289606 100 - 20766785
---ACUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU-----------------GCAGCAGUGGCAGCGUCAAAUAAAAAGGACUCCU
---..........(((...........(((((((((.....)))))))))......((((((((((...-----------------)))))))).))...(((..........)))))). ( -26.60)
>DroPse_CAF1 15948 85 - 1
---AAUGGAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUG-------------------------------CAGCCCCAAAUAAA-GGGACUUCC
---...((((..((.(.((((......(((((((((.....))))))))).......))))..).-------------------------------))..(((.......-)))..)))) ( -18.52)
>DroSim_CAF1 15680 100 - 1
---ACUGAAAAAUGGAAAAUGAAAAACAAAUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU-----------------GCAGCAGUGGCAGCGCCAAAUAAAAAGGACUCCU
---..........(((.(((((...........)))))((((.((((((.........))))))(((((-----------------((.......)))))))..........))))))). ( -24.40)
>DroEre_CAF1 9713 100 - 1
---ACUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU-----------------GCAGCAGUGGCAGCGCCAAAUAAAAAGGACUCCA
---.........((((.((((......(((((((((.....))))))))).......))))...(((((-----------------((.......)))))))..............)))) ( -27.92)
>DroAna_CAF1 1158 117 - 1
AUCGCUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCCAGGCGGUGGCAGUGGCAGUGGCAGUAGCAGAGCCAAAUAAAAGGGACU---
.((.((......(((............(((((((((.....)))))))))......(((((((..(((((.((....))..)))).)..))))).))....)))......)).))..--- ( -36.60)
>DroPer_CAF1 15853 85 - 1
---AAUGGAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUG-------------------------------CAGCCCCAAAUAAA-GGGACUUCC
---...((((..((.(.((((......(((((((((.....))))))))).......))))..).-------------------------------))..(((.......-)))..)))) ( -18.52)
>consensus
___ACUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU_________________GCAGCAGUGGCAGCGCCAAAUAAAAAGGACUCCC
............(((..((((......(((((((((.....))))))))).......))))(((((.............................))))).)))................ (-16.96 = -17.24 +   0.28)

alignment

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secondary structure

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Window 9

Location 17,289,640 – 17,289,732
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.70
Mean single sequence MFE -22.21
Consensus MFE -17.62
Energy contribution -17.79
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.79
SVM decision value 1.30
SVM RNA-class probability 0.939161
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289640 92 + 20766785
-----------AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGU-----GUU---------U---UUUUCGUUGUUUGCUUGUUGAU
-----------((((.(((((((.(((.(((((((((((.....)))))))))))....)))....(((......))-----)..---------.---....)))))))))))....... ( -22.10)
>DroPse_CAF1 15971 94 + 1
---------------CAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUCCAUU-----U------GCCAUUUUUCCCCCCUUGUUUGCUUGUUGAU
---------------((((((.(((((.(((((((((((.....)))))))))))....)))....((.........-----)------)....................)))))))).. ( -19.30)
>DroSim_CAF1 15714 92 + 1
-----------AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAUUUGUUUUUCAUUUUCCAUUUUUCAGU-----GUU---------U---UUUUCGUUGUUUGCUUGUUGAU
-----------((((.(((((((.(((.((((.((((((.....)))))).))))....)))....(((......))-----)..---------.---....)))))))))))....... ( -18.90)
>DroEre_CAF1 9747 92 + 1
-----------AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGU-----GUU---------U---UUUUCGUUGUUUGCUUGUUGAU
-----------((((.(((((((.(((.(((((((((((.....)))))))))))....)))....(((......))-----)..---------.---....)))))))))))....... ( -22.10)
>DroAna_CAF1 1195 120 + 1
UGCCACCGCCUGGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGCGAUGUGUUUUUUGUGUUUUUUGUUUCGUUGUUUGCUUGUUGAU
.((((.....)))).((((((.(((((.(((((((((((.....)))))))))))....)))...........((((((......................))))))...)))))))).. ( -31.55)
>DroPer_CAF1 15876 94 + 1
---------------CAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUCCAUU-----U------GCCAUUUUUCCCCCGUUGUUUGCUUGUUGAU
---------------((((((.(((((.(((((((((((.....)))))))))))....)))....((.........-----)------)....................)))))))).. ( -19.30)
>consensus
___________AGCGCAGCAAUGCGUGUAUAAUUGCUCAGACAAUGAGCAAUUGUUUUUCAUUUUCCAUUUUUCAGU_____GUU_________U___UUUUCGUUGUUUGCUUGUUGAU
...............((((((.(((((.(((((((((((.....)))))))))))....)))....((.....................................))...)))))))).. (-17.62 = -17.79 +   0.17)

alignment

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secondary structure

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Window 0

Location 17,289,640 – 17,289,732
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.70
Mean single sequence MFE -15.77
Consensus MFE -12.60
Energy contribution -12.77
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.80
SVM decision value 0.47
SVM RNA-class probability 0.747842
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289640 92 - 20766785
AUCAACAAGCAAACAACGAAAA---A---------AAC-----ACUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU-----------
.......(((............---.---------...-----........................(((((((((.....)))))))))......(((....))))))----------- ( -15.10)
>DroPse_CAF1 15971 94 - 1
AUCAACAAGCAAACAAGGGGGGAAAAAUGGC------A-----AAUGGAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUG---------------
.......(((((.(......)........((------.-----..(....)................(((((((((.....)))))))))......)).))))).--------------- ( -13.40)
>DroSim_CAF1 15714 92 - 1
AUCAACAAGCAAACAACGAAAA---A---------AAC-----ACUGAAAAAUGGAAAAUGAAAAACAAAUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU-----------
.......(((............---.---------...-----...........................((((((.....)))))).........(((....))))))----------- ( -12.30)
>DroEre_CAF1 9747 92 - 1
AUCAACAAGCAAACAACGAAAA---A---------AAC-----ACUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU-----------
.......(((............---.---------...-----........................(((((((((.....)))))))))......(((....))))))----------- ( -15.10)
>DroAna_CAF1 1195 120 - 1
AUCAACAAGCAAACAACGAAACAAAAAACACAAAAAACACAUCGCUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCCAGGCGGUGGCA
.......................................(((((((......(((............(((((((((.....))))))))).....((((....))))))))))))))... ( -25.10)
>DroPer_CAF1 15876 94 - 1
AUCAACAAGCAAACAACGGGGGAAAAAUGGC------A-----AAUGGAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUG---------------
.......(((((....((...(........)------.-----..))....................(((((((((.....))))))))).........))))).--------------- ( -13.60)
>consensus
AUCAACAAGCAAACAACGAAAA___A_________AAC_____ACUGAAAAAUGGAAAAUGAAAAACAAUUGCUCAUUGUCUGAGCAAUUAUACACGCAUUGCUGCGCU___________
.......(((((........................................(....).........(((((((((.....))))))))).........)))))................ (-12.60 = -12.77 +   0.17)

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 11:42:49 2006