Locus 2577

Sequence ID 2R_DroMel_CAF1
Location 9,092,705 – 9,092,840
Length 135
Max. P 0.997529
window4252 window4253 window4254 window4255

overview

Window 2

Location 9,092,705 – 9,092,821
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.25
Mean single sequence MFE -25.11
Consensus MFE -24.91
Energy contribution -24.77
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -3.82
Structure conservation index 0.99
SVM decision value 2.88
SVM RNA-class probability 0.997529
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9092705 116 + 20766785
-AAUCCCAAUCCGCAUCUCCAUCUCGCUCUCGUGUUGCCAAUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCU---CGUUAAUUGUUGUGGCUUUUUAAUUGGACCCUUUUUUUC
-..................((...(((....))).))((((((((((..((((....(((((((......))))))).---((.....))..))))..))))))))))............ ( -25.00)
>DroPse_CAF1 2338 102 + 1
------------------CCAUCUCUCUCUCGUGUUGCCAAUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCUCCCCGUUAAUUGUCGUGGUUUUUUAAUUGGACCCUUUUUUGC
------------------...................((((((((((..((((....(((((((......))))))).....(........)))))..))))))))))............ ( -25.90)
>DroGri_CAF1 3159 98 + 1
------------------CCCUGUCGCUCUCAUGUUGCCAAUUAAAAUUCCAUUUAUGCCAAGUUAACUCACUUGGCU---CGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUCG-G
------------------...................((((((((((..((((....(((((((......))))))).---...........))))..))))))))))..........-. ( -23.79)
>DroWil_CAF1 4013 92 + 1
------------------------AGCUCUCGUGUUGCCAAUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCU---CGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUUUU-
------------------------.............((((((((((..((((....(((((((......))))))).---((.....))..))))..))))))))))...........- ( -25.30)
>DroAna_CAF1 3104 116 + 1
UAUACACUAUUCGC-UCUCCACCUCUCUCUCGUGUUGCCAAUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCU---CGUUAAUUGUUGUGGCUUUUUAAUUGGACCCUUUUUUUC
...((((.......-................))))..((((((((((..((((....(((((((......))))))).---((.....))..))))..))))))))))............ ( -24.80)
>DroPer_CAF1 3887 102 + 1
------------------CCAUCUCUCUCUCGUGUUGCCAAUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCUCCCCGUUAAUUGUCGUGGUUUUUUAAUUGGACCCUUUUUUGC
------------------...................((((((((((..((((....(((((((......))))))).....(........)))))..))))))))))............ ( -25.90)
>consensus
__________________CCAUCUCGCUCUCGUGUUGCCAAUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCU___CGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUUUUC
.....................................((((((((((..((((....(((((((......)))))))....((.....))..))))..))))))))))............ (-24.91 = -24.77 +  -0.14)

alignment

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secondary structure

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Window 3

Location 9,092,705 – 9,092,821
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.25
Mean single sequence MFE -26.42
Consensus MFE -24.37
Energy contribution -24.53
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -3.21
Structure conservation index 0.92
SVM decision value 2.25
SVM RNA-class probability 0.991102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9092705 116 - 20766785
GAAAAAAAGGGUCCAAUUAAAAAGCCACAACAAUUAACG---AGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAUUGGCAACACGAGAGCGAGAUGGAGAUGCGGAUUGGGAUU-
............((((((((((..((((..(.......)---.(((((((......)))))))....))))..))))))))))(((..((....(........)...))..))).....- ( -29.20)
>DroPse_CAF1 2338 102 - 1
GCAAAAAAGGGUCCAAUUAAAAAACCACGACAAUUAACGGGGAGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAUUGGCAACACGAGAGAGAGAUGG------------------
..........(.((((((((((..((((..(........)...(((((((......)))))))....))))..)))))))))))....(....)........------------------ ( -26.10)
>DroGri_CAF1 3159 98 - 1
C-CGAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACG---AGCCAAGUGAGUUAACUUGGCAUAAAUGGAAUUUUAAUUGGCAACAUGAGAGCGACAGGG------------------
(-(.....))(.((((((((((..(((...(.......)---.(((((((......))))))).....)))..)))))))))))..................------------------ ( -22.90)
>DroWil_CAF1 4013 92 - 1
-AAAAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACG---AGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAUUGGCAACACGAGAGCU------------------------
-.........(.((((((((((..((((..(.......)---.(((((((......)))))))....))))..)))))))))))............------------------------ ( -25.50)
>DroAna_CAF1 3104 116 - 1
GAAAAAAAGGGUCCAAUUAAAAAGCCACAACAAUUAACG---AGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAUUGGCAACACGAGAGAGAGGUGGAGA-GCGAAUAGUGUAUA
..........(.((((((((((..((((..(.......)---.(((((((......)))))))....))))..))))))))))).((((................-.......))))... ( -28.70)
>DroPer_CAF1 3887 102 - 1
GCAAAAAAGGGUCCAAUUAAAAAACCACGACAAUUAACGGGGAGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAUUGGCAACACGAGAGAGAGAUGG------------------
..........(.((((((((((..((((..(........)...(((((((......)))))))....))))..)))))))))))....(....)........------------------ ( -26.10)
>consensus
GAAAAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACG___AGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAUUGGCAACACGAGAGAGAGAUGG__________________
..........(.((((((((((..((((..(.......)....(((((((......)))))))....))))..))))))))))).................................... (-24.37 = -24.53 +   0.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,092,744 – 9,092,840
Length 96
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 80.78
Mean single sequence MFE -19.26
Consensus MFE -16.52
Energy contribution -16.27
Covariance contribution -0.25
Combinations/Pair 1.06
Mean z-score -2.02
Structure conservation index 0.86
SVM decision value 1.13
SVM RNA-class probability 0.919975
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9092744 96 + 20766785
AUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGCUUUUUAAUUGGACCCUUUUUUUCUCCUCCUGCUG-----------GCUGCUUU
(((((((..((((....(((((((......))))))).((.....))..))))..))))))).(((...........)))....((..-----------...))... ( -18.00)
>DroVir_CAF1 2824 84 + 1
AUUAAAAUUCCAUUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUCG-GAG---CUGAUG-------------------
..(((((..((((....(((((((......)))))))............))))..)))))((..(..((.....)-)..---)..)).------------------- ( -19.09)
>DroGri_CAF1 3181 102 + 1
AUUAAAAUUCCAUUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUCG-GUG---CUGGUGGUGCUGCGGCUGCUGCUC-
(((((((..((((....(((((((......)))))))............))))..))))))).(.(((......)-)).---).((..((((....)).))..)).- ( -24.99)
>DroWil_CAF1 4029 76 + 1
AUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUUUU-------------------------------
(((((((..((((....(((((((......))))))).((.....))..))))..)))))))..............------------------------------- ( -17.30)
>DroMoj_CAF1 3171 84 + 1
AUUAAAAUUCCAUUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUCG-GUG---CUGCUG-------------------
(((((((..((((....(((((((......)))))))............))))..))))))).(.(((......)-)).---).....------------------- ( -18.99)
>DroAna_CAF1 3143 91 + 1
AUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGCUUUUUAAUUGGACCCUUUUUUUCUCCUGCGCCCA-----------ACU-----
.((((((..((((....(((((((......))))))).((.....))..))))..))))))((((.(.(............).).)))-----------)..----- ( -17.20)
>consensus
AUUAAAAUUCCACUUAUGCCAAGUUAACUCACUUGGCUCGUUAAUUGUUGUGGUUUUUUAAUUGGACCCUUUUCG_GUG___CUGCUG___________________
(((((((..((((....(((((((......)))))))............))))..)))))))............................................. (-16.52 = -16.27 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,092,744 – 9,092,840
Length 96
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -19.77
Consensus MFE -14.75
Energy contribution -14.75
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.79
Structure conservation index 0.75
SVM decision value 1.36
SVM RNA-class probability 0.945930
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9092744 96 - 20766785
AAAGCAGC-----------CAGCAGGAGGAGAAAAAAAGGGUCCAAUUAAAAAGCCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAU
...((...-----------..))....(((...........))).(((((((..((((..(.......).(((((((......)))))))....))))..))))))) ( -21.50)
>DroVir_CAF1 2824 84 - 1
-------------------CAUCAG---CUC-CGAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAAUGGAAUUUUAAU
-------------------......---.((-((.....(((...........)))..............(((((((......))))))).....))))........ ( -16.20)
>DroGri_CAF1 3181 102 - 1
-GAGCAGCAGCCGCAGCACCACCAG---CAC-CGAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAAUGGAAUUUUAAU
-..((.((....)).))....((((---.((-(......))).)..........................(((((((......))))))).....)))......... ( -20.90)
>DroWil_CAF1 4029 76 - 1
-------------------------------AAAAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAU
-------------------------------..............(((((((..((((..(.......).(((((((......)))))))....))))..))))))) ( -17.70)
>DroMoj_CAF1 3171 84 - 1
-------------------CAGCAG---CAC-CGAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAAUGGAAUUUUAAU
-------------------.....(---.((-(......))).).(((((((..(((...(.......).(((((((......))))))).....)))..))))))) ( -16.40)
>DroAna_CAF1 3143 91 - 1
-----AGU-----------UGGGCGCAGGAGAAAAAAAGGGUCCAAUUAAAAAGCCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAGUGGAAUUUUAAU
-----.((-----------(((((.(............).)))))))(((((..((((..(.......).(((((((......)))))))....))))..))))).. ( -25.90)
>consensus
___________________CAGCAG___CAC_AAAAAAGGGUCCAAUUAAAAAACCACAACAAUUAACGAGCCAAGUGAGUUAACUUGGCAUAAAUGGAAUUUUAAU
..................................((((...((((.(((...........(.......).(((((((......))))))).))).)))).))))... (-14.75 = -14.75 +   0.00)

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 10:33:41 2006