Locus 423

Sequence ID 2R_DroMel_CAF1
Location 2,472,447 – 2,472,569
Length 122
Max. P 0.868180
window824 window825 window826

overview

Window 4

Location 2,472,447 – 2,472,543
Length 96
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 71.33
Mean single sequence MFE -26.45
Consensus MFE -14.03
Energy contribution -14.42
Covariance contribution 0.39
Combinations/Pair 1.19
Mean z-score -1.46
Structure conservation index 0.53
SVM decision value 0.06
SVM RNA-class probability 0.565350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2472447 96 - 20766785
UUUUCCUAACGGGAAACCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCGCGCUUGGCUUAGACGCUCCAAAGUUU--AUUCACGCAUGUGGAAGG----------
((((((....)))))).(((((..((((((.((......))))))))....(((..(((..(((((........))))--).)))))).)))))....---------- ( -29.40)
>DroVir_CAF1 29468 93 - 1
AUCUACUAACGGCAU--UCGCAACUAGCU-GCAAUUAAAUGCGGCUAAUUUC-AAUUAGAUU-------GCAAAGUCACAGU----CCGAGUCCAAAGUUUACCAGCU
..........((.((--(((....(((((-(((......)))))))).....-.....((((-------(........))))----)))))))).............. ( -20.90)
>DroSec_CAF1 26670 96 - 1
UUUUCCUAACGGGAUGUCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCGCGCUUGGCUUAGACGCUCCAAAGUUU--AUUCACGCAUGUGGAAGG----------
..((((....))))..((((((..((((((.((......))))))))....(((..(((..(((((........))))--).)))))).))))))...---------- ( -29.40)
>DroSim_CAF1 26985 96 - 1
UUUUCCUAACGGGAUGCCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCGCGCUUGGCUUAGACGCUCCAAAGUUU--AUUCACGCAUGUGGAAGG----------
..((((....))))...(((((..((((((.((......))))))))....(((..(((..(((((........))))--).)))))).)))))....---------- ( -27.90)
>DroEre_CAF1 25718 76 - 1
UUUUCCUAACGGGAUACCCGCAGUUAGCCGGCAACUAAAUGCGGCUAAUUCCCAAG-------------------UUU--AUCCACGCAUGUGGAC-U----------
..........((((...(((((.((((.......)))).))))).....))))...-------------------...--.(((((....))))).-.---------- ( -22.50)
>DroYak_CAF1 25668 96 - 1
UUUUCCUAACGGGAUGCCCGCAGAUAGCCGGCAAAUAAACGCGGCUAAUUCCCAAGUUGCUGAGACGCCCCAAUGUUU--AUCCACGCAUGUGGAUGA----------
..........(((.((((.((.....)).)))).......((((((........))))))........))).....((--((((((....))))))))---------- ( -28.60)
>consensus
UUUUCCUAACGGGAUGCCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCCCAAUUGGCUUAGACGCUCCAAAGUUU__AUUCACGCAUGUGGAAGG__________
.........(((.....)))....(((((.(((......))))))))..................................(((((....)))))............. (-14.03 = -14.42 +   0.39) 

alignment

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secondary structure

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Window 5

Location 2,472,465 – 2,472,569
Length 104
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 74.79
Mean single sequence MFE -25.77
Consensus MFE -13.99
Energy contribution -16.05
Covariance contribution 2.06
Combinations/Pair 1.10
Mean z-score -1.86
Structure conservation index 0.54
SVM decision value 0.86
SVM RNA-class probability 0.868180
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2472465 104 + 20766785
-AAACUUUGGAGCGUCUAAGCCAAGCGCGAAUUAGCCGCAUUUAGUUGCCGGCUAUCUGCGGGUUUCCCGUUAGGAAAAACAAUUUCAGAAAUGAAAUUAGCAAA
-.......((((((.((......)))))....((((((((......)).)))))))))(((..(((((.....)))))..)(((((((....))))))).))... ( -30.30)
>DroVir_CAF1 29493 83 + 1
GUGACUUUGC-------AAUCUAAUU-GAAAUUAGCCGCAUUUAAUUGC-AGCUAGUUGCGA--AUGCCGUUAGUAGAUAUU---UU----AUUUAAU----AUU
.(((((((((-------..((.....-))(((((((.(((......)))-.)))))))))))--)....))))...((((((---..----....)))----))) ( -16.30)
>DroSec_CAF1 26688 104 + 1
-AAACUUUGGAGCGUCUAAGCCAAGCGCGAAUUAGCCGCAUUUAGUUGCCGGCUAUCUGCGGACAUCCCGUUAGGAAAAAAAAUUUCAGAAAUGAAAUUAGCAAA
-..........((((((..((...))(((...((((((((......)).))))))..))))))).(((.....))).....(((((((....))))))).))... ( -28.10)
>DroSim_CAF1 27003 104 + 1
-AAACUUUGGAGCGUCUAAGCCAAGCGCGAAUUAGCCGCAUUUAGUUGCCGGCUAUCUGCGGGCAUCCCGUUAGGAAAAACAAUUUCAGAAAUGAAAUUAGCAAA
-..........((((.....((.((((((...((((((((......)).))))))..)))(((...)))))).))....))(((((((....))))))).))... ( -29.90)
>DroEre_CAF1 25735 84 + 1
-AAA-------------------CUUGGGAAUUAGCCGCAUUUAGUUGCCGGCUAACUGCGGGUAUCCCGUUAGGAAAAACUAUUUCAGA-AUGAAAUUAGCAAA
-...-------------------...((((..((.(((((.(((((.....))))).))))).))))))((((.........(((((...-..)))))))))... ( -22.60)
>DroYak_CAF1 25686 103 + 1
-AAACAUUGGGGCGUCUCAGCAACUUGGGAAUUAGCCGCGUUUAUUUGCCGGCUAUCUGCGGGCAUCCCGUUAGGAAAAACUAUUUCAGA-AUGAAAUUAGCAAA
-.......(.(((.((((((....))))))....))).)(((.(((((((.((.....)).)))....((((..((((.....))))..)-))))))).)))... ( -27.40)
>consensus
_AAACUUUGGAGCGUCUAAGCCAAGCGCGAAUUAGCCGCAUUUAGUUGCCGGCUAUCUGCGGGCAUCCCGUUAGGAAAAACAAUUUCAGA_AUGAAAUUAGCAAA
................................((((((((......))).))))).((((((.....))).)))........((((((....))))))....... (-13.99 = -16.05 +   2.06) 

alignment

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secondary structure

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dotplot

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Window 6

Location 2,472,465 – 2,472,569
Length 104
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 74.79
Mean single sequence MFE -23.57
Consensus MFE -12.87
Energy contribution -15.23
Covariance contribution 2.36
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.55
SVM decision value 0.42
SVM RNA-class probability 0.730751
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2472465 104 - 20766785
UUUGCUAAUUUCAUUUCUGAAAUUGUUUUUCCUAACGGGAAACCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCGCGCUUGGCUUAGACGCUCCAAAGUUU-
(((((((((((((....)))))))).((((((....))))))...)))))((((((.((......))))))))....(((((......)).)))..........- ( -28.60)
>DroVir_CAF1 29493 83 - 1
AAU----AUUAAAU----AA---AAUAUCUACUAACGGCAU--UCGCAACUAGCU-GCAAUUAAAUGCGGCUAAUUUC-AAUUAGAUU-------GCAAAGUCAC
...----.......----..---.............(((.(--(.((((.(((((-(((......))))))))...((-.....))))-------)).))))).. ( -15.90)
>DroSec_CAF1 26688 104 - 1
UUUGCUAAUUUCAUUUCUGAAAUUUUUUUUCCUAACGGGAUGUCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCGCGCUUGGCUUAGACGCUCCAAAGUUU-
(((((.(((((((....)))))))....((((....)))).....)))))((((((.((......))))))))....(((((......)).)))..........- ( -25.50)
>DroSim_CAF1 27003 104 - 1
UUUGCUAAUUUCAUUUCUGAAAUUGUUUUUCCUAACGGGAUGCCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCGCGCUUGGCUUAGACGCUCCAAAGUUU-
...((.(((((((....)))))))((((((((....)))).((((((..(((((((.((......))))))).))..)))...)))..))))))..........- ( -27.40)
>DroEre_CAF1 25735 84 - 1
UUUGCUAAUUUCAU-UCUGAAAUAGUUUUUCCUAACGGGAUACCCGCAGUUAGCCGGCAACUAAAUGCGGCUAAUUCCCAAG-------------------UUU-
..(((..(((((..-...))))).((..((((....)))).))..)))((((((((.((......)))))))))).......-------------------...- ( -20.60)
>DroYak_CAF1 25686 103 - 1
UUUGCUAAUUUCAU-UCUGAAAUAGUUUUUCCUAACGGGAUGCCCGCAGAUAGCCGGCAAAUAAACGCGGCUAAUUCCCAAGUUGCUGAGACGCCCCAAUGUUU-
...((((.((((..-...))))))))..........(((.((((.((.....)).)))).......((((((........))))))........))).......- ( -23.40)
>consensus
UUUGCUAAUUUCAU_UCUGAAAUAGUUUUUCCUAACGGGAUGCCCGCAGAUAGCCGGCAACUAAAUGCGGCUAAUUCCCAAUUGGCUUAGACGCUCCAAAGUUU_
(((((..((((((....)))))).....((((....)))).....)))))(((((.(((......))))))))................................ (-12.87 = -15.23 +   2.36) 

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 09:38:17 2006