Locus 4660

Sequence ID 3L_DroMel_CAF1
Location 13,192,508 – 13,192,660
Length 152
Max. P 0.971744
window7327 window7328 window7329

overview

Window 7

Location 13,192,508 – 13,192,620
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.04
Mean single sequence MFE -31.74
Consensus MFE -25.98
Energy contribution -25.66
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -2.09
Structure conservation index 0.82
SVM decision value 1.68
SVM RNA-class probability 0.971744
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13192508 112 + 23771897
-----CGAAAUCUUGAAAUCCGUCGCUUGCCGCUUGGCGCUUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUUUUUUCAUAUGCUCCGCGCUCUAUUUU
-----........(((((......((.....))((((((((.(((.((---.(((((((((.....))).)))))).)).)))))))))))....)))))...((.....))........ ( -32.40)
>DroSec_CAF1 43774 111 + 1
-----CGAAAUCUUGAAAUCCGUCGCUUGCCGCUUGGCGCUUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGCUCCGCGCUCUAUUUC
-----.(((((..(((((......((.....))((((((((.(((.((---.(((((((((.....))).)))))).)).)))))))))))...-)))))...((.....))...))))) ( -33.20)
>DroSim_CAF1 42186 111 + 1
-----CGAAAUCUUGAAAUCCGUCGCUUGCCGCUUGGCGCUUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGCUCCGCGCUCUAUUUC
-----.(((((..(((((......((.....))((((((((.(((.((---.(((((((((.....))).)))))).)).)))))))))))...-)))))...((.....))...))))) ( -33.20)
>DroEre_CAF1 47459 104 + 1
-----CGAAAUCUCGAAAUCCGUCUUUU-------GGCGCUUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGCUGCGCGCUCUAUUUC
-----.(((((...((((........((-------((((((.(((.((---.(((((((((.....))).)))))).)).)))))))))))...-))))....((.....))...))))) ( -31.10)
>DroYak_CAF1 43525 112 + 1
AAUCUCGAAAUCUUGAAAUCCGUCGCUU-------GGCGCUUGACUCUUGUUGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGUUCCGCGCUCUAUUUC
......(((....(((((........((-------((((((.(((.((....(((((((((.....))).)))))).)).)))))))))))...-)))))....)))............. ( -28.80)
>consensus
_____CGAAAUCUUGAAAUCCGUCGCUUGCCGCUUGGCGCUUGACUCU___UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU_UUUCAUAUGCUCCGCGCUCUAUUUC
......(((((...((...................((((((.(((.((....(((((((((.....))).)))))).)).)))))))))..............((.....)))).))))) (-25.98 = -25.66 +  -0.32)

alignment

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secondary structure

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Window 8

Location 13,192,508 – 13,192,620
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.04
Mean single sequence MFE -32.04
Consensus MFE -24.03
Energy contribution -25.43
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.75
SVM decision value 0.44
SVM RNA-class probability 0.738858
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13192508 112 - 23771897
AAAAUAGAGCGCGGAGCAUAUGAAAAAAAUUGGCGCUGACACUGACAAGUCGUGUGAAGCACACCUGCA---AGAGUCAAGCGCCAAGCGGCAAGCGACGGAUUUCAAGAUUUCG-----
......((((.....))...(((((....(((((((((((.((..((.((.(((.....))))).))..---)).))).))))))))((.....))......))))).....)).----- ( -31.30)
>DroSec_CAF1 43774 111 - 1
GAAAUAGAGCGCGGAGCAUAUGAAA-AAAUUGGCGCUGACACUGACAAGUCGUGUGAAGCACACCUGCA---AGAGUCAAGCGCCAAGCGGCAAGCGACGGAUUUCAAGAUUUCG-----
(((((...((.....))...(((((-...(((((((((((.((..((.((.(((.....))))).))..---)).))).))))))))((.....))......)))))..))))).----- ( -34.10)
>DroSim_CAF1 42186 111 - 1
GAAAUAGAGCGCGGAGCAUAUGAAA-AAAUUGGCGCUGACACUGACAAGUCGUGUGAAGCACACCUGCA---AGAGUCAAGCGCCAAGCGGCAAGCGACGGAUUUCAAGAUUUCG-----
(((((...((.....))...(((((-...(((((((((((.((..((.((.(((.....))))).))..---)).))).))))))))((.....))......)))))..))))).----- ( -34.10)
>DroEre_CAF1 47459 104 - 1
GAAAUAGAGCGCGCAGCAUAUGAAA-AAAUUGGCGCUGACACUGACAAGUCGUGUGAAGCACACCUGCA---AGAGUCAAGCGCC-------AAAAGACGGAUUUCGAGAUUUCG-----
(((((.((((.....))........-...(((((((((((.((..((.((.(((.....))))).))..---)).))).))))))-------))..........))...))))).----- ( -30.40)
>DroYak_CAF1 43525 112 - 1
GAAAUAGAGCGCGGAACAUAUGAAA-AAAUUGGCGCUGACACUGACAAGUCGUGUGAAGCACACCUGCAACAAGAGUCAAGCGCC-------AAGCGACGGAUUUCAAGAUUUCGAGAUU
(((((....(((........(....-)..(((((((((((.((........(((((...)))))........)).))).))))))-------)))))....))))).............. ( -30.29)
>consensus
GAAAUAGAGCGCGGAGCAUAUGAAA_AAAUUGGCGCUGACACUGACAAGUCGUGUGAAGCACACCUGCA___AGAGUCAAGCGCCAAGCGGCAAGCGACGGAUUUCAAGAUUUCG_____
(((((....(((....(....).......(((((((((((.((........(((((...)))))........)).))).)))))))).......)))....))))).............. (-24.03 = -25.43 +   1.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,192,543 – 13,192,660
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.04
Mean single sequence MFE -32.36
Consensus MFE -27.87
Energy contribution -28.15
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -1.50
Structure conservation index 0.86
SVM decision value 0.77
SVM RNA-class probability 0.846949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13192543 117 + 23771897
UUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUUUUUUCAUAUGCUCCGCGCUCUAUUUUUUCGAGUUUUGUGGCAUAGACAAAGCCAUGGCAGGCAUUU
(((((.((---.(((((((((.....))).)))))).)).))))).(((....(((.((.(((((..((.((((.........))))..))..))))))).)))((....)).))).... ( -34.70)
>DroSec_CAF1 43809 115 + 1
UUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGCUCCGCGCUCUAUUUCUUCGAGUUUUGUGGCAUAGACAAAG-CAUGGCAGACAUUU
(((((.((---.(((((((((.....))).)))))).)).))))).((((.(((-(.((.(((((..((.((((.........))))..))..))))))).))))-..))))........ ( -33.40)
>DroSim_CAF1 42221 115 + 1
UUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGCUCCGCGCUCUAUUUCUUCGAGUUUUGUGGCAUAGACAAAG-CAUGGCAGACAUUU
(((((.((---.(((((((((.....))).)))))).)).))))).((((.(((-(.((.(((((..((.((((.........))))..))..))))))).))))-..))))........ ( -33.40)
>DroEre_CAF1 47487 115 + 1
UUGACUCU---UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGCUGCGCGCUCUAUUUCUUCGAGUUUUGUGGCUUAGACAAAG-CAUGGCAGGCAUUU
.((((.((---.(((((((((.....))).)))))).)).))))((((((.(((-(.((.((.((..((.((((.........))))..))..)).)))).))))-..))))..)).... ( -32.30)
>DroYak_CAF1 43558 118 + 1
UUGACUCUUGUUGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU-UUUCAUAUGUUCCGCGCUCUAUUUCUUUGAGUUUUGUGGCAUGGACAAAG-CAAAGCAGGCAUUU
......((((((((..(((((...)))))...(((((.(((((((((...((..-......))....)))((((.........))))....)))))).))))).)-))..)))))..... ( -28.00)
>consensus
UUGACUCU___UGCAGGUGUGCUUCACACGACUUGUCAGUGUCAGCGCCAAUUU_UUUCAUAUGCUCCGCGCUCUAUUUCUUCGAGUUUUGUGGCAUAGACAAAG_CAUGGCAGGCAUUU
(((((.((....(((((((((.....))).)))))).)).))))).((((..........(((((..((.((((.........))))..))..)))))..........))))........ (-27.87 = -28.15 +   0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:55 2006