Locus 3758

Sequence ID 3L_DroMel_CAF1
Location 10,879,459 – 10,879,581
Length 122
Max. P 0.870290
window5862 window5863 window5864

overview

Window 2

Location 10,879,459 – 10,879,549
Length 90
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 79.38
Mean single sequence MFE -24.34
Consensus MFE -10.09
Energy contribution -10.62
Covariance contribution 0.53
Combinations/Pair 1.13
Mean z-score -2.43
Structure conservation index 0.41
SVM decision value 0.02
SVM RNA-class probability 0.543307
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10879459 90 + 23771897
GGAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGCAAGAGCAGCCAAAAGGCCAA--CCAGC
((.....(((((((((....(((((((.....)))))))(((.....))))))))))))....((....)).(((....)))...--))... ( -27.90)
>DroPse_CAF1 7711 84 + 1
GAAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUUGACUCCCGAGGAG---UCAGUCGC----ACAACCAG-AGCCCAAAACCAAA
.......((.((((....(((((((((.....)))))))))((((((...))))---))...)))----))).....-.............. ( -21.10)
>DroSec_CAF1 11779 86 + 1
GGAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUGGACUCCCGAGACGCAGCGAGCAGC----CCAACCAAAAGGCCAA--CCAGC
((.....(((((((((...((((((((.....))))))))((....))..)))))))))....((----(.........)))...--))... ( -27.00)
>DroEre_CAF1 6915 85 + 1
GGAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGUU-----GGCCAAAAGGCCAA--CCAGC
.......(((((((((....(((((((.....)))))))(((.....)))))))))))).((.(((-----((((....))))))--)..)) ( -34.10)
>DroAna_CAF1 1824 78 + 1
GGAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAACCAAAACCG-----AAACAAAAAACC---------
((........((((((....(((((((.....)))))))(((.....))))))))).......)).-----............--------- ( -14.86)
>DroPer_CAF1 7231 84 + 1
GAAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUUGACUCCCGAGGAG---UCAGUCGC----ACAACCAG-AGCCCAAAACCAAA
.......((.((((....(((((((((.....)))))))))((((((...))))---))...)))----))).....-.............. ( -21.10)
>consensus
GGAACAAUGCUGCGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCCAGCAGC_____CAACCAAAAGGCCAA__CCAGC
........(((((......((((((((.....))))))))...((....)).........)))))........................... (-10.09 = -10.62 +   0.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,879,471 – 10,879,581
Length 110
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 79.84
Mean single sequence MFE -29.58
Consensus MFE -16.85
Energy contribution -18.35
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.57
SVM decision value 0.63
SVM RNA-class probability 0.805997
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10879471 110 + 23771897
CGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGCAAGAGCAGCCAAAAGGCCAACCAGC----CAGCUAUCGGGCCAAAGCCCAAAGGAGUCG----AA
........(((((((.....)))))))((((((((........(((..((.((....)).(((....)))......))----..)))...((((....))))...)))))))----). ( -38.30)
>DroSec_CAF1 11791 110 + 1
CGUUAAAGGUAAUUGUUUGUCAAUUACUGGACUCCCGAGACGCAGCGAGCAGC----CCAACCAAAAGGCCAACCAGCCAGCCAGCUAUCGGUCCAAAACCCAAAGGAGUCG----AA
.......((((((((.....)))))))).((((((.((...((.((.....))----..........(((......))).....))..))(((.....)))....)))))).----.. ( -27.10)
>DroSim_CAF1 7822 101 + 1
CGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGCA-GACCAACCAAAAGGCCAACCAGC------------GGGCCAAAACCCAAAGGAGUCG----AA
........(((((((.....)))))))((((((((.........((.....)).-............((((.......------------.))))..........)))))))----). ( -29.20)
>DroEre_CAF1 6927 101 + 1
CGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGUU-----GGCCAAAAGGCCAACCAGCA---------ACGGGCCAAAACCCAAAGGAGUCGG---AA
.......((((((((.....))))))))(((((((.............((.(((-----((((....)))))))..)).---------..(((......)))...))))))).---.. ( -37.60)
>DroYak_CAF1 7663 112 + 1
CGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGCG--AGCAGCCAAAAGGCCAACCAGCAAACCAGCAAACGGGCCAAAACCCAAAGGAGUCG----AA
........(((((((.....)))))))((((((((......((.((.....)).--.))........((((.....((......)).....))))..........)))))))----). ( -34.00)
>DroAna_CAF1 1836 91 + 1
CGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAACCAAAACCG-----AAACAAAAAACC----------------------CGAAACCCCAAAAGACUCUGGCCAA
.(((...((((((((.....))))).((((.....))))...........))).-----.)))........----------------------.......(((........))).... ( -11.30)
>consensus
CGUUAAAGGUAAUUGUUUGUCAAUUACUCGACUCCCGAGACGCAGCGAGCAGCA____CAACCAAAAGGCCAACCAGC___________CGGGCCAAAACCCAAAGGAGUCG____AA
.......((((((((.....)))))))).((((((......((.....)).................((((....................))))..........))))))....... (-16.85 = -18.35 +   1.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,879,471 – 10,879,581
Length 110
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 79.84
Mean single sequence MFE -36.72
Consensus MFE -21.19
Energy contribution -21.92
Covariance contribution 0.72
Combinations/Pair 1.22
Mean z-score -2.32
Structure conservation index 0.58
SVM decision value 0.87
SVM RNA-class probability 0.870290
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10879471 110 - 23771897
UU----CGACUCCUUUGGGCUUUGGCCCGAUAGCUG----GCUGGUUGGCCUUUUGGCUGCUCUUGCUGCUCGCUGCGUCUCGGGAGUCGAGUAAUUGACAAACAAUUACCUUUAACG
.(----((((((((((((((....))))))((((.(----((.....((((....))))((....)).))).))))......)))))))))(((((((.....)))))))........ ( -43.70)
>DroSec_CAF1 11791 110 - 1
UU----CGACUCCUUUGGGUUUUGGACCGAUAGCUGGCUGGCUGGUUGGCCUUUUGGUUGG----GCUGCUCGCUGCGUCUCGGGAGUCCAGUAAUUGACAAACAAUUACCUUUAACG
..----.(((((((...((((...))))(((.((.(((.(((.(.(..(((....)))..)----.).))).))))))))..)))))))..(((((((.....)))))))........ ( -37.70)
>DroSim_CAF1 7822 101 - 1
UU----CGACUCCUUUGGGUUUUGGCCC------------GCUGGUUGGCCUUUUGGUUGGUC-UGCUGCUCGCUGCGUCUCGGGAGUCGAGUAAUUGACAAACAAUUACCUUUAACG
.(----((((((((..((((....))))------------((.((..((((....))))..))-.)).((.....)).....)))))))))(((((((.....)))))))........ ( -36.90)
>DroEre_CAF1 6927 101 - 1
UU---CCGACUCCUUUGGGUUUUGGCCCGU---------UGCUGGUUGGCCUUUUGGCC-----AACUGCUCGCUGCGUCUCGGGAGUCGAGUAAUUGACAAACAAUUACCUUUAACG
..---.((((((((..((((....))))((---------.(((((((((((....))))-----)))))...)).)).....)))))))).(((((((.....)))))))........ ( -40.90)
>DroYak_CAF1 7663 112 - 1
UU----CGACUCCUUUGGGUUUUGGCCCGUUUGCUGGUUUGCUGGUUGGCCUUUUGGCUGCU--CGCUGCUCGCUGCGUCUCGGGAGUCGAGUAAUUGACAAACAAUUACCUUUAACG
.(----((((((((..((((....))))((..((.(((..((.(((.((((....)))))))--.)).))).)).)).....)))))))))(((((((.....)))))))........ ( -41.30)
>DroAna_CAF1 1836 91 - 1
UUGGCCAGAGUCUUUUGGGGUUUCG----------------------GGUUUUUUGUUU-----CGGUUUUGGUUGCGUCUCGGGAGUCGAGUAAUUGACAAACAAUUACCUUUAACG
....(((((....))))).(((..(----------------------(((...((((((-----...((((((.......))))))(((((....)))))))))))..))))..))). ( -19.80)
>consensus
UU____CGACUCCUUUGGGUUUUGGCCCG___________GCUGGUUGGCCUUUUGGCUG____CGCUGCUCGCUGCGUCUCGGGAGUCGAGUAAUUGACAAACAAUUACCUUUAACG
......((((((((..((((....))))...................((((....)))).......................)))))))).(((((((.....)))))))........ (-21.19 = -21.92 +   0.72)

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 11:05:58 2006