Locus 2596

Sequence ID 2R_DroMel_CAF1
Location 9,165,323 – 9,165,413
Length 90
Max. P 0.970243
window4277 window4278

overview

Window 7

Location 9,165,323 – 9,165,413
Length 90
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 81.63
Mean single sequence MFE -29.23
Consensus MFE -24.52
Energy contribution -25.48
Covariance contribution 0.96
Combinations/Pair 1.08
Mean z-score -3.57
Structure conservation index 0.84
SVM decision value 1.65
SVM RNA-class probability 0.970243
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9165323 90 + 20766785
UUAUUGUGUACUGAAAAAUGCAUUUUUCAUGACAUAA--CAACGACCCGU--U-UGGCAUUGGCAGCCCGAAUUGGGUUGCCAGCCGCC-------CAUU-UC------------
...((((((..(((((((....)))))))..))))))--.........(.--.-((((..(((((((((.....)))))))))))))..-------)...-..------------ ( -30.60)
>DroPse_CAF1 34128 80 + 1
UAAUUGUGUACUGAAAAAUGCAUUUUUCAUGACACAAACCAACGACCCGGCAU-CGGCAUCGGCAUC-------G----GCCAGACCCU-------CCU----------------
...((((((..(((((((....)))))))..))))))...........(((..-..((....))...-------.----))).......-------...---------------- ( -18.30)
>DroSec_CAF1 49693 102 + 1
UUAUUGUGUACUGAAAAAUGCAUUUUUCAUGACAUAA--CAACGACCCGU--U-UGGCAUUGGCAGCCCGAAUUGGGUUGCCAGCCGCC-------CAUU-UCCCAUUUCCCAUU
...((((((..(((((((....)))))))..))))))--.........(.--.-((((..(((((((((.....)))))))))))))..-------)...-.............. ( -30.60)
>DroEre_CAF1 42561 90 + 1
UUAUUGUGUACUGAAAAAUGCAUUUUUCAUGACAUAA--CAACGACCCGU--U-UGGCAUUGGCAGCCCGAAUUGGGUUGCCAGCCGCC-------CAUU-UC------------
...((((((..(((((((....)))))))..))))))--.........(.--.-((((..(((((((((.....)))))))))))))..-------)...-..------------ ( -30.60)
>DroYak_CAF1 40724 97 + 1
UUAUUGUGUACUGAAAAAUGCAUUUUUCAUGACAUAA--CAACGACCCGU--U-UGGCAUUGGCAGCCCGAAUUGGGUUGCCAGCCGCCCGUUUCCCAUU-UC------------
...((((((..(((((((....)))))))..))))))--....((..((.--.-((((..(((((((((.....)))))))))))))..))..)).....-..------------ ( -33.90)
>DroAna_CAF1 43948 92 + 1
UUAUUGUGUACUGAAAAAUGCAUUUUUCAUGACAUAA--CAACGACCCGU--UUUGGCAUUGGCAGCCCGAAUUGGGCUGCCAUCCACC-------CAACACC------------
...((((((..(((((((....)))))))..))))))--.........((--.((((...(((((((((.....))))))))).....)-------))).)).------------ ( -31.40)
>consensus
UUAUUGUGUACUGAAAAAUGCAUUUUUCAUGACAUAA__CAACGACCCGU__U_UGGCAUUGGCAGCCCGAAUUGGGUUGCCAGCCGCC_______CAUU_UC____________
...((((((..(((((((....)))))))..))))))..................(((..(((((((((.....))))))))))))............................. (-24.52 = -25.48 +   0.96)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,165,323 – 9,165,413
Length 90
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 81.63
Mean single sequence MFE -28.62
Consensus MFE -19.87
Energy contribution -20.50
Covariance contribution 0.63
Combinations/Pair 1.08
Mean z-score -2.20
Structure conservation index 0.69
SVM decision value 0.73
SVM RNA-class probability 0.835279
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9165323 90 - 20766785
------------GA-AAUG-------GGCGGCUGGCAACCCAAUUCGGGCUGCCAAUGCCA-A--ACGGGUCGUUG--UUAUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUAA
------------((-..((-------((((..(((((.(((.....))).))))).)))).-.--.))..)).(((--((.(((..(((((((....)))))))..))).))))) ( -27.40)
>DroPse_CAF1 34128 80 - 1
----------------AGG-------AGGGUCUGGC----C-------GAUGCCGAUGCCG-AUGCCGGGUCGUUGGUUUGUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUUA
----------------..(-------(.(..(((((----.-------...((....))..-..)))))..).))...((((((..(((((((....)))))))..))))))... ( -23.90)
>DroSec_CAF1 49693 102 - 1
AAUGGGAAAUGGGA-AAUG-------GGCGGCUGGCAACCCAAUUCGGGCUGCCAAUGCCA-A--ACGGGUCGUUG--UUAUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUAA
..((.....((..(-((((-------((((..(((((.(((.....))).))))).)))).-.--.((.(.(((..--..))).).)).......)))))..)).....)).... ( -29.80)
>DroEre_CAF1 42561 90 - 1
------------GA-AAUG-------GGCGGCUGGCAACCCAAUUCGGGCUGCCAAUGCCA-A--ACGGGUCGUUG--UUAUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUAA
------------((-..((-------((((..(((((.(((.....))).))))).)))).-.--.))..)).(((--((.(((..(((((((....)))))))..))).))))) ( -27.40)
>DroYak_CAF1 40724 97 - 1
------------GA-AAUGGGAAACGGGCGGCUGGCAACCCAAUUCGGGCUGCCAAUGCCA-A--ACGGGUCGUUG--UUAUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUAA
------------((-..(((....).((((..(((((.(((.....))).))))).)))).-.--.))..)).(((--((.(((..(((((((....)))))))..))).))))) ( -31.00)
>DroAna_CAF1 43948 92 - 1
------------GGUGUUG-------GGUGGAUGGCAGCCCAAUUCGGGCUGCCAAUGCCAAA--ACGGGUCGUUG--UUAUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUAA
------------..((((.-------..(((.(((((((((.....)))))))))...))).)--))).....(((--((.(((..(((((((....)))))))..))).))))) ( -32.20)
>consensus
____________GA_AAUG_______GGCGGCUGGCAACCCAAUUCGGGCUGCCAAUGCCA_A__ACGGGUCGUUG__UUAUGUCAUGAAAAAUGCAUUUUUCAGUACACAAUAA
..........................((((..(((((.(((.....))).))))).))))............((((.....(((..(((((((....)))))))..))))))).. (-19.87 = -20.50 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:03 2006