Locus 3024

Sequence ID 2L_DroMel_CAF1
Location 8,619,647 – 8,619,787
Length 140
Max. P 0.997659
window4812 window4813 window4814

overview

Window 2

Location 8,619,647 – 8,619,756
Length 109
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 71.72
Mean single sequence MFE -29.22
Consensus MFE -14.02
Energy contribution -15.42
Covariance contribution 1.39
Combinations/Pair 1.21
Mean z-score -1.67
Structure conservation index 0.48
SVM decision value 0.22
SVM RNA-class probability 0.639528
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8619647 109 + 22407834
UUGCUGGUCCCUGCAGCUU---GUAGCUCAGC--UUGGCUCC-CCGGUUGAAAGCCCACCAGAAGCAGCAUCAGCAGCAGCACCAGCUUGUAU-UUCAUUGUUUUAAAACAAUGUU
..((((((..((((.(((.---((.(((..((--((((....-))(((.(.....).)))..))))))))).))).)))).))))))......-..(((((((....))))))).. ( -32.70)
>DroVir_CAF1 63188 93 + 1
UCGUUGGUU-----AGCUUUCGGGCGCUCAGU--UGGGCUCC---AGCUCUGAGCCCUGGG-CU----CCUC--------UUUUACCAUGUAUUUUCAUUGUUUUAGAACAAUGUU
....((((.-----.......(((.(((((..--.((((((.---......))))))))))-).----))).--------....))))........(((((((....))))))).. ( -28.02)
>DroSec_CAF1 47903 109 + 1
UUGCUGGUCCUUGCAGCUU---GUAGCUCAGC--UUGGCUCC-CCGGUUGAAAGCCCACCAGAAGCAGCAGCAGCGGCAGCACCAGCUUGUAU-UUCAUUGUUUUAAAACAAUGUU
..((((((.((.((.(((.---((.(((..((--((((....-))(((.(.....).)))..))))))).))))).)))).))))))......-..(((((((....))))))).. ( -33.50)
>DroSim_CAF1 53553 109 + 1
UUGCUGGUCCCUGCAGCUU---GUAGCUCAGC--UUGGCUCC-CCGGUUGAAAGCCCACCAGAAGCAGCAGCAGCGGCAGCACCAGCUUGUAU-UUCAUUGUUUUAAAACAAUGUU
..((((((..((((.(((.---((.(((..((--((((....-))(((.(.....).)))..))))))).))))).)))).))))))......-..(((((((....))))))).. ( -35.10)
>DroYak_CAF1 50876 93 + 1
UUGCUGGUCCCUGCAGCUU---GUAGCUCAGC--UCGGCUCCCCCGGUUGAAAGCCCACCAGC-----------------CAGCAGCUUGUAU-UUCAUUGUUUUAAAACAAUGUU
((((((((..((((.....---)))).(((((--.(((.....))))))))..........))-----------------)))))).......-..(((((((....))))))).. ( -26.90)
>DroAna_CAF1 50926 94 + 1
UUGUUGGUCUCUGC--CAU---GUAGCUCAGUCGUUGCCCCU-CCGC------GCCCCCUC-UU---GCUUC-----UAUGACCGGCUUGUAU-UUCAUUGUUUUAAAACAAUGUU
..(((((((.....--...---(((((......)))))....-..((------(.......-.)---))...-----...)))))))......-..(((((((....))))))).. ( -19.10)
>consensus
UUGCUGGUCCCUGCAGCUU___GUAGCUCAGC__UUGGCUCC_CCGGUUGAAAGCCCACCAGAA___GCAUC_____CAGCACCAGCUUGUAU_UUCAUUGUUUUAAAACAAUGUU
..((((((..(((.((((......))))))).....((((............)))).........................)))))).........(((((((....))))))).. (-14.02 = -15.42 +   1.39)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,619,647 – 8,619,756
Length 109
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 71.72
Mean single sequence MFE -34.18
Consensus MFE -16.79
Energy contribution -19.68
Covariance contribution 2.89
Combinations/Pair 1.04
Mean z-score -2.81
Structure conservation index 0.49
SVM decision value 2.90
SVM RNA-class probability 0.997659
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8619647 109 - 22407834
AACAUUGUUUUAAAACAAUGAA-AUACAAGCUGGUGCUGCUGCUGAUGCUGCUUCUGGUGGGCUUUCAACCGG-GGAGCCAA--GCUGAGCUAC---AAGCUGCAGGGACCAGCAA
..(((((((....)))))))..-......((((((.((((.(((..((..((((..(((.((((..(.....)-..))))..--)))))))..)---)))).)))).).))))).. ( -42.00)
>DroVir_CAF1 63188 93 - 1
AACAUUGUUCUAAAACAAUGAAAAUACAUGGUAAAA--------GAGG----AG-CCCAGGGCUCAGAGCU---GGAGCCCA--ACUGAGCGCCCGAAAGCU-----AACCAACGA
..(((((((....)))))))........((((....--------..((----.(-(.((((((((......---.)))))).--..)).)).))(....)..-----.)))).... ( -25.80)
>DroSec_CAF1 47903 109 - 1
AACAUUGUUUUAAAACAAUGAA-AUACAAGCUGGUGCUGCCGCUGCUGCUGCUUCUGGUGGGCUUUCAACCGG-GGAGCCAA--GCUGAGCUAC---AAGCUGCAAGGACCAGCAA
..(((((((....)))))))..-......((((((.((((.(((..((..((((..(((.((((..(.....)-..))))..--)))))))..)---)))).)).)).)))))).. ( -41.70)
>DroSim_CAF1 53553 109 - 1
AACAUUGUUUUAAAACAAUGAA-AUACAAGCUGGUGCUGCCGCUGCUGCUGCUUCUGGUGGGCUUUCAACCGG-GGAGCCAA--GCUGAGCUAC---AAGCUGCAGGGACCAGCAA
..(((((((....)))))))..-......((((((.((((.(((..((..((((..(((.((((..(.....)-..))))..--)))))))..)---)))).)))).).))))).. ( -42.00)
>DroYak_CAF1 50876 93 - 1
AACAUUGUUUUAAAACAAUGAA-AUACAAGCUGCUG-----------------GCUGGUGGGCUUUCAACCGGGGGAGCCGA--GCUGAGCUAC---AAGCUGCAGGGACCAGCAA
..(((((((....)))))))..-........(((((-----------------(((....((((..(......)..))))..--.((((((...---..))).))))).)))))). ( -32.60)
>DroAna_CAF1 50926 94 - 1
AACAUUGUUUUAAAACAAUGAA-AUACAAGCCGGUCAUA-----GAAGC---AA-GAGGGGGC------GCGG-AGGGGCAACGACUGAGCUAC---AUG--GCAGAGACCAACAA
..(((((((....)))))))..-.....((((((((...-----...((---..-......))------((..-....))...))))).)))..---.((--(......))).... ( -21.00)
>consensus
AACAUUGUUUUAAAACAAUGAA_AUACAAGCUGGUGCUG_____GAUGC___UUCUGGUGGGCUUUCAACCGG_GGAGCCAA__GCUGAGCUAC___AAGCUGCAGGGACCAGCAA
..(((((((....))))))).........((((((.........................((((((........)))))).....((((((........))).)))..)))))).. (-16.79 = -19.68 +   2.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,619,678 – 8,619,787
Length 109
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.52
Mean single sequence MFE -31.55
Consensus MFE -13.70
Energy contribution -14.07
Covariance contribution 0.36
Combinations/Pair 1.16
Mean z-score -2.30
Structure conservation index 0.43
SVM decision value 0.75
SVM RNA-class probability 0.841710
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8619678 109 - 22407834
AAUCAAAGUCAGCAGCGCAGCCAAAUGGGGAAACAUUGUUUUAAAACAAUGAA-AUACAAGCUGGUGCUGCUGCUGAUGCUGCUUCUGGUGGGCUUUCAACCGG-GGAGCC
.......((((((((((((.(((....(.....(((((((....)))))))..-...)....)))))).)))))))))...(((((((((.........))).)-))))). ( -37.40)
>DroVir_CAF1 63217 95 - 1
AAUCAAAGCCAGUCGCGCAGCCAAAUGGGGAAACAUUGUUCUAAAACAAUGAAAAUACAUGGUAAAA--------GAGG----AG-CCCAGGGCUCAGAGCU---GGAGCC
........((((((..(.((((...((((....(((((((....)))))))....(((...)))...--------....----..-)))).))))).)).))---)).... ( -24.70)
>DroSec_CAF1 47934 109 - 1
AAUCAAAGUCAGCAGUGCAGCCAAAUGGGAAAACAUUGUUUUAAAACAAUGAA-AUACAAGCUGGUGCUGCCGCUGCUGCUGCUUCUGGUGGGCUUUCAACCGG-GGAGCC
.(((((((((((((((((((((.....(.....(((((((....)))))))..-...)......).)))).))))))))..)))).)))).((((..(.....)-..)))) ( -37.00)
>DroSim_CAF1 53584 109 - 1
AAUCAAAGUCAGCAGCGCAGCCAAAUGGGGAAACAUUGUUUUAAAACAAUGAA-AUACAAGCUGGUGCUGCCGCUGCUGCUGCUUCUGGUGGGCUUUCAACCGG-GGAGCC
.(((((((((((((((((((((.....(.....(((((((....)))))))..-...)......).)))).))))))))..)))).)))).((((..(.....)-..)))) ( -38.90)
>DroYak_CAF1 50907 93 - 1
AAUCAAAGUCAGCAGCGCAGCCAAAUGGGGAAACAUUGUUUUAAAACAAUGAA-AUACAAGCUGCUG-----------------GCUGGUGGGCUUUCAACCGGGGGAGCC
...((.((((((((((....((....)).....(((((((....)))))))..-......)))))))-----------------)))..))((((..(......)..)))) ( -35.10)
>DroMoj_CAF1 74699 94 - 1
AAUCAAAGUCAGUCGCGCAACCAAAUGG-GAAACAUUGUUCUAAAACAAUGAAAAUACAUGGUAAAA--------GAGG----AG-CCCAGGGCCCAGAGCC---AGAGCC
..............(.((.((((..((.-....(((((((....)))))))......))))))....--------..((----.(-((...)))))...)))---...... ( -16.20)
>consensus
AAUCAAAGUCAGCAGCGCAGCCAAAUGGGGAAACAUUGUUUUAAAACAAUGAA_AUACAAGCUGGUG________GAUG____UGCUGGUGGGCUUUCAACCGG_GGAGCC
............((((....((....)).....(((((((....))))))).........))))...........................((((((........)))))) (-13.70 = -14.07 +   0.36)

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 10:42:28 2006