Locus 1231

Sequence ID 3L_DroMel_CAF1
Location 3,497,542 – 3,497,642
Length 100
Max. P 0.925483
window1932 window1933

overview

Window 2

Location 3,497,542 – 3,497,642
Length 100
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 80.08
Mean single sequence MFE -21.48
Consensus MFE -16.37
Energy contribution -16.45
Covariance contribution 0.08
Combinations/Pair 1.21
Mean z-score -2.13
Structure conservation index 0.76
SVM decision value 1.17
SVM RNA-class probability 0.925483
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3497542 100 + 23771897
GCCCUUUUGGCCAACAAGAGGUCUGCAAACAGGCCAAACCUGCAAGGGCCAAGAC----GAUUUACAACCAAAGAUGAUAAAAAAAAAGAACGAAAUUCAACUA
..(.((((((((....((.((((((....))))))....)).....)))))))).----)............................................ ( -19.60)
>DroSec_CAF1 28011 98 + 1
GCCCUUUUGGCCAACAAGAGGUCUGCAAACAGGCCAAACCAGCAAGGGCCAAGAC----GAUUUACAACCAAAGAUGAUAAAA--AAAGAAUGAAAUUCAACUU
((((((((((.(.....).((((((....))))))...)))).))))))......----............(((.(((.....--............))).))) ( -20.03)
>DroSim_CAF1 28396 96 + 1
GCCCUUUUGGCCAACA-GAGGUCUGCAAACAGGCCAAACCUGCAAGGGCCAAGAC----GAUUUACAACCAAAGAUGAUAAA---AAAGAACGAAAUUCAACUA
..(.((((((((..((-(.((((((....))))))....)))....)))))))).----)............((.(((....---............))).)). ( -21.29)
>DroEre_CAF1 43782 96 + 1
GCUCUUUUGGCCAACAAGAGGCCUGCAAACAGGCCAAACCUGCAAGGGCCAAGUC----GAUUUACAGCCAAAGGUAAUAAA----AAGAAUACAAUUCAAGUA
(((..(((((((....((.((((((....))))))....)).....)))))))((----..((((..(((...)))..))))----..))..........))). ( -23.70)
>DroYak_CAF1 29478 96 + 1
GCCCUUUUGGCCAACAAGAGGUCUGCAAACAGGCCAAACCUGCAAGGGCCAAGAC----GAUUUACAGCCAAAGAUGAUAAA----AAGAACACAAAUCGAGGA
..((((((((((....((.((((((....))))))....)).....))))))))(----(((((..................----........)))))).)). ( -22.97)
>DroAna_CAF1 42395 82 + 1
GCCCUUUUGGCCAAGAAGAUCUCUGCAAACAGGCCCCACCAGCAG-GGCUAAAAAGCAGGGCUUAAAG--AAAGAAAUUAAA----AAG---------------
...((((.((((.((.....))((((.....(((((........)-)))).....)))))))).))))--............----...--------------- ( -21.30)
>consensus
GCCCUUUUGGCCAACAAGAGGUCUGCAAACAGGCCAAACCUGCAAGGGCCAAGAC____GAUUUACAACCAAAGAUGAUAAA____AAGAACGAAAUUCAACUA
....((((((((.......((((((....))))))...........)))))))).................................................. (-16.37 = -16.45 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,497,542 – 3,497,642
Length 100
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 80.08
Mean single sequence MFE -23.97
Consensus MFE -15.65
Energy contribution -16.82
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.65
SVM decision value -0.00
SVM RNA-class probability 0.531265
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3497542 100 - 23771897
UAGUUGAAUUUCGUUCUUUUUUUUUAUCAUCUUUGGUUGUAAAUC----GUCUUGGCCCUUGCAGGUUUGGCCUGUUUGCAGACCUCUUGUUGGCCAAAAGGGC
............((((((((..(((((.((.....)).)))))..----.....((((...(((((...((.(((....))).)).))))).)))))))))))) ( -24.20)
>DroSec_CAF1 28011 98 - 1
AAGUUGAAUUUCAUUCUUU--UUUUAUCAUCUUUGGUUGUAAAUC----GUCUUGGCCCUUGCUGGUUUGGCCUGUUUGCAGACCUCUUGUUGGCCAAAAGGGC
(((.(((.((.((..(...--.............)..)).)).))----).))).((((((..(((((.((.(((....))).)).......))))).)))))) ( -19.39)
>DroSim_CAF1 28396 96 - 1
UAGUUGAAUUUCGUUCUUU---UUUAUCAUCUUUGGUUGUAAAUC----GUCUUGGCCCUUGCAGGUUUGGCCUGUUUGCAGACCUC-UGUUGGCCAAAAGGGC
............(((((((---(((((.((.....)).)))))..----....(((((...(((((.....)))))..((((....)-))).)))))))))))) ( -22.80)
>DroEre_CAF1 43782 96 - 1
UACUUGAAUUGUAUUCUU----UUUAUUACCUUUGGCUGUAAAUC----GACUUGGCCCUUGCAGGUUUGGCCUGUUUGCAGGCCUCUUGUUGGCCAAAAGAGC
..(((.........((..----(((((..((...))..)))))..----)).((((((...(((((...((((((....)))))).))))).)))))))))... ( -30.70)
>DroYak_CAF1 29478 96 - 1
UCCUCGAUUUGUGUUCUU----UUUAUCAUCUUUGGCUGUAAAUC----GUCUUGGCCCUUGCAGGUUUGGCCUGUUUGCAGACCUCUUGUUGGCCAAAAGGGC
((((((((((..(..(..----............)..)..)))))----)..((((((...(((((...((.(((....))).)).))))).)))))).)))). ( -26.34)
>DroAna_CAF1 42395 82 - 1
---------------CUU----UUUAAUUUCUUU--CUUUAAGCCCUGCUUUUUAGCC-CUGCUGGUGGGGCCUGUUUGCAGAGAUCUUCUUGGCCAAAAGGGC
---------------...----..........((--((((..(((((((......(((-(((....))))))......))))((.....)).)))..)))))). ( -20.40)
>consensus
UAGUUGAAUUUCGUUCUU____UUUAUCAUCUUUGGCUGUAAAUC____GUCUUGGCCCUUGCAGGUUUGGCCUGUUUGCAGACCUCUUGUUGGCCAAAAGGGC
....................................................((((((...(((((...((.(((....))).)).))))).))))))...... (-15.65 = -16.82 +   1.17)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:41 2006