Locus 2746

Sequence ID 3L_DroMel_CAF1
Location 7,732,470 – 7,732,736
Length 266
Max. P 0.897391
window4293 window4294 window4295

overview

Window 3

Location 7,732,470 – 7,732,588
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.30
Mean single sequence MFE -39.16
Consensus MFE -26.52
Energy contribution -26.72
Covariance contribution 0.20
Combinations/Pair 1.13
Mean z-score -1.76
Structure conservation index 0.68
SVM decision value -0.01
SVM RNA-class probability 0.527070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7732470 118 + 23771897
CAAUAUUACCUGCAACGCGG-GUUAUAUCAUGCAGGGCUCACAAUUUGCGGUUUGUGGACACACCGGACUUUGGUCUAGUCCAGAAGCCAAGUGCGUGGGUAAGUACACAUCAAUGU-AC
...(((.((((((...))))-)).)))(((((((..((.........))(((((.(((((..((((.....))))...))))).)))))...)))))))....(((((......)))-)) ( -37.50)
>DroSec_CAF1 28906 118 + 1
CAAUAUUACCUGCAACGCGGGGUUAUAUUCUGCAGGGUUCACAAUUCGCGAGUUGUGGACACACCGGUCUUUGGUCCAGUCCAGAAGCCAAGUGCGUGGGUAAGUACAAAUCAAUGA-A-
.....(((((..(.(((((((((...))))))).((((((((((((....))))))))))...))((..(((((......)))))..))..))..)..)))))..............-.- ( -38.30)
>DroSim_CAF1 25035 117 + 1
CAAUAUUACCUGCAACGCGG-GUUAUAUCCUGCAGGGUUCACAAUUCGCGAGUUGUGGACACACCGGUCUUUGGUCCAGUCCAGAAGCCAAGUGCGUGGGUAAGUACAAAUCAAUGA-A-
.....(((((..(.((((((-(......))))).((((((((((((....))))))))))...))((..(((((......)))))..))..))..)..)))))..............-.- ( -40.50)
>DroEre_CAF1 28778 119 + 1
CAAUAUUACGUGCAACGCGG-GCUAUGUGUUGGAGGGUUCACAAUUCGCAAGUUGUGGACACACCGGAAUUUGGUCUAGCCCAGAGACCAAGUGUGUGUGUAAGUGCAAAUCCGUGGUAC
...((((((...(((((((.-....)))))))..(((((((((((......)))))).((((((....(((((((((.......)))))))))..)))))).......))))))))))). ( -39.50)
>DroYak_CAF1 27635 119 + 1
CAAUAUCAGCUGCAACGCGG-GUUAUGUGUUGCAAGGUUCACAGUUCGCCAGUUGUGGACACACCGGACUUUGGUCUAGUCCAGAGACCAAGUGUGUGGGUAAGUGCAAAUCAGUGGUGC
...(((((..(((((((((.-....))))))))).(((((((.((((((.....))))))((.(((.((((((((((.......)))))))).)).)))))..)))..))))..))))). ( -40.00)
>consensus
CAAUAUUACCUGCAACGCGG_GUUAUAUCCUGCAGGGUUCACAAUUCGCGAGUUGUGGACACACCGGACUUUGGUCUAGUCCAGAAGCCAAGUGCGUGGGUAAGUACAAAUCAAUGA_AC
.....(((((..(..(((((.((........))...((((((((((....))))))))))...))((..(((((......)))))..))..))).)..)))))................. (-26.52 = -26.72 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,732,509 – 7,732,628
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.84
Mean single sequence MFE -21.14
Consensus MFE -17.47
Energy contribution -17.31
Covariance contribution -0.16
Combinations/Pair 1.19
Mean z-score -0.14
Structure conservation index 0.83
SVM decision value 0.57
SVM RNA-class probability 0.785398
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7732509 119 - 23771897
UAUAAAAUCCUAUAGCACUAACUUAAAUUGUUUGUACAUUGU-ACAUUGAUGUGUACUUACCCACGCACUUGGCUUCUGGACUAGACCAAAGUCCGGUGUGUCCACAAACCGCAAAUUGU
.............................((((((.....((-((((....))))))......(((((((.(((((.(((......)))))))).)))))))..)))))).......... ( -27.10)
>DroSec_CAF1 28946 110 - 1
UUAAAAAUCCUAUAGCUUUAACUUCAAUUGUA---------U-UCAUUGAUUUGUACUUACCCACGCACUUGGCUUCUGGACUGGACCAAAGACCGGUGUGUCCACAACUCGCGAAUUGU
................................---------.-.....(((((((........(((((((.(((((.(((......)))))).))))))))).........))))))).. ( -18.13)
>DroSim_CAF1 25074 110 - 1
UUCAAAAUCCUAUAGCUUUAACUUCGAUUGUA---------U-UCAUUGAUUUGUACUUACCCACGCACUUGGCUUCUGGACUGGACCAAAGACCGGUGUGUCCACAACUCGCGAAUUGU
.........................((.....---------.-))...(((((((........(((((((.(((((.(((......)))))).))))))))).........))))))).. ( -18.23)
>DroEre_CAF1 28817 115 - 1
UGCAACUUCAAUUA-----AACCAAAGUCACUCGAACCCUGUACCACGGAUUUGCACUUACACACACACUUGGUCUCUGGGCUAGACCAAAUUCCGGUGUGUCCACAACUUGCGAAUUGU
.((((.........-----.....((((....((((.((........)).)))).))))((((((....(((((((.......)))))))......)))))).......))))....... ( -21.50)
>DroYak_CAF1 27674 94 - 1
UGCAAAAUCUGAUA--------------------------GCACCACUGAUUUGCACUUACCCACACACUUGGUCUCUGGACUAGACCAAAGUCCGGUGUGUCCACAACUGGCGAACUGU
((((((.((.....--------------------------........)))))))).......(((((((.((.((.(((......))).)).)))))))))(((....)))........ ( -20.72)
>consensus
UGCAAAAUCCUAUAGC__UAACUUAAAUUGUA________GU_CCAUUGAUUUGUACUUACCCACGCACUUGGCUUCUGGACUAGACCAAAGUCCGGUGUGUCCACAACUCGCGAAUUGU
................................................(((((((........(((((((.((.((.(((......))).)).))))))))).........))))))).. (-17.47 = -17.31 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,732,628 – 7,732,736
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.67
Mean single sequence MFE -31.34
Consensus MFE -12.06
Energy contribution -12.38
Covariance contribution 0.32
Combinations/Pair 1.33
Mean z-score -2.01
Structure conservation index 0.38
SVM decision value 1.00
SVM RNA-class probability 0.897391
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7732628 108 - 23771897
UUGCAGCUUGCAGGAUAGAAACGUCCAUUGCGAGGGGGUGUCAAAACUGGACAACUCAAUGCGAGGGAUUCUAGAAAUAGGAUGCAAU---AGCAAAU---------ACAUAAUGUGUCU
((((..((((((((((......)))).....(((....((((.......)))).)))..))))))(.((((((....)))))).)...---.))))((---------((.....)))).. ( -30.80)
>DroSec_CAF1 29056 108 - 1
UUGCAGCUGGCAGGAUAGAAACGUCCAUUGCGUGGAGGUGUCAAAACUGGACAGCUCCAUGCGAGGGAUUCUAGAAAUAUGAUGCAAU---ACCAAAU---------ACAUAAUGAGUCU
(((((..........((((...((((.((((((((((.((((.......)))).)))))))))).)))))))).........))))).---.......---------............. ( -35.31)
>DroSim_CAF1 25184 108 - 1
UUGCAGCUGGCAGGAUAGAAACGUCCAUUGCGUGGAGGUGUCAAAGCUGGACAGCUCCAUGCGAGGGAUUCUAGAAAUAGGAUGCAAU---ACCAAAU---------ACAUAAUGAGUCU
(((((.(((......((((...((((.((((((((((.((((.......)))).)))))))))).))))))))....)))..))))).---.......---------............. ( -37.00)
>DroEre_CAF1 28932 118 - 1
UGGCAGCUUGCCGGAACGAAACUUCCAUGGCUGGGUGAUUUCAAAGCGGGACAACUUAGUGCGAGCGAGUCUAUACAUAG--AUAAAUAGAUCUAUAGAUAAAGUAACUAUAAUAAGGCU
.(((.((((((.((((......))))...(((((((..(..(.....)..)..)))))))))))))..(((((....(((--((......)))))))))).................))) ( -29.50)
>DroYak_CAF1 27768 108 - 1
UUGCAGCUCUUCGGAUAGAAACGUCCAUGGCUGGGUGUUUCCAAAACUGGACAACUUGAUGCAAUCGAGGCUAUACAAAGGGAUAAGU---UACAAAG---------AUAUAACGAGGCU
..((..(((((.(.((((....(((((.(..((((....))))...))))))..((((((...)))))).)))).).)))))....((---((.....---------...))))...)). ( -24.10)
>consensus
UUGCAGCUGGCAGGAUAGAAACGUCCAUUGCGGGGAGGUGUCAAAACUGGACAACUCAAUGCGAGGGAUUCUAGAAAUAGGAUGCAAU___ACCAAAU_________ACAUAAUGAGUCU
(((((.((.(((((((......))))..))).))(((.((((.......)))).)))..)))))........................................................ (-12.06 = -12.38 +   0.32)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:45 2006