Locus 7630

Sequence ID X_DroMel_CAF1
Location 19,040,301 – 19,040,472
Length 171
Max. P 0.963096
window12522 window12523 window12524

overview

Window 2

Location 19,040,301 – 19,040,392
Length 91
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 73.93
Mean single sequence MFE -26.00
Consensus MFE -16.94
Energy contribution -19.07
Covariance contribution 2.12
Combinations/Pair 1.23
Mean z-score -1.53
Structure conservation index 0.65
SVM decision value 0.70
SVM RNA-class probability 0.827404
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19040301 91 + 22224390
UACGGACUGAGGACUUUGUGCCUGUAUAUCAGUAACAGAAGGAGAUGCAAGCU------------UCGUAACUUCGGUUACGAUC---UGCUGGUUUUGCUCCUGA
..............(((((..(((.....)))..)))))(((((..((.(((.------------(((((((....)))))))..---.))).))....))))).. ( -29.80)
>DroSec_CAF1 9069 94 + 1
UACGCACUGAGGACUUUGUACGUGUAUAUCAGUAACAACAGGAGAUGCAAGCU------------UCGUAACUUCGGUUACGAUAUUAUCCUGGUCUUGUUCCUGA
.....(((((..((.........))...))))).....(((((...(((((((------------(((((((....))))))).........)).)))))))))). ( -27.00)
>DroYak_CAF1 8714 103 + 1
UACAAUCUGAUGACUUUCUACCUGUAUAUCAGUUACAACCGGAGAUGCUAGCUGAAAACUUUCUUUUGGGAUUUCGGUUUCUGUC---UGUUGGUCUUGCUCCUGA
......((((((((.........)).)))))).....((((((((((..((((((((.(((......))).))))))))..))))---).)))))........... ( -21.20)
>consensus
UACGAACUGAGGACUUUGUACCUGUAUAUCAGUAACAACAGGAGAUGCAAGCU____________UCGUAACUUCGGUUACGAUC___UGCUGGUCUUGCUCCUGA
.....(((((..((.........))...))))).....(((((...(((((((............(((((((....))))))).........)).)))))))))). (-16.94 = -19.07 +   2.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,040,327 – 19,040,432
Length 105
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.62
Mean single sequence MFE -30.33
Consensus MFE -18.17
Energy contribution -18.63
Covariance contribution 0.46
Combinations/Pair 1.31
Mean z-score -1.64
Structure conservation index 0.60
SVM decision value 0.50
SVM RNA-class probability 0.761870
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19040327 105 + 22224390
UAUCAGUAACAGAAGGAGAUGCAAGCU------------UCGUAACUUCGGUUACGAUC---UGCUGGUUUUGCUCCUGAAUCUCAGCAGAAAACGAGAGAUUUUCCCAUUGGAUUUCGG
..(((((......(((((..((.(((.------------(((((((....)))))))..---.))).))....)))))(((((((............)))))))....)))))....... ( -30.90)
>DroSec_CAF1 9095 108 + 1
UAUCAGUAACAACAGGAGAUGCAAGCU------------UCGUAACUUCGGUUACGAUAUUAUCCUGGUCUUGUUCCUGAAUCUCAGCAGGAUUUGGGAGAUUUUCCCAUUGGAUUUCGG
...............(((((.(((...------------(((((((....)))))))........(((.....((((..(((((.....)))))..))))......)))))).))))).. ( -31.80)
>DroYak_CAF1 8740 117 + 1
UAUCAGUUACAACCGGAGAUGCUAGCUGAAAACUUUCUUUUGGGAUUUCGGUUUCUGUC---UGUUGGUCUUGCUCCUGAAUUUCAGCUUCAAACGGGAGAUUUUUCUCUUGGAUUUCAA
..((((...((((((((((((..((((((((.(((......))).))))))))..))))---).)))))..))...))))..............(((((((....)))))))........ ( -28.30)
>consensus
UAUCAGUAACAACAGGAGAUGCAAGCU____________UCGUAACUUCGGUUACGAUC___UGCUGGUCUUGCUCCUGAAUCUCAGCAGAAAACGGGAGAUUUUCCCAUUGGAUUUCGG
.........(((..(((((.(((((((............(((((((....))))))).........)).)))))))..(((((((............))))))))))..)))........ (-18.17 = -18.63 +   0.46)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,040,355 – 19,040,472
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 65.55
Mean single sequence MFE -33.70
Consensus MFE -17.10
Energy contribution -20.33
Covariance contribution 3.24
Combinations/Pair 1.28
Mean z-score -1.96
Structure conservation index 0.51
SVM decision value 1.55
SVM RNA-class probability 0.963096
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19040355 117 + 22224390
CGUAACUUCGGUUACGAUC---UGCUGGUUUUGCUCCUGAAUCUCAGCAGAAAACGAGAGAUUUUCCCAUUGGAUUUCGGAGACAGCCGAGUAAUCCUCCUGGGUCUCGGUUAUAGUCUG
((((((....)))))).((---((((((..((.(....)))..))))))))...(((((.....(((....)))))))).(((((((((((..((((....)))))))))))...)))). ( -40.70)
>DroSec_CAF1 9123 120 + 1
CGUAACUUCGGUUACGAUAUUAUCCUGGUCUUGUUCCUGAAUCUCAGCAGGAUUUGGGAGAUUUUCCCAUUGGAUUUCGGAGACAAUCGGGUAAUCCUCCUGGAUCUCGGUUAUAGUUUG
((((((....))))))...........(((((..(((..(((((.....)))))..)))((...(((....)))..)).)))))(((((((..((((....)))))))))))........ ( -38.90)
>DroYak_CAF1 8780 89 + 1
UGGGAUUUCGGUUUCUGUC---UGUUGGUCUUGCUCCUGAAUUUCAGCUUCAAACGGGAGAUUUUUCUCUUGGAUUUCAAAGACAAUCGGGC----------------------------
.(..((....))..).(((---((...(((((....(((.....))).......(((((((....))))))).......)))))...)))))---------------------------- ( -21.50)
>consensus
CGUAACUUCGGUUACGAUC___UGCUGGUCUUGCUCCUGAAUCUCAGCAGAAAACGGGAGAUUUUCCCAUUGGAUUUCGGAGACAAUCGGGUAAUCCUCCUGG_UCUCGGUUAUAGU_UG
((((((....))))))...........(((((....(((.....)))..........(((((((.......))))))).)))))(((((((..((((....)))))))))))........ (-17.10 = -20.33 +   3.24)

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 12:43:48 2006