Locus 9624

Sequence ID 3R_DroMel_CAF1
Location 25,415,979 – 25,416,071
Length 92
Max. P 0.757415
window15383 window15384

overview

Window 3

Location 25,415,979 – 25,416,071
Length 92
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 76.10
Mean single sequence MFE -33.82
Consensus MFE -14.61
Energy contribution -15.83
Covariance contribution 1.23
Combinations/Pair 1.29
Mean z-score -1.98
Structure conservation index 0.43
SVM decision value 0.02
SVM RNA-class probability 0.545155
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25415979 92 + 27905053
AUUUGGCAUC----UGGAUAG-CGUUUCCGAGAUUACGGACACCUCGGCGAGCAGGCUGGUUUG--GUUGUCGGAUGCGUUGUAGGAAGCUUUCUCCAG----
....(((.((----(..((((-(((.(((((.(...(((((....((((......)))))))))--..).))))).))))))).))).)))........---- ( -30.10)
>DroPse_CAF1 110456 96 + 1
GUCUGGCACGUAUCCAGAUCGGAGUCGACGAGA-----GCGAGCUCCGCAAGCAG-CUG-UUUGUUGAAGUCGGUCGCAUUCUGGCCAAUGAUCGUCAGAAUA
.((((((.........((((((..((((((((.-----...((((.(....).))-)).-))))))))..))))))((......))........))))))... ( -32.90)
>DroSec_CAF1 99727 92 + 1
AUUUGGCAUC----UGGAUAG-CGUGUCCGAGAUUACGGACACCUGGGCGAGCAGGCUGGUUUG--GUUGUCGGAUGCCUUGUAGGAAGUUUUCUCCAG----
((..((((((----((.((((-((((((((......))))))).(..((.((....)).))..)--)))))))))))))..)).(((.......)))..---- ( -36.30)
>DroSim_CAF1 100234 92 + 1
AUUUGGCAUC----UGGAUAG-CGUGUCCGAGAUUACGGACACCUGGGCGAGCAGGCUGGUUUG--GUUGUCGGAUGCCUUGUAGGAAGCUUUCUCCAG----
((..((((((----((.((((-((((((((......))))))).(..((.((....)).))..)--)))))))))))))..)).(((.......)))..---- ( -36.30)
>DroEre_CAF1 106065 92 + 1
AUUUGGCAUU----UGGAUAG-CGUGUCCGCGAUUUCGGACACCUGGCCGAGCAGGCUGGUUUG--GUUAUCAGAUGCCUUGUAGGAAGCUUGCUCCAG----
((..((((((----((.((((-((((((((......)))))))(..(((.....)))..)....--)))))))))))))..)).(((.(....))))..---- ( -38.30)
>DroYak_CAF1 107828 92 + 1
AUUUGGCAUC----UGGUUUC-CGUUUCCUUGAUUUCGGACACUUGGGUGAGCAGGCUGGUUUG--GUUAUCAGAUGCCUUGUAGGAAGCUUGCUCCAG----
((..((((((----((((..(-((..((((((...(((..(....)..))).))))..))..))--)..))))))))))..)).(((.(....))))..---- ( -29.00)
>consensus
AUUUGGCAUC____UGGAUAG_CGUGUCCGAGAUUACGGACACCUGGGCGAGCAGGCUGGUUUG__GUUGUCGGAUGCCUUGUAGGAAGCUUUCUCCAG____
....((((((.............(((((((......))))))).....(((((......))))).........)))))).....(((.......)))...... (-14.61 = -15.83 +   1.23)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,415,979 – 25,416,071
Length 92
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 76.10
Mean single sequence MFE -24.71
Consensus MFE -13.94
Energy contribution -15.75
Covariance contribution 1.81
Combinations/Pair 1.20
Mean z-score -1.71
Structure conservation index 0.56
SVM decision value 0.49
SVM RNA-class probability 0.757415
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25415979 92 - 27905053
----CUGGAGAAAGCUUCCUACAACGCAUCCGACAAC--CAAACCAGCCUGCUCGCCGAGGUGUCCGUAAUCUCGGAAACG-CUAUCCA----GAUGCCAAAU
----(((((...(((..........(((..(......--.......)..)))...(((((((.......)))))))....)-)).))))----)......... ( -21.12)
>DroPse_CAF1 110456 96 - 1
UAUUCUGACGAUCAUUGGCCAGAAUGCGACCGACUUCAACAAA-CAG-CUGCUUGCGGAGCUCGC-----UCUCGUCGACUCCGAUCUGGAUACGUGCCAGAC
...((((.((........(((((.((.((.((((.........-..(-(.....))((((....)-----))).))))..)))).))))).....)).)))). ( -22.42)
>DroSec_CAF1 99727 92 - 1
----CUGGAGAAAACUUCCUACAAGGCAUCCGACAAC--CAAACCAGCCUGCUCGCCCAGGUGUCCGUAAUCUCGGACACG-CUAUCCA----GAUGCCAAAU
----..((((.....)))).....((((((.(.....--.......(((((......)))))(((((......)))))...-.....).----)))))).... ( -26.90)
>DroSim_CAF1 100234 92 - 1
----CUGGAGAAAGCUUCCUACAAGGCAUCCGACAAC--CAAACCAGCCUGCUCGCCCAGGUGUCCGUAAUCUCGGACACG-CUAUCCA----GAUGCCAAAU
----..((((.....)))).....((((((.(.....--.......(((((......)))))(((((......)))))...-.....).----)))))).... ( -26.90)
>DroEre_CAF1 106065 92 - 1
----CUGGAGCAAGCUUCCUACAAGGCAUCUGAUAAC--CAAACCAGCCUGCUCGGCCAGGUGUCCGAAAUCGCGGACACG-CUAUCCA----AAUGCCAAAU
----..((((....))))......(((((.((.....--.......(((.....))).(((((((((......))))))).-))...))----.))))).... ( -27.60)
>DroYak_CAF1 107828 92 - 1
----CUGGAGCAAGCUUCCUACAAGGCAUCUGAUAAC--CAAACCAGCCUGCUCACCCAAGUGUCCGAAAUCAAGGAAACG-GAAACCA----GAUGCCAAAU
----..((((....))))......((((((((.....--.....................((.(((........))).))(-....)))----)))))).... ( -23.30)
>consensus
____CUGGAGAAAGCUUCCUACAAGGCAUCCGACAAC__CAAACCAGCCUGCUCGCCCAGGUGUCCGUAAUCUCGGACACG_CUAUCCA____GAUGCCAAAU
......((((.....)))).....((((((..................(((......)))(((((((......))))))).............)))))).... (-13.94 = -15.75 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:31 2006