Locus 3958

Sequence ID 2R_DroMel_CAF1
Location 13,054,642 – 13,054,852
Length 210
Max. P 0.513050
window6391 window6392

overview

Window 1

Location 13,054,642 – 13,054,738
Length 96
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 79.86
Mean single sequence MFE -28.82
Consensus MFE -17.47
Energy contribution -17.20
Covariance contribution -0.27
Combinations/Pair 1.48
Mean z-score -1.50
Structure conservation index 0.61
SVM decision value -0.05
SVM RNA-class probability 0.509108
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13054642 96 + 20766785
CCAGGAGCAGUCCAAAAGCAAGUCCGGAAAAUUGGGCUCUGAUCUGAUUGGUCAGCUAAGUGGACAGAAGCCUGCGAGUUUCUUGAUGGGGAAACA
.((((..(.(((((..(((.(((((((....))))))).(((((.....))))))))...))))).)...))))...((((((......)))))). ( -32.40)
>DroSec_CAF1 3390 96 + 1
CCAGGAGCAGUCCAAAAGCAAGUCCGGUAAAUUGGGAUCCGAUCUGAUUGGUCAGCUAAGUGGACAGAAACCUGCGAGUUUCUUGAUGGGGAAACA
.((((..(.(((((..(((..((((.(.....).))))..((((.....)))).)))...))))).)...))))...((((((......)))))). ( -28.90)
>DroSim_CAF1 3342 96 + 1
CCAGGAGCAGUCCAAAAGCAAGUCCGGUAAAUUGGGCUCCGAUCUGAUUGGUCAGCUAAGUGGACAGAAGCCUGCGAGUUUCUUGAUGGGUAAACA
(((....(((((((..(((.(((((((....)))))))..((((.....)))).)))...)))))((((((......)))))))).)))....... ( -28.60)
>DroEre_CAF1 3332 96 + 1
CCAGGAGCAGUCGAAAAGCGAGUCCGGAAAACUGGGCUCUAAUCUAAUUGGUCAGCUAAGUGGGCAGAAUCCUGCGAGAUUCCUGAUGGACAAACA
(((..((.((((.......((((((((....))))))))....(((.((((....)))).)))((((....))))..)))).))..)))....... ( -28.80)
>DroYak_CAF1 3314 96 + 1
CCAGGAGCAGUCCAAAAGCGAGUCCGGAAAACUGGGCUCCAAUCUGAUUGGUCAGCUAAGUGCGCAGAAUUCUACGAGAUUCUUAAUAGGAAAACA
((..((.(((((.....(.((((((((....))))))))).....))))).)).((.....))..((((((......)))))).....))...... ( -24.90)
>DroAna_CAF1 3220 96 + 1
UCAGGAGCAGGCCAAGAGCGACUUUAGUAAACUGAACUCUGACUUAGUGGCCCAGCUCAGCGAUGUGAAUCCUCCACAGUUCCUGAUAGACGGGGA
((((((((.(((((.((((((.(((((....))))).)).).)))..)))))...........((((.......)))))))))))).......... ( -29.30)
>consensus
CCAGGAGCAGUCCAAAAGCAAGUCCGGAAAACUGGGCUCCGAUCUGAUUGGUCAGCUAAGUGGACAGAAUCCUGCGAGUUUCUUGAUGGGCAAACA
(((..((..(((((..(((.(((((((....)))))))..((((.....)))).)))...))))).(((((......)))))))..)))....... (-17.47 = -17.20 +  -0.27)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,054,738 – 13,054,852
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 84.44
Mean single sequence MFE -39.57
Consensus MFE -29.51
Energy contribution -29.98
Covariance contribution 0.48
Combinations/Pair 1.31
Mean z-score -1.74
Structure conservation index 0.75
SVM decision value -0.04
SVM RNA-class probability 0.513050
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13054738 114 - 20766785
UGUUUGAGGCACAAUUUCAGGCAACGUCUGGAGGGCAGGCCCUUCAACUCACUUGGAGGCAUGGGAGGGAAGAACACGCUCUGAAAUCUCCUAUGGCACACACUGCGAUAUAGA
(((((((((.....)))))))))..((((((((((....))))))).(((.....))).(((((((((..(((......)))....)))))))))(((.....))))))..... ( -35.70)
>DroVir_CAF1 5109 114 - 1
UGCUUGAGGCACAGUUUCAGACAACGACUCGUGGGCAGUCCCUGAAACUGAGCGAACGGCACGGGCGCCAGGAAGACGCCUUUAAACAGCCUCGGACAAUUGCUUCGAUACAGA
...(((((((((((((((((...((..((....))..))..)))))))))..(((..(((..(((((.(.....).))))).......))))))......))))))))...... ( -34.10)
>DroSec_CAF1 3486 114 - 1
UGUUUGAGGCACAAUUUCAGGCAACGUCUGGAGGGCAGGCCCUUCAACUCACUUGGUGGCAUGGGAGGGAAGAACACGCUCUGAAACCUCCUAUGGCACACAGUACGAUAUAGA
(((((((((.....))))))))).(((.(((((((....)))))))....(((..(((.(((((((((..(((......)))....))))))))).)))..))))))....... ( -43.00)
>DroSim_CAF1 3438 114 - 1
UGUUUGAGGCAUAAUUUCAGGCAACGUCUGGAGGGCAGGCCCUUCAACUCACUUGGUGGCAUGGGAGGGAAGAACACGCUCUGAAACCUCCUAUGGCACACAGUGCGAUAUAGA
(((((((((.....)))))))))..((((((((((....)))))))...((((..(((.(((((((((..(((......)))....))))))))).)))..)))).)))..... ( -44.90)
>DroEre_CAF1 3428 114 - 1
UGUUUGAGGCACAAUUUCAGGCAUCGCCUGGAGGGCAGACCCUUCAACUCGCUUGGAGGCAGGGGUGGGAAGAACACGCUUUGAAACUUCCUAUGGCACACACUGCGAUAUAGA
.((((((((.....))))))))(((((.(((((((....)))))))....(((.(((((((((((((.......))).)))))...)))))...))).......)))))..... ( -37.20)
>DroYak_CAF1 3410 114 - 1
UGUUUGAGGCACAAUUUCAGGCAACGCCUGGAGGGCAGGCCCUUCAACUCACUUGGCGGCAUGGGUGGGAAGAAGACGCUCUGAAACCUCUUGUGGCACAAACUGCGAUAAAGA
.(((((.(.(((((...(((((...)))))((((.(((((.((((..((((((((......))))))))..))))..)).)))...))))))))).).)))))........... ( -42.50)
>consensus
UGUUUGAGGCACAAUUUCAGGCAACGUCUGGAGGGCAGGCCCUUCAACUCACUUGGAGGCAUGGGAGGGAAGAACACGCUCUGAAACCUCCUAUGGCACACACUGCGAUAUAGA
(((((((((.....))))))))).(((.(((((((....)))))))...........(.(((((((((..(((......)))....))))))))).).......)))....... (-29.51 = -29.98 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:19 2006