Locus 4998

Sequence ID 3R_DroMel_CAF1
Location 13,163,940 – 13,164,073
Length 133
Max. P 0.690297
window8171 window8172

overview

Window 1

Location 13,163,940 – 13,164,045
Length 105
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 88.50
Mean single sequence MFE -26.67
Consensus MFE -23.78
Energy contribution -24.12
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.89
SVM decision value 0.33
SVM RNA-class probability 0.690297
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13163940 105 - 27905053
----GUUUCGCGCACCAAGCCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGAAUAACGAAAGACCAUCUCGA
----((((((((((..((((.((..(((.((((...(((.((.......)).)))..)))))))...)))))).)))))))))).((((....(....)....)))).. ( -28.60)
>DroSec_CAF1 193289 105 - 1
----GUUUCGCGCACCAAGCCGUCUGCACAAUAAUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGGAUAACGAAAGACCAUCUCGA
----((((((((((..((((.((..(((.(((((..(((.((.......)).))).))))))))...)))))).)))))))))).((((....(....)....)))).. ( -28.20)
>DroSim_CAF1 178619 105 - 1
----GUUUCGCGCACCAAGCCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCGAAGCGGAGGAUAACGAAAGACCAACUCGA
----((((((((((..((((.((..(((.((((...(((.((.......)).)))..)))))))...)))))).)))))))))).(((.....(....).....))).. ( -27.80)
>DroEre_CAF1 184336 109 - 1
GAGCGUUCCACUAACCAAGCCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCAAAGCGGAGGAUAACGAAAGACCAUCUCGA
(((.(((.....)))......(((((((.......)))...(((((((((...........(((((.((((....)))).))))))))))))))...))))...))).. ( -26.80)
>DroYak_CAF1 192372 98 - 1
A-----------CACCAAGCCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCAAAGCGGAGGAUAACGAAAGACCAUCUCGA
.-----------.........(((((((.......)))...(((((((((...........(((((.((((....)))).))))))))))))))...))))........ ( -26.10)
>DroAna_CAF1 180975 91 - 1
------------------CCCGUCUGCACAAUAUUUGCCCAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCAAAGCGGAGAAUAACGGAAGACUAUCACGA
------------------..(((..(((.......)))..((((.(((...((((((..(((((((.((((....)))).))))))))))))).))).))))...))). ( -22.50)
>consensus
____GUUUCGCGCACCAAGCCGUCUGCACAAUAUUUGCACAGUUAUCCUUUUUGUUUUAUUUGCUUAGCGCUUCUGUGCAAAGCGGAGGAUAACGAAAGACCAUCUCGA
.....................(((((((.......)))...(((((((((...........(((((.((((....)))).))))))))))))))...))))........ (-23.78 = -24.12 +   0.33)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 13,163,980 – 13,164,073
Length 93
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 79.90
Mean single sequence MFE -25.28
Consensus MFE -14.38
Energy contribution -14.38
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.57
SVM decision value 0.13
SVM RNA-class probability 0.599029
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13163980 93 + 27905053
GCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGGCUUGGUGCGCGAAAC------UGGAGACGGGC--UGG------GGGGAGUGGUGAAA
(((((((........(.....).....(((..((.....))..)))...))))))).(((....(------((....)))((--(..------....))).)))... ( -22.40)
>DroSec_CAF1 193329 99 + 1
GCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAUUAUUGUGCAGACGGCUUGGUGCGCGAAAC------UGGAGACGGGUGAUGGU-AGCCGGGGAGCGG-GGAA
(((((((........(.....).....(((..((.....))..)))...))))))).(((....(------(((..((.(....).))-..))))...))).-.... ( -26.90)
>DroSim_CAF1 178659 100 + 1
GCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGGCUUGGUGCGCGAAAC------UGGAGACGGUCGAUGGU-CGCCGGGGAGCGGGGGAA
(((((((........(.....).....(((..((.....))..)))...))))))).(((....(------(((.(((........))-).))))...)))...... ( -28.80)
>DroEre_CAF1 184376 102 + 1
GCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGGCUUGGUUAGUGGAACGCUCGCUGGGGA-----GCUGGGGAGCUGCGGAGCUGGGAAA
(((..(((...................(((..((.....))..))).(.(((.....))).)...((((.(..(...-----.)..).)))))))..)))....... ( -30.10)
>DroYak_CAF1 192412 91 + 1
GCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGGCUUGGUG-----------UGCUGGUGU-----GAUGGUGUGAUGGUGAGCUGGGAAA
.((.(((..((...(((...(..(((.(((..((.....))..))).((((......-----------.)))).)))-----..)..)))....))..))).))... ( -18.20)
>consensus
GCUAAGCAAAUAAAACAAAAAGGAUAACUGUGCAAAUAUUGUGCAGACGGCUUGGUGCGCGAAAC______UGGAGACGG__GAUGGU_AGCCGGGGAGCGGGGAAA
(((((((........(.....).....(((..((.....))..)))...)))))))................................................... (-14.38 = -14.38 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:55 2006