Locus 1850

Sequence ID 2L_DroMel_CAF1
Location 5,088,581 – 5,088,737
Length 156
Max. P 0.532560
window2979 window2980

overview

Window 9

Location 5,088,581 – 5,088,697
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.57
Mean single sequence MFE -27.57
Consensus MFE -18.19
Energy contribution -19.00
Covariance contribution 0.81
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value -0.00
SVM RNA-class probability 0.532560
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5088581 116 - 22407834
GUAACCGGAAAGAAUGCUCUGCUAUCUGAAGGCGGGACUAGCGUGCUAAG-AACU---GCGAUAGCGGAGCAACAAACAACAGCAUUGGAACAACAUUUACCUAACAUAAUUUAGCACUC
......((......((((((((((((.....((((..((((....)).))-..))---))))))))))))))..............((......))....)).................. ( -27.50)
>DroSec_CAF1 17964 118 - 1
GUAACCGGAAAGAAUGCUCUGCUAUCUGAGGGCG-CACUCGCAUGCUAAG-AACAGCAGCGAUAGCGGAGCAACAAACAACAGCAUUGGAACAACAUUUAUCUAACAUAAUUUAGCACUC
......(((.(((.((((((((((((.(((....-..)))((.((((...-...))))))))))))))))))..............((......))))).)))................. ( -31.30)
>DroSim_CAF1 20585 118 - 1
GUAACCGGAAAGAAUGCUCUGCUAUCUGAGGACG-CACUCGCAUGCUAAG-AACAGCAGCGAUAGCGGAGCAACAAACAACAGCAUUGGAACAACAUUUACCUAACAUAAUUUAGCACUC
......((......((((((((((((.(((....-..)))((.((((...-...))))))))))))))))))..............((......))....)).................. ( -31.90)
>DroYak_CAF1 19519 96 - 1
GUAACCGGAAAGAAUGUUCUGCUAUCUGAGG----CACUCGCAUGCUAAGGAACACC--CGAUAGCGGCGCAA------------------CAACAUUUACCUAACAUAAUUUAGCACUC
......((...(((((((((((((((...((----((......))))..((.....)--))))))))).....------------------.))))))).)).................. ( -19.60)
>consensus
GUAACCGGAAAGAAUGCUCUGCUAUCUGAGGGCG_CACUCGCAUGCUAAG_AACAGC_GCGAUAGCGGAGCAACAAACAACAGCAUUGGAACAACAUUUACCUAACAUAAUUUAGCACUC
..............((((((((((((.(((.......)))....((............))))))))))))))................................................ (-18.19 = -19.00 +   0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,088,621 – 5,088,737
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.20
Mean single sequence MFE -30.10
Consensus MFE -21.69
Energy contribution -22.50
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.54
Structure conservation index 0.72
SVM decision value -0.01
SVM RNA-class probability 0.530375
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5088621 116 - 22407834
GUGGCACCAUAAAUUCUGAUCAACUAUUAGUGCAUGAAAAGUAACCGGAAAGAAUGCUCUGCUAUCUGAAGGCGGGACUAGCGUGCUAAG-AACU---GCGAUAGCGGAGCAACAAACAA
(((....)))...(((((....(((.((........)).)))...)))))....((((((((((((.....((((..((((....)).))-..))---))))))))))))))........ ( -29.80)
>DroSec_CAF1 18004 118 - 1
GUGGCACCAUAAAUUCUGAUCAACUAUUAGUGCAUGAAAAGUAACCGGAAAGAAUGCUCUGCUAUCUGAGGGCG-CACUCGCAUGCUAAG-AACAGCAGCGAUAGCGGAGCAACAAACAA
(((....)))...(((((....(((.((........)).)))...)))))....((((((((((((.(((....-..)))((.((((...-...))))))))))))))))))........ ( -34.20)
>DroSim_CAF1 20625 118 - 1
GUGGCACCAUAAAUUCUGAUCAACUAUUAGUGCAUGAAAAGUAACCGGAAAGAAUGCUCUGCUAUCUGAGGACG-CACUCGCAUGCUAAG-AACAGCAGCGAUAGCGGAGCAACAAACAA
(((....)))...(((((....(((.((........)).)))...)))))....((((((((((((.(((....-..)))((.((((...-...))))))))))))))))))........ ( -34.20)
>DroYak_CAF1 19548 107 - 1
GUGGCCCCAUAAAUUCUGAUCAACUAUUAGUGCAUGAAAAGUAACCGGAAAGAAUGUUCUGCUAUCUGAGG----CACUCGCAUGCUAAGGAACACC--CGAUAGCGGCGCAA-------
(((....)))...(((((....(((.((........)).)))...)))))....(((.((((((((...((----((......))))..((.....)--))))))))).))).------- ( -22.20)
>consensus
GUGGCACCAUAAAUUCUGAUCAACUAUUAGUGCAUGAAAAGUAACCGGAAAGAAUGCUCUGCUAUCUGAGGGCG_CACUCGCAUGCUAAG_AACAGC_GCGAUAGCGGAGCAACAAACAA
(((....)))...(((((....(((.((........)).)))...)))))....((((((((((((.(((.......)))....((............))))))))))))))........ (-21.69 = -22.50 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:55 2006