Locus 8187

Sequence ID X_DroMel_CAF1
Location 20,348,356 – 20,348,475
Length 119
Max. P 0.999993
window13458 window13459

overview

Window 8

Location 20,348,356 – 20,348,475
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.41
Mean single sequence MFE -35.62
Consensus MFE -24.80
Energy contribution -30.18
Covariance contribution 5.38
Combinations/Pair 1.26
Mean z-score -3.79
Structure conservation index 0.70
SVM decision value 5.77
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20348356 119 + 22224390
UCGAGAGAAGGCUCGACCAGACCAAAGAGAUAUGAUGAUAUGAUAUCAAAGUUUUUGGUUCGCCGAGCCGGAUGUUGCAUGAAAAAAAUUGUGCACUUCCUUGCAA-UUUUACCAUUCAA
((....)).((((((..(..(((((((((((((.((...)).)))))....))))))))..).))))))(((.((.(((..(......)..))))).)))......-............. ( -32.90)
>DroSec_CAF1 16277 111 + 1
CCAAUAUCCGGCUCGAG-GGACCAAAAUGAUAUGAUGA-----UAGCAAAGUUUUCGGUCCGCCAAGCCGGAUGUUGCAUUAAA--AAUAGUGCAGUUCCUUGCAA-UUUUCCCAUUCAA
.((((((((((((.(..-((((((((((..(((....)-----)).....))))).)))))..).)))))))))))).......--.....(((((....))))).-............. ( -33.80)
>DroEre_CAF1 13050 100 + 1
CCAUAAUCCGGCUCGAG-GGACCAUAAAGAUAUGUUUA-----UAGCGUAGAUUUUGGUCCAUUGAGCCGG-----------UA--AAUAAUGCAGUUGCUUGCAA-UUUGCCCAUUAAU
.........(((((((.-((((((.(((..(((((...-----..)))))..))))))))).)))))))((-----------((--(((..(((((....))))))-))))))....... ( -38.20)
>DroYak_CAF1 16826 112 + 1
ACAAUAUCCGGCUCGAG-GGACCACCAAUAUAUGUUAA-----UGUGGUUGUCUUUGGUCCUUCGUGCCGCAUAUUGCAUUAAA--AACAGUGCAGUUCUUUGCAAAAUUUCCCAUUAAA
.((((((.((((.((((-((((((.((((((((....)-----))).))))....)))))))))).)))).)))))).......--.....(((((....)))))............... ( -37.60)
>consensus
CCAAUAUCCGGCUCGAG_GGACCAAAAAGAUAUGAUGA_____UAGCAAAGUUUUUGGUCCGCCGAGCCGGAUGUUGCAUUAAA__AAUAGUGCAGUUCCUUGCAA_UUUUCCCAUUAAA
.((((((((((((((...(((((((((...(((((((......)))))))..)))))))))..))))))))))))))..............(((((....)))))............... (-24.80 = -30.18 +   5.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,348,356 – 20,348,475
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.41
Mean single sequence MFE -32.88
Consensus MFE -20.00
Energy contribution -22.56
Covariance contribution 2.56
Combinations/Pair 1.17
Mean z-score -3.04
Structure conservation index 0.61
SVM decision value 4.82
SVM RNA-class probability 0.999953
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20348356 119 - 22224390
UUGAAUGGUAAAA-UUGCAAGGAAGUGCACAAUUUUUUUCAUGCAACAUCCGGCUCGGCGAACCAAAAACUUUGAUAUCAUAUCAUCAUAUCUCUUUGGUCUGGUCGAGCCUUCUCUCGA
((((..((.....-(((((.(((((..........))))).)))))...))((((((((.(((((((.....((((........))))......)))))).).)))))))).....)))) ( -31.50)
>DroSec_CAF1 16277 111 - 1
UUGAAUGGGAAAA-UUGCAAGGAACUGCACUAUU--UUUAAUGCAACAUCCGGCUUGGCGGACCGAAAACUUUGCUA-----UCAUCAUAUCAUUUUGGUCC-CUCGAGCCGGAUAUUGG
........(((((-(((((......))))..)))--)))....(((.(((((((((((.(((((((((....((.((-----(....))).)))))))))))-.))))))))))).))). ( -37.50)
>DroEre_CAF1 13050 100 - 1
AUUAAUGGGCAAA-UUGCAAGCAACUGCAUUAUU--UA-----------CCGGCUCAAUGGACCAAAAUCUACGCUA-----UAAACAUAUCUUUAUGGUCC-CUCGAGCCGGAUUAUGG
........(((..-(((....))).)))......--..-----------(((((((...((((((.((.........-----...........)).))))))-...)))))))....... ( -26.05)
>DroYak_CAF1 16826 112 - 1
UUUAAUGGGAAAUUUUGCAAAGAACUGCACUGUU--UUUAAUGCAAUAUGCGGCACGAAGGACCAAAGACAACCACA-----UUAACAUAUAUUGGUGGUCC-CUCGAGCCGGAUAUUGU
.......((((((..((((......))))..)))--)))...(((((((.((((.(((.((((((....(((.....-----..........))).))))))-.))).)))).))))))) ( -36.46)
>consensus
UUGAAUGGGAAAA_UUGCAAGGAACUGCACUAUU__UUUAAUGCAACAUCCGGCUCGACGGACCAAAAACUACGAUA_____UCAACAUAUCUUUUUGGUCC_CUCGAGCCGGAUAUUGG
...............((((......))))..................((((((((((..(((((((((.........................)))))))))...))))))))))..... (-20.00 = -22.56 +   2.56)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:01 2006