Locus 1832

Sequence ID 2L_DroMel_CAF1
Location 5,063,979 – 5,064,163
Length 184
Max. P 0.996013
window2939 window2940

overview

Window 9

Location 5,063,979 – 5,064,072
Length 93
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 67.37
Mean single sequence MFE -37.60
Consensus MFE -9.37
Energy contribution -8.76
Covariance contribution -0.61
Combinations/Pair 1.64
Mean z-score -4.32
Structure conservation index 0.25
SVM decision value 2.64
SVM RNA-class probability 0.996013
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5063979 93 - 22407834
GAAGGGGGGGGGGGGGGUUGAGA---GAGAGGUUGAGUUGAAGGUACAGCGUG--UGU--AAG-CUGUGUUUGUCUUUACCUUCUUUCUUU----------------CUCCCUUUCU
(((((((((..((..((((....---))(((((.(((....(..((((((...--...--..)-)))))..)..))).)))))))..))..----------------))))))))). ( -41.30)
>DroSec_CAF1 11060 89 - 1
GCUGGGUGACAGGGAGGUUGA-------GAGGUUGAGUUGGAGGUAAAGCGUG--UGU--AAG-CUGUGUUUGUCUUUACCUUCUUUCCUU----------------CUCCCUUUCU
....(....)((..(((..((-------((((..(((..((((((((((((.(--..(--...-..)..).)).)))))))))).))))))----------------))))))..)) ( -29.20)
>DroSim_CAF1 11527 89 - 1
GCUGGGGGGGAGGGGGGGUGA-------GAGGUUGAGUUGGAGGUAAAGCGUG--UGU--AAG-CUGUGUUUGUCUUUACCUUCUUUCCUU----------------CUCCCUUUCU
...(..((((((((((((.((-------.((((.(((.(..(.(...(((...--...--..)-)).).)..).))).)))))).))))))----------------))))))..). ( -35.00)
>DroEre_CAF1 11417 93 - 1
GGUGGGGGGAGGGAGAGGUGGGAGGUGAGAGGUUG-----UAGGUAUAGCGUGUGUGU--AAG-CUGUGUUUGUCUUCACCUGCUUUCUUU----------------CUCCCUCCCU
.....(((((((((((((.((.((((((.(((...-----((..((((((........--..)-)))))..))))))))))).))...)))----------------)))))))))) ( -42.70)
>DroYak_CAF1 11317 105 - 1
---GAGGGAAGGGGGA----GGAGGUGAGAGGUUGUGUUUUAGGUACAGCGUG--UGU--AAG-CUAUGUUUGUCUUCGUCUUCUUUCUUUCGACCACCCUCCCUACCUCCCUCCCU
---((((((..(((((----((.(((((((((..(......(((.((((((((--(..--..)-).))).)))))))......)..)))))).)))..)))))))...))))))... ( -38.60)
>DroAna_CAF1 9835 89 - 1
GC---GGAGAAAGAGGGAAGA-------AAGGUGGGUAGAAAGGUGAGGCGUG--UGUAUAAGCCUGUGUUUGUAUUUGCCUUUCUUUCUU----------------CUGGCUUGCU
((---(.((..((((((((((-------((((..((((.(((..(.((((...--.......)))))..))).))))..))))))))))))----------------))..))))). ( -38.80)
>consensus
GCUGGGGGGAAGGGGGGGUGA_______GAGGUUGAGUUGAAGGUAAAGCGUG__UGU__AAG_CUGUGUUUGUCUUUACCUUCUUUCCUU________________CUCCCUUUCU
..........(((((((...........((((.......(((((((.((((....................)).)).)))))))...))))................)))))))... ( -9.37 =  -8.76 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,064,072 – 5,064,163
Length 91
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -22.77
Consensus MFE -17.49
Energy contribution -17.68
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -1.65
Structure conservation index 0.77
SVM decision value 0.14
SVM RNA-class probability 0.603990
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5064072 91 - 22407834
AAACAAGCC---GAAAAUCAGCUGUUUCCUAGGUACAAUUUGGCAAGCGGAACAAACGGAAGUGGAAACGAAACAGCUGG-------UACCAAACAUG---AAG
.........---....((((((((((((...........................((....))(....))))))))))))-------)..........---... ( -21.90)
>DroSec_CAF1 11149 90 - 1
AAACAAGCC---GAAAAUCAGCUGUUUCCUAGGUACAAUUUGGCAAGCGGAACAAGCGGAAGUGGA-ACGAAACAGCUGG-------UACAAAACAGG---GUG
......(((---....((((((((((((..........(((.(....).)))...((....))...-..)))))))))))-------).(......))---)). ( -22.30)
>DroSim_CAF1 11616 91 - 1
AAACAAGCC---GAAAAUCAGCUGUUUCCUAGGUACAAUUUGGCAAGCGGAACAAGCGGAAGUGGAAACGAAACAGCUGG-------UACAAAACAGG---GUG
......(((---....((((((((((((...........................((....))(....))))))))))))-------).(......))---)). ( -23.50)
>DroEre_CAF1 11510 94 - 1
AAACAAGCC---GAAAAUCAGCUGUUUCCUAGGUACAAUUUGGCAUGCGGAACAAGCGGAAGUGGAAACGAAACAGCUGG-------UACAAAACUAAGUGAUG
.........---....((((((((((((..........(((.((.((.....)).)).)))..(....))))))))))))-------)................ ( -23.30)
>DroYak_CAF1 11422 88 - 1
AAACAAGCC---GAAAAUCAGCUGUUUCCUAGGUACAAUUUGGCAGACGGAACAAGCGGAAGUGGAAGCGAAACAGCUGC-------UACAAGCGUAC------
......((.---......((((((((((((........((((.....))))....((....))...)).)))))))))).-------.....))....------ ( -20.92)
>DroPer_CAF1 9093 99 - 1
AAACAAACCCCAGAGUAUCAGCUGUUUCCUCGGUACACUUUGGCAA-CGGAACAGGCGGAAGUGGAAACGAAACAUAUGCCCGCCUCCACCCAAUAGG----UG
......((((((((((....((((......))))..)))))))...-.(((...(((((..(((...........)))..))))))))........))----). ( -24.70)
>consensus
AAACAAGCC___GAAAAUCAGCUGUUUCCUAGGUACAAUUUGGCAAGCGGAACAAGCGGAAGUGGAAACGAAACAGCUGG_______UACAAAACAGG____UG
..................((((((((((...........................((....))(....)))))))))))......................... (-17.49 = -17.68 +   0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:17 2006