Locus 7704

Sequence ID 3L_DroMel_CAF1
Location 20,606,801 – 20,606,893
Length 92
Max. P 0.629437
window12530 window12531

overview

Window 0

Location 20,606,801 – 20,606,893
Length 92
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.50
Mean single sequence MFE -23.05
Consensus MFE -17.08
Energy contribution -17.68
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.74
SVM decision value 0.02
SVM RNA-class probability 0.544706
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20606801 92 + 23771897
GGAAGCAG-------------AAA-AAAAGUGAAGAAAAAUGAGCUGCAAGA----AAAGAGCUCAAGAGCAGCUCCCACGGUAGCUGAAUUGGU----------AACUCCUGCGCCAUU
((..((((-------------...-...............((((((......----....))))))....(((((((...)).))))).......----------.....)))).))... ( -21.80)
>DroSec_CAF1 51671 92 + 1
GGAAGCAG-------------AAA-AAAAGUGAAGAAAAAUGAGCUGCAAGA----AAAGAGCUCAAGAGCAGCUCCCACGGUAGCUGAAUUGGU----------AACUCCUGCGCCAUU
((..((((-------------...-...............((((((......----....))))))....(((((((...)).))))).......----------.....)))).))... ( -21.80)
>DroAna_CAF1 73572 119 + 1
GGAAGCAGGGGUACUAACAAAAAA-AAAAGGCAGAAAAAAUGAGCAGCCAGAAAAAAAAGAGCUCAAGAGCAGCUCCCACGGUAGCUGGAUUGGUUUCCACAGCCAACUCCUGGGCCAUU
((...(((((((............-....(((..............)))..........((((((....).)))))....(((.(.((((......))))).))).)))))))..))... ( -29.94)
>DroSim_CAF1 46466 93 + 1
GGAAGCAG-------------AAAAAAAAGUGAAGAAAAAUGAGCUGCAAGA----AAAGAGCUCAAGAGCAGCUCCCACGGUAGCUGAAUUGGU----------AACUCCUGCGCCAUU
((..((((-------------...................((((((......----....))))))....(((((((...)).))))).......----------.....)))).))... ( -21.80)
>DroEre_CAF1 44200 91 + 1
GGAAGCAG-------------ACA--AAAGUGAAGAAAAAUGAGCUGCAAGA----AAAGAGCUCAAGAGCAGCUCCCACGGUAGCGGAAUUGGU----------AACUCCUGCACCAUU
((.(((..-------------((.--...)).........((((((......----....))))))......))).))..(((.(((((......----------...))).)))))... ( -19.90)
>consensus
GGAAGCAG_____________AAA_AAAAGUGAAGAAAAAUGAGCUGCAAGA____AAAGAGCUCAAGAGCAGCUCCCACGGUAGCUGAAUUGGU__________AACUCCUGCGCCAUU
((..((((................................((((((..............))))))....(((((((...)).)))))......................)))).))... (-17.08 = -17.68 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,606,801 – 20,606,893
Length 92
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.50
Mean single sequence MFE -24.24
Consensus MFE -16.22
Energy contribution -16.46
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.86
Structure conservation index 0.67
SVM decision value 0.20
SVM RNA-class probability 0.629437
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20606801 92 - 23771897
AAUGGCGCAGGAGUU----------ACCAAUUCAGCUACCGUGGGAGCUGCUCUUGAGCUCUUU----UCUUGCAGCUCAUUUUUCUUCACUUUU-UUU-------------CUGCUUCC
......(((((((..----------.(((............)))(((((((....(((.....)----))..)))))))................-)))-------------)))).... ( -22.20)
>DroSec_CAF1 51671 92 - 1
AAUGGCGCAGGAGUU----------ACCAAUUCAGCUACCGUGGGAGCUGCUCUUGAGCUCUUU----UCUUGCAGCUCAUUUUUCUUCACUUUU-UUU-------------CUGCUUCC
......(((((((..----------.(((............)))(((((((....(((.....)----))..)))))))................-)))-------------)))).... ( -22.20)
>DroAna_CAF1 73572 119 - 1
AAUGGCCCAGGAGUUGGCUGUGGAAACCAAUCCAGCUACCGUGGGAGCUGCUCUUGAGCUCUUUUUUUUCUGGCUGCUCAUUUUUUCUGCCUUUU-UUUUUUGUUAGUACCCCUGCUUCC
...((((((((((((((.((.(....)))..)))))).)).)))((((.(((...(((.........))).))).)))).........)))....-......(..((((....))))..) ( -29.30)
>DroSim_CAF1 46466 93 - 1
AAUGGCGCAGGAGUU----------ACCAAUUCAGCUACCGUGGGAGCUGCUCUUGAGCUCUUU----UCUUGCAGCUCAUUUUUCUUCACUUUUUUUU-------------CUGCUUCC
......(((((((..----------.(((............)))(((((((....(((.....)----))..))))))).................)))-------------)))).... ( -22.20)
>DroEre_CAF1 44200 91 - 1
AAUGGUGCAGGAGUU----------ACCAAUUCCGCUACCGUGGGAGCUGCUCUUGAGCUCUUU----UCUUGCAGCUCAUUUUUCUUCACUUU--UGU-------------CUGCUUCC
.(((((((.(((((.----------....))))))).)))))((((((......(((((((...----....).)))))).........((...--.))-------------..)))))) ( -25.30)
>consensus
AAUGGCGCAGGAGUU__________ACCAAUUCAGCUACCGUGGGAGCUGCUCUUGAGCUCUUU____UCUUGCAGCUCAUUUUUCUUCACUUUU_UUU_____________CUGCUUCC
((((((((((((..............(((............)))(((((.(....)))))).......)))))).)).))))...................................... (-16.22 = -16.46 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:27 2006