Locus 4306

Sequence ID	3L_DroMel_CAF1
Location	12,642,183 – 12,642,293
Length	110
Max. P	0.825458

overview

Window 1

Location	12,642,183 – 12,642,293
Length	110
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.42
Mean single sequence MFE	-34.42
Consensus MFE	-23.37
Energy contribution	-24.73
Covariance contribution	1.36
Combinations/Pair	1.07
Mean z-score	-2.15
Structure conservation index	0.68
SVM decision value	0.70
SVM RNA-class probability	0.825458
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12642183 110 + 23771897
AACGGAACUGCGUGGAACGCGCAAACUGAGCGCCA--------GAGGUCGCCACUCUACAUAAAUAGUUUGUGACCUUUCGCUUGUUUUACAAACAAGCA-GUGAACAGUUGGCGUCGC
..(((...((((((...))))))..))).((((((--------((((((((....(((......)))...))))))))..(((((((.....))))))).-.........))))))... ( -37.20)
>DroVir_CAF1 6430 111 + 1
AAUGG---UGUGCG-AAC--ACAAACACUGCGCCAGAGGCA-AGAGGUCGCCACUCUACACAAAUAGUUUGUGACCUUUUGGUUGUUUUACAAACAAGCC-CCAAACAGUUGGCGUCGA
....(---(((...-.))--)).....(.(((((((..(((-(((((((((....(((......)))...))))))))))).(((((.....)))))...-.....)..))))))).). ( -33.00)
>DroEre_CAF1 6505 110 + 1
AACGGAACUGCGUGGAACUCGCAAACUGAGCGCCA--------GAGGUCGCCACUCUACAUAAAUAGUUUGUGACCUUUCGCUUGUUUUACAAACAAGCU-CCCAACAGUUGGCGUCGC
..(((...((((.......))))..))).((((((--------((((((((....(((......)))...))))))))..(((((((.....))))))).-.........))))))... ( -34.10)
>DroYak_CAF1 5915 110 + 1
AACGGAACUGCGUGGCACUCGCUAACUGGGCGCCA--------GAGGUCGCCACUCUACAUAAAUAGUUUGUGACCUCUCGCUUGUUUUACAAACAAGCU-CCCAACAGCUGGCGUCGC
..(((....(((.......)))...)))(((((((--------((((((((....(((......)))...))))))))..(((((((.....))))))).-.........))))))).. ( -39.00)
>DroMoj_CAF1 6989 106 + 1
AAUGG---UGUGCG-AAC--ACAAACACUGCGCCAGCGGCAAAGAGGUCGCCACUCUACACAAAUAGUUUGUGACCUUUUGGUUGUUUUACAAACAAGCCCCCAAACAGUUU-------
....(---(((...-.))--))((((...((....))(((.((((((((((....(((......)))...))))))))))..(((((.....))))))))........))))------- ( -26.50)
>DroAna_CAF1 7049 110 + 1
AACGGAACUGCGUCGAGCACACAAACGCAGCGCCA--------GAGGUCGCCACUCUACAUAAAUAGUUUGUGACCUUUCGCUUGUUUUACAAACAAGCU-CCAAACAGCUGGCGUCGA
..(((..((((((...........))))))(((((--------((((((((....(((......)))...)))))))...(((((((.....))))))).-........))))))))). ( -36.70)
>consensus
AACGGAACUGCGUGGAAC_CACAAACUCAGCGCCA________GAGGUCGCCACUCUACAUAAAUAGUUUGUGACCUUUCGCUUGUUUUACAAACAAGCU_CCAAACAGUUGGCGUCGC
........((((.......))))......((((((........((((((((....(((......)))...))))))))..(((((((.....)))))))...........))))))... (-23.37 = -24.73 +   1.36)

alignment

secondary structure

dotplot

Window 2

Location	12,642,183 – 12,642,293
Length	110
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.42
Mean single sequence MFE	-36.07
Consensus MFE	-22.64
Energy contribution	-23.50
Covariance contribution	0.86
Combinations/Pair	1.08
Mean z-score	-1.60
Structure conservation index	0.63
SVM decision value	-0.01
SVM RNA-class probability	0.530924
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12642183 110 - 23771897
GCGACGCCAACUGUUCAC-UGCUUGUUUGUAAAACAAGCGAAAGGUCACAAACUAUUUAUGUAGAGUGGCGACCUC--------UGGCGCUCAGUUUGCGCGUUCCACGCAGUUCCGUU
(.(((((.(((((..(.(-((((((((.....)))))))...(((((.((..((((....))))..))..))))).--------.)).)..))))).))(((.....))).))).)... ( -33.60)
>DroVir_CAF1 6430 111 - 1
UCGACGCCAACUGUUUGG-GGCUUGUUUGUAAAACAACCAAAAGGUCACAAACUAUUUGUGUAGAGUGGCGACCUCU-UGCCUCUGGCGCAGUGUUUGU--GUU-CGCACA---CCAUU
...............(((-.(((((.(((.....))).)))..(..(((((((...((((((..((.(((((....)-)))).)).)))))).))))))--)..-)))...---))).. ( -31.10)
>DroEre_CAF1 6505 110 - 1
GCGACGCCAACUGUUGGG-AGCUUGUUUGUAAAACAAGCGAAAGGUCACAAACUAUUUAUGUAGAGUGGCGACCUC--------UGGCGCUCAGUUUGCGAGUUCCACGCAGUUCCGUU
..((((..((((((..((-(((((((.....((((.((((..(((((.((..((((....))))..))..))))).--------...))))..)))))))))))))..)))))).)))) ( -38.30)
>DroYak_CAF1 5915 110 - 1
GCGACGCCAGCUGUUGGG-AGCUUGUUUGUAAAACAAGCGAGAGGUCACAAACUAUUUAUGUAGAGUGGCGACCUC--------UGGCGCCCAGUUAGCGAGUGCCACGCAGUUCCGUU
(((.(((..((((..(((-.(((((((((.....))))))(((((((.((..((((....))))..))..))))))--------)))).)))...))))..)))...)))......... ( -40.10)
>DroMoj_CAF1 6989 106 - 1
-------AAACUGUUUGGGGGCUUGUUUGUAAAACAACCAAAAGGUCACAAACUAUUUGUGUAGAGUGGCGACCUCUUUGCCGCUGGCGCAGUGUUUGU--GUU-CGCACA---CCAUU
-------........(((..(((((.(((.....))).)))..(..(((((((...((((((..((((((((.....)))))))).)))))).))))))--)..-)))...---))).. ( -35.10)
>DroAna_CAF1 7049 110 - 1
UCGACGCCAGCUGUUUGG-AGCUUGUUUGUAAAACAAGCGAAAGGUCACAAACUAUUUAUGUAGAGUGGCGACCUC--------UGGCGCUGCGUUUGUGUGCUCGACGCAGUUCCGUU
..((((((((........-.(((((((.....)))))))...(((((.((..((((....))))..))..))))))--------))))((((((((.(....)..))))))))...))) ( -38.20)
>consensus
GCGACGCCAACUGUUUGG_AGCUUGUUUGUAAAACAAGCGAAAGGUCACAAACUAUUUAUGUAGAGUGGCGACCUC________UGGCGCUCAGUUUGCG_GUUCCACGCAGUUCCGUU
....(((((...........(((((((.....)))))))...(((((.((..((((....))))..))..))))).........)))))........(((.......)))......... (-22.64 = -23.50 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:08 2006