Locus 3867

Sequence ID 3L_DroMel_CAF1
Location 11,193,438 – 11,193,605
Length 167
Max. P 0.770185
window6018 window6019

overview

Window 8

Location 11,193,438 – 11,193,544
Length 106
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 84.22
Mean single sequence MFE -29.63
Consensus MFE -20.66
Energy contribution -21.97
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -3.01
Structure conservation index 0.70
SVM decision value 0.53
SVM RNA-class probability 0.770185
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11193438 106 - 23771897
CCCAAAUCAUAAUCAAAUUGGGAACAAGGCCAAAACGAAG-AGAUUUGUUCCGAAUCUGUUUGAUUCUUGGCCGCUGGCCAAGAAUGAAUGCC---UUAAAUUUUGAUUG
.........((((((((..(....)(((((.....((((.-(((((((...))))))).))))((((((((((...))))))))))....)))---))....)))))))) ( -34.70)
>DroSec_CAF1 2585 106 - 1
UCCAAAUCAUAAUCAAUUUGGGAACAAGGCCAAAACGAAG-AGAUUUGUUCCGAAUCUGUUUGAUUUUUGGCCGCUGGCCAACAAUUAAUGCC---ACAAAUUUUGAUUG
.........(((((((((((.......((((((((((((.-(((((((...))))))).))))..))))))))..((((...........)))---))))))..)))))) ( -29.70)
>DroSim_CAF1 2426 106 - 1
CCCAAAUCAUAAUCAAUUUGGGAACAAGGCCAAAACGAAG-AGAUUUGUUCCGAAUCUGUUUGAUUCUUGGCCGCUGGCCAACAAUUAAUGCC---ACAAAUUUUGAUUU
(((((((........)))))))..(((((((((((((((.-(((((((...))))))).)))).)).))))))(.((((...........)))---)).....))).... ( -30.00)
>DroEre_CAF1 2846 106 - 1
CCCAAAUCAUUAUCAAUUUGGGAACAAGGCCAAAACCAAG-AGAUUUGUGCCGAAUCUGUUUGAUUCUUGGGCGCUGGCCAAGAAUUAAUGCC---ACACAUUUUUAUUG
(((((((........))))))).....(((..........-(((((((...)))))))..(((((((((((.(...).))))))))))).)))---.............. ( -28.90)
>DroYak_CAF1 2535 106 - 1
CCCAAAUCACGAUCAAUUUGGGAACAAGGCCAAAAGCAAG-AGAUUUGUUCCGAAUCUGUUUGAUUCUUGGACGCUGGCCAAGAAUUAAUGCC---ACACAUUUUGAUUG
.........(((((((..((((((((((.((........)-.).))))))))........(((((((((((.(....))))))))))))....---...))..))))))) ( -28.70)
>DroAna_CAF1 2391 109 - 1
CCGAAA-CUUAAUCAAUUUUAGAGCAAGGCCAUAACCAAGAAGAUUUGUUCUGAUUCCAUUUGAUUCUUGGCUAUACGCCAAGAAAUAAUUUUUCUCUAAGAUUAGGCUA
......-(((((((....((((((((((................))))))))))..........((((((((.....))))))))...............)))))))... ( -25.79)
>consensus
CCCAAAUCAUAAUCAAUUUGGGAACAAGGCCAAAACCAAG_AGAUUUGUUCCGAAUCUGUUUGAUUCUUGGCCGCUGGCCAAGAAUUAAUGCC___ACAAAUUUUGAUUG
(((((((........))))))).....(((...........((((((.....))))))..((((((((((((.....)))))))))))).)))................. (-20.66 = -21.97 +   1.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,193,504 – 11,193,605
Length 101
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 78.54
Mean single sequence MFE -20.28
Consensus MFE -10.48
Energy contribution -10.87
Covariance contribution 0.39
Combinations/Pair 1.18
Mean z-score -2.00
Structure conservation index 0.52
SVM decision value 0.29
SVM RNA-class probability 0.670485
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11193504 101 - 23771897
GACAGGUC-UUGACGGCAAAAUCAAGAAC-CUACAAAUUUAAUAAUACAACUAAUUGGGCGUGCCCAAAUCAUAAUCAAAUUGGGAACAAGGCCAAAACGAAG
...(((((-((((........))))).))-))......................((((.(...(((((............))))).....).))))....... ( -19.80)
>DroPse_CAF1 2480 90 - 1
GACAUUCCCCUGA---------CAAGAAACACCCAAAUUU--UGAU-CAACCAAUUAAGCAGGCCUAAA-CACGAUCAAUUUGGGAACAAGGCCACAGCGGAG
.....(((.(((.---------(((((..........)))--))..-..............(((((...-..(((.....)))......))))).))).))). ( -16.70)
>DroSec_CAF1 2651 86 - 1
----GGUC-UA-----------CAAGAGC-CUACAAAUUGAAUAAUACAACUAAUUGGGCGUGUCCAAAUCAUAAUCAAUUUGGGAACAAGGCCAAAACGAAG
----((((-(.-----------.....((-(((....(((.......))).....)))))((..((((((........))))))..)).)))))......... ( -19.60)
>DroSim_CAF1 2492 90 - 1
GACAGGUC-UU-----------CAAGAGC-CUACAAAUUGAAUAAUACAACUAAUUGGGCGUGCCCAAAUCAUAAUCAAUUUGGGAACAAGGCCAAAACGAAG
....((((-((-----------.....((-(((....(((.......))).....)))))((.(((((((........))))))).))))))))......... ( -22.40)
>DroEre_CAF1 2912 101 - 1
GACAGGUC-UUGACGGCAUAUUCAAGAGC-CCACAAAUUUAAUAAUACAACUAAUUAGGCAUGCCCAAAUCAUUAUCAAUUUGGGAACAAGGCCAAAACCAAG
....((((-(((..(((..........))-)................................(((((((........)))))))..)))))))......... ( -21.60)
>DroYak_CAF1 2601 101 - 1
GACAGGUC-GUGACGGCAUAUUCAAGAGC-CAACAAAUUUAAUAAUACAACUAAUUAGGCGUGCCCAAAUCACGAUCAAUUUGGGAACAAGGCCAAAAGCAAG
....((((-((((.(((((........((-(..........................))))))))....))))))))..(((((........)))))...... ( -21.57)
>consensus
GACAGGUC_UUGA_________CAAGAGC_CUACAAAUUUAAUAAUACAACUAAUUAGGCGUGCCCAAAUCAUAAUCAAUUUGGGAACAAGGCCAAAACGAAG
.........................................................(((.(.(((((((........)))))))....).)))......... (-10.48 = -10.87 +   0.39)

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 11:08:42 2006