Locus 8705

Sequence ID 3L_DroMel_CAF1
Location 22,603,117 – 22,603,240
Length 123
Max. P 0.976008
window14264 window14265 window14266

overview

Window 4

Location 22,603,117 – 22,603,207
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 83.21
Mean single sequence MFE -21.59
Consensus MFE -19.40
Energy contribution -19.34
Covariance contribution -0.06
Combinations/Pair 1.05
Mean z-score -2.67
Structure conservation index 0.90
SVM decision value 1.76
SVM RNA-class probability 0.976008
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22603117 90 - 23771897
AAGUAGAAUAGCAGGCUUAUCACAUGUUUAAUUCA-AUCUGCUGUGAGAUUCUUCUAUUCUACUUUCGAC-AACACCCGUUAACAUCACACC
(((((((((((.(((....(((((.((........-....)))))))...))).))))))))))).....-..................... ( -19.20)
>DroVir_CAF1 75040 91 - 1
AAGUAGAAUAGCAGGCUUAUCACAUGUACAAUUCA-ACCUAGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGCUAGCGUCUUUUU
(((((((((((.(((....((((((..........-.....))))))...))).)))))))))))..(((..............)))..... ( -20.30)
>DroGri_CAF1 64873 91 - 1
AAGUAGAAUAGCAGGCUUAUCACAUGUAACAUUCG-ACAUGGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGCUAGCGUCACAUU
(((((((((((.((.(((((..(((((........-)))))..)))))...)).)))))))))))..(((..............)))..... ( -24.14)
>DroWil_CAF1 83740 92 - 1
AAGUAGAAUAGCAGGCUUAUCACAUGUUCCCUUUACAACCGGUGUGAGAUUCUUCUAUUCUACUUUCGAAAAGCACCCGAUAACAACAAAAU
(((((((((((.(((....(((((((((........)))..))))))...))).)))))))))))(((.........)))............ ( -20.20)
>DroMoj_CAF1 93858 91 - 1
AAGUAGAAUAGCAGGCUUAUCACAUGUACCAUUUG-ACCGAGUGUGAGAUUCUUCUAUUCUACUUUCGACAAGCACCAGUCAGCGUCGUUUU
(((((((((((.(((....((((((..........-.....))))))...))).))))))))))).((((..((........)))))).... ( -23.76)
>DroAna_CAF1 58072 90 - 1
AAGUAGAAUAGCAGGCUUAUCACAGGUUCC-UUUA-ACCCACUGUGAGAUUCUUCUAUUCUACUUUCGAGAAACACCCGUAAACACCGAUCU
(((((((((((.(((....((((((.....-....-.....))))))...))).)))))))))))........................... ( -21.94)
>consensus
AAGUAGAAUAGCAGGCUUAUCACAUGUACCAUUCA_ACCUAGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGUUAACAUCAAAUU
(((((((((((.(((....((((((................))))))...))).)))))))))))........................... (-19.40 = -19.34 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,603,129 – 22,603,240
Length 111
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.93
Mean single sequence MFE -28.39
Consensus MFE -23.01
Energy contribution -23.04
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.76
Structure conservation index 0.81
SVM decision value 0.94
SVM RNA-class probability 0.886824
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22603129 111 + 23771897
ACGGGUGUU-GUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGAUUGAAUUAAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAUAGACACGCCGAUCGU-GGAAAAUCCUCGA
.((((((((-.....(((((((((((.((....(((((.................))))).....)).)))))))))))......))))).))).(((.-((.....)).))) ( -33.63)
>DroVir_CAF1 75052 111 + 1
GCUGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACACUAGGUUGAAUUGUACAUGUGAUAAGCCUGCUAUUCUACUUGCCAA-UCCACACCGAUCAA-AAUAUAUAGAGAA
..((((((..((.(.(((((((((((.((....(((((....((........)).))))).....)).)))))))))))..).)-)..)))))).....-............. ( -25.10)
>DroPse_CAF1 71552 112 + 1
ACGGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCGGAUUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAUACACACCGAUCGU-GCUAGCCAUAUCC
.(((((((.......(((((((((((.((....(((((..(............).))))).....)).))))))))))).......)))).))).....-............. ( -27.74)
>DroGri_CAF1 64885 111 + 1
GCUGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACACCAUGUCGAAUGUUACAUGUGAUAAGCCUGCUAUUCUACUUGCCAA-UCCACACCGAUCAG-AGUAAAACAAAAA
..((((((..((.(.(((((((((((.((....(((((...(((........)))))))).....)).)))))))))))..).)-)..)))))).....-............. ( -25.10)
>DroAna_CAF1 58084 112 + 1
ACGGGUGUUUCUCGAAAGUAGAAUAGAAGAAUCUCACAGUGGGUUAAA-GGAACCUGUGAUAAGCCUGCUAUUCUACUUGCUAAAAACCCACCGGUCGUUGGAAUAUUCUUGG
..(((((((((.((((((((((((((.((....((((((.(..(....-.)..))))))).....)).)))))))))))........((....)))))..))))))))).... ( -31.00)
>DroPer_CAF1 78700 112 + 1
ACGGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCGGAUUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAUACACACCGAUCNN-NNNNNNNNNNNNN
.(((((((.......(((((((((((.((....(((((..(............).))))).....)).))))))))))).......)))).))).....-............. ( -27.74)
>consensus
ACGGGUGUUUGUCGAAAGUAGAAUAGAAGAAUCUCACAGCAGAUUGAAUGGAACAUGUGAUAAGCCUGCUAUUCUACUUGCCAAAUACACACCGAUCGU_GGUAAAUACAUAA
...(((((.......(((((((((((.((....(((((.................))))).....)).))))))))))).........))))).................... (-23.01 = -23.04 +   0.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,603,129 – 22,603,240
Length 111
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.93
Mean single sequence MFE -31.67
Consensus MFE -25.80
Energy contribution -26.46
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.83
Structure conservation index 0.81
SVM decision value 1.58
SVM RNA-class probability 0.965335
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22603129 111 - 23771897
UCGAGGAUUUUCC-ACGAUCGGCGUGUCUAUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUUAAUUCAAUCUGCUGUGAGAUUCUUCUAUUCUACUUUCGAC-AACACCCGU
(((.((.....))-.))).(((.((((...(((.(((((((((((.(((....(((((.((............)))))))...))).))))))))))))))..-.))))))). ( -33.30)
>DroVir_CAF1 75052 111 - 1
UUCUCUAUAUAUU-UUGAUCGGUGUGGA-UUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUACAAUUCAACCUAGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGC
.............-......(((((...-((((.(((((((((((.(((....((((((...............))))))...))).)))))))))))))))...)))))... ( -31.16)
>DroPse_CAF1 71552 112 - 1
GGAUAUGGCUAGC-ACGAUCGGUGUGUAUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAAUCCGCUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCCGU
.(((...(....)-...)))(((((....((((.(((((((((((.(((....(((((.((............)))))))...))).)))))))))))))))...)))))... ( -30.00)
>DroGri_CAF1 64885 111 - 1
UUUUUGUUUUACU-CUGAUCGGUGUGGA-UUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUAACAUUCGACAUGGUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCAGC
.............-......(((((...-((((.(((((((((((.((.(((((..(((((........)))))..)))))...)).)))))))))))))))...)))))... ( -34.50)
>DroAna_CAF1 58084 112 - 1
CCAAGAAUAUUCCAACGACCGGUGGGUUUUUAGCAAGUAGAAUAGCAGGCUUAUCACAGGUUCC-UUUAACCCACUGUGAGAUUCUUCUAUUCUACUUUCGAGAAACACCCGU
...................(((.(.((((((.(.(((((((((((.(((....((((((.....-.........))))))...))).))))))))))).).)))))).)))). ( -31.74)
>DroPer_CAF1 78700 112 - 1
NNNNNNNNNNNNN-NNGAUCGGUGUGUAUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAAUCCGCUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCCGU
.............-.....(((.((((..((((.(((((((((((.(((....(((((.((............)))))))...))).)))))))))))))))...))))))). ( -29.30)
>consensus
UCAUGGAUAUACC_ACGAUCGGUGUGUAUUUGGCAAGUAGAAUAGCAGGCUUAUCACAUGUUCCAUUCAACCCGCUGUGAGAUUCUUCUAUUCUACUUUCGACAAACACCCGU
....................(((((....((((.(((((((((((.(((....(((((.................)))))...))).)))))))))))))))...)))))... (-25.80 = -26.46 +   0.67)

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 13:22:45 2006