Locus 4353

Sequence ID 3L_DroMel_CAF1
Location 12,778,253 – 12,778,388
Length 135
Max. P 0.979283
window6738 window6739 window6740

overview

Window 8

Location 12,778,253 – 12,778,348
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 75.67
Mean single sequence MFE -23.52
Consensus MFE -16.73
Energy contribution -16.12
Covariance contribution -0.61
Combinations/Pair 1.21
Mean z-score -0.90
Structure conservation index 0.71
SVM decision value 0.06
SVM RNA-class probability 0.561992
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12778253 95 + 23771897
UAGGUAAAUGGAAGGUAUUUAUUUGUUUUGAAGAGUUUAUUUUCUUACCUUGCGAUGACGUCCUUUGUAGACGACGGCAAAGGCGCCAUGGCCCA
.(((((...((((((((...((((........)))).))))))))))))).((.(((.((.(((((((........))))))))).))).))... ( -26.30)
>DroVir_CAF1 39895 82 + 1
UAGAUAAAC--AAGAUAUUG---------AUGUGA--CGUUUGCUUACCUUGCGAUGACGUCCUUUGUAGACCACAGCAAAGGCGCCAUGGCCAA
........(--((....)))---------..((((--.(....)))))...((.(((.((.(((((((........))))))))).))).))... ( -17.00)
>DroPse_CAF1 45844 88 + 1
-----AAAU-GACGAAAUUAAAGUGUUUUUU-UAUUAUUAGUUCUUACCUUGCGGUGACGCCCUUUGUAGACGACAGCAAAGGCGCCAUGGCCAA
-----.(((-((.(((((......))))).)-))))...............((.(((.((((.(((((........))))))))).))).))... ( -20.00)
>DroSec_CAF1 20206 95 + 1
UAGGUAAAUGGAAGAUAUUUAUUUGUUUUGAAGAGUUUCGCUUCUUACCUUGCGAUGACGUCCUUUGUAGACGACGGCAAAGGCGCCGUGGCCCA
.((((((....((((((......))))))((((.......)))))))))).((.(((.((.(((((((........))))))))).))).))... ( -25.30)
>DroSim_CAF1 19530 95 + 1
UAGGUAAAUAGAAGAUAUUUAUUUGUUUUGAAGAGUUUCGCUUCUUACCUUGCGAUGACGUCCUUUGUAGACGACGGCAAAGGCGCCGUGGCCCA
.((((((....((((((......))))))((((.......)))))))))).((.(((.((.(((((((........))))))))).))).))... ( -25.30)
>DroMoj_CAF1 33287 90 + 1
CAGUUAAAC--AAUUAAUUA-GUUGCAUUACAUGG--CAAUUUCUUACCUUGCGGUGACGUCCUUUGUAGACCACGGCGAAGGCGCCGUGGCCAA
.......((--((.(((..(-(((((........)--)))))..)))....(((....)))...)))).(.((((((((....)))))))).).. ( -27.20)
>consensus
UAGGUAAAU_GAAGAUAUUUAUUUGUUUUGAAGAGUUUAAUUUCUUACCUUGCGAUGACGUCCUUUGUAGACGACGGCAAAGGCGCCAUGGCCAA
...................................................((.(((.((.(((((((........))))))))).))).))... (-16.73 = -16.12 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,778,253 – 12,778,348
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 75.67
Mean single sequence MFE -23.74
Consensus MFE -16.19
Energy contribution -15.22
Covariance contribution -0.97
Combinations/Pair 1.31
Mean z-score -2.09
Structure conservation index 0.68
SVM decision value 1.83
SVM RNA-class probability 0.979283
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12778253 95 - 23771897
UGGGCCAUGGCGCCUUUGCCGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGAAAAUAAACUCUUCAAAACAAAUAAAUACCUUCCAUUUACCUA
(((((.((((((((((((..(....)..)))))).)))))).))(((((((((........)))..............)))))))))........ ( -22.33)
>DroVir_CAF1 39895 82 - 1
UUGGCCAUGGCGCCUUUGCUGUGGUCUACAAAGGACGUCAUCGCAAGGUAAGCAAACG--UCACAU---------CAAUAUCUU--GUUUAUCUA
...((.((((((((((((..(....)..)))))).)))))).)).((((((((((...--......---------.......))--)))))))). ( -25.39)
>DroPse_CAF1 45844 88 - 1
UUGGCCAUGGCGCCUUUGCUGUCGUCUACAAAGGGCGUCACCGCAAGGUAAGAACUAAUAAUA-AAAAAACACUUUAAUUUCGUC-AUUU-----
.((((...(((((((((..(((.....))))))))))))(((....)))..............-..................)))-)...----- ( -21.80)
>DroSec_CAF1 20206 95 - 1
UGGGCCACGGCGCCUUUGCCGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGAAGCGAAACUCUUCAAAACAAAUAAAUAUCUUCCAUUUACCUA
(((((.((((((....)))))).)))))....(((....(((....)))..((((.......)))).................)))......... ( -21.40)
>DroSim_CAF1 19530 95 - 1
UGGGCCACGGCGCCUUUGCCGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGAAGCGAAACUCUUCAAAACAAAUAAAUAUCUUCUAUUUACCUA
(((((.((((((....)))))).)))))...(((.....(((....)))..((((.......))))........((((((.....))))))))). ( -21.20)
>DroMoj_CAF1 33287 90 - 1
UUGGCCACGGCGCCUUCGCCGUGGUCUACAAAGGACGUCACCGCAAGGUAAGAAAUUG--CCAUGUAAUGCAAC-UAAUUAAUU--GUUUAACUG
..((((((((((....)))))))))).((((.((......))(((.(((((....)))--)).)))........-.......))--))....... ( -30.30)
>consensus
UGGGCCACGGCGCCUUUGCCGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGAAAAGAAACUAUUCAAAACAAAUAAAUAUCUUC_AUUUACCUA
..(((.((((((....)))))).((((.....)))))))(((....))).............................................. (-16.19 = -15.22 +  -0.97)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,778,272 – 12,778,388
Length 116
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.41
Mean single sequence MFE -32.38
Consensus MFE -24.00
Energy contribution -25.03
Covariance contribution 1.03
Combinations/Pair 1.03
Mean z-score -1.61
Structure conservation index 0.74
SVM decision value 0.61
SVM RNA-class probability 0.798869
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12778272 116 - 23771897
AAUAUUGUCGGGGAAUAUGAAUACAGCUCCAAGGAUAUGCUGGGCCAUGGCGCCUUUGCCGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGAAAAUAAACUCUUCAAAACAAAUA
..((((.((((((....((....)).)))).......((((..((.((((((((((((..(....)..)))))).)))))).))..)))).)).)))).................. ( -28.30)
>DroVir_CAF1 39912 105 - 1
AAUAUUGUCGGGGAAUAUGAAUACAGCUCCAAGGAUAUGCUUGGCCAUGGCGCCUUUGCUGUGGUCUACAAAGGACGUCAUCGCAAGGUAAGCAAACG--UCACAU---------C
.(((((.(.((((....((....)).)))).).)))))(((((((.((((((((((((..(....)..)))))).)))))).))....))))).....--......---------. ( -28.70)
>DroPse_CAF1 45857 115 - 1
AAUAUUGUCGGGGAGUAUGAAUACAGCUCCAAGGAUAUGCUUGGCCAUGGCGCCUUUGCUGUCGUCUACAAAGGGCGUCACCGCAAGGUAAGAACUAAUAAUA-AAAAAACACUUU
..((((((..((((((.((....))))))).......(((((.((..((((((((((..(((.....)))))))))))))..)).)))))....)..))))))-............ ( -31.80)
>DroWil_CAF1 33381 108 - 1
AAUAUUGUUGGGGACUAUGAAUACAGCUCCAAGGAUAUGCUUGGCCAUGGGGCCUUUGCUGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGU--------UCUUAAUUAUAAUUA
..(((.((((((((((.........((((((.((.((....)).)).))))))((((((((.(((((.....))))).))..))))))..)))--------))))))).))).... ( -34.70)
>DroMoj_CAF1 33304 113 - 1
AAUAUUGUCGGGGAAUAUGAAUACAGCUCCAAGGAUAUGCUUGGCCACGGCGCCUUCGCCGUGGUCUACAAAGGACGUCACCGCAAGGUAAGAAAUUG--CCAUGUAAUGCAAC-U
.(((((.(.((((....((....)).)))).).)))))((..((((((((((....))))))))))((((..((......))....(((((....)))--)).))))..))...-. ( -38.20)
>DroAna_CAF1 14979 108 - 1
AAUAUUGUCGGGGACUAUGAAUACAGCUCCAAGGAUAUGCUUGGCCACGGCGCCUUUGCCGUCGUCUACAAGGGUCGUCAUCGCAAGGUAAGCAUCCAGUCUCCUCUC--------
.........((((((((((..(((.((.(((((......)))))....((((((((((..(....)..)))))).))))...))...)))..)))..)))))))....-------- ( -32.60)
>consensus
AAUAUUGUCGGGGAAUAUGAAUACAGCUCCAAGGAUAUGCUUGGCCAUGGCGCCUUUGCCGUCGUCUACAAAGGACGUCAUCGCAAGGUAAGAAAACA__CUAUUAAA_ACAA__A
.(((((.(.((((....((....)).)))).).)))))((((.((.((((((((((((..(....)..)))))).)))))).)).))))........................... (-24.00 = -25.03 +   1.03)

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 11:20:23 2006