Locus 5908

Sequence ID 2L_DroMel_CAF1
Location 16,693,838 – 16,693,952
Length 114
Max. P 0.989408
window9381 window9382 window9383 window9384

overview

Window 1

Location 16,693,838 – 16,693,936
Length 98
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.51
Mean single sequence MFE -21.32
Consensus MFE -18.69
Energy contribution -18.69
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.94
Structure conservation index 0.88
SVM decision value 1.69
SVM RNA-class probability 0.972188
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16693838 98 + 22407834
----------UUGCACUAUUUA--------UCAU-UUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUCACGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
----------..(((..(....--------....-)..))).....(((((((((...((((.(((((.((...(((.....)))..)).))))).))))...)))))))))..... ( -20.70)
>DroPse_CAF1 166736 108 + 1
CC--------AUGCACUUUUUGUUCUCCUUUAAU-UUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUUUUGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
.(--------(.(((....(((........))).-...)))))...(((((((((...((((.(((((.((....(((.....))).)).))))).))))...)))))))))..... ( -22.50)
>DroGri_CAF1 93186 105 + 1
CCACACACAAUUGCAAUUUCUU--------UCAU-UUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUC---UAUAUCUUGUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
............((((......--------....-..)))).....(((((((((...((((.(((((.(...(---........)...)))))).))))...)))))))))..... ( -21.30)
>DroWil_CAF1 250552 98 + 1
----------UCCCUCCA-UCA--------UCAUUUUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUUUUGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
----------........-...--------................(((((((((...((((.(((((.((....(((.....))).)).))))).))))...)))))))))..... ( -21.30)
>DroMoj_CAF1 75429 90 + 1
---------CAC---U---CUU--------UCAU-UUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUU---CACAUAUUGUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
---------...---.---...--------....-...........(((((((((...((((.(((((.((...---((.....)).)).))))).))))...)))))))))..... ( -19.60)
>DroPer_CAF1 168629 108 + 1
CC--------AUGCACUUUUUGUUCUCCUUUAAU-UUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUUUUGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
.(--------(.(((....(((........))).-...)))))...(((((((((...((((.(((((.((....(((.....))).)).))))).))))...)))))))))..... ( -22.50)
>consensus
__________AUGCACUUUUUA________UCAU_UUUUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUUUUGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCA
..............................................(((((((((...((((.(((((.((................)).))))).))))...)))))))))..... (-18.69 = -18.69 +  -0.00)

alignment

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secondary structure

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Window 2

Location 16,693,838 – 16,693,936
Length 98
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.51
Mean single sequence MFE -21.34
Consensus MFE -19.95
Energy contribution -19.95
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.26
Structure conservation index 0.93
SVM decision value 1.95
SVM RNA-class probability 0.983701
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16693838 98 - 22407834
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCGUGAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAA-AUGA--------UAAAUAGUGCAA----------
((...(((((((((...((((.(((((....(((.......))).....))))).))))...)))))))))...))(((...-((..--------...))..)))..---------- ( -23.20)
>DroPse_CAF1 166736 108 - 1
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCAAAAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAA-AUUAAAGGAGAACAAAAAGUGCAU--------GG
((...(((((((((...((((.(((((......................))))).))))...)))))))))...))(((...-...................)))..--------.. ( -20.30)
>DroGri_CAF1 93186 105 - 1
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUACAAGAUAUA---GAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAA-AUGA--------AAGAAAUUGCAAUUGUGUGUGG
((...(((((((((...((((.(((((.............---......))))).))))...)))))))))...))(((..(-((..--------((....))...)))...))).. ( -22.61)
>DroWil_CAF1 250552 98 - 1
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCAAAAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAAAAUGA--------UGA-UGGAGGGA----------
((...(((((((((...((((.(((((......................))))).))))...)))))))))...))...........--------...-........---------- ( -19.95)
>DroMoj_CAF1 75429 90 - 1
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUACAAUAUGUG---AAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAA-AUGA--------AAG---A---GUG---------
((...(((((((((...((((.(((((.........(((.---...)))))))).))))...)))))))))...))......-....--------...---.---...--------- ( -21.70)
>DroPer_CAF1 168629 108 - 1
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCAAAAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAA-AUUAAAGGAGAACAAAAAGUGCAU--------GG
((...(((((((((...((((.(((((......................))))).))))...)))))))))...))(((...-...................)))..--------.. ( -20.30)
>consensus
UGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCAAAAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAAAA_AUGA________AAAAAAGUGCAA__________
((...(((((((((...((((.(((((......................))))).))))...)))))))))...))......................................... (-19.95 = -19.95 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,693,856 – 16,693,952
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.04
Mean single sequence MFE -28.55
Consensus MFE -24.99
Energy contribution -24.99
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.31
Structure conservation index 0.88
SVM decision value 2.16
SVM RNA-class probability 0.989408
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16693856 96 + 22407834
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUCACGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUAAC------------------------
..((((...(((((((((...((((.(((((.((...(((.....)))..)).))))).))))...)))))))))...))))..............------------------------ ( -26.40)
>DroVir_CAF1 83421 106 + 1
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUU---UACAGUUUGUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUGCCACCGCCC--------GCAC---CC
..((((...(((((((((...((((.(((((.(....---(((.....))).)))))).))))...)))))))))...))))......(((..((....))..--------))).---.. ( -29.90)
>DroGri_CAF1 93214 107 + 1
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUC---UAUAUCUUGUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUGCCACCGCCU--------GCAC--CCC
..((((...(((((((((...((((.(((((.(...(---........)...)))))).))))...)))))))))...))))......(((..((....))..--------))).--... ( -29.50)
>DroWil_CAF1 250570 103 + 1
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUUUUGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUGCCAACGCA------------C-----
..((((...(((((((((...((((.(((((.((....(((.....))).)).))))).))))...)))))))))...))))......(((........)))------------.----- ( -29.10)
>DroYak_CAF1 148403 103 + 1
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUCGCGCACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUAACAGCGCA------------C-----
..((((((.(((((((((...((((.(((((.((...(((.....)))..)).))))).))))...)))))))))....(((.......))).))))))...------------.----- ( -29.50)
>DroMoj_CAF1 75442 117 + 1
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUU---CACAUAUUGUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUGACACCGCCCAACCGCUCGCACAAUCC
..((((...(((((((((...((((.(((((.((...---((.....)).)).))))).))))...)))))))))...))))....((((..(((....((......)))))..)))).. ( -26.90)
>consensus
UUGCUGUUUCUUUGGUAUUCUAGCUGUAGAUUGUUUC___CACAUUGUAUAUCAUCUAAAGCUUUUAUACCAAAGCUCCAGCUUAAAUUGCUUGACACCGCC____________C_____
..((((...(((((((((...((((.(((((.((................)).))))).))))...)))))))))...))))...................................... (-24.99 = -24.99 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,693,856 – 16,693,952
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.04
Mean single sequence MFE -31.82
Consensus MFE -27.12
Energy contribution -27.45
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -4.44
Structure conservation index 0.85
SVM decision value 2.04
SVM RNA-class probability 0.986260
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16693856 96 - 22407834
------------------------GUUAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCGUGAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
------------------------..............((((...(((((((((...((((.(((((....(((.......))).....))))).))))...)))))))))...)))).. ( -28.60)
>DroVir_CAF1 83421 106 - 1
GG---GUGC--------GGGCGGUGGCAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUACAAACUGUA---AAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
..---.(((--------..((....))..)))......((((...(((((((((...((((.(((((..(((.....)))---......))))).))))...)))))))))...)))).. ( -34.20)
>DroGri_CAF1 93214 107 - 1
GGG--GUGC--------AGGCGGUGGCAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUACAAGAUAUA---GAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
...--.(((--------..((....))..)))......((((...(((((((((...((((.(((((.............---......))))).))))...)))))))))...)))).. ( -32.31)
>DroWil_CAF1 250570 103 - 1
-----G------------UGCGUUGGCAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCAAAAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
-----.------------(((........)))......((((...(((((((((...((((.(((((......................))))).))))...)))))))))...)))).. ( -29.65)
>DroYak_CAF1 148403 103 - 1
-----G------------UGCGCUGUUAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUAUACAAUGUGCGCGAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
-----.------------...(((....))).......((((...(((((((((...((((.(((((......................))))).))))...)))))))))...)))).. ( -30.35)
>DroMoj_CAF1 75442 117 - 1
GGAUUGUGCGAGCGGUUGGGCGGUGUCAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUACAAUAUGUG---AAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
(((((((..((((.(.....).)).))..)))))))..((((...(((((((((...((((.(((((.........(((.---...)))))))).))))...)))))))))...)))).. ( -35.80)
>consensus
_____G____________GGCGGUGGCAAGCAAUUUAAGCUGGAGCUUUGGUAUAAAAGCUUUAGAUGAUACAAAAUGUG___AAAACAAUCUACAGCUAGAAUACCAAAGAAACAGCAA
...................((........)).......((((...(((((((((...((((.(((((......................))))).))))...)))))))))...)))).. (-27.12 = -27.45 +   0.33)

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 11:56:09 2006