Locus 4752

Sequence ID 2L_DroMel_CAF1
Location 13,572,070 – 13,572,226
Length 156
Max. P 0.996107
window7516 window7517 window7518

overview

Window 6

Location 13,572,070 – 13,572,186
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.88
Mean single sequence MFE -34.46
Consensus MFE -24.58
Energy contribution -25.98
Covariance contribution 1.40
Combinations/Pair 1.06
Mean z-score -3.06
Structure conservation index 0.71
SVM decision value 1.25
SVM RNA-class probability 0.936062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13572070 116 + 22407834
UUGCUUGAUUUGCAUAUGUGAGCGUGUGUAUUCUGCACACAGAAUUUUCUUGUUGCGCUUUUUAUACCCAUUACCCUUGCGCUAAGCGGGUAUAUUAAAUUAUGUGCAAUUUAUG----C
..((.(((.(((((((((.((((((((((.....))))))(((....)))......))))..(((((((.........((.....)))))))))......))))))))).))).)----) ( -31.20)
>DroSec_CAF1 5399 116 + 1
UUGCUUGAUUUGCAUAUGUGAGCGCGUGUGUUCUGCACACAGAAUUUUCUUGUUGCGCUUUUUAUACCCAUUACCCUUGGGCUAAGCGGGUAUAUAACAUUUCGAGCAAUUUAUG----C
((((((((..((.......(((((((((((.....)))))(((....)))....))))))..(((((((.(((((....)).)))..)))))))...))..))))))))......----. ( -39.90)
>DroSim_CAF1 4943 116 + 1
UUGCUUGAUUUGCAUAUGUGAGCGUGUGUGUUCUGCACACAGAAUUUUCUUGUUGCGCUUUUUAUACCCAUUACCCUUGGACUAAGCGGGUAUAUUAGAUUUCGUGCAAUUUUUG----C
..((..((.((((((....(((((((((((.....)))))(((....)))....))))))..(((((((.(((((...))..)))..))))))).........)))))).))..)----) ( -30.20)
>DroEre_CAF1 5851 115 + 1
UUGCUAGAUUUGCAUAUGUGAGCGUGUGUGUUCUGCACACAGAAUUUUCUUGUUGCGCUU-UUAUACCCCUUACCCAUGGGUAAGGCGGGUAUAUCACAUUUCCAGCAUUUUGUG----C
..((..((..(((..(((((((((((((((.....)))))(((....)))....))))..-.(((((((((((((....))))))..))))))))))))).....)))..))..)----) ( -38.50)
>DroYak_CAF1 2516 120 + 1
UUGCUUGAUUUGCAUAUGUGAGCGUGUGUGUUCUGCACACAGAAUUUUCUUGUUGCGCUUUUUAUACCCAUUACCCUUGGGCAAAGAGGGUAUCUUACAUUUUGAGCAAUUUAUGUUUGU
(((((..(..((..((((.(((((((((((.....)))))(((....)))....))))))..)))).....(((((((.......))))))).....))..)..)))))........... ( -32.50)
>consensus
UUGCUUGAUUUGCAUAUGUGAGCGUGUGUGUUCUGCACACAGAAUUUUCUUGUUGCGCUUUUUAUACCCAUUACCCUUGGGCUAAGCGGGUAUAUUACAUUUCGAGCAAUUUAUG____C
((((((((...........(((((((((((.....)))))(((....)))....))))))..(((((((....((....))......))))))).......))))))))........... (-24.58 = -25.98 +   1.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,572,070 – 13,572,186
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.88
Mean single sequence MFE -31.90
Consensus MFE -22.38
Energy contribution -22.46
Covariance contribution 0.08
Combinations/Pair 1.09
Mean z-score -3.98
Structure conservation index 0.70
SVM decision value 1.69
SVM RNA-class probability 0.972339
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13572070 116 - 22407834
G----CAUAAAUUGCACAUAAUUUAAUAUACCCGCUUAGCGCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCUGUGUGCAGAAUACACACGCUCACAUAUGCAAAUCAAGCAA
(----((((....((...........((((((((.(((.(.....).)))))))))))....(((((...(((....))).)))))...........)).....)))))........... ( -27.40)
>DroSec_CAF1 5399 116 - 1
G----CAUAAAUUGCUCGAAAUGUUAUAUACCCGCUUAGCCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCUGUGUGCAGAACACACGCGCUCACAUAUGCAAAUCAAGCAA
.----......(((((.((..(((..((((((((.(((.((....)))))))))))))...(((((....(((....)))(((((.....)))))))))).......)))..)).))))) ( -34.00)
>DroSim_CAF1 4943 116 - 1
G----CAAAAAUUGCACGAAAUCUAAUAUACCCGCUUAGUCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCUGUGUGCAGAACACACACGCUCACAUAUGCAAAUCAAGCAA
(----(.....(((((..........((((((((.(((.(.....).)))))))))))...((((.....(((....)))(((((.....))))).))))......))))).....)).. ( -26.50)
>DroEre_CAF1 5851 115 - 1
G----CACAAAAUGCUGGAAAUGUGAUAUACCCGCCUUACCCAUGGGUAAGGGGUAUAA-AAGCGCAACAAGAAAAUUCUGUGUGCAGAACACACACGCUCACAUAUGCAAAUCUAGCAA
.----.......(((((((..((((.(((((((..((((((....))))))))))))).-..(((((...(((....))).)))))....))))...((........))...))))))). ( -41.20)
>DroYak_CAF1 2516 120 - 1
ACAAACAUAAAUUGCUCAAAAUGUAAGAUACCCUCUUUGCCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCUGUGUGCAGAACACACACGCUCACAUAUGCAAAUCAAGCAA
...........(((((.....((((..((((((...(((((....))))).))))))....((((.....(((....)))(((((.....))))).))))......)))).....))))) ( -30.40)
>consensus
G____CAUAAAUUGCUCGAAAUGUAAUAUACCCGCUUAGCCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCUGUGUGCAGAACACACACGCUCACAUAUGCAAAUCAAGCAA
............(((...........(((((((.....(((....)))...)))))))....(((((...(((....))).)))))...........((........)).......))). (-22.38 = -22.46 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,572,110 – 13,572,226
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.76
Mean single sequence MFE -24.43
Consensus MFE -10.12
Energy contribution -10.60
Covariance contribution 0.48
Combinations/Pair 1.19
Mean z-score -2.51
Structure conservation index 0.41
SVM decision value 2.65
SVM RNA-class probability 0.996107
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13572110 116 - 22407834
UACUAUUAAACUCUUUUAAAAGUAAAUAUCUAAUUGGGUUG----CAUAAAUUGCACAUAAUUUAAUAUACCCGCUUAGCGCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCU
((((.(((((....))))).)))).........((..((((----(.(((((((....))))))).((((((((.(((.(.....).)))))))))))......)))))..))....... ( -23.20)
>DroSec_CAF1 5439 94 - 1
----------------------UAAAUAUCUUUUUGGGUUG----CAUAAAUUGCUCGAAAUGUUAUAUACCCGCUUAGCCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCU
----------------------......((((.(((.((((----((.....)))...........((((((((.(((.((....)))))))))))))...))).))).))))....... ( -23.50)
>DroSim_CAF1 4983 94 - 1
----------------------UAAAUAUAUGAUUGGGCUG----CAAAAAUUGCACGAAAUCUAAUAUACCCGCUUAGUCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCU
----------------------........((.(((.((((----((.....)))...........((((((((.(((.(.....).)))))))))))...))).))))).......... ( -19.90)
>DroEre_CAF1 5891 103 - 1
UGACAGC-AAA-----------UAAAGAUUUGGGUGGCUUG----CACAAAAUGCUGGAAAUGUGAUAUACCCGCCUUACCCAUGGGUAAGGGGUAUAA-AAGCGCAACAAGAAAAUUCU
...((((-(..-----------.......((..(((.....----)))..)))))))....((((.(((((((..((((((....))))))))))))).-...))))............. ( -27.20)
>DroYak_CAF1 2556 119 - 1
UGACAGC-AAAUCCAUUAAAAAUAAUCAUUUGGAUGCGCUACAAACAUAAAUUGCUCAAAAUGUAAGAUACCCUCUUUGCCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCU
.......-..(((((...............)))))(((((...........((((.......)))).((((((...(((((....))))).))))))....))))).............. ( -28.36)
>consensus
U___A___AA____________UAAAUAUCUGAUUGGGUUG____CAUAAAUUGCUCGAAAUGUAAUAUACCCGCUUAGCCCAAGGGUAAUGGGUAUAAAAAGCGCAACAAGAAAAUUCU
............................(((..(((.(((.....((.....))............(((((((.....(((....)))...)))))))...))).)))..)))....... (-10.12 = -10.60 +   0.48)

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 11:26:21 2006