Locus 5843

Sequence ID X_DroMel_CAF1
Location 15,103,936 – 15,104,061
Length 125
Max. P 0.972569
window9479 window9480 window9481

overview

Window 9

Location 15,103,936 – 15,104,035
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.57
Mean single sequence MFE -32.40
Consensus MFE -27.05
Energy contribution -27.17
Covariance contribution 0.11
Combinations/Pair 1.21
Mean z-score -2.60
Structure conservation index 0.83
SVM decision value 1.22
SVM RNA-class probability 0.932633
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15103936 99 - 22224390
GGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUUC------------------CCUA-CUUU--CUCCCUUGCUUU
((.(((..(.((((((...(((.((((((....)))))).))).))).....(((.((....)))))))).)..))).)------------------)...-....--............ ( -31.90)
>DroSec_CAF1 16700 99 - 1
GGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUUC------------------UUCA-CUUU--CUCCUUUGCUUU
.(((((((..(((((.........(((((....)))))((.....)).......)))))..))))).))(((.......------------------..))-)...--............ ( -32.30)
>DroSim_CAF1 20984 99 - 1
GGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUUU------------------CCCA-CUUU--CUCCUUUGCUUU
.(((((((..(((((.........(((((....)))))((.....)).......)))))..))))).))(((.......------------------..))-)...--............ ( -31.80)
>DroEre_CAF1 24347 98 - 1
GGCGGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUC-------------------CCCA-CUUU--CUCCUUUGCUUU
.(((((((..(((((.........(((((....)))))((.....)).......)))))..)))).)))(((......-------------------..))-)...--............ ( -34.10)
>DroYak_CAF1 21811 117 - 1
GGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUUCGCCUCGCGUGUACCUUCCACUUCCACUUCCACUUUCCUA-CUUU--CUCCUUUGCUUU
((.(((..(.((((((...(((.((((((....)))))).))).))).....(((.((....)))))))).)..))).)).....................-....--............ ( -32.80)
>DroPer_CAF1 58517 101 - 1
GGCAGCUCCGCGCGUAUUUGUCUCGCUUGUAAAGGAGCGCAAUUUUCAAUUUAAGCGCGCUCGUUUCGCGUGUGCCUC-------------------UGCAUCCUUGGCACCGAUGCCUU
((((....((((((.........)))..(.(((.((((((..((........))..)))))).))))))).(((((..-------------------.........)))))...)))).. ( -31.50)
>consensus
GGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUUC__________________CCCA_CUUU__CUCCUUUGCUUU
.(((((((..(((((.........(((((....)))))((.....)).......)))))..))))).))................................................... (-27.05 = -27.17 +   0.11)

alignment

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secondary structure

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Window 0

Location 15,103,956 – 15,104,061
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.45
Mean single sequence MFE -34.97
Consensus MFE -18.54
Energy contribution -18.87
Covariance contribution 0.34
Combinations/Pair 1.24
Mean z-score -1.75
Structure conservation index 0.53
SVM decision value 0.09
SVM RNA-class probability 0.579070
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15103956 105 + 22224390
-GAAGGUACACGCGAGGCGGACGCGCUCAAAUUGCAAAUUGCGCUCGUUUACAAGCGAAAUAAAUGCGCGAGCGCCUGCCAUUUGGCAAAAGUCAGCCA--------------UGCUCCA
-...((.....(((.(((.(((((((((.....((.....))((.((((((.........)))))).)))))))).((((....))))...))).))).--------------))).)). ( -37.70)
>DroPse_CAF1 31419 109 + 1
-----------GCGAAACGAACGCGCUUAAAUUGCAAAUUGCGCUCCUUUACAAGCGAGACAAAUACGCGCGGACCUGCCAUUUGGCGAAAGUCGGCCAUCCCACGCCAGACCUACGCCA
-----------(((.......(((((.......((.....))((((((.....)).))).)......)))))(((.((((....))))...)))(((........))).......))).. ( -28.40)
>DroSim_CAF1 21004 105 + 1
-AAAGGUACACGCGAGGCGGACGCGCUCAAAUUGCAAAUUGCGCUCGUUUACAAGCGAAAUAAAUGCGCGAGCGCCUGCCAUUUGGCAAAAGUCAGCCA--------------UGCUCCA
-...((.....(((.(((.(((((((((.....((.....))((.((((((.........)))))).)))))))).((((....))))...))).))).--------------))).)). ( -37.70)
>DroEre_CAF1 24367 104 + 1
--GAGGUACACGCGAGGCGGACGCGCUCAAAUUGCAAAUUGCGCUCGUUUACAAGCGAAAUAAAUGCGCGAGCGCCCGCCAUUUGGCAGGAGUCAGCCA--------------UGCCCCA
--..((.....(((.(((.(((((((((.....((.....))((.((((((.........)))))).))))))))(((((....))).)).))).))).--------------))).)). ( -37.80)
>DroYak_CAF1 21848 106 + 1
GGAAGGUACACGCGAGGCGAACGCGCUCAAAUUGCAAAUUGCGCUCGUUUACAAGCGAAAUAAAUGCGCGAGCGCCUGCCAUUUGGCAAGAGUCAGGCA--------------UGCUCCA
....((..((.((.(((((..(((((.......((.....))..(((((....))))).......)))))..)))))(((....))).........)).--------------))..)). ( -35.30)
>DroPer_CAF1 58540 108 + 1
--GAGGCACACGCGAAACGAGCGCGCUUAAAUUGAAAAUUGCGCUCCUUUACAAGCGAGACAAAUACGCGCGGAGCUGCCAUUUG----------GCCAUCCCACGCCAGACCUACGCCA
--..(((...(((.(((.(((((((.((........)).))))))).)))....)))..........(((.(((...(((....)----------))..)))..))).........))). ( -32.90)
>consensus
__AAGGUACACGCGAGGCGAACGCGCUCAAAUUGCAAAUUGCGCUCGUUUACAAGCGAAAUAAAUGCGCGAGCGCCUGCCAUUUGGCAAAAGUCAGCCA______________UGCUCCA
....(((...(((.((((((..((((..............))))))))))....)))...((((((.(((......)))))))))..........)))...................... (-18.54 = -18.87 +   0.34)

alignment

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secondary structure

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Window 1

Location 15,103,956 – 15,104,061
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.45
Mean single sequence MFE -41.28
Consensus MFE -25.78
Energy contribution -26.37
Covariance contribution 0.59
Combinations/Pair 1.22
Mean z-score -2.37
Structure conservation index 0.62
SVM decision value 1.70
SVM RNA-class probability 0.972569
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15103956 105 - 22224390
UGGAGCA--------------UGGCUGACUUUUGCCAAAUGGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUUC-
.((.(((--------------((((.(((..(((((....)))))(((((((.(((...(((.((((((....)))))).))).)))....)))))))))).)))....)))).))...- ( -42.60)
>DroPse_CAF1 31419 109 - 1
UGGCGUAGGUCUGGCGUGGGAUGGCCGACUUUCGCCAAAUGGCAGGUCCGCGCGUAUUUGUCUCGCUUGUAAAGGAGCGCAAUUUGCAAUUUAAGCGCGUUCGUUUCGC-----------
(((((.(((((.(((........)))))))).)))))...((.(.(..(((((....((((..(((((......)))))......)))).....)))))..).).))..----------- ( -36.60)
>DroSim_CAF1 21004 105 - 1
UGGAGCA--------------UGGCUGACUUUUGCCAAAUGGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUUU-
.((.(((--------------((((.(((..(((((....)))))(((((((.(((...(((.((((((....)))))).))).)))....)))))))))).)))....)))).))...- ( -42.60)
>DroEre_CAF1 24367 104 - 1
UGGGGCA--------------UGGCUGACUCCUGCCAAAUGGCGGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUC--
.((..((--------------((((.(((..(((((....)))))(((((((.(((...(((.((((((....)))))).))).)))....)))))))))).)))....)))..))..-- ( -45.00)
>DroYak_CAF1 21848 106 - 1
UGGAGCA--------------UGCCUGACUCUUGCCAAAUGGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUUCGCCUCGCGUGUACCUUCC
.((.(((--------------(((........((((....))))((((..(((((.........(((((....)))))((.....)).......)))))..))))..)))))).)).... ( -43.40)
>DroPer_CAF1 58540 108 - 1
UGGCGUAGGUCUGGCGUGGGAUGGC----------CAAAUGGCAGCUCCGCGCGUAUUUGUCUCGCUUGUAAAGGAGCGCAAUUUUCAAUUUAAGCGCGCUCGUUUCGCGUGUGCCUC--
.((((........(((((((...((----------(....)))...)))))))..........(((.((.(((.((((((..((........))..)))))).))))).)))))))..-- ( -37.50)
>consensus
UGGAGCA______________UGGCUGACUUUUGCCAAAUGGCAGGCGCUCGCGCAUUUAUUUCGCUUGUAAACGAGCGCAAUUUGCAAUUUGAGCGCGUCCGCCUCGCGUGUACCUU__
.....................((((........))))....(((((((..(((((.........(((((....)))))((.....)).......)))))..))))).))........... (-25.78 = -26.37 +   0.59)

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 11:57:42 2006