Locus 6437

Sequence ID 3L_DroMel_CAF1
Location 17,222,169 – 17,222,312
Length 143
Max. P 0.999934
window10323 window10324 window10325

overview

Window 3

Location 17,222,169 – 17,222,273
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.03
Mean single sequence MFE -38.04
Consensus MFE -35.22
Energy contribution -34.90
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -3.06
Structure conservation index 0.93
SVM decision value 4.65
SVM RNA-class probability 0.999934
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17222169 104 + 23771897
----------------UCGGCGGCGGAAAUGUUUGCCUUGUUUACAGCGCAGUGCAUAAAUUUGCAAUUGCAUGCGCACAGAUACUGAUGCAAUGGUGCGUGCAUUUCCGCUUGCUACUA
----------------..((((((((((((((.(((.(..((....((((((((((......))).)))))..))((((((...))).)))))..).))).)))))))))).)))).... ( -39.30)
>DroSec_CAF1 105744 96 + 1
----------------UCGGCGGCGGAAAUGUUUGCCUUGUUUACAGCGCAGUGCAUAAAUUUGCAAUUGCAUGCGCACAGAUACUGAUGCAAUGGUGCGUGUAUUUCCGCC--------
----------------.....((((((((((..(((.(..((....((((((((((......))).)))))..))((((((...))).)))))..).)))..))))))))))-------- ( -34.20)
>DroSim_CAF1 99484 96 + 1
----------------UCGGCGGCGGAAAUGUUUGCCUUGUUUACAGCGCAGUGCAUAAAUUUGCAAUUGCAUGCGCACAGAUACUGAUGCAAUGGUGCGUGCAUUUCCGCU--------
----------------.....(((((((((((.(((.(..((....((((((((((......))).)))))..))((((((...))).)))))..).))).)))))))))))-------- ( -35.50)
>DroEre_CAF1 109310 100 + 1
----------------UCGGCGGCGGAAAUGUUUGCCUUGUUUACAGCGCAGUGCAUAAAUUUGCAAUUGCAUGCGCACAGAUACUGAUGCAAUGGUGCGUGCAUUUCCGCUUGCC----
----------------..((((((((((((((.(((.(..((....((((((((((......))).)))))..))((((((...))).)))))..).))).)))))))))).))))---- ( -40.30)
>DroYak_CAF1 111925 116 + 1
GCGAAUACUCGAAUACUCGGUGGCGGAAAUGUUUGCCUUGUUUACAGCGCAGUGCAUAAAUUUGCAAUUGCAUGCGCACAGAUACUGAUGCAAUGGUGCGUGCAUUUCCGCUUGCU----
((((.(((.(((....))))))((((((((((.(((.(..((....((((((((((......))).)))))..))((((((...))).)))))..).))).)))))))))))))).---- ( -40.90)
>consensus
________________UCGGCGGCGGAAAUGUUUGCCUUGUUUACAGCGCAGUGCAUAAAUUUGCAAUUGCAUGCGCACAGAUACUGAUGCAAUGGUGCGUGCAUUUCCGCUUGC_____
.....................(((((((((((.(((.(..((....((((((((((......))).)))))..))((((((...))).)))))..).))).)))))))))))........ (-35.22 = -34.90 +  -0.32)

alignment

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secondary structure

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Window 4

Location 17,222,169 – 17,222,273
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -33.08
Consensus MFE -29.56
Energy contribution -29.76
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.89
SVM decision value 3.97
SVM RNA-class probability 0.999734
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17222169 104 - 23771897
UAGUAGCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAACAAGGCAAACAUUUCCGCCGCCGA----------------
.....((..(((((((((..(((((...(((....)))...)))))...(((..((((......)))).)))(((........)))...))))))))).))...---------------- ( -31.60)
>DroSec_CAF1 105744 96 - 1
--------GGCGGAAAUACACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAACAAGGCAAACAUUUCCGCCGCCGA----------------
--------(((((((((...(((((...(((....)))...)))))...(((..((((......)))).)))(((........)))....))))))))).....---------------- ( -32.00)
>DroSim_CAF1 99484 96 - 1
--------AGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAACAAGGCAAACAUUUCCGCCGCCGA----------------
--------.(((((((((..(((((...(((....)))...)))))...(((..((((......)))).)))(((........)))...)))))))))......---------------- ( -30.50)
>DroEre_CAF1 109310 100 - 1
----GGCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAACAAGGCAAACAUUUCCGCCGCCGA----------------
----(((..(((((((((..(((((...(((....)))...)))))...(((..((((......)))).)))(((........)))...))))))))).)))..---------------- ( -35.60)
>DroYak_CAF1 111925 116 - 1
----AGCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAACAAGGCAAACAUUUCCGCCACCGAGUAUUCGAGUAUUCGC
----.....(((((((((..(((((...(((....)))...)))))...(((..((((......)))).)))(((........)))...)))))))))...(((((((....))))))). ( -35.70)
>consensus
_____GCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAACAAGGCAAACAUUUCCGCCGCCGA________________
.........(((((((((..(((((...(((....)))...)))))...(((..((((......)))).)))(((........)))...)))))))))...................... (-29.56 = -29.76 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,222,193 – 17,222,312
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.32
Mean single sequence MFE -25.52
Consensus MFE -19.56
Energy contribution -19.76
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.77
SVM decision value 0.56
SVM RNA-class probability 0.780816
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17222193 119 - 23771897
GCGCCUCUU-CACACACCCACACACCUACACAGCCGCAUAUAGUAGCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAA
.........-...................(((((.((........))..((((...(((((((((...(((....)))...)))))..))))..((((......)))))))))))))... ( -29.00)
>DroSec_CAF1 105768 104 - 1
GCCCCUCUU-CACACAC------ACGCACACACCCACAC---------GGCGGAAAUACACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAA
.........-.......------..............((---------(((.........(((((...(((....)))...)))))...(((..((((......)))).))))))))... ( -21.40)
>DroSim_CAF1 99508 104 - 1
GCCCCUCUU-CACACAC------ACGAACACAGCCACAC---------AGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAA
.........-.......------......(((((.....---------.((((...(((((((((...(((....)))...)))))..))))..((((......)))))))))))))... ( -24.90)
>DroEre_CAF1 109334 109 - 1
GCCCCCUUUUUCCACAC------ACACCCACACCCACAC-----GGCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAA
.................------..............((-----(((..((((...(((((((((...(((....)))...)))))..))))..((((......)))))))))))))... ( -25.80)
>DroYak_CAF1 111965 102 - 1
GCCCCCUUU-------C------ACACACGCACCCACAC-----AGCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAA
.........-------.------..............((-----(((..((((...(((((((((...(((....)))...)))))..))))..((((......)))))))))))))... ( -26.50)
>consensus
GCCCCUCUU_CACACAC______ACACACACACCCACAC______GCAAGCGGAAAUGCACGCACCAUUGCAUCAGUAUCUGUGCGCAUGCAAUUGCAAAUUUAUGCACUGCGCUGUAAA
.................................................((((...(((((((((...(((....)))...)))))..))))..((((......))))))))........ (-19.56 = -19.76 +   0.20)

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 12:18:41 2006