Locus 2880

Sequence ID 3L_DroMel_CAF1
Location 8,223,285 – 8,223,390
Length 105
Max. P 0.999773
window4496 window4497 window4498 window4499

overview

Window 6

Location 8,223,285 – 8,223,377
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 88.57
Mean single sequence MFE -27.26
Consensus MFE -19.48
Energy contribution -20.52
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.83
Structure conservation index 0.71
SVM decision value 1.26
SVM RNA-class probability 0.937515
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8223285 92 + 23771897
GAUUCUCGAAAGGGGUUGUGUGUGGUUGGUUGGUGCUUUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUA
....(((....)))(((((((.(((((((..((((((((....((....))...))))))))))))))))))))))(((.....)))..... ( -26.70)
>DroSec_CAF1 45781 90 + 1
GAUUCUCGAAAGGGGUUGU--GUGGUUGGUCGGUGCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUA
...((((....)))).(((--(((.(((...((((.((((.((((((((.((.....)).))))))))..)))).))))...))).)))))) ( -29.50)
>DroSim_CAF1 43696 90 + 1
GAUUCUCGAAAGGGGUUGU--GUGGUUGGUUGGUGCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUA
...((((....)))).(((--(((.(((..(((((.((((.((((((((.((.....)).))))))))..)))).)))))..))).)))))) ( -31.00)
>DroEre_CAF1 49103 80 + 1
GA--CUCGA--GGGGUUUG--GCG------UGGGGCCGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUA
((--((...--..))))((--(((------(...((.((..((((((((.((.....)).)))))))).)))).))))))............ ( -24.20)
>DroYak_CAF1 47390 83 + 1
GAUUCUCGA-UGGGGUUGU--GUG------UGGGCCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCACAUAGGUGCAUA
........(-((.(.((((--(((------.(.(..((((.((((((((.((.....)).))))))))..)))).).)))))))).).))). ( -24.90)
>consensus
GAUUCUCGAAAGGGGUUGU__GUGGUUGGUUGGUGCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUA
....(((....))).......(((......(((((.((((.((((((((.((.....)).))))))))..)))).)))))......)))... (-19.48 = -20.52 +   1.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,223,285 – 8,223,377
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 88.57
Mean single sequence MFE -16.42
Consensus MFE -13.88
Energy contribution -13.96
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -1.69
Structure conservation index 0.85
SVM decision value 0.89
SVM RNA-class probability 0.874842
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8223285 92 - 23771897
UAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCAAAGCACCAACCAACCACACACAACCCCUUUCGAGAAUC
............(((.(((.....((((((((.((.....)).))))))))....))).))).............................. ( -13.60)
>DroSec_CAF1 45781 90 - 1
UAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGCACCGACCAACCAC--ACAACCCCUUUCGAGAAUC
............(((((.(((((.((((((((.((.....)).))))))))..)).))).)).))).....--................... ( -16.80)
>DroSim_CAF1 43696 90 - 1
UAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGCACCAACCAACCAC--ACAACCCCUUUCGAGAAUC
............(((.((((.(..((((((((.((.....)).)))))))).).)))).))).........--................... ( -16.30)
>DroEre_CAF1 49103 80 - 1
UAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACGGCCCCA------CGC--CAAACCCC--UCGAG--UC
............((((((.((((.((((((((.((.....)).))))))))..)).))...)------)))--))......--.....--.. ( -18.40)
>DroYak_CAF1 47390 83 - 1
UAUGCACCUAUGUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGGCCCA------CAC--ACAACCCCA-UCGAGAAUC
..........(((((.(((.....((((((((.((.....)).)))))))).....))))))------)).--.........-......... ( -17.00)
>consensus
UAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGCACCAACCAACCAC__ACAACCCCUUUCGAGAAUC
............(((.((((.(..((((((((.((.....)).)))))))).).)))).))).............................. (-13.88 = -13.96 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,223,299 – 8,223,390
Length 91
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 86.93
Mean single sequence MFE -29.54
Consensus MFE -23.28
Energy contribution -24.80
Covariance contribution 1.52
Combinations/Pair 1.07
Mean z-score -3.84
Structure conservation index 0.79
SVM decision value 3.27
SVM RNA-class probability 0.998896
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8223299 91 + 23771897
GUUGUGUGUGGUUGGUUGGUGCUUUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUA----UAUGCACAUAUAU
(((((((.(((((((..((((((((....((....))...))))))))))))))))))))))...(((((.(((((..----..))))).))))) ( -27.90)
>DroSec_CAF1 45795 93 + 1
GUUGU--GUGGUUGGUCGGUGCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUAUACAUAUGCACAUAUAU
.....--..........((((.((((.((((((((.((.....)).))))))))..)))).))))(((((.(((((((....))))))).))))) ( -30.10)
>DroSim_CAF1 43710 93 + 1
GUUGU--GUGGUUGGUUGGUGCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUAUACAUAUGCACAUAUUU
.((((--(((((.(.....(((.((..((((((((.((.....)).)))))))).))))).))))))))))(((((((....)))))))...... ( -30.00)
>DroEre_CAF1 49113 83 + 1
GUUUG--GCG------UGGGGCCGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUAUA--U--GCACAUAUAU
...((--(((------(...((.((..((((((((.((.....)).)))))))).)))).))))))((((.(((((....--)--)))).)))). ( -30.40)
>DroYak_CAF1 47403 85 + 1
GUUGU--GUG------UGGGCCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCACAUAGGUGCAUAUA--UGUGCACAUGUAU
....(--(((------(((...((((.((((((((.((.....)).))))))))..))))...))))))).((((((...--.))))))...... ( -29.30)
>consensus
GUUGU__GUGGUUGGUUGGUGCUGUGGAAUUGAAAAGCGAAAAGCAUUUCAAUUAACGCAACGCCAUAUAGGUGCAUAUA__UAUGCACAUAUAU
.................((((.((((.((((((((.((.....)).))))))))..)))).))))(((((.(((((((....))))))).))))) (-23.28 = -24.80 +   1.52)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,223,299 – 8,223,390
Length 91
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 86.93
Mean single sequence MFE -24.20
Consensus MFE -20.60
Energy contribution -21.72
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -4.18
Structure conservation index 0.85
SVM decision value 4.05
SVM RNA-class probability 0.999773
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8223299 91 - 23771897
AUAUAUGUGCAUA----UAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCAAAGCACCAACCAACCACACACAAC
.((((.(((((..----..))))).))))(((.(((.....((((((((.((.....)).))))))))....))).)))................ ( -21.10)
>DroSec_CAF1 45795 93 - 1
AUAUAUGUGCAUAUGUAUAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGCACCGACCAACCAC--ACAAC
.((((.(((((((....))))))).))))(((((.(((((.((((((((.((.....)).))))))))..)).))).)).))).....--..... ( -26.70)
>DroSim_CAF1 43710 93 - 1
AAAUAUGUGCAUAUGUAUAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGCACCAACCAACCAC--ACAAC
..(((.(((((((....))))))).))).(((.((((.(..((((((((.((.....)).)))))))).).)))).))).........--..... ( -25.00)
>DroEre_CAF1 49113 83 - 1
AUAUAUGUGC--A--UAUAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACGGCCCCA------CGC--CAAAC
.((((.((((--(--....))))).))))((((((.((((.((((((((.((.....)).))))))))..)).))...)------)))--))... ( -25.90)
>DroYak_CAF1 47403 85 - 1
AUACAUGUGCACA--UAUAUGCACCUAUGUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGGCCCA------CAC--ACAAC
......(((((..--....)))))...(((((.(((.....((((((((.((.....)).)))))))).....))))))------)).--..... ( -22.30)
>consensus
AUAUAUGUGCAUA__UAUAUGCACCUAUAUGGCGUUGCGUUAAUUGAAAUGCUUUUCGCUUUUCAAUUCCACAGCACCAACCAACCAC__ACAAC
(((((.(((((((....))))))).)))))((.((((.(..((((((((.((.....)).)))))))).).)))).))................. (-20.60 = -21.72 +   1.12)

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 10:44:03 2006