Locus 619

Sequence ID 3R_DroMel_CAF1
Location 2,292,117 – 2,292,267
Length 150
Max. P 0.862911
window985 window986

overview

Window 5

Location 2,292,117 – 2,292,228
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.38
Mean single sequence MFE -31.14
Consensus MFE -12.42
Energy contribution -14.34
Covariance contribution 1.92
Combinations/Pair 1.19
Mean z-score -1.93
Structure conservation index 0.40
SVM decision value 0.84
SVM RNA-class probability 0.862911
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2292117 111 - 27905053
GAUUGCCACACUCCAGUUGCCUACUUCAAGGCGGCGGUGAAAAGACA--CUUUUAAUGUGGAAACAGGGCAGUGAACUAC-----AGUGAAAAGUGUCCCACAAACUGGCAACUUG--CU
..((((((((((...(((((((......)))))))))))....((((--(((((..(((((..((......))...))))-----)...)))))))))........))))))....--.. ( -37.20)
>DroSec_CAF1 28375 111 - 1
GAUUGCCACACUCCAGUUGCCUACUUUAAGGCGUUGCUGAAAAGUCA--GUUUAAAUGUGGAAACAGGGCAGUGAACUAC-----UGGGAAAAGUGUCCCACAAACUGGCAACUUG--CU
..((((((.....(((((((((......)))))..))))...(((.(--(((((..(.((....)).)....))))))))-----)((((......))))......))))))....--.. ( -32.30)
>DroSim_CAF1 30001 111 - 1
GAUUGCCACACUCCAGUUGCCUACUUUAAGGCGGCGCUGAAAAGUCA--GUUUAAAUGUGGAAACAGGGCAGUGAACUAC-----UGGGAAAAGUGUCCCACAAACUGGCAACUUG--CU
..((((((((((((.(((((((......)))))))(((((....)))--)).......((....)).)).))))......-----(((((......))))).....))))))....--.. ( -36.60)
>DroYak_CAF1 27200 103 - 1
GACUGCCUCACUUCGGCUGCCUACAUUAAGGCGGCGCUAAAAAGUCA--GUUUAAAUGAGUAAACAGGAC--UAAACUAC-----AGUGAAAAGUGUCCCACAAACUGGCAA--------
...(((((((((...(((((((......))))))).......((((.--(((((......)))))..)))--).......-----)))))...(((...))).....)))).-------- ( -29.10)
>DroAna_CAF1 27956 107 - 1
AAUC-----------GCUGCCUACUUUCUGGCUCUUUUGAAAAUUCCUCCUUUGAAUUAGGAAG-GGUUUAUUCCACUAUGGAAAUGGGUCACAUGCUCCACAAA-UGUCCACUCGUGUA
....-----------...(((........)))........((((((.((((.......)))).)-))))).((((.....))))((((((.((((.........)-)))..))))))... ( -20.50)
>consensus
GAUUGCCACACUCCAGUUGCCUACUUUAAGGCGGCGCUGAAAAGUCA__GUUUAAAUGUGGAAACAGGGCAGUGAACUAC_____UGGGAAAAGUGUCCCACAAACUGGCAACUUG__CU
..(((((........(((((((......)))))))...................................................((((......)))).......)))))........ (-12.42 = -14.34 +   1.92)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,292,150 – 2,292,267
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.99
Mean single sequence MFE -32.11
Consensus MFE -9.70
Energy contribution -11.52
Covariance contribution 1.82
Combinations/Pair 1.35
Mean z-score -1.69
Structure conservation index 0.30
SVM decision value -0.01
SVM RNA-class probability 0.526512
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2292150 117 - 27905053
AAAUAUGCUGGCC-CAUCUGCACUCUUGUGUGGAUGAUUCGAUUGCCACACUCCAGUUGCCUACUUCAAGGCGGCGGUGAAAAGACA--CUUUUAAUGUGGAAACAGGGCAGUGAACUAC
......((((.((-((((..(((....)))..)))).........(((((.....(((((((......)))))))((((......))--)).....))))).....)).))))....... ( -39.90)
>DroSec_CAF1 28408 117 - 1
AAAUAUGCUGGCC-CAUCUGCACUCUUGUGUGCGAGUUUCGAUUGCCACACUCCAGUUGCCUACUUUAAGGCGUUGCUGAAAAGUCA--GUUUAAAUGUGGAAACAGGGCAGUGAACUAC
......((((.((-(..(((.(((..((((.((((.......))))))))...(((((((((......)))))..))))...)))))--)........((....)))))))))....... ( -33.10)
>DroSim_CAF1 30034 117 - 1
AAAUAUGCUGGCC-CAUCUGCACUCUUGUGUGCGAGUUUCGAUUGCCACACUCCAGUUGCCUACUUUAAGGCGGCGCUGAAAAGUCA--GUUUAAAUGUGGAAACAGGGCAGUGAACUAC
......((((.((-(...(((((......)))))...........(((((.....(((((((......)))))))(((((....)))--)).....))))).....)))))))....... ( -37.30)
>DroYak_CAF1 27227 103 - 1
AAAUAUGCUGGCA-C-UUUGCUCUC--G---------UUUGACUGCCUCACUUCGGCUGCCUACAUUAAGGCGGCGCUAAAAAGUCA--GUUUAAAUGAGUAAACAGGAC--UAAACUAC
.......(((((.-.-...)).(((--(---------((((((((.((.......(((((((......))))))).......)).))--).)))))))))....)))...--........ ( -27.34)
>DroAna_CAF1 27995 105 - 1
AAAUAUGCUGGGUGUAUUUGUUUUCAUCCG---GAUGUUCAAUC-----------GCUGCCUACUUUCUGGCUCUUUUGAAAAUUCCUCCUUUGAAUUAGGAAG-GGUUUAUUCCACUAU
..((((.(((((((..........))))))---)))))((((..-----------...(((........)))....))))((((((.((((.......)))).)-))))).......... ( -22.90)
>consensus
AAAUAUGCUGGCC_CAUCUGCACUCUUGUGUG_GAGUUUCGAUUGCCACACUCCAGUUGCCUACUUUAAGGCGGCGCUGAAAAGUCA__GUUUAAAUGUGGAAACAGGGCAGUGAACUAC
.....(((((.((.....(.(((....(((((..............)))))....(((((((......)))))))......................))).)....)).)))))...... ( -9.70 = -11.52 +   1.82)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:38 2006