Locus 8472

Sequence ID 3R_DroMel_CAF1
Location 22,606,147 – 22,606,277
Length 130
Max. P 0.998223
window13629 window13630 window13631

overview

Window 9

Location 22,606,147 – 22,606,242
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.65
Mean single sequence MFE -22.28
Consensus MFE -14.86
Energy contribution -15.16
Covariance contribution 0.30
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.67
SVM decision value 2.14
SVM RNA-class probability 0.988938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22606147 95 + 27905053
AAAUAUCGUGUGCAAAA---------ACAAACCACUUCGUUUCCCAUCACUGAACUUUAAGGGGUGGCAAUAGCAGA--UGCGAAAGCAAA-A-------------AGCGAAAGCAAAUA
.......((.(((....---------..((((......)))).(((((.((........)).))))).....))).)--)((....))...-.-------------.((....))..... ( -20.60)
>DroSec_CAF1 54500 95 + 1
AAAUAUCGCGUGCAAAA---------ACAAACCACUUCGUUUCCCAUCACUGAACUUUAAGGGGUGGCAAUGGCAGA--UGCGAAAGCAAA-A-------------AGCGAAAGCAAAUA
.......((((......---------)).........((((..(((((.((........)).))))).))))))...--(((....)))..-.-------------.((....))..... ( -21.50)
>DroSim_CAF1 56289 108 + 1
AAAUAUCGUGUGCAAAA---------ACAAACCACUUCGUUUCCCAUCACUGAACUUUAAGGGGUGGCAAUGGCAGA--UGCGAAAGCAAA-AAGCGAAAGCAAAAAGCGAAAGCAAAUA
........(((......---------))).....(((((((..(((((.((........)).))))).))))).)).--(((....)))..-..((....)).....((....))..... ( -25.80)
>DroEre_CAF1 62426 94 + 1
AAAUAUCGUGUGCAAAA---------ACAAACCACUUCGUUUCCCAUCACUGAACAUUGAGGGGUGGCAAAAGCAAG----------------AGCAACAGCAA-AAGCGAAAGCAAAUA
.....((((.(((....---------............((..(((.(((........))).)))..))....((...----------------.))....))).-..))))......... ( -19.00)
>DroYak_CAF1 56852 119 + 1
AAAUAUCGUUUGCAAAAACAUGCAAAACAAACCACUUCGUUUCCCAUCACUGAACAUUAAAGGGUGGCAAAAGCAAAAUAGCAAAAGCAAGAAAGCAUAAGCGA-AAGCGAAAGCAAAUA
.......((((((......((((...............((((.(((((.((.........)))))))...))))......((....))......))))..((..-..))....)))))). ( -24.50)
>consensus
AAAUAUCGUGUGCAAAA_________ACAAACCACUUCGUUUCCCAUCACUGAACUUUAAGGGGUGGCAAUAGCAGA__UGCGAAAGCAAA_AAGC___AGC_A_AAGCGAAAGCAAAUA
..........(((...............((((......)))).(((((.((........)).))))).....))).....((....))...................((....))..... (-14.86 = -15.16 +   0.30)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,606,178 – 22,606,277
Length 99
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 81.60
Mean single sequence MFE -32.60
Consensus MFE -26.98
Energy contribution -27.32
Covariance contribution 0.34
Combinations/Pair 1.04
Mean z-score -3.14
Structure conservation index 0.83
SVM decision value 3.04
SVM RNA-class probability 0.998223
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22606178 99 + 27905053
UUCCCAUCACUGAACUUUAAGGGGUGGCAAUAGCAGA--UGCGAAAGCAAA-A-------------AGCGAAAGCAAAUACCCAUGAGGUUGGAUUCCGCCUCCUUUAGCUCAGU
........(((((.((..(((((((((((((..((..--(((....)))..-.-------------.((....)).........))..))))....))))).)))).)).))))) ( -33.00)
>DroSec_CAF1 54531 99 + 1
UUCCCAUCACUGAACUUUAAGGGGUGGCAAUGGCAGA--UGCGAAAGCAAA-A-------------AGCGAAAGCAAAUACCCAUGAGGUUGGAUUCCGCCUCCUUAAGCUCAGU
........(((((.(((.(((((((((((((..((..--(((....)))..-.-------------.((....)).........))..))))....))))).))))))).))))) ( -33.70)
>DroSim_CAF1 56320 112 + 1
UUCCCAUCACUGAACUUUAAGGGGUGGCAAUGGCAGA--UGCGAAAGCAAA-AAGCGAAAGCAAAAAGCGAAAGCAAAUACCCAUGAGGUUGGAUUCCGCCUCCUUAAGCUCAGU
........(((((.(((.(((((((((((((..((..--(((....)))..-..((....)).....((....)).........))..))))....))))).))))))).))))) ( -38.20)
>DroEre_CAF1 62457 98 + 1
UUCCCAUCACUGAACAUUGAGGGGUGGCAAAAGCAAG----------------AGCAACAGCAA-AAGCGAAAGCAAAUACCCAUGAGGUUGGAUUUUGCCUCCUUAAGCUCAGU
........(((((...((((((((((((....((...----------------.))....))..-..((....))...)))))..(((((........))))))))))..))))) ( -29.10)
>DroYak_CAF1 56892 114 + 1
UUCCCAUCACUGAACAUUAAAGGGUGGCAAAAGCAAAAUAGCAAAAGCAAGAAAGCAUAAGCGA-AAGCGAAAGCAAAUACCCAUGAGGUUGGAUUCCGCCUCCUUAAGCUCAGU
........(((((...((((.(((((((....((......))....((......))....))..-..((....))...)))))..(((((.((...))))))).))))..))))) ( -29.00)
>consensus
UUCCCAUCACUGAACUUUAAGGGGUGGCAAUAGCAGA__UGCGAAAGCAAA_AAGC___AGC_A_AAGCGAAAGCAAAUACCCAUGAGGUUGGAUUCCGCCUCCUUAAGCUCAGU
........(((((.(.((((((((((((....))......((....))...................((....))...)))))..(((((........))))))))))).))))) (-26.98 = -27.32 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 22,606,178 – 22,606,277
Length 99
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 81.60
Mean single sequence MFE -30.06
Consensus MFE -24.22
Energy contribution -24.14
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.79
Structure conservation index 0.81
SVM decision value 0.70
SVM RNA-class probability 0.827117
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22606178 99 - 27905053
ACUGAGCUAAAGGAGGCGGAAUCCAACCUCAUGGGUAUUUGCUUUCGCU-------------U-UUUGCUUUCGCA--UCUGCUAUUGCCACCCCUUAAAGUUCAGUGAUGGGAA
((((((((...((((((((((((((......))))).)))))))))((.-------------.-..(((....)))--...))................))))))))........ ( -28.60)
>DroSec_CAF1 54531 99 - 1
ACUGAGCUUAAGGAGGCGGAAUCCAACCUCAUGGGUAUUUGCUUUCGCU-------------U-UUUGCUUUCGCA--UCUGCCAUUGCCACCCCUUAAAGUUCAGUGAUGGGAA
(((((((((((((.((.((....((......))((((..(((....((.-------------.-...))....)))--..))))....)).)))))).)))))))))........ ( -30.80)
>DroSim_CAF1 56320 112 - 1
ACUGAGCUUAAGGAGGCGGAAUCCAACCUCAUGGGUAUUUGCUUUCGCUUUUUGCUUUCGCUU-UUUGCUUUCGCA--UCUGCCAUUGCCACCCCUUAAAGUUCAGUGAUGGGAA
(((((((((((((.((.((....((......))((((..(((....((.....))....((..-...))....)))--..))))....)).)))))).)))))))))........ ( -32.80)
>DroEre_CAF1 62457 98 - 1
ACUGAGCUUAAGGAGGCAAAAUCCAACCUCAUGGGUAUUUGCUUUCGCUU-UUGCUGUUGCU----------------CUUGCUUUUGCCACCCCUCAAUGUUCAGUGAUGGGAA
...((((....((((((((((((((......))))).)))))))))((..-..))....)))----------------)..((....))..(((.(((........))).))).. ( -28.90)
>DroYak_CAF1 56892 114 - 1
ACUGAGCUUAAGGAGGCGGAAUCCAACCUCAUGGGUAUUUGCUUUCGCUU-UCGCUUAUGCUUUCUUGCUUUUGCUAUUUUGCUUUUGCCACCCUUUAAUGUUCAGUGAUGGGAA
(((((((((((((((((((((((((......))))).)))))))))....-..((....((......((....))......))....))......)))).)))))))........ ( -29.20)
>consensus
ACUGAGCUUAAGGAGGCGGAAUCCAACCUCAUGGGUAUUUGCUUUCGCUU_U_GCU___GCUU_UUUGCUUUCGCA__UCUGCUAUUGCCACCCCUUAAAGUUCAGUGAUGGGAA
(((((((((((((((((((((((((......))))).))))))).....................................((....))....)))))).)))))))........ (-24.22 = -24.14 +  -0.08)

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 13:12:10 2006