Locus 1684

Sequence ID X_DroMel_CAF1
Location 4,707,995 – 4,708,123
Length 128
Max. P 0.996642
window2769 window2770 window2771

overview

Window 9

Location 4,707,995 – 4,708,088
Length 93
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.60
Mean single sequence MFE -30.00
Consensus MFE -19.64
Energy contribution -20.87
Covariance contribution 1.23
Combinations/Pair 1.14
Mean z-score -2.13
Structure conservation index 0.65
SVM decision value 2.73
SVM RNA-class probability 0.996642
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4707995 93 - 22224390
UCAAUAUGCCUUGAAAGGGUUGCGGGUUGCGG-----------AAAAG----CAGCUGCGGUGGCUUAAGUGAGGCAUAAGAAAAUAAUUAAAAACAGAAAG------------CGAUUU
....(((((((((...((((..(.((((((..-----------....)----)))))...)..))))...))))))))).......................------------...... ( -25.70)
>DroPse_CAF1 21092 119 - 1
UCAAUAUGCCAC-AAAGGGUUGCAGAGAGGGGCUGGUGGCUGGUGCGGCCGUUGGCUGUGGUGGCUUAAGUGAGGCAUAAGAAAAUAAUUAAAAACACAAAAGAGCCGAACACACAGUUU
....((((((.(-(..((((..(.....(.((((..((((((...))))))..)))).).)..))))...)).))))))............................((((.....)))) ( -32.60)
>DroPer_CAF1 20512 116 - 1
UCAAUAUGCCAC-AAAGGGUUGCAGAGAGGGGCC-AUGGCUGGUGAGGCCGUUGGCUGUGGUGGCUUAAGUGAGGCAUAAGAAAAUAAUUAAAAACACAAAAGAGCCGAAC--ACAGUUU
....((((((.(-(..((((..(.....(.((((-((((((.....))))).))))).).)..))))...)).))))))................................--....... ( -31.70)
>consensus
UCAAUAUGCCAC_AAAGGGUUGCAGAGAGGGGC___UGGCUGGUGAGGCCGUUGGCUGUGGUGGCUUAAGUGAGGCAUAAGAAAAUAAUUAAAAACACAAAAGAGCCGAAC__ACAGUUU
....((((((......((((..(.....(.((((.((((((.....)))))).)))).).)..))))......))))))......................................... (-19.64 = -20.87 +   1.23)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,708,023 – 4,708,123
Length 100
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.65
Mean single sequence MFE -25.47
Consensus MFE -16.90
Energy contribution -16.73
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.66
SVM decision value 0.43
SVM RNA-class probability 0.732101
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4708023 100 + 22224390
UUAUGCCUCACUUAAGCCACCGCAGCUG----CUUUU-----------CCGCAACCCGCAACCCUUUCAAGGCAUAUUGAGUGCUUUGUAAUUUUUGCGGUUUUUAAGCCUUUUC-----
..........((((((..((((((((((----(....-----------..)))....))........((((((((.....)))))))).......)))))).)))))).......----- ( -23.20)
>DroPse_CAF1 21132 119 + 1
UUAUGCCUCACUUAAGCCACCACAGCCAACGGCCGCACCAGCCACCAGCCCCUCUCUGCAACCCUUU-GUGGCAUAUUGAGUGCUUUGUAAUUUUUGUGGGUCUUAAGCCUUUCCACCAC
..........((((((.(.((((((((...))).((((((((((((((.......))).........-)))))....)).))))...........)))))).))))))............ ( -26.60)
>DroPer_CAF1 20550 118 + 1
UUAUGCCUCACUUAAGCCACCACAGCCAACGGCCUCACCAGCCAU-GGCCCCUCUCUGCAACCCUUU-GUGGCAUAUUGAGUGCUUUGUAAUUUUUGUGGGUCUUAAGCCUUUCCACCAC
..........((((((.(.(((((((((..(((.......))).)-))).......(((((......-..(((((.....)))))))))).....)))))).))))))............ ( -26.60)
>consensus
UUAUGCCUCACUUAAGCCACCACAGCCAACGGCCUCACCAGCCA___GCCCCUCUCUGCAACCCUUU_GUGGCAUAUUGAGUGCUUUGUAAUUUUUGUGGGUCUUAAGCCUUUCCACCAC
..........((((((...((((((.....(((.......)))..............((((.........(((((.....))))))))).....))))))..))))))............ (-16.90 = -16.73 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,708,023 – 4,708,123
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.65
Mean single sequence MFE -33.38
Consensus MFE -22.87
Energy contribution -24.21
Covariance contribution 1.34
Combinations/Pair 1.11
Mean z-score -1.75
Structure conservation index 0.69
SVM decision value 0.83
SVM RNA-class probability 0.861651
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4708023 100 - 22224390
-----GAAAAGGCUUAAAAACCGCAAAAAUUACAAAGCACUCAAUAUGCCUUGAAAGGGUUGCGGGUUGCGG-----------AAAAG----CAGCUGCGGUGGCUUAAGUGAGGCAUAA
-----......((((...................))))......(((((((((...((((..(.((((((..-----------....)----)))))...)..))))...))))))))). ( -27.11)
>DroPse_CAF1 21132 119 - 1
GUGGUGGAAAGGCUUAAGACCCACAAAAAUUACAAAGCACUCAAUAUGCCAC-AAAGGGUUGCAGAGAGGGGCUGGUGGCUGGUGCGGCCGUUGGCUGUGGUGGCUUAAGUGAGGCAUAA
((((.(.............)))))....................((((((.(-(..((((..(.....(.((((..((((((...))))))..)))).).)..))))...)).)))))). ( -36.92)
>DroPer_CAF1 20550 118 - 1
GUGGUGGAAAGGCUUAAGACCCACAAAAAUUACAAAGCACUCAAUAUGCCAC-AAAGGGUUGCAGAGAGGGGCC-AUGGCUGGUGAGGCCGUUGGCUGUGGUGGCUUAAGUGAGGCAUAA
((((.(.............)))))....................((((((.(-(..((((..(.....(.((((-((((((.....))))).))))).).)..))))...)).)))))). ( -36.12)
>consensus
GUGGUGGAAAGGCUUAAGACCCACAAAAAUUACAAAGCACUCAAUAUGCCAC_AAAGGGUUGCAGAGAGGGGC___UGGCUGGUGAGGCCGUUGGCUGUGGUGGCUUAAGUGAGGCAUAA
...........(((((((..((((............((((((..............))).))).......((((.((((((.....)))))).))))))))...)))))))......... (-22.87 = -24.21 +   1.34)

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 10:16:38 2006