Locus 6144

Sequence ID 2R_DroMel_CAF1
Location 19,334,732 – 19,334,875
Length 143
Max. P 0.982471
window9840 window9841 window9842 window9843

overview

Window 0

Location 19,334,732 – 19,334,835
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 94.27
Mean single sequence MFE -19.58
Consensus MFE -15.62
Energy contribution -15.42
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.12
SVM RNA-class probability 0.592857
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19334732 103 + 20766785
AUAUGCGGGGAAAUUUAACUUUCGCAUAAAAAUGUCAAAAUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAAAAAAA
.((((((..(.........)..))))))..............(.(((..........((((....((((.....))))...)))).....))).)........ ( -21.26)
>DroSec_CAF1 12713 101 + 1
AUAUGCGGGGAAAUUUAACUUUCGCAUAAAAAUGUCAAAAUAGGGAAAACUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAAA--AA
.((((((..(.........)..))))))....(((....((((......))))(((.((((....((((.....))))...)))).....))))))...--.. ( -23.30)
>DroSim_CAF1 12890 101 + 1
AUAUGCGGGGAAAUUUAACUUUCGCAUAAAAAUGUCAAAAUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAAA--AA
.((((((..(.........)..))))))..............(.(((..........((((....((((.....))))...)))).....))).)....--.. ( -21.26)
>DroEre_CAF1 12806 94 + 1
A-----GGGA-AAUUUAACUUUCGCAUAAAAAUGUCAAAAUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAA---AA
.-----(.((-(((((..(((..((((....))))......)))..)))))(..(..((((....((((.....))))...))))..)..))).)...---.. ( -15.70)
>DroYak_CAF1 13147 95 + 1
A-----GGGAAAAUUUAACUUUCGCAUAAAAAUGUCAAAAUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAA---AA
.-----(.((((((((..(((..((((....))))......)))..)))))......((((....((((.....))))...)))).....))).)...---.. ( -16.40)
>consensus
AUAUGCGGGGAAAUUUAACUUUCGCAUAAAAAUGUCAAAAUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAAA__AA
......(.((((((((...((((((((....))))....((((......)))))))).(((....((((.....))))...)))))))).))).)........ (-15.62 = -15.42 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,334,732 – 19,334,835
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -17.05
Consensus MFE -14.68
Energy contribution -14.52
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.67
Structure conservation index 0.86
SVM decision value 1.30
SVM RNA-class probability 0.939769
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19334732 103 - 20766785
UUUUUUUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAUUUUGACAUUUUUAUGCGAAAGUUAAAUUUCCCCGCAUAU
.......((((........(((((..(((.....)))...)))))......((((((((.(.................).))))))))........))))... ( -18.03)
>DroSec_CAF1 12713 101 - 1
UU--UUUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAGUUUUCCCUAUUUUGACAUUUUUAUGCGAAAGUUAAAUUUCCCCGCAUAU
..--...((((........(((((..(((.....)))...)))))......................((.((((....((....)).)))).))..))))... ( -17.80)
>DroSim_CAF1 12890 101 - 1
UU--UUUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAUUUUGACAUUUUUAUGCGAAAGUUAAAUUUCCCCGCAUAU
..--...((((........(((((..(((.....)))...)))))......((((((((.(.................).))))))))........))))... ( -18.03)
>DroEre_CAF1 12806 94 - 1
UU---UUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAUUUUGACAUUUUUAUGCGAAAGUUAAAUU-UCCC-----U
((---((((((........(((((..(((.....)))...)))))...(((.(((.......))).)))........)))))))).......-....-----. ( -15.70)
>DroYak_CAF1 13147 95 - 1
UU---UUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAUUUUGACAUUUUUAUGCGAAAGUUAAAUUUUCCC-----U
((---((((((........(((((..(((.....)))...)))))...(((.(((.......))).)))........))))))))............-----. ( -15.70)
>consensus
UU__UUUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAUUUUGACAUUUUUAUGCGAAAGUUAAAUUUCCCCGCAUAU
.....((((((........(((((..(((.....)))...)))))...(((.(((.......))).)))........)))))).................... (-14.68 = -14.52 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,334,771 – 19,334,875
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 97.41
Mean single sequence MFE -28.16
Consensus MFE -28.22
Energy contribution -28.04
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -4.14
Structure conservation index 1.00
SVM decision value 1.75
SVM RNA-class probability 0.975609
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19334771 104 + 20766785
AUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAAAAAAAAGGAAGAGAAAGCGAACAGGAAAACUAUAAUGCAGCCCGU
...(((...((((((...((((....((((.....))))...))))..((((((((...................))))))))......))))))....))).. ( -28.51)
>DroSim_CAF1 12929 102 + 1
AUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAAA--AAAGGAAGAGAAAGUGAACAGGAAAACUAUAAUGCAGCCCAU
...(((...((((((...((((....((((.....))))...))))..((((((((....--.............))))))))......))))))....))).. ( -26.73)
>DroEre_CAF1 12839 101 + 1
AUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAA---AAAGGAAGAGAAAGCGAACAGGAAAACUAUAAUGCAGCCCAU
...(((...((((((...((((....((((.....))))...))))..((((((((...---.............))))))))......))))))....))).. ( -28.69)
>DroYak_CAF1 13181 101 + 1
AUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAA---AAAGGAAGAGAAAGCGAACAGGAAAACUAUAAUGCAGCCCAU
...(((...((((((...((((....((((.....))))...))))..((((((((...---.............))))))))......))))))....))).. ( -28.69)
>consensus
AUAGGGAAAAUUAUGAAAUGCCAAAAGGCGGAAAACGCUGUCGGCGGAUUGUUCGCAAA___AAAGGAAGAGAAAGCGAACAGGAAAACUAUAAUGCAGCCCAU
...(((...((((((...((((....((((.....))))...))))..((((((((...................))))))))......))))))....))).. (-28.22 = -28.04 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,334,771 – 19,334,875
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 97.41
Mean single sequence MFE -21.76
Consensus MFE -21.28
Energy contribution -21.54
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.98
SVM decision value 1.92
SVM RNA-class probability 0.982471
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19334771 104 - 20766785
ACGGGCUGCAUUAUAGUUUUCCUGUUCGCUUUCUCUUCCUUUUUUUUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAU
..(((....(((((........(((((((...................)))))))....(((((..(((.....)))...))))).....)))))...)))... ( -23.21)
>DroSim_CAF1 12929 102 - 1
AUGGGCUGCAUUAUAGUUUUCCUGUUCACUUUCUCUUCCUUU--UUUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAU
..(((....(((((........(((((.(.............--....).)))))....(((((..(((.....)))...))))).....)))))...)))... ( -17.63)
>DroEre_CAF1 12839 101 - 1
AUGGGCUGCAUUAUAGUUUUCCUGUUCGCUUUCUCUUCCUUU---UUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAU
..(((....(((((........(((((((.............---...)))))))....(((((..(((.....)))...))))).....)))))...)))... ( -23.09)
>DroYak_CAF1 13181 101 - 1
AUGGGCUGCAUUAUAGUUUUCCUGUUCGCUUUCUCUUCCUUU---UUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAU
..(((....(((((........(((((((.............---...)))))))....(((((..(((.....)))...))))).....)))))...)))... ( -23.09)
>consensus
AUGGGCUGCAUUAUAGUUUUCCUGUUCGCUUUCUCUUCCUUU___UUUGCGAACAAUCCGCCGACAGCGUUUUCCGCCUUUUGGCAUUUCAUAAUUUUCCCUAU
..(((....(((((........(((((((...................)))))))....(((((..(((.....)))...))))).....)))))...)))... (-21.28 = -21.54 +   0.25)

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 12:03:55 2006