Locus 6746

Sequence ID X_DroMel_CAF1
Location 16,761,027 – 16,761,167
Length 140
Max. P 0.836242
window11034 window11035 window11036

overview

Window 4

Location 16,761,027 – 16,761,128
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.87
Mean single sequence MFE -24.20
Consensus MFE -17.94
Energy contribution -18.50
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 0.73
SVM RNA-class probability 0.836242
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16761027 101 + 22224390
GUUCACGCGCUCUUCGAGUCACAAAUUCAACUGUCACUGCCAUAACACCCAGUC-CCAUAUAUAAUGCAUGUGAAGUCACAUGCCAUAUAGUGACAAGUCAC------------------
.................(((((.........((..((((..........)))).-.))(((((...(((((((....))))))).)))))))))).......------------------ ( -21.60)
>DroSec_CAF1 47822 99 + 1
--UCACGCGCUCUUCGAGUCACAAAUUCAACUGUCACUGCCAUAACACCCAGUC-CCAUAUAUAAUGCAUGUGAAGUCACAUGCCGCAAAGUGACGAGUCAC------------------
--......((((...((((.....))))....((((((((....((.....)).-...........(((((((....))))))).))..))))))))))...------------------ ( -22.40)
>DroSim_CAF1 45751 99 + 1
--UCACGCGCUCUUCGAGUCACAAAUUCGACUGUCACUGCCAUAACACCCAGUC-CCAUAUAUAAUGCAUGUGAAGUCACAUGCCGCAUAGUGACGAGUCAC------------------
--......((((.((((((.....))))))..(((((((.....((.....)).-...........(((((((....)))))))....)))))))))))...------------------ ( -25.50)
>DroYak_CAF1 40012 116 + 1
----UCGUGCUCUUCACGCCGCAAAUUCAACUGUCACUGCCAUAACACCAAGUCCCCAUAUAUAAUGCAUGUGAAGUCACAUGCCGUAUAGUGACGAGUCACUCACUAGUCGAAUCGGAU
----.((((.....))))(((...((((.((((((((((.....((.....)).............(((((((....)))))))....)))))))(((...)))...))).))))))).. ( -27.30)
>consensus
__UCACGCGCUCUUCGAGUCACAAAUUCAACUGUCACUGCCAUAACACCCAGUC_CCAUAUAUAAUGCAUGUGAAGUCACAUGCCGCAUAGUGACGAGUCAC__________________
......(.((((...))))).........((((((((((.....((.....)).............(((((((....)))))))....))))))).)))..................... (-17.94 = -18.50 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,761,027 – 16,761,128
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.87
Mean single sequence MFE -32.55
Consensus MFE -28.41
Energy contribution -27.48
Covariance contribution -0.94
Combinations/Pair 1.19
Mean z-score -1.63
Structure conservation index 0.87
SVM decision value 0.52
SVM RNA-class probability 0.768776
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16761027 101 - 22224390
------------------GUGACUUGUCACUAUAUGGCAUGUGACUUCACAUGCAUUAUAUAUGG-GACUGGGUGUUAUGGCAGUGACAGUUGAAUUUGUGACUCGAAGAGCGCGUGAAC
------------------....((.(((.((((((((((((((....)))))))....)))))))-))).))(((((.....(((.((((......)))).))).....)))))...... ( -31.10)
>DroSec_CAF1 47822 99 - 1
------------------GUGACUCGUCACUUUGCGGCAUGUGACUUCACAUGCAUUAUAUAUGG-GACUGGGUGUUAUGGCAGUGACAGUUGAAUUUGUGACUCGAAGAGCGCGUGA--
------------------(((.(((((((((..((.(((((((....)))))))......(((((-.((...)).)))))))))))))((((........))))....))))))....-- ( -30.10)
>DroSim_CAF1 45751 99 - 1
------------------GUGACUCGUCACUAUGCGGCAUGUGACUUCACAUGCAUUAUAUAUGG-GACUGGGUGUUAUGGCAGUGACAGUCGAAUUUGUGACUCGAAGAGCGCGUGA--
------------------(((.(((((((((..((.(((((((....)))))))......(((((-.((...)).)))))))))))))(((((......)))))....))))))....-- ( -32.40)
>DroYak_CAF1 40012 116 - 1
AUCCGAUUCGACUAGUGAGUGACUCGUCACUAUACGGCAUGUGACUUCACAUGCAUUAUAUAUGGGGACUUGGUGUUAUGGCAGUGACAGUUGAAUUUGCGGCGUGAAGAGCACGA----
..(((((((((((.....((.(((.((((..((((.(((((((....))))))).........(....)...))))..))))))).))))))))))...)))((((.....)))).---- ( -36.60)
>consensus
__________________GUGACUCGUCACUAUACGGCAUGUGACUUCACAUGCAUUAUAUAUGG_GACUGGGUGUUAUGGCAGUGACAGUUGAAUUUGUGACUCGAAGAGCGCGUGA__
..................(((.(((((((((.....(((((((....)))))))............(((.....))).....)))))).((((......)))).....))))))...... (-28.41 = -27.48 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,761,067 – 16,761,167
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.08
Mean single sequence MFE -22.62
Consensus MFE -15.70
Energy contribution -15.70
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.69
SVM decision value 0.14
SVM RNA-class probability 0.601952
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16761067 100 + 22224390
CAUAACACCCAGUC-CCAUAUAUAAUGCAUGUGAAGUCACAUGCCAUAUAGUGACAAGUCAC-------------------GUAUUGCAUCACAAAAAAAUCUUAGACAACUGCCAGAGU
...........(((-...(((((...(((((((....))))))).)))))((((....))))-------------------........................)))............ ( -18.90)
>DroSec_CAF1 47860 99 + 1
CAUAACACCCAGUC-CCAUAUAUAAUGCAUGUGAAGUCACAUGCCGCAAAGUGACGAGUCAC-------------------GGAUUGCAUCACAAA-ACAUCUUAGACAAUUGCCAGAGU
...........(((-...........(((((((....))))))).((((.((((....))))-------------------...))))........-........)))............ ( -21.90)
>DroSim_CAF1 45789 99 + 1
CAUAACACCCAGUC-CCAUAUAUAAUGCAUGUGAAGUCACAUGCCGCAUAGUGACGAGUCAC-------------------GGAUUGCAUCACAAA-ACAUCUUAGACAAUUGCCAGAGU
.........(((((-(..........(((((((....)))))))......((((....))))-------------------)))))).........-....................... ( -21.80)
>DroYak_CAF1 40048 119 + 1
CAUAACACCAAGUCCCCAUAUAUAAUGCAUGUGAAGUCACAUGCCGUAUAGUGACGAGUCACUCACUAGUCGAAUCGGAUUGGAUUGCAUCAGAGA-AAAUCUUAGACAAUCGCCAGAGU
..........(((((...........(((((((....)))))))((..((((((........))))))..))....))))).(((((..((.(((.-....))).)))))))........ ( -27.90)
>consensus
CAUAACACCCAGUC_CCAUAUAUAAUGCAUGUGAAGUCACAUGCCGCAUAGUGACGAGUCAC___________________GGAUUGCAUCACAAA_AAAUCUUAGACAAUUGCCAGAGU
...........(((............(((((((....)))))))......((((....))))...........................................)))............ (-15.70 = -15.70 +   0.00)

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 12:21:48 2006