Locus 3957

Sequence ID X_DroMel_CAF1
Location 10,516,711 – 10,516,905
Length 194
Max. P 0.927239
window6498 window6499

overview

Window 8

Location 10,516,711 – 10,516,825
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.23
Mean single sequence MFE -23.44
Consensus MFE -11.54
Energy contribution -11.66
Covariance contribution 0.12
Combinations/Pair 1.22
Mean z-score -2.01
Structure conservation index 0.49
SVM decision value 1.18
SVM RNA-class probability 0.927239
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10516711 114 + 22224390
UACACAAAACCAACCACCCGUUCUGUUCCCC-GCUUUUCUCUCGGUGUAGGCUCACAAAAUCGAAAUGUUAAAAAAAAAAAA----AAUGUAAAGAGCGAGAA-AAGGGGAGCAAAUUUU
.......................((((((((-..(((((.(((.(((......))).........(((((............----)))))...))).)))))-..))))))))...... ( -23.80)
>DroSec_CAF1 48313 96 + 1
UACGCAAAACCA----------------CCC-GCUUUUCUCUCGGUGUAGGCUCACAAAAUCGAAAUGUUGAAAAAAAAAAAUAUA------AAGAGCGAGAA-AAGGGGAGCAAAUUUU
............----------------(((-.((((((((.(.(((......)))....((...(((((..........))))).------..))).)))))-)))))).......... ( -19.50)
>DroSim_CAF1 51803 102 + 1
UACGCAAAACCA----------------CCC-GCUUUUCUCUCGGUGUAGGCUCACAAAAUCGAAAUGUUGAAAAAAAAAAAUAUAAAUGCAAAGAGCGAGAA-AAGGGGAGCAAAUUUU
............----------------(((-.(((((((((((((...(.....)...))))).........................((.....)))))))-)))))).......... ( -20.60)
>DroEre_CAF1 50284 106 + 1
-------ACCAACCCACCC-UCCUAUUCCCUAUUUUUUCUCUCGGUGUAGGCUCACAAAAUCGAAAUGUUGGA----AAAAACA-AAAUGGAAAGAGCGGGAG-AAGGGGCGCAAAUUUU
-------...........(-((((.(((((..(((((((..(((((...(.....)...)))))..((((...----...))))-....)))))))..)))))-.))))).......... ( -24.00)
>DroYak_CAF1 49780 100 + 1
-------CAGCACCCACCC-U-----------UUUUUUCGCUCUGUGUAGGCUCACAAAAUCGAAAUGUUGAACAAAAAAAGUA-AAAGGCAAAGAGAGGGAAAAAGGGGUGCAAAUUUU
-------..((((((.(((-(-----------((((((.(((.((((......))))...((((....))))............-...)))))))))))))......))))))....... ( -29.30)
>consensus
UAC_CAAAACCA_CCACCC_U_______CCC_GCUUUUCUCUCGGUGUAGGCUCACAAAAUCGAAAUGUUGAAAAAAAAAAAUA_AAAUGCAAAGAGCGAGAA_AAGGGGAGCAAAUUUU
............................(((...(((((.(((.(((......)))....((((....))))......................))).)))))...)))........... (-11.54 = -11.66 +   0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,516,790 – 10,516,905
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.17
Mean single sequence MFE -22.02
Consensus MFE -15.82
Energy contribution -15.95
Covariance contribution 0.13
Combinations/Pair 1.14
Mean z-score -1.42
Structure conservation index 0.72
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10516790 115 + 22224390
AA----AAUGUAAAGAGCGAGAA-AAGGGGAGCAAAUUUUGUAGCUGGUAGGCAAAAAGCUGGCAACAAAUGAUGAAAUGCUAAAAUGCAUAUAGCAGCAAUGGAGUGGGUAUGUUUUUU
..----...............((-((((.(.((..((((..(.((((.(((((.....)))(....)..........((((......)))).)).)))).)..))))..)).).)))))) ( -21.70)
>DroSim_CAF1 51866 108 + 1
AAUAUAAAUGCAAAGAGCGAGAA-AAGGGGAGCAAAUUUUGUAGUUGGUAGGCAAAAAGCUGGCAACAAAUGAUGAAAUGCUAAAAUGCAUAUAGCGGCAAGGGAGUGG-----------
........(((.....((.....-........((...(((((.((..((.........))..)).)))))...))..((((......))))...)).))).........----------- ( -17.00)
>DroEre_CAF1 50352 118 + 1
AACA-AAAUGGAAAGAGCGGGAG-AAGGGGCGCAAAUUUUGUAGUUGGCAGGCAAAAAGCUGGCAACAAAUGAUGAAAUGCUAAAAUGCAUAUAGCGGCAAGGGACUGGGCAUGUUUUUU
....-......((((((((.(..-.((.(.(((....(((((.((..((.........))..)).))))).......((((......))))...))).)......))...).)))))))) ( -24.80)
>DroYak_CAF1 49841 119 + 1
AGUA-AAAGGCAAAGAGAGGGAAAAAGGGGUGCAAAUUUUGCAGUUGGCGGGCAAAAAGCUGGCAACAAAUGAUGAAAUGCAAAAAUGCAUAUAGCGGCCAUGGAGUGGGUGUGGAUUUU
.(((-(((.(((..................)))...)))))).((((.(.(((.....))).)))))..........(((((....)))))...(((.((((...)))).)))....... ( -24.57)
>consensus
AAUA_AAAUGCAAAGAGCGAGAA_AAGGGGAGCAAAUUUUGUAGUUGGCAGGCAAAAAGCUGGCAACAAAUGAUGAAAUGCUAAAAUGCAUAUAGCGGCAAGGGAGUGGGUAUGUUUUUU
................................((..((((((.((((((.(((.....))).)).............((((......)))).)))).))))))...))............ (-15.82 = -15.95 +   0.13)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:44 2006