Locus 1549

Sequence ID X_DroMel_CAF1
Location 4,460,037 – 4,460,171
Length 134
Max. P 0.930513
window2536 window2537 window2538 window2539

overview

Window 6

Location 4,460,037 – 4,460,156
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.49
Mean single sequence MFE -42.80
Consensus MFE -34.36
Energy contribution -34.88
Covariance contribution 0.52
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.80
SVM decision value 1.07
SVM RNA-class probability 0.909556
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4460037 119 + 22224390
AAAAAAAUAGGCGACGCGCGCCUUUUCAAUAACCUUUAUCAGGUGGGUGACUGUUUUCUGUGGGCGGA-AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUAUCACUGGUGACAACA
.........((((.(((.((((..((((((..((((...((((.((....))....)))).))).)..-)))))).)))))))..))))..((((((.(((....)))..)))))).... ( -41.00)
>DroSec_CAF1 61587 118 + 1
AAAAAAAUAGGCGACGCGCGCCUUUUCAAUAACCUUUAUCAGGUGGGUGACUGUUUU-UGUGGGUGGA-AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCACUGGUGACAACA
.........((((.(((.((((..((((((.((((.....(((..(....)..))).-...))))...-)))))).)))))))..))))..((((((.(((....)))..)))))).... ( -43.80)
>DroSim_CAF1 66808 118 + 1
AAAAAAAUAGGCGACGCGCGCCUUUUCAAUAACCUUUAUCAGGUGGGUGACUGUUUU-UGUGGGUGGA-AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCGCUGGUGACAGCA
.........((((.(((.((((..((((((.((((.....(((..(....)..))).-...))))...-)))))).)))))))..))))..(((.....))).....((((....)))). ( -43.50)
>DroEre_CAF1 65039 116 + 1
AAA---GAAUGCGGCGCGCGCCUUUUCAAUAACCUUUAUCAGGUGGGUGACUGGUUU-UGUGGGUGGAAAUUGGGUGGUGGCGGGUGGCCAGUCACCUUGACAUGUCACUGGUGACAACA
...---......(((((.((((..((((((.((((..(((((........)))))..-...))))....))))))....)))).)).))).((((((.(((....)))..)))))).... ( -40.00)
>DroYak_CAF1 62297 112 + 1
-------AAUGCGGCGCGCGCCUUUUUAAUAACCUUUAUCAGGUGGGUGACUGCUAU-UGUGGGUGGCUUUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCACUGGUGACAACA
-------..((.(((((.((((.........((((.((...((..(....)..))..-)).)))).(((.......))))))).)))))))((((((.(((....)))..)))))).... ( -45.70)
>consensus
AAAAAAAUAGGCGACGCGCGCCUUUUCAAUAACCUUUAUCAGGUGGGUGACUGUUUU_UGUGGGUGGA_AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCACUGGUGACAACA
.........((((.(((.((((..((((((.((((....(((........)))........))))....)))))).)))))))..))))..((((((.(((....)))..)))))).... (-34.36 = -34.88 +   0.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,460,037 – 4,460,156
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.49
Mean single sequence MFE -31.96
Consensus MFE -25.34
Energy contribution -26.38
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.53
Structure conservation index 0.79
SVM decision value 0.27
SVM RNA-class probability 0.660678
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4460037 119 - 22224390
UGUUGUCACCAGUGAUAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU-UCCGCCCACAGAAAACAGUCACCCACCUGAUAAAGGUUAUUGAAAAGGCGCGCGUCGCCUAUUUUUUU
....((((((..(((....))).))))))(((((...(((((((......(-((........))).....(((...((((.....))))...)))...)))).)))..)))))....... ( -34.20)
>DroSec_CAF1 61587 118 - 1
UGUUGUCACCAGUGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU-UCCACCCACA-AAAACAGUCACCCACCUGAUAAAGGUUAUUGAAAAGGCGCGCGUCGCCUAUUUUUUU
...(((((....)))))..(((((((((((((((....)))(.....)...-..........-....)))))))).((((.....))))..))))..(((((.....)))))........ ( -32.80)
>DroSim_CAF1 66808 118 - 1
UGCUGUCACCAGCGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU-UCCACCCACA-AAAACAGUCACCCACCUGAUAAAGGUUAUUGAAAAGGCGCGCGUCGCCUAUUUUUUU
.((((....))))......(((((((((((((((....)))(.....)...-..........-....)))))))).((((.....))))..))))..(((((.....)))))........ ( -32.50)
>DroEre_CAF1 65039 116 - 1
UGUUGUCACCAGUGACAUGUCAAGGUGACUGGCCACCCGCCACCACCCAAUUUCCACCCACA-AAACCAGUCACCCACCUGAUAAAGGUUAUUGAAAAGGCGCGCGCCGCAUUC---UUU
...(((((....)))))..(((((((((((((..............................-...))))))))).((((.....))))..))))...(((....)))......---... ( -29.21)
>DroYak_CAF1 62297 112 - 1
UGUUGUCACCAGUGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAAAGCCACCCACA-AUAGCAGUCACCCACCUGAUAAAGGUUAUUAAAAAGGCGCGCGCCGCAUU-------
((.(((((....)))))...)).(((((((((((....)))((.........))........-....)))))))).((((.....)))).........(((....))).....------- ( -31.10)
>consensus
UGUUGUCACCAGUGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU_UCCACCCACA_AAAACAGUCACCCACCUGAUAAAGGUUAUUGAAAAGGCGCGCGUCGCCUAUUUUUUU
...(((((....)))))..(((((((((((((((....)))(.....)...................)))))))).((((.....))))..))))..(((((.....)))))........ (-25.34 = -26.38 +   1.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,460,077 – 4,460,171
Length 94
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 90.10
Mean single sequence MFE -38.50
Consensus MFE -28.34
Energy contribution -29.02
Covariance contribution 0.69
Combinations/Pair 1.18
Mean z-score -2.87
Structure conservation index 0.74
SVM decision value 1.00
SVM RNA-class probability 0.897548
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4460077 94 + 22224390
AGGUGGGUGACUGUUUUCUGUGGGCGGA-AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUAUCACUGGUGACAACAGUAACAACAAUAAAA-------
..((..((.(((((((((((....))))-).((((((.(....).))))))((((((.(((....)))..)))))))))))).)).)).......------- ( -30.70)
>DroSec_CAF1 61627 100 + 1
AGGUGGGUGACUGUUUU-UGUGGGUGGA-AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCACUGGUGACAACAGCAACAACAAUAACACCCAUUA
.((((((((..((((.(-(((.(.((..-..((((((.(....).))))))((((((.(((....)))..))))))..)).).)))).)))).)))))))). ( -39.20)
>DroSim_CAF1 66848 100 + 1
AGGUGGGUGACUGUUUU-UGUGGGUGGA-AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCGCUGGUGACAGCAGCAACAACAAUAACACCCAUUA
(((..(....)..))).-.(((((((..-(((((((((((((....)))..))))))......(((.((((....)))).)))....))))..))))))).. ( -42.70)
>DroEre_CAF1 65076 101 + 1
AGGUGGGUGACUGGUUU-UGUGGGUGGAAAUUGGGUGGUGGCGGGUGGCCAGUCACCUUGACAUGUCACUGGUGACAACAGCAACAACACCAACACCCAUUA
.((((((((..((((.(-(((.(.((......((((((((((.....)))).)))))).....(((((....))))).)).).)))).)))).)))))))). ( -41.40)
>consensus
AGGUGGGUGACUGUUUU_UGUGGGUGGA_AUUGGGUGGCGGCGGGUGCCCAGUCACCUUGACAUGUCACUGGUGACAACAGCAACAACAAUAACACCCAUUA
.((((((((..((((...(((..((......((((((.(....).))))))((((((.(((....)))..))))))....)).)))..)))).)))))))). (-28.34 = -29.02 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,460,077 – 4,460,171
Length 94
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 90.10
Mean single sequence MFE -31.62
Consensus MFE -23.71
Energy contribution -24.90
Covariance contribution 1.19
Combinations/Pair 1.11
Mean z-score -3.06
Structure conservation index 0.75
SVM decision value 1.21
SVM RNA-class probability 0.930513
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4460077 94 - 22224390
-------UUUUAUUGUUGUUACUGUUGUCACCAGUGAUAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU-UCCGCCCACAGAAAACAGUCACCCACCU
-------.....(((.((((((((.......))))))))...)))(((((((((((....))).........(-((........)))..))))))))..... ( -26.00)
>DroSec_CAF1 61627 100 - 1
UAAUGGGUGUUAUUGUUGUUGCUGUUGUCACCAGUGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU-UCCACCCACA-AAAACAGUCACCCACCU
...((((((..((((..((.((....((((((..(((....))).))))))..(((....))))).)).))))-..))))))..-................. ( -32.30)
>DroSim_CAF1 66848 100 - 1
UAAUGGGUGUUAUUGUUGUUGCUGCUGUCACCAGCGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU-UCCACCCACA-AAAACAGUCACCCACCU
....(((((...(((.((((((((.......))))))))...)))(((((((((((....)))(.....)...-..........-....))))))))))))) ( -32.70)
>DroEre_CAF1 65076 101 - 1
UAAUGGGUGUUGGUGUUGUUGCUGUUGUCACCAGUGACAUGUCAAGGUGACUGGCCACCCGCCACCACCCAAUUUCCACCCACA-AAACCAGUCACCCACCU
...(((((((((((.((((.(.((..((((((..(((....))).))))))((((.....))))............)).).)))-).))))).))))))... ( -35.50)
>consensus
UAAUGGGUGUUAUUGUUGUUGCUGUUGUCACCAGUGACAUGUCAAGGUGACUGGGCACCCGCCGCCACCCAAU_UCCACCCACA_AAAACAGUCACCCACCU
....(((((...(((.((((((((.......))))))))...)))(((((((((((....)))(.....)...................))))))))))))) (-23.71 = -24.90 +   1.19)

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 10:13:09 2006