Locus 5189

Sequence ID 3L_DroMel_CAF1
Location 14,292,480 – 14,292,702
Length 222
Max. P 0.985470
window8215 window8216 window8217

overview

Window 5

Location 14,292,480 – 14,292,582
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -21.50
Consensus MFE -14.90
Energy contribution -14.57
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -1.28
Structure conservation index 0.69
SVM decision value 0.10
SVM RNA-class probability 0.582286
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14292480 102 + 23771897
GGGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCACAUAAAAUUAUUAUGUGACGAGGAACGUGGGAUGCGAAUAUAUGGUGGUAGU-GGGG-----------------GGAAAAGCG
...(((.((((((((....))).(((.((......(((((((.....)))))))(((.....))).)).)))............)))))-.)))-----------------......... ( -22.50)
>DroSec_CAF1 117728 101 + 1
GGGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCACAUAAAAUUAUUAUGUGACGAGGAACGUGGGAUGCGAAAAUC-GGGGGUUGU-GGGG-----------------GGAAAAGGG
...(((..((.((((....))))((((((......(((((((.....))))))).(((....(((.....)))....))-)..))))))-))..-----------------)))...... ( -25.30)
>DroSim_CAF1 117829 101 + 1
GGGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCACAUAAAAUUAUUAUGUGACGAGGAACGUGGGAUGCGAAAAUC-GGGGGUUGU-GGGG-----------------CGAAAAGGG
..((((.....((((....))))((((((......(((((((.....))))))).(((....(((.....)))....))-)..))))))-.)))-----------------)........ ( -25.70)
>DroEre_CAF1 117861 100 + 1
GGGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCACAUAAAAUUAUUAUGUGACGAGGAACGUGGGGAGUGAAAAUC-GGGGGUCGU-GGGGAAGGG------------------GGG
...(((..((.((((....))))((.(((......(((((((.....))))))).(((...((.......)).....))-)..))).))-.))..))).------------------... ( -19.10)
>DroYak_CAF1 121617 119 + 1
GGGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCACAUAAAAUUAUUAUGUGACGAGGAACGUGGGGAGCGAAAAUC-GGUGGUCGUUGGGGAAGGGAAAGGGAAAGGGGAAAAAGCG
...(((..((...(.....(.((((.((((.....(((((((.....))))))).(((....(((.....)))....))-).)))).)))).).....)....))..))).......... ( -22.30)
>DroAna_CAF1 112730 85 + 1
AAGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCAUAUAAAAUUAUUAUGUGACGAGGAACGUGGGGAAUGAGCACC-AGGA----------------------------------GG
..(.(((....((((....)))).))).).....((((((((.....))))))).)......(.(((..........))-).).----------------------------------.. ( -14.10)
>consensus
GGGUCUGACUAUGCAAAAAUGCAGCAGCCAAAAAGCACAUAAAAUUAUUAUGUGACGAGGAACGUGGGAAGCGAAAAUC_GGGGGUCGU_GGGG_________________GGAAAAGGG
.((.(((....((((....)))).))))).....((((((((.....))))))).)......(((.....)))............................................... (-14.90 = -14.57 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,292,480 – 14,292,582
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -17.78
Consensus MFE -17.42
Energy contribution -17.58
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.98
SVM decision value 2.01
SVM RNA-class probability 0.985470
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14292480 102 - 23771897
CGCUUUUCC-----------------CCCC-ACUACCACCAUAUAUUCGCAUCCCACGUUCCUCGUCACAUAAUAAUUUUAUGUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACCC
.........-----------------....-.................................(.(((((((.....))))))))..((((((((.((((....))))))))))))... ( -18.30)
>DroSec_CAF1 117728 101 - 1
CCCUUUUCC-----------------CCCC-ACAACCCCC-GAUUUUCGCAUCCCACGUUCCUCGUCACAUAAUAAUUUUAUGUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACCC
.........-----------------....-........(-((....((.......))....))).(((((((.....)))))))...((((((((.((((....))))))))))))... ( -18.70)
>DroSim_CAF1 117829 101 - 1
CCCUUUUCG-----------------CCCC-ACAACCCCC-GAUUUUCGCAUCCCACGUUCCUCGUCACAUAAUAAUUUUAUGUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACCC
.........-----------------....-........(-((....((.......))....))).(((((((.....)))))))...((((((((.((((....))))))))))))... ( -18.70)
>DroEre_CAF1 117861 100 - 1
CCC------------------CCCUUCCCC-ACGACCCCC-GAUUUUCACUCCCCACGUUCCUCGUCACAUAAUAAUUUUAUGUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACCC
...------------------.........-.........-.......................(.(((((((.....))))))))..((((((((.((((....))))))))))))... ( -18.30)
>DroYak_CAF1 121617 119 - 1
CGCUUUUUCCCCUUUCCCUUUCCCUUCCCCAACGACCACC-GAUUUUCGCUCCCCACGUUCCUCGUCACAUAAUAAUUUUAUGUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACCC
..............................((((.....(-(.....)).......))))....(.(((((((.....))))))))..((((((((.((((....))))))))))))... ( -18.90)
>DroAna_CAF1 112730 85 - 1
CC----------------------------------UCCU-GGUGCUCAUUCCCCACGUUCCUCGUCACAUAAUAAUUUUAUAUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACUU
..----------------------------------....-((.((...........)).))..(((..((((.....))))........((((((.((((....))))))))))))).. ( -13.80)
>consensus
CCCUUUUCC_________________CCCC_ACAACCCCC_GAUUUUCGCACCCCACGUUCCUCGUCACAUAAUAAUUUUAUGUGCUUUUUGGCUGCUGCAUUUUUGCAUAGUCAGACCC
................................................................(.(((((((.....))))))))..((((((((.((((....))))))))))))... (-17.42 = -17.58 +   0.17)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,292,582 – 14,292,702
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 97.28
Mean single sequence MFE -30.33
Consensus MFE -28.71
Energy contribution -28.68
Covariance contribution -0.03
Combinations/Pair 1.09
Mean z-score -0.82
Structure conservation index 0.95
SVM decision value 0.04
SVM RNA-class probability 0.553499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14292582 120 + 23771897
GAGGACAAUGCUUAAAGGCAUUUCGGACUCGGCCAAAAAUCAGACUCAGCAUGUGCGCAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUCG
(((..(((((((....))))))..)..)))(((.........(((((.((....))((.....))((((...(((....))).)))).....)))))...((((((....))))))))). ( -32.30)
>DroSec_CAF1 117829 120 + 1
GAGGACAAUGCUCAAAGGCAUUUCGGACUCGGCCAAAAAUCAGACUCAGCAUGUGCGCAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUCG
(((..(((((((....))))))..)..)))(((.........(((((.((....))((.....))((((...(((....))).)))).....)))))...((((((....))))))))). ( -31.90)
>DroSim_CAF1 117930 120 + 1
GAGGACAAUGCUCAAAGGCAUUUCGGACUCGGCCAAAAAUCAGACUCAGCAUGUGCGCAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUCG
(((..(((((((....))))))..)..)))(((.........(((((.((....))((.....))((((...(((....))).)))).....)))))...((((((....))))))))). ( -31.90)
>DroEre_CAF1 117961 120 + 1
UAGGACAAUGCUCAAAGGCAUUUCGGACUCGGCCAAAAAUCAGACUCAGCAUGUGCGCAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUCG
...((.((((((....))))))))((......))........(((......((.((.......)).))....(((((...(((....)))..)))))...((((((....))))))))). ( -28.30)
>DroYak_CAF1 121736 120 + 1
AGGGACAACGCUCAAAGGCAUUUUGGACUUGGCCAAAAAUCAGACUCAGCAUGUGCGCAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUCG
...(((...(((.....((.((((((......))))))..........((....))))....))).......(((((...(((....)))..)))))...((((((....))))))))). ( -30.70)
>DroAna_CAF1 112815 120 + 1
AGGGACAAUGCUCAAAGGCAUUUCGGACUCGGCCAAAAAUCAGACUCAGCAUGUGCACAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUUG
...((.((((((....))))))))((......))............((((.((.((.......)).))....(((((...(((....)))..)))))...((((((....)))))))))) ( -26.90)
>consensus
GAGGACAAUGCUCAAAGGCAUUUCGGACUCGGCCAAAAAUCAGACUCAGCAUGUGCGCAUAAAGCUCAAAUAAACUCAAGUUGUUGACAAAGGGGUUAAAGGCCAUAAUUGUGGCCGUCG
(((..(((((((....))))))..)..)))(((.........(((((.((....)).......(.((((...(((....))).)))))....)))))...((((((....))))))))). (-28.71 = -28.68 +  -0.03)

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 11:44:09 2006