Locus 3760

Sequence ID X_DroMel_CAF1
Location 9,968,536 – 9,968,718
Length 182
Max. P 0.998577
window6174 window6175 window6176

overview

Window 4

Location 9,968,536 – 9,968,653
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.31
Mean single sequence MFE -27.25
Consensus MFE -19.75
Energy contribution -19.62
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.51
Structure conservation index 0.72
SVM decision value 0.04
SVM RNA-class probability 0.554337
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9968536 117 - 22224390
ACCAACUAUCCA-ACCCACUUUUCUGUGGGAAAAUCCCGAACGAAACUCAACAAAGAGGUUUUUUUUUUCGUUUUUGGCCAAGGCUUUUUCGCACACCUGUCCAGGUGGUAAAUUUGU--
.((((.......-.(((((......)))))........(((((((((((......)))........)))))))))))).((((((......)).(((((....))))).....)))).-- ( -26.90)
>DroSec_CAF1 9013 111 - 1
ACCGACUAUCCA-ACCCACUUUUCUGUGGGAAAAUCCCGAACGAAACUCAACAAAGAGGUUUUUU--------UUUGGCCAAGGCUUUUUCGCACACCUGUCCAGAUGGUAAAUUUUUUA
....((((((..-.(((((......)))))...........((((((((......))).......--------...(((....))).)))))............)))))).......... ( -23.00)
>DroEre_CAF1 1180 116 - 1
ACCGACUGUGCA-ACCCACUUUGCUGUGGGAAAAACC-CAACGAAACUCCACAAAGAAAAGGUUUUCUUAUUUUUUGGCCAAGGCUUUUUCACACACCUGUCCAGGUGGUAAAUUUGU--
((((.(((..((-.(((((......))))).......-....((((.....(((((((.(((....))).)))))))((....))..)))).......))..))).))))........-- ( -28.20)
>DroYak_CAF1 1184 114 - 1
ACCGACGGUCCAAACCCACUUUUCUGUGGGAAAAACC-AAACGGAAUUCAACAAAGAAAAUGUUUUUU---UUUCUUGCCAAGGCUUUUUCGCACACCUGUACAGGUGGUAAAUUGGU--
.(((..(((.....(((((......)))))....)))-...))).........(((((((.......)---))))))(((((.((......)).(((((....))))).....)))))-- ( -30.90)
>consensus
ACCGACUAUCCA_ACCCACUUUUCUGUGGGAAAAACC_GAACGAAACUCAACAAAGAAAAUGUUUUUU___UUUUUGGCCAAGGCUUUUUCGCACACCUGUCCAGGUGGUAAAUUUGU__
..............(((((......)))))............(((((((......)))...................((....))..))))((.(((((....))))))).......... (-19.75 = -19.62 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,968,574 – 9,968,686
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 73.57
Mean single sequence MFE -19.55
Consensus MFE -10.26
Energy contribution -10.57
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.96
Structure conservation index 0.52
SVM decision value 3.15
SVM RNA-class probability 0.998577
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9968574 112 - 22224390
UUUCUCAUAACCCUUCCCC-------CAAAAAACCAAAAAACCAACUAUCCA-ACCCACUUUUCUGUGGGAAAAUCCCGAACGAAACUCAACAAAGAGGUUUUUUUUUUCGUUUUUGGCC
..................(-------((((((...((((((((.........-.(((((......)))))........((.......))........))))))))......))))))).. ( -20.90)
>DroSec_CAF1 9053 111 - 1
UUUCUCAUAACCCUUCCCAACAACAAAAAAAAACCAAAAAACCGACUAUCCA-ACCCACUUUUCUGUGGGAAAAUCCCGAACGAAACUCAACAAAGAGGUUUUUU--------UUUGGCC
.......................((((((((((((.................-.(((((......)))))........((.......))........))))))))--------))))... ( -22.00)
>DroEre_CAF1 1218 100 - 1
-UUCUCACAACACUUCUCC-------CA----------AAACCGACUGUGCA-ACCCACUUUGCUGUGGGAAAAACC-CAACGAAACUCCACAAAGAAAAGGUUUUCUUAUUUUUUGGCC
-.................(-------((----------(((.....((((..-.(((((......))))).......-....(.....)))))((((((....))))))...)))))).. ( -16.40)
>DroYak_CAF1 1222 98 - 1
-UUCUCAUAACACUUCGCC-------CA----------AAACCGACGGUCCAAACCCACUUUUCUGUGGGAAAAACC-AAACGGAAUUCAACAAAGAAAAUGUUUUUU---UUUCUUGCC
-...............((.-------..----------...(((..(((.....(((((......)))))....)))-...))).........(((((((.......)---)))))))). ( -18.90)
>consensus
_UUCUCAUAACACUUCCCC_______CA__________AAACCGACUAUCCA_ACCCACUUUUCUGUGGGAAAAACC_GAACGAAACUCAACAAAGAAAAUGUUUUUU___UUUUUGGCC
.........................................((((.........(((((......)))))................(((......)))................)))).. (-10.26 = -10.57 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,968,614 – 9,968,718
Length 104
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 77.13
Mean single sequence MFE -18.24
Consensus MFE -10.35
Energy contribution -10.10
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.83
Structure conservation index 0.57
SVM decision value 0.01
SVM RNA-class probability 0.538790
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9968614 104 - 22224390
GUUUCUUGGUUUGCAUGGCAUGCUGCACAAUUUUUCUCAUAACCCUUCCCC-------CAAAAAACCAAAAAACCAACUAUCCA-ACCCACUUUUCUGUGGGAAAAUCCCGA
((((.(((((((...(((................................)-------))..))))))).))))..........-.(((((......))))).......... ( -18.25)
>DroSec_CAF1 9085 106 - 1
GUUUCUGGGUUUGC-----AUGCUGCACAAUUUUUCUCAUAACCCUUCCCAACAACAAAAAAAAACCAAAAAACCGACUAUCCA-ACCCACUUUUCUGUGGGAAAAUCCCGA
...((.((((((((-----.....))..........................................................-.(((((......))))).)))))).)) ( -16.00)
>DroEre_CAF1 1258 87 - 1
GUUUCUAGGCUUGC-----AUGCUGCAGAAUU-UUCUCACAACACUUCUCC-------CA----------AAACCGACUGUGCA-ACCCACUUUGCUGUGGGAAAAACC-CA
..((((.(((....-----..)))..))))((-(((((((((((..((...-------..----------.....)).)))(((-(......))))))))))))))...-.. ( -18.00)
>DroYak_CAF1 1259 88 - 1
GUUUCUGGGCUUGC-----AUGCUGCACAAUU-UUCUCAUAACACUUCGCC-------CA----------AAACCGACGGUCCAAACCCACUUUUCUGUGGGAAAAACC-AA
((((.(((((.(((-----.....)))....(-(......))......)))-------))----------))))....(((.....(((((......)))))....)))-.. ( -20.70)
>consensus
GUUUCUGGGCUUGC_____AUGCUGCACAAUU_UUCUCAUAACACUUCCCC_______CA__________AAACCGACUAUCCA_ACCCACUUUUCUGUGGGAAAAACC_GA
........((..((.......)).))............................................................(((((......))))).......... (-10.35 = -10.10 +  -0.25)

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 11:07:44 2006