Locus 4544

Sequence ID X_DroMel_CAF1
Location 11,961,118 – 11,961,336
Length 218
Max. P 0.979494
window7472 window7473 window7474

overview

Window 2

Location 11,961,118 – 11,961,220
Length 102
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -30.85
Consensus MFE -18.09
Energy contribution -18.34
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -2.57
Structure conservation index 0.59
SVM decision value 0.58
SVM RNA-class probability 0.787648
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11961118 102 - 22224390
AAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCUUAGUGGA---UGGCGUGGGUGGCGCCAGUGGAAAGUGCUGGGGUAAUGGGA
......((((((.(((.((.(((..(......)....(((((((....)))))))..))).---)).))).)))))).(((((.......))))).......... ( -35.00)
>DroSec_CAF1 405 101 - 1
AAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCGUAGUGGA---UGGCGUGGGUGGCGC-AAUGGAAAGUGCUGGGGUAAUGGGA
......((((((.(((.((.(((..(......)......(((((....)))))....))).---)).))).))))))((-(.(....).)))............. ( -29.70)
>DroSim_CAF1 406 101 - 1
AAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCGUAGUGGA---UGGCGUGGGUGGCGC-AGUGGAAAGUGCUGGGGUAAUGGGA
......((((((.(((.((.(((..(......)......(((((....)))))....))).---)).))).))))))((-(.(....).)))............. ( -31.80)
>DroEre_CAF1 983 85 - 1
AAAGUUGCCACUGAUG-CGGCCAAGGAAAAUGCAGAAAAGCU-GCAAACUGGCAUAGCGGCUGG------------------UGGAAAUUGCUGGGGUAGUGGGC
.......((((((.(.-((((.........(((((.....))-))).((..((......))..)------------------).......)))).).)))))).. ( -26.90)
>consensus
AAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCGUAGUGGA___UGGCGUGGGUGGCGC_AGUGGAAAGUGCUGGGGUAAUGGGA
...((((((.....((.((((..................)))).))..(..(((............((((.....))))..........)))..))))))).... (-18.09 = -18.34 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,961,158 – 11,961,260
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.82
Mean single sequence MFE -31.95
Consensus MFE -24.59
Energy contribution -25.36
Covariance contribution 0.77
Combinations/Pair 1.14
Mean z-score -1.81
Structure conservation index 0.77
SVM decision value 0.54
SVM RNA-class probability 0.773443
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11961158 102 - 22224390
GGGGGUUUUCAUCCACGGUAGCUCUUUUUUUGGUUAAUGAAAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCUUAGUGGA------------------U
..........((((((....((..(((((((((((..(....)...((((....)))))))))))))))..))....(((((((....))))))).)))))------------------) ( -34.40)
>DroSec_CAF1 444 102 - 1
GGGAGUUUUCAUCCACGGUAGCUCUUUUUUUGGUUAAUGAAAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCGUAGUGGA------------------U
..........((((((....((..(((((((((((..(....)...((((....)))))))))))))))..))......(((((....)))))...)))))------------------) ( -32.80)
>DroSim_CAF1 445 102 - 1
GGGGGUUCUCAUCCACGGUAGCUCUUUUUUUGGUUAAUGAAAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCGUAGUGGA------------------U
(((....)))((((((....((..(((((((((((..(....)...((((....)))))))))))))))..))......(((((....)))))...)))))------------------) ( -33.70)
>DroEre_CAF1 1006 102 - 1
GGUGGUUUCCAUCUACGGUAGCUCUUUUUUUGGUUAAUGAAAAGUUGCCACUGAUG-CGGCCAAGGAAAAUGCAGAAAAGCU-GCAAACUGGCAUAGCGGCUGG----------------
..(((((..((((...(((((((.(((.((.....)).))).)))))))...))))-.))))).......(((((.....))-)))..(..((......))..)---------------- ( -27.50)
>DroYak_CAF1 1005 111 - 1
GGUGGUUUUCAUCUACGGUAGCUCUUU-UUUGGUUAAUGAAAAGUUGCCACUGAUGGCGACCAAAGAAAAUGCAGAAAAGC--------UGGCGUUGUGGAUGGUUUGGAUGGCGUGGAU
.((.(((((((((((((...(((((((-((((...........(((((((....)))))))...........)))))))).--------.)))..)))))))))...)))).))...... ( -31.35)
>consensus
GGGGGUUUUCAUCCACGGUAGCUCUUUUUUUGGUUAAUGAAAAGUUGCCACUGAUGGCGGCCAAAGAAAAUGCAGAAAAGCCGGCAAACUGGCGUAGUGGA__________________U
...........(((((....((..(((((((((((..(....)...((((....)))))))))))))))..))......(((((....)))))...)))))................... (-24.59 = -25.36 +   0.77)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,961,220 – 11,961,336
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 81.38
Mean single sequence MFE -21.97
Consensus MFE -14.03
Energy contribution -14.70
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -3.02
Structure conservation index 0.64
SVM decision value 1.84
SVM RNA-class probability 0.979494
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11961220 116 + 22224390
UCAUUAACCAAAAAAAGAGCUACCGUGGAUGAAAACCCCCAUCAUACAUGCUAAAAA-AAAAGACACUUGCCAAUGAACACUGGCUGAAAU-UAAAAAAAAAAAUAGUUUUACUUACA
...............(((((((..(((((((........)))).)))..........-...........((((........))))......-............)))))))....... ( -14.50)
>DroEre_CAF1 1068 113 + 1
UCAUUAACCAAAAAAAGAGCUACCGUAGAUGGAAACCACCAUCAUGCAUGCUUAAAA--AAAGACACUUGCCAGUGGACACUGGCAAAAAUU-UGGAAAAAA--UUGUUUCACUUUCC
.......(((((....((((...(((.(((((......))))))))...))))....--........((((((((....))))))))...))-)))......--.............. ( -28.60)
>DroYak_CAF1 1077 113 + 1
UCAUUAACCAAA-AAAGAGCUACCGUAGAUGAAAACCACCAUCAUGUAUGCUCAAAAAAAAAAACACUUGCCAAAGGACACUGGCAAAAAA--UGGUGACAA--UAGUUUUCCUUAUC
............-...((((...(((.((((........)))))))...)))).......(((((..((((((........))))))....--((....)).--..)))))....... ( -22.80)
>consensus
UCAUUAACCAAAAAAAGAGCUACCGUAGAUGAAAACCACCAUCAUGCAUGCUAAAAA_AAAAGACACUUGCCAAUGGACACUGGCAAAAAU__UGGAAAAAA__UAGUUUUACUUACC
................((((...(((.((((........)))))))...))))..............((((((........))))))............................... (-14.03 = -14.70 +   0.67)

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 11:27:46 2006