Locus 5590

Sequence ID X_DroMel_CAF1
Location 14,433,367 – 14,433,558
Length 191
Max. P 0.991287
window9075 window9076 window9077 window9078 window9079

overview

Window 5

Location 14,433,367 – 14,433,464
Length 97
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 83.77
Mean single sequence MFE -32.06
Consensus MFE -27.42
Energy contribution -27.86
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.44
Structure conservation index 0.86
SVM decision value -0.05
SVM RNA-class probability 0.507771
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14433367 97 - 22224390
GUGCGCCGGCGCUGCGAGAGUCGAGCUUUUCCCGCAGAAUACCGGUUUCCCAU--------------UUCCCGACUUUUGGCUAUUUUUGGCCCAGAGUCGCUAUAC--AUAU
..(((((((..(((((.(((........))).)))))....))))).......--------------.....((((((.(((((....))))).)))))))).....--.... ( -34.50)
>DroSec_CAF1 12712 97 - 1
GUGCGCCGGCGCUGCGAGAGCCGAGCUUUUACCGCAGAAUACCGGUUUCCCAU--------------UUCCCGACUUUUGGCUAUUUUUGGCCCAGAGUCGCUGUAU--AUAU
(((((((((..((((((((((...)))))...)))))....))))).......--------------....(((((((.(((((....))))).)))))))..))))--.... ( -35.60)
>DroSim_CAF1 23935 97 - 1
GUGCGCCGGCGCUGCGAGAGCCGAGCUUUUACCACAGAAUACCGGUUUCCCAU--------------UUCCCGACUUUUGGCUAUUUUUGGCCCAGAGUCGCUGUAC--AUAU
(((((((((..(((.((((((...))))))....)))....))))).......--------------....(((((((.(((((....))))).)))))))..))))--.... ( -33.10)
>DroEre_CAF1 12434 110 - 1
GAGCGCCGGCGCCGCGAGAGCCGAGCUUUC-CUGCAGAAUACCGGUUUCCCGUUUCCCAUUUCCCAUUUCCCGACUUU--GCUAUUUUUGGCCCAGAGUCGAGCCACACACAU
((((..((((..(....).)))).))))..-..((.(((...(((....))).)))...............(((((((--((((....))))..))))))).))......... ( -28.70)
>DroYak_CAF1 12576 98 - 1
GAGCGCCGGCGCUGGGAGAGUCGAGCUUUU-CCGCAGAAUACUGGUUUCCCAUU-------------UUCCCGACUUU-GGCUAUUUUUGGCCCAGACUCGAGCCACACAAAU
.......(((((.(((((((.....)))))-)))).(((...(((....)))..-------------))).(((.(((-(((((....))).))))).))).)))........ ( -28.40)
>consensus
GUGCGCCGGCGCUGCGAGAGCCGAGCUUUU_CCGCAGAAUACCGGUUUCCCAU______________UUCCCGACUUUUGGCUAUUUUUGGCCCAGAGUCGCUCUAC__AUAU
....(((((..((((((((((...))))))...))))....))))).........................(((((((.(((((....))))).)))))))............ (-27.42 = -27.86 +   0.44)

alignment

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secondary structure

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Window 6

Location 14,433,398 – 14,433,504
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.65
Mean single sequence MFE -41.62
Consensus MFE -39.04
Energy contribution -38.28
Covariance contribution -0.76
Combinations/Pair 1.16
Mean z-score -1.50
Structure conservation index 0.94
SVM decision value 0.77
SVM RNA-class probability 0.846586
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14433398 106 + 22224390
CAAAAGUCGGGAA--------------AUGGGAAACCGGUAUUCUGCGGGAAAAGCUCGACUCUCGCAGCGCCGGCGCACUGAAUGAUGUCCUUGCCAGGACAUCUCGCUGCCAUUGCUG
.....(((((...--------------.(((....))).....((((((((..........))))))))..)))))(((.(((..((((((((....))))))))))).)))........ ( -39.60)
>DroSec_CAF1 12743 106 + 1
CAAAAGUCGGGAA--------------AUGGGAAACCGGUAUUCUGCGGUAAAAGCUCGGCUCUCGCAGCGCCGGCGCACUGAAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUG
....(((((((((--------------.(((....)))...))))((.......)).)))))....(((((.((((((...((..((((((((....)))))))))))).)))).))))) ( -40.50)
>DroSim_CAF1 23966 106 + 1
CAAAAGUCGGGAA--------------AUGGGAAACCGGUAUUCUGUGGUAAAAGCUCGGCUCUCGCAGCGCCGGCGCACUGUAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUG
....(((((((..--------------.(((....))).(((......)))....)))))))....(((((.(((((....((..((((((((....))))))))..))))))).))))) ( -39.80)
>DroEre_CAF1 12467 117 + 1
--AAAGUCGGGAAAUGGGAAAUGGGAAACGGGAAACCGGUAUUCUGCAG-GAAAGCUCGGCUCUCGCGGCGCCGGCGCUCUGGACGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUG
--.....(((((..((((...((((((.(((....)))...)))).)).-.....))))..)))))(((((.((((((....((.((((((((....)))))))))))).)))).))))) ( -45.90)
>DroYak_CAF1 12609 105 + 1
C-AAAGUCGGGAA-------------AAUGGGAAACCAGUAUUCUGCGG-AAAAGCUCGACUCUCCCAGCGCCGGCGCUCUGGAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUUGCUG
.-..(((((((((-------------..(((....)))...))))((..-....)).)))))....(((((.((((((....((.((((((((....)))))))))))).)))).))))) ( -42.30)
>consensus
CAAAAGUCGGGAA______________AUGGGAAACCGGUAUUCUGCGG_AAAAGCUCGGCUCUCGCAGCGCCGGCGCACUGAAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUG
....(((((((.................(((....))).....((........)))))))))....(((((.((((((.......((((((((....))))))))..)).)))).))))) (-39.04 = -38.28 +  -0.76)

alignment

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secondary structure

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Window 7

Location 14,433,424 – 14,433,534
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 92.72
Mean single sequence MFE -43.60
Consensus MFE -36.90
Energy contribution -36.98
Covariance contribution 0.08
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.85
SVM decision value 1.99
SVM RNA-class probability 0.984891
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14433424 110 + 22224390
AUUCUGCGGGAAAAGCUCGACUCUCGCAGCGCCGGCGCACUGAAUGAUGUCCUUGCCAGGACAUCUCGCUGCCAUUGCUGAUAACAAUCCGCAGGCUGUGUUAUCGCCGC
...((((((((..........))))))))...(((((........((((((((....)))))))).(((.(((..(((.(((....))).)))))).)))....))))). ( -41.00)
>DroSec_CAF1 12769 110 + 1
AUUCUGCGGUAAAAGCUCGGCUCUCGCAGCGCCGGCGCACUGAAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUGAUAACAAUUCGCAGGCUGUGUUAUCGCCGC
.....((((..(.(((.((((.((.((((((.((((((...((..((((((((....)))))))))))).)))).))))((.......)))))))))).))).)..)))) ( -44.30)
>DroSim_CAF1 23992 110 + 1
AUUCUGUGGUAAAAGCUCGGCUCUCGCAGCGCCGGCGCACUGUAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUGAUAACAAUUCGCAGGCUGUGUUAUCGCCGC
.....((((..(.(((.((((.((.((((((.(((((....((..((((((((....))))))))..))))))).))))((.......)))))))))).))).)..)))) ( -43.10)
>DroEre_CAF1 12505 109 + 1
AUUCUGCAG-GAAAGCUCGGCUCUCGCGGCGCCGGCGCUCUGGACGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUGAUAGCAAUUCGCAGGCGGCGUUAUCGCCGC
...((((.(-((..(((((((....((((((((((....))))..((((((((....)))))))).))))))....)))))..))..)))))))((((((....)))))) ( -49.50)
>DroYak_CAF1 12635 109 + 1
AUUCUGCGG-AAAAGCUCGACUCUCCCAGCGCCGGCGCUCUGGAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUUGCUGAUAACAAUUCGCAGGCUGCGUUAUCGCCGC
...((((((-(.......(.....).(((((.((((((....((.((((((((....)))))))))))).)))).))))).......)))))))((.(((....))).)) ( -40.10)
>consensus
AUUCUGCGG_AAAAGCUCGGCUCUCGCAGCGCCGGCGCACUGAAUGAUGUCCUUGCCAGGACAUCUCGCUGCCGUCGCUGAUAACAAUUCGCAGGCUGUGUUAUCGCCGC
...((((((.......(((((....((((((.(((....)))...((((((((....)))))))).))))))....))))).......))))))((.(((....))).)) (-36.90 = -36.98 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,433,424 – 14,433,534
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 92.72
Mean single sequence MFE -45.40
Consensus MFE -38.04
Energy contribution -38.24
Covariance contribution 0.20
Combinations/Pair 1.12
Mean z-score -2.22
Structure conservation index 0.84
SVM decision value 2.26
SVM RNA-class probability 0.991287
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14433424 110 - 22224390
GCGGCGAUAACACAGCCUGCGGAUUGUUAUCAGCAAUGGCAGCGAGAUGUCCUGGCAAGGACAUCAUUCAGUGCGCCGGCGCUGCGAGAGUCGAGCUUUUCCCGCAGAAU
((((.((.......(((.(((.((((((..((....))..)))..((((((((....))))))))....))).))).)))(((.((.....)))))...))))))..... ( -43.60)
>DroSec_CAF1 12769 110 - 1
GCGGCGAUAACACAGCCUGCGAAUUGUUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUUCAGUGCGCCGGCGCUGCGAGAGCCGAGCUUUUACCGCAGAAU
((((.(((((((..(....)....)))))))(((..((((..((.((((((((....))))))))...((((((....))))))))...)))).)))....))))..... ( -45.80)
>DroSim_CAF1 23992 110 - 1
GCGGCGAUAACACAGCCUGCGAAUUGUUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUACAGUGCGCCGGCGCUGCGAGAGCCGAGCUUUUACCACAGAAU
.(((((((((((..(....)....)))))))((((.((((.(((.((((((((....))))))))......))))))).))))......))))................. ( -41.50)
>DroEre_CAF1 12505 109 - 1
GCGGCGAUAACGCCGCCUGCGAAUUGCUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCGUCCAGAGCGCCGGCGCCGCGAGAGCCGAGCUUUC-CUGCAGAAU
((((((....))))))(((((..(((((..(......)..)))))((((((((....))))))))....(((((..((((..(....).)))).))))).-.)))))... ( -50.10)
>DroYak_CAF1 12635 109 - 1
GCGGCGAUAACGCAGCCUGCGAAUUGUUAUCAGCAACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUCCAGAGCGCCGGCGCUGGGAGAGUCGAGCUUUU-CCGCAGAAU
((.(((....))).))(((((.........((((..((((.((((((((((((....)))))))).))....))))))..))))((((((.....)))))-))))))... ( -46.00)
>consensus
GCGGCGAUAACACAGCCUGCGAAUUGUUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUCCAGUGCGCCGGCGCUGCGAGAGCCGAGCUUUU_CCGCAGAAU
((((.(((((((..(....)....)))))))(((..((((.....((((((((....))))))))...((((((....)))))).....)))).)))....))))..... (-38.04 = -38.24 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,433,464 – 14,433,558
Length 94
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 92.56
Mean single sequence MFE -34.34
Consensus MFE -26.58
Energy contribution -26.62
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.00
Structure conservation index 0.77
SVM decision value 0.79
SVM RNA-class probability 0.852611
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14433464 94 - 22224390
GCGUUG-UGGCAGUGAAAGUUUUGUGCGGCGAUAACACAGCCUGCGGAUUGUUAUCAGCAAUGGCAGCGAGAUGUCCUGGCAAGGACAUCAUUCA
((((((-(.((.((...........)).)).)))))...((((((.(((....))).)))..))).))..((((((((....))))))))..... ( -32.90)
>DroSec_CAF1 12809 94 - 1
GCGGUGUUGGCAGUGAAAGU-UGGUGCGGCGAUAACACAGCCUGCGAAUUGUUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUUCA
((.(..(..((.......))-..)..).))(((((((..(....)....))))))).((.......))..((((((((....))))))))..... ( -32.10)
>DroSim_CAF1 24032 94 - 1
GCGGUGUUGGCAGUGAAAGU-UUGUGCGGCGAUAACACAGCCUGCGAAUUGUUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUACA
.((.(((((((.((((.(((-(((((.(((.........))))))))))).))))..))..))))).)).((((((((....))))))))..... ( -32.80)
>DroEre_CAF1 12544 93 - 1
GCGUGG-UGGCAGUGAAAGU-UUUUGCGGCGAUAACGCCGCCUGCGAAUUGCUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCGUCCA
((.(((-(((((((....((-....((((((....))))))..))..))))))))))))((((....)..((((((((....))))))))))).. ( -41.60)
>DroYak_CAF1 12674 93 - 1
GCGGUG-UGGCAGUGAAAGU-UUUUGCGGCGAUAACGCAGCCUGCGAAUUGUUAUCAGCAACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUCCA
(((.((-(.((.(..((...-.))..).)).))).))).((((((..((....))..)))..))).(.((((((((((....)))))))).))). ( -32.30)
>consensus
GCGGUG_UGGCAGUGAAAGU_UUGUGCGGCGAUAACACAGCCUGCGAAUUGUUAUCAGCGACGGCAGCGAGAUGUCCUGGCAAGGACAUCAUCCA
((..((.(((((((..........((((((.........))).))).))))))).))((....)).))..((((((((....))))))))..... (-26.58 = -26.62 +   0.04)

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 11:51:44 2006