Locus 8224

Sequence ID 3R_DroMel_CAF1
Location 22,059,518 – 22,059,655
Length 137
Max. P 0.999862
window13247 window13248 window13249 window13250

overview

Window 7

Location 22,059,518 – 22,059,627
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.96
Mean single sequence MFE -44.84
Consensus MFE -38.47
Energy contribution -39.75
Covariance contribution 1.28
Combinations/Pair 1.03
Mean z-score -3.88
Structure conservation index 0.86
SVM decision value 4.29
SVM RNA-class probability 0.999862
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22059518 109 + 27905053
CCGAGCAGUGCUU-UUUCACCUGCCCAACUGGAG----CGUCUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG---GUUUUCCAGUUGGCCAGAA---
..((((...))))-......(((.((((((((((----((.((((.((((((.((((((((.....))))))))......)))..))))))).))---...)))))))))).)))..--- ( -39.70)
>DroSec_CAF1 51586 109 + 1
CCGAGCAGUGCUU-UUCCACCUGGCCAACUGGAG----CGACUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUC---GUUUUCCAGUUGGCCAUAA---
..((((...))))-.......(((((((((((((----(((((((.((((((.((((((((.....))))))))......)))..))))))).))---))..))))))))))))...--- ( -48.20)
>DroSim_CAF1 44265 109 + 1
CCGAGCAGUGCUU-UUCCACCUGGCCAACUGGAG----CGACUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG---GCUUUCCAGUUGGCCAGAA---
..((((...))))-......((((((((((((((----(((((((.((((((.((((((((.....))))))))......)))..))))))))))---...))))))))))))))..--- ( -51.40)
>DroEre_CAF1 46041 112 + 1
CCGAGCAGUGCUU-UUCCACUUGGCCAACUGGUG----CGUAUUUCGCAGGCGUCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG---GUUUUCCAGUUGGCCAGAAUGC
....((((((...-...)))((((((((((((((----((.....))))((((((((((((.....))))))).))....)))............---.....))))))))))))..))) ( -37.90)
>DroYak_CAF1 53855 119 + 1
CCGAGCAGUGCUUUUUCCACCUGGCCAACUGGAGCGAGCGUCUUUCGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUGGUGGUUUUCCAGUUGGCCAGAAA-C
..((((...)))).......((((((((((((((((((.....))))).(((.((((((((.....))))))))......)))....(((.....)))....)))))))))))))...-. ( -47.00)
>consensus
CCGAGCAGUGCUU_UUCCACCUGGCCAACUGGAG____CGUCUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG___GUUUUCCAGUUGGCCAGAA___
..((((...)))).......((((((((((((((.......((((.((((((.((((((((.....))))))))......)))..))))))).........))))))))))))))..... (-38.47 = -39.75 +   1.28)

alignment

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secondary structure

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Window 8

Location 22,059,518 – 22,059,627
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.96
Mean single sequence MFE -43.38
Consensus MFE -36.73
Energy contribution -36.93
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -4.30
Structure conservation index 0.85
SVM decision value 4.06
SVM RNA-class probability 0.999779
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22059518 109 - 27905053
---UUCUGGCCAACUGGAAAAC---CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGACG----CUCCAGUUGGGCAGGUGAAA-AAGCACUGCUCGG
---..(((.(((((((((....---(..(((((((..(((......((((((((.....)))))))).)))))).))))..)----.))))))))).)))(((...-...)))....... ( -39.70)
>DroSec_CAF1 51586 109 - 1
---UUAUGGCCAACUGGAAAAC---GAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGUCG----CUCCAGUUGGCCAGGUGGAA-AAGCACUGCUCGG
---...((((((((((((...(---((.(((((((..(((......((((((((.....)))))))).)))))).)))))))----.))))))))))))((((...-...))))...... ( -47.30)
>DroSim_CAF1 44265 109 - 1
---UUCUGGCCAACUGGAAAGC---CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGUCG----CUCCAGUUGGCCAGGUGGAA-AAGCACUGCUCGG
---..(((((((((((((..((---..((((((((..(((......((((((((.....)))))))).)))))).))))).)----))))))))))))))(((...-...)))....... ( -48.30)
>DroEre_CAF1 46041 112 - 1
GCAUUCUGGCCAACUGGAAAAC---CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGACGCCUGCGAAAUACG----CACCAGUUGGCCAAGUGGAA-AAGCACUGCUCGG
((....(((((((((((.....---............(((.......(((((((.....)))))))..)))((((.....))----)))))))))))))((((...-...)))))).... ( -38.90)
>DroYak_CAF1 53855 119 - 1
G-UUUCUGGCCAACUGGAAAACCACCAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCGAAAGACGCUCGCUCCAGUUGGCCAGGUGGAAAAAGCACUGCUCGG
.-...(((((((((((((...........((.((....))))....((((((((.....)))))))).((..(((.....)))..)))))))))))))))(..(........)..).... ( -42.70)
>consensus
___UUCUGGCCAACUGGAAAAC___CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGACG____CUCCAGUUGGCCAGGUGGAA_AAGCACUGCUCGG
......((((((((((((.............((((..(((......((((((((.....)))))))).)))))))............))))))))))))((((.......))))...... (-36.73 = -36.93 +   0.20)

alignment

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secondary structure

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Window 9

Location 22,059,553 – 22,059,655
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.96
Mean single sequence MFE -33.34
Consensus MFE -24.73
Energy contribution -25.13
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.74
SVM decision value 0.37
SVM RNA-class probability 0.708725
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22059553 102 + 27905053
UCUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG---GUUUUCCAGUUGGCCAGAA---------------UGUCAGUCAGCAGUUAGUUAGCCUUUGG
.(((((((.(((.((((((((.....))))))))(((((((((((.......(((---(....))))))))))))))---------------)))).).))))))............... ( -34.81)
>DroSec_CAF1 51621 102 + 1
ACUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUC---GUUUUCCAGUUGGCCAUAA---------------UGUCAGUCAGCAGUUAGUUAGCCUUUGG
((((((((.(((.((((((((.....))))))))(((.(((((((((.((.....---))....)).))))))).))---------------)))).).))))))).............. ( -30.00)
>DroSim_CAF1 44300 102 + 1
ACUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG---GCUUUCCAGUUGGCCAGAA---------------UGUCAGUCAGCAGUUAGUUAGCCUUUGG
((((((((.(((.((((((((.....))))))))(((((((((((((...((...---.))...)).))))))))))---------------)))).).))))))).............. ( -35.30)
>DroEre_CAF1 46076 110 + 1
UAUUUCGCAGGCGUCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG---GUUUUCCAGUUGGCCAGAAUGCCAGAA-------UGUCAGUCAGCAGUUAGUUCGCCUUUGG
.....((.(((((((((((((.....))))))(((((((((((((.......(((---(....)))))))))))))))))..)).-------(((......))).......))))).)). ( -32.81)
>DroYak_CAF1 53895 119 + 1
UCUUUCGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUGGUGGUUUUCCAGUUGGCCAGAAA-CCAGCAGUCCAGCAGUCAGUCAGCAGUUAGUUAGCCUUUGG
.....((.((((.((((((((.....))))))))...(((((.(.(((....(((.(((((((((....))...))))-))).)))....))).)..)))))..........)))).)). ( -33.80)
>consensus
UCUGUUGCAGGCGGCAUUUUCAUAUUGAAAAUGCAUUUUGGCCAGUGCACAGUUG___GUUUUCCAGUUGGCCAGAA_______________UGUCAGUCAGCAGUUAGUUAGCCUUUGG
........((((.((((((((.....)))))))).((((((((((((.................)).))))))))))...................................)))).... (-24.73 = -25.13 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,059,553 – 22,059,655
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.96
Mean single sequence MFE -27.14
Consensus MFE -21.68
Energy contribution -21.72
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.80
SVM decision value 0.78
SVM RNA-class probability 0.848712
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22059553 102 - 27905053
CCAAAGGCUAACUAACUGCUGACUGACA---------------UUCUGGCCAACUGGAAAAC---CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGA
(((..(((((..................---------------...)))))...))).....---...(((((((..(((......((((((((.....)))))))).)))))).)))). ( -24.90)
>DroSec_CAF1 51621 102 - 1
CCAAAGGCUAACUAACUGCUGACUGACA---------------UUAUGGCCAACUGGAAAAC---GAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGU
(((..(((((..(((.(((.....).))---------------))))))))...))).....---..((((((((..(((......((((((((.....)))))))).)))))).))))) ( -25.90)
>DroSim_CAF1 44300 102 - 1
CCAAAGGCUAACUAACUGCUGACUGACA---------------UUCUGGCCAACUGGAAAGC---CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGU
.....((((.......(((.....).))---------------(((..(....)..))))))---).((((((((..(((......((((((((.....)))))))).)))))).))))) ( -27.30)
>DroEre_CAF1 46076 110 - 1
CCAAAGGCGAACUAACUGCUGACUGACA-------UUCUGGCAUUCUGGCCAACUGGAAAAC---CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGACGCCUGCGAAAUA
....(((((.................((-------((.((((......((((..(((....)---))..)).))....)))).))))(((((((.....))))))).)))))........ ( -28.70)
>DroYak_CAF1 53895 119 - 1
CCAAAGGCUAACUAACUGCUGACUGACUGCUGGACUGCUGG-UUUCUGGCCAACUGGAAAACCACCAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCGAAAGA
....((((....................((..(..((((((-((((..(....)..).))))))........))))..))......((((((((.....)))))))).)))).(....). ( -28.90)
>consensus
CCAAAGGCUAACUAACUGCUGACUGACA_______________UUCUGGCCAACUGGAAAAC___CAACUGUGCACUGGCCAAAAUGCAUUUUCAAUAUGAAAAUGCCGCCUGCAACAGA
....((((......................................((((((....(...((........)).)..))))))....((((((((.....)))))))).))))........ (-21.68 = -21.72 +   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 13:05:57 2006