Locus 5719

Sequence ID 3L_DroMel_CAF1
Location 15,598,232 – 15,598,432
Length 200
Max. P 0.983226
window9050 window9051 window9052 window9053

overview

Window 0

Location 15,598,232 – 15,598,352
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -33.58
Consensus MFE -26.96
Energy contribution -27.44
Covariance contribution 0.48
Combinations/Pair 1.14
Mean z-score -1.55
Structure conservation index 0.80
SVM decision value 0.33
SVM RNA-class probability 0.693769
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15598232 120 - 23771897
CGAGAAUUAGCUGGGCAAAUAUGCUAAGAUUUUAUAGCCUCGCAAGUGGCGGAGAUUAAACGAAACGGAGCAGAGCUCCGGAGUAAUUACAAAUGUUUUCCCUCAUUUCCACUUGGCAAA
(.((......)).).......(((((((........(((.(....).)))((((((.........((((((...))))))(((..(..((....))..)..))))))))).))))))).. ( -37.10)
>DroSec_CAF1 21492 120 - 1
CGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCUCGCAAGUGGCAGAGAUUAAACGAAACGGAGCAGAGCUCCGCAGUAAUGACAAAUGUUUUCCCUCAUUUCCACUUGGCAAA
((((.....((((...((((........))))..))))))))(((((((..(((...(((((...((((((...))))))((....)).....)))))...)))....)))))))..... ( -31.20)
>DroSim_CAF1 21226 120 - 1
CGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCUCGCAAGUGGCAGAGAUUAAACGAAACGGAGCAGAGCUCCGGAGUAAUGACAAAUGUUUUCCCUCAUUUCCACUUGGCAAA
((((.....((((...((((........))))..))))))))(((((((.(((............((((((...))))))(((..(.(((....))).)..))).))))))))))..... ( -31.10)
>DroEre_CAF1 21469 120 - 1
CGAGAAUUAGUUGGGCAAAUAUGCGGAGCUUUUACAGCCUCCAAAGUGGCGGAGAUUAAACGAAACGAGGCAGAGUUCCAGAGUAAUGGCAAAUGUUUUCCCUCAUUUCCACUUGGCAAA
((((.((((.((..(((....)))((((((((....(((((....((..((.........))..))))))))))))))).)).))))((.(((((........))))))).))))..... ( -30.10)
>DroYak_CAF1 22887 119 - 1
UGAGAAUUAGCAGGGCAAAUAUGCGGAGGUUUUACAGCCUCGAAAGGGGCGGAGAUUAAACGAAACGGAGCAGAGCUCCGGAGUAAUGACAAAUGUU-UCCCUCAUUUCCACUUGGCAAA
.....................(((.(((........(((((....)))))((((((.........((((((...))))))(((....(((....)))-...))))))))).))).))).. ( -38.40)
>consensus
CGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCUCGCAAGUGGCGGAGAUUAAACGAAACGGAGCAGAGCUCCGGAGUAAUGACAAAUGUUUUCCCUCAUUUCCACUUGGCAAA
.....................(((.(((........(((.(....).)))((((((.........((((((...))))))(((..(.(((....))).)..))))))))).))).))).. (-26.96 = -27.44 +   0.48)

alignment

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secondary structure

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Window 1

Location 15,598,272 – 15,598,392
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -37.54
Consensus MFE -28.94
Energy contribution -28.66
Covariance contribution -0.28
Combinations/Pair 1.24
Mean z-score -1.51
Structure conservation index 0.77
SVM decision value 0.01
SVM RNA-class probability 0.541084
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15598272 120 - 23771897
GAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCUAAGAUUUUAUAGCCUCGCAAGUGGCGGAGAUUAAACGAAACGGAGCAGAGCUCCG
.......(((((((((((((....((..(((.((......)).)))...)).))))))))...)))))(((((...(((.(....).))).))))).........((((((...)))))) ( -36.80)
>DroSec_CAF1 21532 120 - 1
GAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCUCGCAAGUGGCAGAGAUUAAACGAAACGGAGCAGAGCUCCG
...(((((....((((((((....((..(((.((......)).)))...)).)))))))).(((((.(.........).)))))...))))).............((((((...)))))) ( -37.40)
>DroSim_CAF1 21266 120 - 1
GAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCUCGCAAGUGGCAGAGAUUAAACGAAACGGAGCAGAGCUCCG
...(((((....((((((((....((..(((.((......)).)))...)).)))))))).(((((.(.........).)))))...))))).............((((((...)))))) ( -37.40)
>DroEre_CAF1 21509 120 - 1
GGGCUGCCUUGGAUUUAGCCAUAUGCACUUCACGUGUAAUCGAGAAUUAGUUGGGCAAAUAUGCGGAGCUUUUACAGCCUCCAAAGUGGCGGAGAUUAAACGAAACGAGGCAGAGUUCCA
((((((((((((((((.(((((.(((((.....)))))................(((....)))((((((.....)).))))...)))))..)))))........))))))))...))). ( -34.20)
>DroYak_CAF1 22926 120 - 1
GGGCUGCCUUGGAUGAGUCCAUAUGCACUUCACGUGUAAUUGAGAAUUAGCAGGGCAAAUAUGCGGAGGUUUUACAGCCUCGAAAGGGGCGGAGAUUAAACGAAACGGAGCAGAGCUCCG
....(((((((..(((.((((..(((((.....)))))..)).)).))).)))))))......((..((((((...(((((....))))).))))))...))...((((((...)))))) ( -41.90)
>consensus
GAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCUCGCAAGUGGCGGAGAUUAAACGAAACGGAGCAGAGCUCCG
(((((..(((.(((((((((....((..(((.((......)).)))...)).)))))))).......((((((...(((.(....).))).))))))........).)))...))))).. (-28.94 = -28.66 +  -0.28)

alignment

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secondary structure

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Window 2

Location 15,598,312 – 15,598,432
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.50
Mean single sequence MFE -30.28
Consensus MFE -23.52
Energy contribution -23.56
Covariance contribution 0.04
Combinations/Pair 1.16
Mean z-score -1.50
Structure conservation index 0.78
SVM decision value 0.07
SVM RNA-class probability 0.568606
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15598312 120 + 23771897
AGGCUAUAAAAUCUUAGCAUAUUUGCCCAGCUAAUUCUCGAUUACACGUGAAGUGCAUAAGGGCAAAUCCAAGGCAGCUCACGUGUAAAACGUCGAUUUACUGAGUGAACUACUUAAUGA
..((((........))))...((..(.(((..((((..((.((((((((((..(((....(((....)))...)))..))))))))))..))..))))..))).)..))........... ( -32.50)
>DroSec_CAF1 21572 120 + 1
AGGCUGUAAAAUCUUCGCAUAUUUGCCCAGCUAAUUCUCGAUUACACGUGAAGUGCAUAAGGGCAAAUCCAAGGCAGCUCACGUGUAAAAUGUCGAUUUGCUGAGUGAAUUACUUAAUGA
....................(((..(.((((......((((((((((((((..(((....(((....)))...)))..)))))))))....)))))...)))).)..))).......... ( -31.30)
>DroSim_CAF1 21306 120 + 1
AGGCUGUAAAAUCUUCGCAUAUUUGCCCAGCUAAUUCUCGAUUACACGUGAAGUGCAUAAGGGCAAAUCCAAGGCAGCUCACGUGUAAAAUGUCGAUUUGCUGAGUGAAUUACUUAAUGA
....................(((..(.((((......((((((((((((((..(((....(((....)))...)))..)))))))))....)))))...)))).)..))).......... ( -31.30)
>DroEre_CAF1 21549 110 + 1
AGGCUGUAAAAGCUCCGCAUAUUUGCCCAACUAAUUCUCGAUUACACGUGAAGUGCAUAUGGCUAAAUCCAAGGCAGCCCACGUGUAAGAUGUCGAUUUCCAGAGGGAAU----------
.((((.....))))..(((....)))((..((.....(((((((((((((...(((...(((......)))..)))...))))))))....))))).....))..))...---------- ( -28.20)
>DroYak_CAF1 22966 120 + 1
AGGCUGUAAAACCUCCGCAUAUUUGCCCUGCUAAUUCUCAAUUACACGUGAAGUGCAUAUGGACUCAUCCAAGGCAGCCCACGUGUAAAAUGUCGAUUUUCAGAGUGAAUUACUUUAUGA
..((.(........).))..(((..(.(((..((((..((.(((((((((...(((...((((....))))..)))...)))))))))..))..))))..))).)..))).......... ( -28.10)
>consensus
AGGCUGUAAAAUCUUCGCAUAUUUGCCCAGCUAAUUCUCGAUUACACGUGAAGUGCAUAAGGGCAAAUCCAAGGCAGCUCACGUGUAAAAUGUCGAUUUGCUGAGUGAAUUACUUAAUGA
..((.(........).))..(((..(.(((..((((..((.((((((((((..(((....((......))...)))..))))))))))..))..))))..))).)..))).......... (-23.52 = -23.56 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,598,312 – 15,598,432
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.50
Mean single sequence MFE -33.14
Consensus MFE -27.54
Energy contribution -27.10
Covariance contribution -0.44
Combinations/Pair 1.21
Mean z-score -2.23
Structure conservation index 0.83
SVM decision value 1.94
SVM RNA-class probability 0.983226
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15598312 120 - 23771897
UCAUUAAGUAGUUCACUCAGUAAAUCGACGUUUUACACGUGAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCUAAGAUUUUAUAGCCU
.......(((((((((...(((((.......)))))..)))))))))(((((((((((((....((..(((.((......)).)))...)).))))))))...)))))............ ( -33.30)
>DroSec_CAF1 21572 120 - 1
UCAUUAAGUAAUUCACUCAGCAAAUCGACAUUUUACACGUGAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCU
.......((((.((..(((((...((((....(((((((((((.(((...((......))....))).)))))))))))))))......)))))(((....)))...))..))))..... ( -33.40)
>DroSim_CAF1 21306 120 - 1
UCAUUAAGUAAUUCACUCAGCAAAUCGACAUUUUACACGUGAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCU
.......((((.((..(((((...((((....(((((((((((.(((...((......))....))).)))))))))))))))......)))))(((....)))...))..))))..... ( -33.40)
>DroEre_CAF1 21549 110 - 1
----------AUUCCCUCUGGAAAUCGACAUCUUACACGUGGGCUGCCUUGGAUUUAGCCAUAUGCACUUCACGUGUAAUCGAGAAUUAGUUGGGCAAAUAUGCGGAGCUUUUACAGCCU
----------...((..((((...((((....(((((((((((.(((..(((......)))...))).)))))))))))))))...))))..))(((....)))((.(((.....))))) ( -31.90)
>DroYak_CAF1 22966 120 - 1
UCAUAAAGUAAUUCACUCUGAAAAUCGACAUUUUACACGUGGGCUGCCUUGGAUGAGUCCAUAUGCACUUCACGUGUAAUUGAGAAUUAGCAGGGCAAAUAUGCGGAGGUUUUACAGCCU
.......((((((..(((((..((((..((..(((((((((((.(((..((((....))))...))).))))))))))).)).).)))..)))))..))).)))..((((......)))) ( -33.70)
>consensus
UCAUUAAGUAAUUCACUCAGCAAAUCGACAUUUUACACGUGAGCUGCCUUGGAUUUGCCCUUAUGCACUUCACGUGUAAUCGAGAAUUAGCUGGGCAAAUAUGCGAAGAUUUUACAGCCU
..........(((..((((((...((((....(((((((((((.(((...((......))....))).)))))))))))))))......))))))..))).................... (-27.54 = -27.10 +  -0.44)

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 11:57:37 2006