Locus 7989

Sequence ID X_DroMel_CAF1
Location 19,883,318 – 19,883,573
Length 255
Max. P 0.961970
window13105 window13106 window13107 window13108 window13109

overview

Window 5

Location 19,883,318 – 19,883,429
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.07
Mean single sequence MFE -28.75
Consensus MFE -21.20
Energy contribution -21.96
Covariance contribution 0.76
Combinations/Pair 1.05
Mean z-score -1.88
Structure conservation index 0.74
SVM decision value 1.05
SVM RNA-class probability 0.906613
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19883318 111 + 22224390
ACUGACAAGAUAUAUGAUGGCAAACUUUAGCCAGCUUGCGUUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGU-----CCCCCCAA-CAACCAUAU---CCCCA
........(((((....((((........))))....(((((((((((.((((((((((.......))))))))))))))))..)))))-----........-.....))))---).... ( -30.00)
>DroSec_CAF1 37072 102 + 1
ACUGACAAGAUAUAUGAUGGCAAACUUUAGCCAGCUU------------GUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGCCACCUCCACCCAA-CGA-----CCACCCCCC
...((((((........((((........)))).)))------------)))(((((((.......)))))))((((.........))))............-...-----......... ( -25.40)
>DroSim_CAF1 27798 120 + 1
ACUGACAAGAUAUAUGAUGGCAAACUUUAGCCAGCUUGCGUUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGCCACCUCCCCCCAAACAACCCCUCCUCCCCCC
...((..((........((((........))))....(((((((((((.((((((((((.......))))))))))))))))..)))))....................))..))..... ( -29.20)
>DroEre_CAF1 16892 103 + 1
ACUGACAAGAUAUAUGAUGGCAAACUUUUGCCAGCUUGCGUUGCUUUUUGUCGUUGGCCGCUCGCAGGCAAAUGGUUAAAGUUUGAUAU-----CCCC-CAA-CACUCAC----------
...............((((.((((((((.(((((((((((..(((..........)))....)))))))...)))).)))))))).)))-----)...-...-.......---------- ( -28.20)
>DroYak_CAF1 13543 98 + 1
ACUGACAAGAUAUAUGAUGGCAAACUUUUGCCAGCUUGCGUUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGUAAAAGUUUGAUAU-----CCCU-CCA-CU---------------
...............((((.((((((((((((((((((((..((...............)).)))))))...))))))))))))).)))-----)...-...-..--------------- ( -30.96)
>consensus
ACUGACAAGAUAUAUGAUGGCAAACUUUAGCCAGCUUGCGUUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGU_____CCCCCCAA_CAA_C_______CCCC_
....................((((((((.(((((((((((..((...............)).)))))))...)))).))))))))................................... (-21.20 = -21.96 +   0.76)

alignment

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secondary structure

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Window 6

Location 19,883,358 – 19,883,469
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.39
Mean single sequence MFE -26.99
Consensus MFE -21.38
Energy contribution -22.54
Covariance contribution 1.16
Combinations/Pair 1.04
Mean z-score -1.46
Structure conservation index 0.79
SVM decision value 1.53
SVM RNA-class probability 0.961970
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19883358 111 + 22224390
UUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGU-----CCCCCCAA-CAACCAUAU---CCCCACACUACUAUCCCAUGCGUGGCAUUUGAAAUGCUAAUGGCA
.....((((((((((((((.......))))))))))))))(.(((.((.-----.....)).-))).)....---...............((((...((((((.....)))))))))).. ( -26.80)
>DroSec_CAF1 37109 105 + 1
---------GUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGCCACCUCCACCCAA-CGA-----CCACCCCCCUCCCACUUUCCCAUACGUGGCAUUUGAAAUGCUAAUGGCA
---------((((((((((.......)))))))))).....((.((((((((..........-...-----.........................)))))))).))..(((.....))) ( -25.46)
>DroSim_CAF1 27838 120 + 1
UUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGCCACCUCCCCCCAAACAACCCCUCCUCCCCCCUCGCACUUUCCCAUGCGUGGCAUUUGAAAUGCUAAUGGCA
....(((((((((((((((.......))))))))))))))).....(((((..............................((((........))))((((((.....)))))).))))) ( -33.70)
>DroEre_CAF1 16932 99 + 1
UUGCUUUUUGUCGUUGGCCGCUCGCAGGCAAAUGGUUAAAGUUUGAUAU-----CCCC-CAA-CACUCAC--------------UUGCCACCAUGCGUGGCAUUUGAAAUGCUAAUGGCA
........((((((((((.(((....)))....................-----....-...-...(((.--------------.((((((.....))))))..)))...)))))))))) ( -26.20)
>DroYak_CAF1 13583 94 + 1
UUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGUAAAAGUUUGAUAU-----CCCU-CCA-CU-------------------UCUCCUCCAUGCGUGGCAUUUGAAAUGCUAAUGGCA
....(((((..((((((((.......))))))))..)))))........-----....-...-..-------------------.........(((.((((((.....))))))...))) ( -22.80)
>consensus
UUGCUUUUUGUCGUUUGCCGCUCGCAGGCAAAUGGCAAAAGUUUGAUGU_____CCCCCCAA_CAA_C_______CCCC_____ACUCUCCCAUGCGUGGCAUUUGAAAUGCUAAUGGCA
....(((((((((((((((.......))))))))))))))).................................................((((...((((((.....)))))))))).. (-21.38 = -22.54 +   1.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,883,429 – 19,883,536
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.31
Mean single sequence MFE -29.02
Consensus MFE -23.82
Energy contribution -24.22
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.82
SVM decision value 0.04
SVM RNA-class probability 0.555874
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19883429 107 + 22224390
CACUACUAUCCCAUGCGUGGCAUUUGAAAUGCUAAUGGCAGAUGAGCUUAGGCCAAAAGCUGAAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC-------------
................(((((((.....))))...((((.....(((((.(((.....))).)))))((....))...))))..(((.......))).)))......------------- ( -24.20)
>DroSec_CAF1 37174 107 + 1
UCCCACUUUCCCAUACGUGGCAUUUGAAAUGCUAAUGGCAGAUGAGCUUAGGCCAAGAGCUGGAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC-------------
.................((((.(((((...(((..((((..(......)..))))..)))(((..((((....))))..)))...))))))))).............------------- ( -27.70)
>DroSim_CAF1 27918 107 + 1
UCGCACUUUCCCAUGCGUGGCAUUUGAAAUGCUAAUGGCAGAUGAGCUUAGGCCAAGAGCUGGAGCUGGAAAUCCAGAGCCAAGGACAAAGUCAGACACACAGAAAC-------------
.((((........))))((((.((((....(((..((((..(......)..))))..)))(((..((((....))))..)))....)))))))).............------------- ( -29.50)
>DroEre_CAF1 16995 103 + 1
----UUGCCACCAUGCGUGGCAUUUGAAAUGCUAAUGGCAGAUGAGCUUAGGCCAAAAGCUGGAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC-------------
----.((((((.....))))))((((....(((..((((..(......)..))))..)))(((..((((....))))..)))..(((.......)))...))))...------------- ( -31.50)
>DroYak_CAF1 13641 116 + 1
----UCUCCUCCAUGCGUGGCAUUUGAAAUGCUAAUGGCAGAUGAGCUUAGGCCAGAAGCUGGAGCUGAAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAGUCGAAGGCUCGAA
----((..(((((.((.((((((.....)))))).((((..(......)..))))...)))))))..)).......(((((...(((.......))).....(.....)...)))))... ( -32.20)
>consensus
____ACUCUCCCAUGCGUGGCAUUUGAAAUGCUAAUGGCAGAUGAGCUUAGGCCAAAAGCUGGAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC_____________
................(((...(((((...(((..((((..(......)..))))..)))(((..((((....))))..))).........)))))..)))................... (-23.82 = -24.22 +   0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,883,469 – 19,883,573
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.76
Mean single sequence MFE -31.16
Consensus MFE -24.56
Energy contribution -24.96
Covariance contribution 0.40
Combinations/Pair 1.09
Mean z-score -2.01
Structure conservation index 0.79
SVM decision value 1.12
SVM RNA-class probability 0.918306
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19883469 104 + 22224390
GAUGAGCUUAGGCCAAAAGCUGAAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC----------------UUGAAGGCUGGAGGCCUCAUAAUUGAAUGUUUGGCCA
..(((.(((.((((...(((....)))((....)).).))).))))))..((((((((..(((....----------------.(((.(((.....))))))...)))..)))))))).. ( -28.30)
>DroSec_CAF1 37214 104 + 1
GAUGAGCUUAGGCCAAGAGCUGGAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC----------------UCGAAGGCUGGAGGCCUCAUAAUUGAAUGUUUGGCCA
..........(((((((((.(((..((((....))))..)))..(((.......))).........)----------------))((.(((.....)))))............)))))). ( -32.30)
>DroSim_CAF1 27958 104 + 1
GAUGAGCUUAGGCCAAGAGCUGGAGCUGGAAAUCCAGAGCCAAGGACAAAGUCAGACACACAGAAAC----------------UCGAAGGCUGGAGGCCUCAUAAUUGAAUGUUUGGCCA
..........(((((((((.(((..((((....))))..)))..(((...))).............)----------------))((.(((.....)))))............)))))). ( -30.80)
>DroEre_CAF1 17031 104 + 1
GAUGAGCUUAGGCCAAAAGCUGGAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC----------------UCGAAGGCUGGAGGCCUCAUAAUUGAAUGUUUGGCCA
..........(((((((...(((..((((....))))..)))..(((.......)))..........----------------..((.(((.....)))))...........))))))). ( -30.10)
>DroYak_CAF1 13677 120 + 1
GAUGAGCUUAGGCCAGAAGCUGGAGCUGAAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAGUCGAAGGCUCGAAGACUCGAAGACUGGAGGCCUCAUAAUUGAAUGUUUGGCCA
..........(((((((..(((((........))))).(((..((((...(((.(((.........)))...)))((((....)))).))))...)))..............))))))). ( -34.30)
>consensus
GAUGAGCUUAGGCCAAAAGCUGGAGCUGGAAAUCCAGAGCCAAAGUCAAAGUCAGACACACAGAAAC________________UCGAAGGCUGGAGGCCUCAUAAUUGAAUGUUUGGCCA
..........(((((((...(((..((((....))))..)))..(((.......)))............................((.(((.....)))))...........))))))). (-24.56 = -24.96 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,883,469 – 19,883,573
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.76
Mean single sequence MFE -28.98
Consensus MFE -22.92
Energy contribution -22.84
Covariance contribution -0.08
Combinations/Pair 1.14
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.57
SVM RNA-class probability 0.783846
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19883469 104 - 22224390
UGGCCAAACAUUCAAUUAUGAGGCCUCCAGCCUUCAA----------------GUUUCUGUGUGUCUGACUUUGACUUUGGCUCUGGAUUUCCAGCUUCAGCUUUUGGCCUAAGCUCAUC
.((((((((((..((((..(((((.....)))))..)----------------)))...))))(((.......)))...((((((((....))))....)))).)))))).......... ( -27.40)
>DroSec_CAF1 37214 104 - 1
UGGCCAAACAUUCAAUUAUGAGGCCUCCAGCCUUCGA----------------GUUUCUGUGUGUCUGACUUUGACUUUGGCUCUGGAUUUCCAGCUCCAGCUCUUGGCCUAAGCUCAUC
.((((((............(((((.....))))).((----------------((........(((.......)))..(((..((((....))))..))))))))))))).......... ( -29.80)
>DroSim_CAF1 27958 104 - 1
UGGCCAAACAUUCAAUUAUGAGGCCUCCAGCCUUCGA----------------GUUUCUGUGUGUCUGACUUUGUCCUUGGCUCUGGAUUUCCAGCUCCAGCUCUUGGCCUAAGCUCAUC
.((((((((((..((((..(((((.....)))))..)----------------)))...))))..............((((..((((....))))..))))...)))))).......... ( -28.20)
>DroEre_CAF1 17031 104 - 1
UGGCCAAACAUUCAAUUAUGAGGCCUCCAGCCUUCGA----------------GUUUCUGUGUGUCUGACUUUGACUUUGGCUCUGGAUUUCCAGCUCCAGCUUUUGGCCUAAGCUCAUC
.((((((((((..((((..(((((.....)))))..)----------------)))...))))(((.......))).((((..((((....))))..))))...)))))).......... ( -29.90)
>DroYak_CAF1 13677 120 - 1
UGGCCAAACAUUCAAUUAUGAGGCCUCCAGUCUUCGAGUCUUCGAGCCUUCGACUUUCUGUGUGUCUGACUUUGACUUUGGCUCUGGAUUUUCAGCUCCAGCUUCUGGCCUAAGCUCAUC
.(((((...............((((...((((...(((((...(......)(((.........))).))))).))))..))))(((((........)))))....))))).......... ( -29.60)
>consensus
UGGCCAAACAUUCAAUUAUGAGGCCUCCAGCCUUCGA________________GUUUCUGUGUGUCUGACUUUGACUUUGGCUCUGGAUUUCCAGCUCCAGCUUUUGGCCUAAGCUCAUC
.((((((............(((((.....))))).............................(((.......))).((((..((((....))))..))))...)))))).......... (-22.92 = -22.84 +  -0.08)

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 12:52:32 2006