Locus 636

Sequence ID 2L_DroMel_CAF1
Location 1,897,214 – 1,897,421
Length 207
Max. P 0.927550
window1036 window1037 window1038 window1039 window1040

overview

Window 6

Location 1,897,214 – 1,897,321
Length 107
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.74
Mean single sequence MFE -35.00
Consensus MFE -27.84
Energy contribution -27.73
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.80
SVM decision value 0.70
SVM RNA-class probability 0.825677
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1897214 107 + 22407834
UUAAAACUAAACUGUGCCGGCAGUUUGGAAAUUUCACACAUUGCGGCUAAAGAGUUUUCUCAGUUGGCAGUGGCAAAUUACAGUUGCAAACAAUGCGACGAUGC-------------CAC
......(((((((((....))))))))).................(((((.(((....)))..))))).((((((.......((((((.....))))))..)))-------------))) ( -31.10)
>DroEre_CAF1 62104 111 + 1
-UAUAACUAAACUGUGCCGGCAGUUUGGAAAUUUCACACAUUCCGGCUAAAGAGUUUUCUCAGUUGGCAGUGGCAAAUUACAGUUGCAAACAAUGCGACGAUGCCUUGC--------CAC
-.....(((((((((....))))))))).................(((((.(((....)))..))))).(((((((..((..((((((.....))))))..))..))))--------))) ( -34.40)
>DroYak_CAF1 71431 119 + 1
-UAUAACUAAACUGCGCCGGCAGUUUGGAAAUUUCACACAUUCCGGCUAAAGAGUUUUCUCAGUUGGCAGUGGCAAAUUACAGUUGCGAACAAUGCGACGAUGCCUUGCCUCAUGGCCAC
-.....(((((((((....)))))))))................(((((..(((....)))....(((((.((((.......((((((.....))))))..)))))))))...))))).. ( -39.50)
>consensus
_UAUAACUAAACUGUGCCGGCAGUUUGGAAAUUUCACACAUUCCGGCUAAAGAGUUUUCUCAGUUGGCAGUGGCAAAUUACAGUUGCAAACAAUGCGACGAUGCCUUGC________CAC
......(((((((((....))))))))).(((((..(((...((((((...(((....)))))))))..)))..)))))...((((((.....))))))..................... (-27.84 = -27.73 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,897,294 – 1,897,384
Length 90
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 75.38
Mean single sequence MFE -31.60
Consensus MFE -13.44
Energy contribution -13.87
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -2.93
Structure conservation index 0.43
SVM decision value 1.18
SVM RNA-class probability 0.927550
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1897294 90 + 22407834
CAGUUGCAAACAAUGCGACGAUGC-------------CACAUGG--------CCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA------GCUACAGUUACACG
.(((((((....(((((..(((((-------------(...(((--------(.((.(((....))).))))))..)))))).....))))).))))------)))........... ( -28.30)
>DroEre_CAF1 62183 101 + 1
CAGUUGCAAACAAUGCGACGAUGCCUUGC--------CACAUGGCCAAAUGCCCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA--------CACAAAUACACG
..((((((.....))))))((((((((((--------(....)))........(((.(((....))).)))...)))))))).....(((....)))--------............ ( -27.60)
>DroYak_CAF1 71510 109 + 1
CAGUUGCGAACAAUGCGACGAUGCCUUGCCUCAUGGCCACAUGGCCAAAUGGCCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA--------CACAAAUACACG
..((((((....(((((..(((((((((((...(((((....)))))...)))(((.(((....))).)))...)))))))).....))))).))))--------.))......... ( -36.70)
>DroAna_CAF1 65844 108 + 1
CAGUUAUAAACAAUUCUGCC-UGCCUUGC--------CACAUGCCCCGUCCAACAGUUGCAGUUGCAAUUGUCAGAGGAAUUAAUAAUGCAUGUGCUGGCCAGGCAACAGACACACA
..............((((..-(((((.((--------(((((((.((.((..((((((((....))))))))..))))..........))))))...))).))))).))))...... ( -33.80)
>consensus
CAGUUGCAAACAAUGCGACGAUGCCUUGC________CACAUGGCCAAAUG_CCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA________CACAAAUACACG
..((((((.....))))))..................(((((...........(((.(((....))).)))......((((.....)))))))))...................... (-13.44 = -13.87 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,897,294 – 1,897,384
Length 90
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 75.38
Mean single sequence MFE -32.83
Consensus MFE -15.65
Energy contribution -15.40
Covariance contribution -0.25
Combinations/Pair 1.23
Mean z-score -2.18
Structure conservation index 0.48
SVM decision value 0.17
SVM RNA-class probability 0.618847
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1897294 90 - 22407834
CGUGUAACUGUAGC------UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGG--------CCAUGUG-------------GCAUCGUCGCAUUGUUUGCAACUG
.(((((.(....).------))))).((((....((((((..(...(((.(((....))).)))(--------((....)-------------))...)..))))))..)))).... ( -25.40)
>DroEre_CAF1 62183 101 - 1
CGUGUAUUUGUG--------UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGGGCAUUUGGCCAUGUG--------GCAAGGCAUCGUCGCAUUGUUUGCAACUG
.((((((....)--------))))).((((....((((((....(((...(((...(((.....(((.....))).....--------)))..)))..)))))))))..)))).... ( -30.10)
>DroYak_CAF1 71510 109 - 1
CGUGUAUUUGUG--------UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGGCCAUUUGGCCAUGUGGCCAUGAGGCAAGGCAUCGUCGCAUUGUUCGCAACUG
.......(((((--------.(((.((((.......((((((....(((.(((....))).)))(((...(((((....)))))...))).))))))....))))))).)))))... ( -36.80)
>DroAna_CAF1 65844 108 - 1
UGUGUGUCUGUUGCCUGGCCAGCACAUGCAUUAUUAAUUCCUCUGACAAUUGCAACUGCAACUGUUGGACGGGGCAUGUG--------GCAAGGCA-GGCAGAAUUGUUUAUAACUG
......((((((((((.(((...((((((.........(((((..(((.((((....)))).)))..)).))))))))))--------)).)))))-.))))).............. ( -39.00)
>consensus
CGUGUAUCUGUG________UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGG_CAUUUGGCCAUGUG________GCAAGGCAUCGUCGCAUUGUUUGCAACUG
.((((((.(((((......))))).))))))...((((((..(.......(((....)))..(((((....)))))......................)..)))))).......... (-15.65 = -15.40 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,897,321 – 1,897,421
Length 100
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 83.03
Mean single sequence MFE -23.20
Consensus MFE -18.05
Energy contribution -18.44
Covariance contribution 0.39
Combinations/Pair 1.07
Mean z-score -1.53
Structure conservation index 0.78
SVM decision value -0.01
SVM RNA-class probability 0.528254
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1897321 100 + 22407834
AUGG--------CCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCAGCUACAGUUACACGGCUAGAAAAAAAUGGGAAAUAC---UAAAGCCGUUGACGG
....--------((...((.(((((((.....((...((((.....)))).))))))))).))((((.((((((.........(((......)---)).)))))))))))) ( -23.10)
>DroEre_CAF1 62215 108 + 1
AUGGCCAAAUGCCCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA--CACAAAUACACGGCUAGAAAA-AAUGGAAAUAAAAAAAACAGCAGUCGACGA
.(((((.(((((((((.(((....))).))).....)))))).....(((....)))--...........))))).....-.............................. ( -20.10)
>DroYak_CAF1 71550 108 + 1
AUGGCCAAAUGGCCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA--CACAAAUACACGGCUAGAAAA-AAUGGCAAAUAAACACACAGCCGUCGACGG
.(((((....)))))..(((....)))..((((.(((((........(((....)))--............((((.....-..)))).............))).)))))). ( -26.40)
>consensus
AUGGCCAAAUG_CCAAAUGCAGUUGCAAUUGUCAGAGGCAUUAAUAAUGCAUGUGCA__CACAAAUACACGGCUAGAAAA_AAUGGAAAAUAAA_AAACAGCCGUCGACGG
.(((((....)))))..(((....))).(((((....((((.....)))).((((....)))).....((((((.........................)))))).))))) (-18.05 = -18.44 +   0.39)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,897,321 – 1,897,421
Length 100
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 83.03
Mean single sequence MFE -24.62
Consensus MFE -17.69
Energy contribution -18.97
Covariance contribution 1.28
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.72
SVM decision value 0.13
SVM RNA-class probability 0.599309
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1897321 100 - 22407834
CCGUCAACGGCUUUA---GUAUUUCCCAUUUUUUUCUAGCCGUGUAACUGUAGCUGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGG--------CCAU
..((((((((((...---...................)))))).....(((((.((((((.((((.....))))...)).....)))).)))))..)))--------)... ( -20.35)
>DroEre_CAF1 62215 108 - 1
UCGUCGACUGCUGUUUUUUUUAUUUCCAUU-UUUUCUAGCCGUGUAUUUGUG--UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGGGCAUUUGGCCAU
..(((((.((((..................-..........((((((....)--)))))..((((.....))))......(((.(((....))).))))))).)))))... ( -23.10)
>DroYak_CAF1 71550 108 - 1
CCGUCGACGGCUGUGUGUUUAUUUGCCAUU-UUUUCUAGCCGUGUAUUUGUG--UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGGCCAUUUGGCCAU
..(((((((((((((.((......))))).-......))))))(((((...(--(((....))))....)))))...))))...(((....)))..(((((....))))). ( -30.41)
>consensus
CCGUCGACGGCUGUAU_UUUAUUUCCCAUU_UUUUCUAGCCGUGUAUUUGUG__UGCACAUGCAUUAUUAAUGCCUCUGACAAUUGCAACUGCAUUUGG_CAUUUGGCCAU
..(((((((((((.......................)))))))((((.(((....))).))))..............))))...(((....)))..(((((....))))). (-17.69 = -18.97 +   1.28)

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 09:41:34 2006