Locus 734

Sequence ID X_DroMel_CAF1
Location 1,995,922 – 1,996,116
Length 194
Max. P 0.983933
window1186 window1187 window1188 window1189

overview

Window 6

Location 1,995,922 – 1,996,042
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.75
Mean single sequence MFE -23.62
Consensus MFE -20.11
Energy contribution -20.03
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.98
Structure conservation index 0.85
SVM decision value 1.96
SVM RNA-class probability 0.983933
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1995922 120 + 22224390
AACCCACCCCUUUCCACCAUUUUCCGUGGCCUGUACAAACCGAUUUCCCAAACAAACAUUAUACAAUUACCCUCAAAAGGGGAUCCAUUCUGAUGUCCCAAGGGGUGUACACGUAAUCCC
....((((((((.((((........))))..........................((((((........((((....)))).........))))))...))))))))............. ( -24.53)
>DroSec_CAF1 27915 118 + 1
AACCCACCCCUUUCCACCAUUUUCCGUGGCCUGUACAAACCGAUUUCCCAAACAAACAUUAUACAAUUUCCCUCAAAAGGGGAUCCAUUCUGAGUUCCCAAGGGGUGUA--UGUAAUCCC
....((((((((.((((........)))).................................................(((((..(.....)..)))))))))))))..--......... ( -24.90)
>DroSim_CAF1 22120 118 + 1
AACCCACCCCUUUCCACCAUUUUCCGUGGCCUGUACAAACCGAUUUCCCAAACAAACGUUAUACAAUUACCCUCAAAAGGAGAUCCAUUCUGAGUUCCCAAGGGGUGUA--UGUAAUCCC
....((((((((.((((........))))............(((((((..............................)))))))..............))))))))..--......... ( -22.31)
>DroEre_CAF1 17698 118 + 1
AACCCACCCUCUUCCACCAUUUUCCGUGGCCUGUGCAAACCGAUUUCCCAAGCAAACAUUAAACAAUUACCCUCAAAAGGAGAUCCAUUCCGAUGUCCCAAGGGGUGUG--CGGAAUACC
..(((((((((((((((........))))....(((...............)))........................(((.(((......))).))).)))))).)))--.))...... ( -23.06)
>DroYak_CAF1 28527 118 + 1
AACCCACCCUCUUCCACCAUUUUCCGUGGUCCGUACAAACCGAUUUCCCAAACAAACAUUAAACAAUUACCCUCAAAAGGGGAUCCAUUCCGAUGUCCCAAGGGGUGCA--CGGAAUCCC
.....................((((((((((.((....)).))).......................((((((.....(((((((......))).))))..))))))))--))))).... ( -23.30)
>consensus
AACCCACCCCUUUCCACCAUUUUCCGUGGCCUGUACAAACCGAUUUCCCAAACAAACAUUAUACAAUUACCCUCAAAAGGGGAUCCAUUCUGAUGUCCCAAGGGGUGUA__CGUAAUCCC
....((((((((.((((........))))............(((((((..............................)))))))..............))))))))............. (-20.11 = -20.03 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,995,962 – 1,996,081
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.52
Mean single sequence MFE -31.34
Consensus MFE -24.88
Energy contribution -26.08
Covariance contribution 1.20
Combinations/Pair 1.10
Mean z-score -1.81
Structure conservation index 0.79
SVM decision value 0.83
SVM RNA-class probability 0.860890
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1995962 119 + 22224390
CGAUUUCCCAAACAAACAUUAUACAAUUACCCUCAAAAGGGGAUCCAUUCUGAUGUCCCAAGGGGUGUACACGUAAUCCCACCCCUAAGAUCAUUAGGGGUGUGAACGAGC-GUAGGAAU
....((((.............((((....((((.....(((((((......))).)))).)))).)))).((((..((.(((((((((.....))))))))).))....))-)).)))). ( -35.00)
>DroSec_CAF1 27955 117 + 1
CGAUUUCCCAAACAAACAUUAUACAAUUUCCCUCAAAAGGGGAUCCAUUCUGAGUUCCCAAGGGGUGUA--UGUAAUCCCACCCCUAACAUCAUUAAGGGUGUGAACAAGC-GUAGGAAU
...........................((((((....))))))(((((.((..((((...(((((((..--........))))))).(((((......))))))))).)).-)).))).. ( -28.30)
>DroSim_CAF1 22160 117 + 1
CGAUUUCCCAAACAAACGUUAUACAAUUACCCUCAAAAGGAGAUCCAUUCUGAGUUCCCAAGGGGUGUA--UGUAAUCCCACCCCUAAGAUCAUUAAGGGUGUGAACAAGC-GUAGGAAU
....((((.......(((((.((((..((((((.....((((.((......)).))))...))))))..--)))).((.(((((.(((.....))).))))).))...)))-)).)))). ( -28.30)
>DroEre_CAF1 17738 118 + 1
CGAUUUCCCAAGCAAACAUUAAACAAUUACCCUCAAAAGGAGAUCCAUUCCGAUGUCCCAAGGGGUGUG--CGGAAUACCACCCUGAAGAUCAUUAGGGGUGUGAACGAGCCGUUGGAAU
....((((...................((((((.....(((.(((......))).)))...)))))).(--(((..(((..((((((......))))))..)))......)))).)))). ( -29.20)
>DroYak_CAF1 28567 117 + 1
CGAUUUCCCAAACAAACAUUAAACAAUUACCCUCAAAAGGGGAUCCAUUCCGAUGUCCCAAGGGGUGCA--CGGAAUCCCACCCCUAAGAUCAUUAGGGGUGUAAACGAGC-GUUGGAAU
.............................((((....)))).....(((((((((..(...(((((...--....)))))((((((((.....))))))))......)..)-)))))))) ( -35.90)
>consensus
CGAUUUCCCAAACAAACAUUAUACAAUUACCCUCAAAAGGGGAUCCAUUCUGAUGUCCCAAGGGGUGUA__CGUAAUCCCACCCCUAAGAUCAUUAGGGGUGUGAACGAGC_GUAGGAAU
....((((...................((((((.....(((.(((......))).)))...))))))....(((..((.(((((((((.....))))))))).))))).......)))). (-24.88 = -26.08 +   1.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,995,962 – 1,996,081
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.52
Mean single sequence MFE -35.70
Consensus MFE -27.84
Energy contribution -28.04
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -1.73
Structure conservation index 0.78
SVM decision value 0.53
SVM RNA-class probability 0.769539
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1995962 119 - 22224390
AUUCCUAC-GCUCGUUCACACCCCUAAUGAUCUUAGGGGUGGGAUUACGUGUACACCCCUUGGGACAUCAGAAUGGAUCCCCUUUUGAGGGUAAUUGUAUAAUGUUUGUUUGGGAAAUCG
.((((((.-((..((((.(((((((((.....))))))))))))).(((((((((.(((((((((..((......)))))).....)))))....))))).))))..)).)))))).... ( -38.60)
>DroSec_CAF1 27955 117 - 1
AUUCCUAC-GCUUGUUCACACCCUUAAUGAUGUUAGGGGUGGGAUUACA--UACACCCCUUGGGAACUCAGAAUGGAUCCCCUUUUGAGGGAAAUUGUAUAAUGUUUGUUUGGGAAAUCG
.((((((.-((..((((.((((((((((...))))))))))))))...(--(((((((...)))..(((((((.((....)))))))))......))))).......)).)))))).... ( -36.20)
>DroSim_CAF1 22160 117 - 1
AUUCCUAC-GCUUGUUCACACCCUUAAUGAUCUUAGGGGUGGGAUUACA--UACACCCCUUGGGAACUCAGAAUGGAUCUCCUUUUGAGGGUAAUUGUAUAACGUUUGUUUGGGAAAUCG
.((((((.-((.((((..(((((((((.....))))))))).((((((.--....(((...)))..(((((((.((....))))))))).))))))....))))...)).)))))).... ( -37.40)
>DroEre_CAF1 17738 118 - 1
AUUCCAACGGCUCGUUCACACCCCUAAUGAUCUUCAGGGUGGUAUUCCG--CACACCCCUUGGGACAUCGGAAUGGAUCUCCUUUUGAGGGUAAUUGUUUAAUGUUUGCUUGGGAAAUCG
.((((...(((.((((.(((.((((.(((.(((...(((((((.....)--).)))))...))).)))(((((.((....)))))))))))....)))..))))...)))..)))).... ( -29.10)
>DroYak_CAF1 28567 117 - 1
AUUCCAAC-GCUCGUUUACACCCCUAAUGAUCUUAGGGGUGGGAUUCCG--UGCACCCCUUGGGACAUCGGAAUGGAUCCCCUUUUGAGGGUAAUUGUUUAAUGUUUGUUUGGGAAAUCG
.(((((((-(..((((..(((((((((.....)))))))))..((((((--((..((....))..)).)))))).....((((....)))).........))))..)).))))))..... ( -37.20)
>consensus
AUUCCUAC_GCUCGUUCACACCCCUAAUGAUCUUAGGGGUGGGAUUACG__UACACCCCUUGGGACAUCAGAAUGGAUCCCCUUUUGAGGGUAAUUGUAUAAUGUUUGUUUGGGAAAUCG
.(((((...((.((((.((((((.......(((.(((((((............))))))).)))...((((((.((....)))))))))))....)))..))))...))..))))).... (-27.84 = -28.04 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,996,002 – 1,996,116
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.65
Mean single sequence MFE -29.95
Consensus MFE -23.46
Energy contribution -23.58
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -1.55
Structure conservation index 0.78
SVM decision value 0.11
SVM RNA-class probability 0.590658
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1996002 114 - 22224390
CAAAUAGU--CCUAUUUGGCUCCCCCUGCCAUUUUC---AAUUCCUAC-GCUCGUUCACACCCCUAAUGAUCUUAGGGGUGGGAUUACGUGUACACCCCUUGGGACAUCAGAAUGGAUCC
......((--((((..((((.......)))).....---......(((-((..((((.(((((((((.....)))))))))))))...))))).......)))))).............. ( -35.20)
>DroSec_CAF1 27995 112 - 1
CAAAUAGU--CCUAUUUGGCUCCCCCUGCCAUUUUC---AAUUCCUAC-GCUUGUUCACACCCUUAAUGAUGUUAGGGGUGGGAUUACA--UACACCCCUUGGGAACUCAGAAUGGAUCC
((((((..--..))))))..........(((((((.---(.((((((.-....((((.((((((((((...))))))))))))))....--.........)))))).).))))))).... ( -27.97)
>DroSim_CAF1 22200 112 - 1
CAAAUAGU--CCUAUUUGGCUCCCCCUGCCAUUUUC---AAUUCCUAC-GCUUGUUCACACCCUUAAUGAUCUUAGGGGUGGGAUUACA--UACACCCCUUGGGAACUCAGAAUGGAUCU
((((((..--..))))))..........(((((((.---(.((((((.-....((((.(((((((((.....)))))))))))))....--.........)))))).).))))))).... ( -27.47)
>DroEre_CAF1 17778 116 - 1
CGAAUAGU--CCUAUUUGGCUCCCGCUGCAUUUUUCAGGAAUUCCAACGGCUCGUUCACACCCCUAAUGAUCUUCAGGGUGGUAUUCCG--CACACCCCUUGGGACAUCGGAAUGGAUCU
.(((((((--(......(((....)))..........((....))...)))).)))).(((((....((.....))))))).(((((((--....(((...)))....)))))))..... ( -27.30)
>DroYak_CAF1 28607 114 - 1
--AAUAGUCUCCUAUUUGGCUCGC-CUGCAUUUUUCAGAAAUUCCAAC-GCUCGUUUACACCCCUAAUGAUCUUAGGGGUGGGAUUCCG--UGCACCCCUUGGGACAUCGGAAUGGAUCC
--.......(((......((....-..))...........(((((...-((.((.(..(((((((((.....)))))))))..)...))--.)).(((...))).....))))))))... ( -31.80)
>consensus
CAAAUAGU__CCUAUUUGGCUCCCCCUGCCAUUUUC___AAUUCCUAC_GCUCGUUCACACCCCUAAUGAUCUUAGGGGUGGGAUUACG__UACACCCCUUGGGACAUCAGAAUGGAUCC
(((((((....)))))))((.......))......................((((((.(((((((((.....)))))))))..............(((...)))......)))))).... (-23.46 = -23.58 +   0.12)

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 09:52:29 2006