Locus 166

Sequence ID X_DroMel_CAF1
Location 619,902 – 620,059
Length 157
Max. P 0.930004
window263 window264 window265

overview

Window 3

Location 619,902 – 620,001
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.59
Mean single sequence MFE -22.83
Consensus MFE -21.08
Energy contribution -21.25
Covariance contribution 0.17
Combinations/Pair 1.13
Mean z-score -1.47
Structure conservation index 0.92
SVM decision value 0.74
SVM RNA-class probability 0.838686
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 619902 99 - 22224390
UGUACUCAGUGGCAGAGCAAAAAAUUGGUCACUCUUCUUUAUUUGGGCUCUCUGUU--C--U-A-C-C--CACU-CGACUCUUAGCCUUAACAAAGAAAGAGACAUUUA-----------
(((.(((((((((.((........)).)))))).((((((.((.(((((....(((--.--.-.-.-.--....-.)))....))))).)).)))))).))))))....----------- ( -21.60)
>DroVir_CAF1 4198 107 - 1
UGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUUAUUUGGGCCUUUUGUU--C--ACAAUU---CCAUUUGACUUUUGGCCUUAACAAAGACAGAGACAGCACUACA-C-----
(((.(((((((((..(((....)))..))))))..(((((.((.(((((....((.--.--.(((..---....)))))....))))).)).)))))..))))))........-.----- ( -22.60)
>DroGri_CAF1 4149 110 - 1
UGUACUCAGUGGCAUAUUGAAAAAUUGGUCACUCUUCUUUAUUUGGGCCUUUUGUUUUC--GAAUUUA--CUAU-UGACUUUUGGCCUUAACAAAGAAAGAGACAGAACAACAAC-----
(((.(((((((((..(((....)))..)))))).((((((.((.(((((....(((...--.......--....-.)))....))))).)).)))))).))))))..........----- ( -26.26)
>DroWil_CAF1 5115 112 - 1
UGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUUAUUUGGGCCUUUUGUU--UACU-A-U-U--CUAU-UGACUUUUGGCCUUAACGAAGAAAGAGACAGCUUGAAAAAGAAAA
(((.(((((((((..(((....)))..)))))).(((((..((.(((((....(((--....-.-.-.--....-.)))....))))).))..))))).)))))).(((....))).... ( -26.80)
>DroMoj_CAF1 3919 105 - 1
UGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUAAUUUGGGUCUUUUGUU--C--GCA-UU---CCAU-UGACUUUUGGCCUUAACAAAGAAAGAGACAGCACUACU-C-----
(((.(((((((((..(((....)))..)))))).(((((.....(((((....(((--.--...-..---....-.)))....))))).....))))).))))))........-.----- ( -19.10)
>DroAna_CAF1 4393 101 - 1
UGUACUCAGUGGCAGAUUAAAAAAUUGGACACUCUUCUUUAUUUGGGCCUUUUGUU--C--U-U-C-AAUCCUU-UGACUUUUGGCCUUAACAAAGAAAGAGAUAAUCU-----------
....(((((((...((((....))))...)))).((((((.((.(((((.......--.--.-(-(-((....)-))).....))))).)).)))))).))).......----------- ( -20.64)
>consensus
UGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUUAUUUGGGCCUUUUGUU__C__U_A_U____CCAU_UGACUUUUGGCCUUAACAAAGAAAGAGACAGCAC_ACA_C_____
(((.(((((((((..(((....)))..)))))).((((((.((.(((((....(((....................)))....))))).)).)))))).))))))............... (-21.08 = -21.25 +   0.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 619,961 – 620,059
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.42
Mean single sequence MFE -29.47
Consensus MFE -22.11
Energy contribution -22.14
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.75
SVM decision value 0.59
SVM RNA-class probability 0.793048
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 619961 98 + 22224390
AAAGAAGAGUGACCAAUUUUUUGCUCUGCCACUGAGUACACUGCCAUCAGAGCGAC-----------GC---AUAA----AGC-UCACUCUCUGACGGCAAAUCGGCGUGGCCU---GUA
.....((((..(........)..))))(((((...((....((((.((((((.((.-----------((---....----.))-))...)))))).)))).....)))))))..---... ( -29.60)
>DroVir_CAF1 4265 102 + 1
AAAGAAGAGUGACCAAUUUUUUAAUAUGCCACUGAGUACACUGCCAUCAGAGCGAC-----------ACGGCCAAAAG--GCCUUCACUCUCUGACGGCAAAUCGGCGUGGCUA---U--
...(((((((.....))))))).....(((((...((....((((.((((((.(..-----------..((((....)--)))....).)))))).)))).....)))))))..---.-- ( -33.10)
>DroGri_CAF1 4219 106 + 1
AAAGAAGAGUGACCAAUUUUUCAAUAUGCCACUGAGUACACUGCCAUCAGAGCGAC------CA---AUGGCUAAAAGAAGCCUUCACUCUCUGACGGCAAAUCGGCGUGGCCU---A--
...(((((((.....))))))).....(((((...((....((((.((((((.(..------..---..((((......))))....).)))))).)))).....)))))))..---.-- ( -32.70)
>DroWil_CAF1 5187 113 + 1
AAAGAAGAGUGACCAAUUUUUUAAUAUGCCACUGAGUACACUGCCAUCAAAGCGACAUGGACCAUUUGC---AUGG----ACCUUCACUCUCUGACGGCAAAUCGGCGUGGCCUUAUAUA
...(((((((.....))))))).....(((((...((....((((.(((.((.(....((.((((....---))))----.))....).)).))).)))).....)))))))........ ( -24.80)
>DroMoj_CAF1 3984 101 + 1
UAAGAAGAGUGACCAAUUUUUUAAUAUGCCACUGAGUACACUGCCAUCAGAGCGAC-----------UA-UCCCAAGG--GAUUUCACUCUCUGACGGCAAAUCGGCGUGGCCU---A--
...(((((((.....))))))).....(((((...((....((((.((((((.(..-----------.(-(((....)--)))....).)))))).)))).....)))))))..---.-- ( -30.50)
>DroAna_CAF1 4454 97 + 1
AAAGAAGAGUGUCCAAUUUUUUAAUCUGCCACUGAGUACACUGCCAUCAGAGCGAC-----------GCC--AUGG----AGC-UCACUCUCUGACGGCAAAUCGGCGUGGCCU---A--
...(((((((.....))))))).....(((((...((....((((.((((((.((.-----------((.--....----.))-))...)))))).)))).....)))))))..---.-- ( -26.10)
>consensus
AAAGAAGAGUGACCAAUUUUUUAAUAUGCCACUGAGUACACUGCCAUCAGAGCGAC___________GC___AUAA____ACCUUCACUCUCUGACGGCAAAUCGGCGUGGCCU___A__
...(((((((.....))))))).....(((((...((....((((.((((((.(.................................).)))))).)))).....)))))))........ (-22.11 = -22.14 +   0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 619,961 – 620,059
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.42
Mean single sequence MFE -36.07
Consensus MFE -26.79
Energy contribution -26.65
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -2.74
Structure conservation index 0.74
SVM decision value 1.20
SVM RNA-class probability 0.930004
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 619961 98 - 22224390
UAC---AGGCCACGCCGAUUUGCCGUCAGAGAGUGA-GCU----UUAU---GC-----------GUCGCUCUGAUGGCAGUGUACUCAGUGGCAGAGCAAAAAAUUGGUCACUCUUCUUU
...---..(((((......((((((((((((.(...-((.----....---))-----------..).))))))))))))........))))).((.(((....))).)).......... ( -35.64)
>DroVir_CAF1 4265 102 - 1
--A---UAGCCACGCCGAUUUGCCGUCAGAGAGUGAAGGC--CUUUUGGCCGU-----------GUCGCUCUGAUGGCAGUGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUU
--.---..(((((......(((((((((((..((((.(((--(....))))..-----------.)))))))))))))))........)))))........................... ( -39.54)
>DroGri_CAF1 4219 106 - 1
--U---AGGCCACGCCGAUUUGCCGUCAGAGAGUGAAGGCUUCUUUUAGCCAU---UG------GUCGCUCUGAUGGCAGUGUACUCAGUGGCAUAUUGAAAAAUUGGUCACUCUUCUUU
--.---.(((((.((((..((((((((((((.((.((((((......)))).)---).------).).)))))))))))).........))))..(((....)))))))).......... ( -36.80)
>DroWil_CAF1 5187 113 - 1
UAUAUAAGGCCACGCCGAUUUGCCGUCAGAGAGUGAAGGU----CCAU---GCAAAUGGUCCAUGUCGCUUUGAUGGCAGUGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUU
........(((((......(((((((((..((((((.((.----((((---....)))).))...)))))))))))))))........)))))........................... ( -36.54)
>DroMoj_CAF1 3984 101 - 1
--U---AGGCCACGCCGAUUUGCCGUCAGAGAGUGAAAUC--CCUUGGGA-UA-----------GUCGCUCUGAUGGCAGUGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUA
--.---..(((((......(((((((((((..((((.(((--(....)))-).-----------.)))))))))))))))........)))))........................... ( -35.14)
>DroAna_CAF1 4454 97 - 1
--U---AGGCCACGCCGAUUUGCCGUCAGAGAGUGA-GCU----CCAU--GGC-----------GUCGCUCUGAUGGCAGUGUACUCAGUGGCAGAUUAAAAAAUUGGACACUCUUCUUU
--.---..(((((......((((((((((((.(...-(((----....--)))-----------..).))))))))))))........)))))........................... ( -32.74)
>consensus
__U___AGGCCACGCCGAUUUGCCGUCAGAGAGUGAAGGC____UUAU___GC___________GUCGCUCUGAUGGCAGUGUACUCAGUGGCAUAUUAAAAAAUUGGUCACUCUUCUUU
........(((((......((((((((((((.(.................................).))))))))))))........)))))........................... (-26.79 = -26.65 +  -0.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:48 2006