Locus 4156

Sequence ID 2L_DroMel_CAF1
Location 11,956,708 – 11,956,881
Length 173
Max. P 0.998004
window6557 window6558 window6559 window6560

overview

Window 7

Location 11,956,708 – 11,956,801
Length 93
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 89.66
Mean single sequence MFE -21.30
Consensus MFE -18.92
Energy contribution -18.84
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -2.31
Structure conservation index 0.89
SVM decision value 2.98
SVM RNA-class probability 0.998004
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11956708 93 + 22407834
UGCAAGAAAUGAAUUUCAUCUGGAGAUAAUUCGCAUUUUUAUGAUGAAAUUAAGUCGACUCUUGCAAUUGUUUUU-----UUUUUCAAUUGCAGCUGG
.((..((....((((((((((((((((.......))))))).)))))))))...))......((((((((.....-----.....))))))))))... ( -22.70)
>DroSec_CAF1 176075 89 + 1
UGCAAGAAAUGAAUUUCAUCUGGAGAUAAUUCACAUUUUUAUGAUGAAAUUAAGUCGGGUCUUGCAAUUGUUU---------UUUCAAUUGCAACUGG
.((..((....((((((((((((((((.......))))))).)))))))))...))..)).(((((((((...---------...))))))))).... ( -23.50)
>DroSim_CAF1 142474 89 + 1
UGCAAGAAAUGAAUUUCAUCUGGGGGUAAUUCACAUUUUUAUGAUGAAAUUAAGUCGGCUCUUGCAAUUGUUU---------UUUCAAUUGCAACUGA
.((..((....((((((((((((((((.......))))))).)))))))))...)).))..(((((((((...---------...))))))))).... ( -22.00)
>DroEre_CAF1 151005 89 + 1
UGCAAGAAAUGAAUUUCAUCUGGAGAUAAUUCGCAUUUUUAUGAUGAAAUUAAGUCCGCUCUUGCCAUUGUUA---------UUUCAAUUGCAACUGC
.....((....((((((((((((((((.......))))))).)))))))))...)).((..((((.((((...---------...)))).))))..)) ( -20.10)
>DroYak_CAF1 146823 98 + 1
UGCAAGAAAUGAAUUUCAUCUGGAGAUAAUUCGCAUUUUUAUGAUCAAAUUAAGUCAGCUCUUGCAAUUGUUUUUUUUUUUUUUUCAAUUGCAACUGC
(((((....((((........((((((((((.(((......((((........)))).....)))))))))))))........)))).)))))..... ( -18.19)
>consensus
UGCAAGAAAUGAAUUUCAUCUGGAGAUAAUUCGCAUUUUUAUGAUGAAAUUAAGUCGGCUCUUGCAAUUGUUU_________UUUCAAUUGCAACUGC
.....((....((((((((((((((((.......))))))).)))))))))...)).....(((((((((...............))))))))).... (-18.92 = -18.84 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,956,708 – 11,956,801
Length 93
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 89.66
Mean single sequence MFE -16.86
Consensus MFE -12.53
Energy contribution -12.93
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.74
SVM decision value 0.75
SVM RNA-class probability 0.841302
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11956708 93 - 22407834
CCAGCUGCAAUUGAAAAA-----AAAAACAAUUGCAAGAGUCGACUUAAUUUCAUCAUAAAAAUGCGAAUUAUCUCCAGAUGAAAUUCAUUUCUUGCA
...((.(((((((.....-----.....)))))))(((((..((....((((((((......................))))))))))..))))))). ( -16.75)
>DroSec_CAF1 176075 89 - 1
CCAGUUGCAAUUGAAA---------AAACAAUUGCAAGACCCGACUUAAUUUCAUCAUAAAAAUGUGAAUUAUCUCCAGAUGAAAUUCAUUUCUUGCA
....(((((((((...---------...))))))))).....((..((((((((((......................))))))))).)..))..... ( -15.65)
>DroSim_CAF1 142474 89 - 1
UCAGUUGCAAUUGAAA---------AAACAAUUGCAAGAGCCGACUUAAUUUCAUCAUAAAAAUGUGAAUUACCCCCAGAUGAAAUUCAUUUCUUGCA
....(((((((((...---------...)))))))))..((.((..((((((((((......................))))))))).)..))..)). ( -17.25)
>DroEre_CAF1 151005 89 - 1
GCAGUUGCAAUUGAAA---------UAACAAUGGCAAGAGCGGACUUAAUUUCAUCAUAAAAAUGCGAAUUAUCUCCAGAUGAAAUUCAUUUCUUGCA
((....)).((((...---------...)))).((((((..(((..(((((((((.......))).))))))..))).((((.....)))))))))). ( -18.00)
>DroYak_CAF1 146823 98 - 1
GCAGUUGCAAUUGAAAAAAAAAAAAAAACAAUUGCAAGAGCUGACUUAAUUUGAUCAUAAAAAUGCGAAUUAUCUCCAGAUGAAAUUCAUUUCUUGCA
(((((((((((((...............))))))))).....((..(((((((..(((....))))))))))..)).(((((.....))))).)))). ( -16.66)
>consensus
CCAGUUGCAAUUGAAA_________AAACAAUUGCAAGAGCCGACUUAAUUUCAUCAUAAAAAUGCGAAUUAUCUCCAGAUGAAAUUCAUUUCUUGCA
.................................(((((((..((....((((((((......................))))))))))..))))))). (-12.53 = -12.93 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,956,726 – 11,956,841
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.19
Mean single sequence MFE -24.99
Consensus MFE -16.91
Energy contribution -17.91
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.68
SVM decision value 0.41
SVM RNA-class probability 0.725687
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11956726 115 + 22407834
UCUGGAGAUAAUUCGCAUUUUUAUGAUGAAAUUAAGUCGACUCUUGCAAUUGUUUUU-----UUUUUCAAUUGCAGCUGGCAAGCUAGUGUAUAUAAACCUACUUGGGUGUGCCACUAUU
...(..(((......((((.....)))).......)))..)..(((((((((.....-----.....))))))))).(((((.(((...(((........)))...))).)))))..... ( -23.02)
>DroSec_CAF1 176093 106 + 1
UCUGGAGAUAAUUCACAUUUUUAUGAUGAAAUUAAGUCGGGUCUUGCAAUUGUUU---------UUUCAAUUGCAACUGGCAAGCUA---UAU--AUAACAACUUGGGUGUGCCACUAUU
.((.((..((((((((((....))).)).)))))..)).))..(((((((((...---------...))))))))).(((((.(((.---...--...........))).)))))..... ( -23.06)
>DroSim_CAF1 142492 108 + 1
UCUGGGGGUAAUUCACAUUUUUAUGAUGAAAUUAAGUCGGCUCUUGCAAUUGUUU---------UUUCAAUUGCAACUGACAAGCUA---UAUAUAUACCGACUUGGGUGUGCCACUAUU
..(((.((((.(((((((....))).)))).(((((((((...(((((((((...---------...)))))))))((....))...---........)))))))))...)))).))).. ( -28.60)
>DroYak_CAF1 146841 111 + 1
UCUGGAGAUAAUUCGCAUUUUUAUGAUCAAAUUAAGUCAGCUCUUGCAAUUGUUUUUUUUUUUUUUUCAAUUGCAACUGCCAAUCUU---UAU----ACCCACAUGGGUGUGCCAAUC--
..(((((((..............((((........))))((..(((((((((...............)))))))))..))..)))).---(((----((((....))))))))))...-- ( -25.26)
>consensus
UCUGGAGAUAAUUCACAUUUUUAUGAUGAAAUUAAGUCGGCUCUUGCAAUUGUUU_________UUUCAAUUGCAACUGGCAAGCUA___UAU__AUACCAACUUGGGUGUGCCACUAUU
..(((......(((((((....))).)))).....(((((...(((((((((...............))))))))))))))..............(((((......))))).)))..... (-16.91 = -17.91 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,956,766 – 11,956,881
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.42
Mean single sequence MFE -24.06
Consensus MFE -12.50
Energy contribution -14.06
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.15
Structure conservation index 0.52
SVM decision value -0.02
SVM RNA-class probability 0.524190
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11956766 115 + 22407834
CUCUUGCAAUUGUUUUU-----UUUUUCAAUUGCAGCUGGCAAGCUAGUGUAUAUAAACCUACUUGGGUGUGCCACUAUUGAGUGAACCAUUGAUUUAAGAAAUAAAGCCUUUAUUUCUG
((((((((((((.....-----.....))))))))).(((((.(((...(((........)))...))).))))).....)))...............((((((((.....)))))))). ( -26.00)
>DroSec_CAF1 176133 106 + 1
GUCUUGCAAUUGUUU---------UUUCAAUUGCAACUGGCAAGCUA---UAU--AUAACAACUUGGGUGUGCCACUAUUGAGUGCACCAUUGAUUUAAGAAAUAAAGCCUUUAUUUCUG
((((((((((((...---------...)))))))))..)))......---...--...........((((..(((....)).)..)))).........((((((((.....)))))))). ( -27.20)
>DroSim_CAF1 142532 108 + 1
CUCUUGCAAUUGUUU---------UUUCAAUUGCAACUGACAAGCUA---UAUAUAUACCGACUUGGGUGUGCCACUAUUGAGUGAACCAUUGAUUUAAGAAAUAAAGCCUUUAUUUCUG
(..(((((((((...---------...)))))))))..).(((....---....((((((......)))))).((((....)))).....))).....((((((((.....)))))))). ( -23.40)
>DroYak_CAF1 146881 109 + 1
CUCUUGCAAUUGUUUUUUUUUUUUUUUCAAUUGCAACUGCCAAUCUU---UAU----ACCCACAUGGGUGUGCCAAUC----GUUAUCCACUGAUUUAAGACAUAAAUCUGCCUUUCCUA
...(((((((((...............)))))))))..((.......---(((----((((....)))))))......----..........((((((.....)))))).))........ ( -19.66)
>consensus
CUCUUGCAAUUGUUU_________UUUCAAUUGCAACUGGCAAGCUA___UAU__AUACCAACUUGGGUGUGCCACUAUUGAGUGAACCAUUGAUUUAAGAAAUAAAGCCUUUAUUUCUG
...(((((((((...............))))))))).(((((..((....................))..))))).......................((((((((.....)))))))). (-12.50 = -14.06 +   1.56)

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 11:11:01 2006