Locus 7556

Sequence ID X_DroMel_CAF1
Location 18,827,087 – 18,827,362
Length 275
Max. P 0.999986
window12394 window12395 window12396 window12397 window12398 window12399

overview

Window 4

Location 18,827,087 – 18,827,202
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 65.50
Mean single sequence MFE -26.47
Consensus MFE -17.94
Energy contribution -16.83
Covariance contribution -1.10
Combinations/Pair 1.24
Mean z-score -1.50
Structure conservation index 0.68
SVM decision value 2.55
SVM RNA-class probability 0.995188
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18827087 115 + 22224390
CUUAGUUUUCAACUUUAACUAGCAGUGACUAUAAGGAAGCAUGAAAAAAGGUGAAAUUCCUCGCAGUGUAAGUGAGUCUCUUCGCUGGCCAUUUUAGCCCGCAAAUGGGUUUCCU
..(((((.....((......))....)))))..(((((((.........((((((....(((((.......)))))....))))))..((((((........))))))))))))) ( -25.60)
>DroSec_CAF1 63926 95 + 1
CUUACUUUUC---UUACAGUUACAGUUUCU-----------------UAGGCGAAAUUUCUCGCAGUGUGAGUGAGUCCAUUCGCUGGCCAUUUUAGCCCGCAAAUGGGUUUCCU
(((((((...---.(((.((...((((((.-----------------.....))))))....)).))).)))))))((((((.((.(((.......))).)).))))))...... ( -22.90)
>DroEre_CAF1 61778 92 + 1
AUUUCU-----------------------UGUAAGGAAAUAUGAAAAUAGGCAAAGUUUCUCGCAGUGUGAGUGAGUCCAUUUGUUGGCCAUUUUGGCCCGCAAAUGGGUUUCCU
......-----------------------....(((((((...................(((((.......))))).((((((((.((((.....)))).))))))))))))))) ( -30.90)
>consensus
CUUACUUUUC___UU__A_U__CAGU__CU_UAAGGAA__AUGAAAAUAGGCGAAAUUUCUCGCAGUGUGAGUGAGUCCAUUCGCUGGCCAUUUUAGCCCGCAAAUGGGUUUCCU
.................................................((((((....(((((.......)))))....)))))).........((((((....)))))).... (-17.94 = -16.83 +  -1.10)

alignment

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secondary structure

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Window 5

Location 18,827,087 – 18,827,202
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 65.50
Mean single sequence MFE -24.67
Consensus MFE -19.91
Energy contribution -20.47
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -2.06
Structure conservation index 0.81
SVM decision value 5.43
SVM RNA-class probability 0.999986
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18827087 115 - 22224390
AGGAAACCCAUUUGCGGGCUAAAAUGGCCAGCGAAGAGACUCACUUACACUGCGAGGAAUUUCACCUUUUUUCAUGCUUCCUUAUAGUCACUGCUAGUUAAAGUUGAAAACUAAG
(((.......(((((.((((.....)))).)))))((((.((.(((.......))))).)))).))).((((((.((((.....((((....))))....))))))))))..... ( -23.90)
>DroSec_CAF1 63926 95 - 1
AGGAAACCCAUUUGCGGGCUAAAAUGGCCAGCGAAUGGACUCACUCACACUGCGAGAAAUUUCGCCUA-----------------AGAAACUGUAACUGUAA---GAAAAGUAAG
.(....)((((((((.((((.....)))).)))))))).............(((((....)))))...-----------------..........(((....---....)))... ( -23.90)
>DroEre_CAF1 61778 92 - 1
AGGAAACCCAUUUGCGGGCCAAAAUGGCCAACAAAUGGACUCACUCACACUGCGAGAAACUUUGCCUAUUUUCAUAUUUCCUUACA-----------------------AGAAAU
((((((.(((((((..((((.....))))..))))))).(((.(.......).)))....................))))))....-----------------------...... ( -26.20)
>consensus
AGGAAACCCAUUUGCGGGCUAAAAUGGCCAGCGAAUGGACUCACUCACACUGCGAGAAAUUUCGCCUAUUUUCAU__UUCCUUA_AG__ACUG__A_U__AA___GAAAAGUAAG
(((....((((((((.((((.....)))).)))))))).(((.(.......).)))........)))................................................ (-19.91 = -20.47 +   0.56)

alignment

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secondary structure

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Window 6

Location 18,827,127 – 18,827,220
Length 93
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 87.10
Mean single sequence MFE -27.59
Consensus MFE -25.93
Energy contribution -24.82
Covariance contribution -1.10
Combinations/Pair 1.18
Mean z-score -0.93
Structure conservation index 0.94
SVM decision value -0.06
SVM RNA-class probability 0.505383
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18827127 93 + 22224390
AUGAAAAAAGGUGAAAUUCCUCGCAGUGUAAGUGAGUCUCUUCGCUGGCCAUUUUAGCCCGCAAAUGGGUUUCCUCGUUUCCUUGGCCGCGUG
.........((((((....(((((.......)))))....))))))(((((....((((((....))))))............)))))..... ( -24.19)
>DroSec_CAF1 63953 86 + 1
-------UAGGCGAAAUUUCUCGCAGUGUGAGUGAGUCCAUUCGCUGGCCAUUUUAGCCCGCAAAUGGGUUUCCUCGUUUCCUUGGCCGCGUG
-------..((((((....(((((.......)))))....))))))(((((....((((((....))))))............)))))..... ( -26.79)
>DroEre_CAF1 61795 93 + 1
AUGAAAAUAGGCAAAGUUUCUCGCAGUGUGAGUGAGUCCAUUUGUUGGCCAUUUUGGCCCGCAAAUGGGUUUCCUCGUUUCCUUGGCCGCGUG
.........(((.(((...(((((...))))).((((((((((((.((((.....)))).)))))))))....))).....))).)))..... ( -31.80)
>consensus
AUGAAAAUAGGCGAAAUUUCUCGCAGUGUGAGUGAGUCCAUUCGCUGGCCAUUUUAGCCCGCAAAUGGGUUUCCUCGUUUCCUUGGCCGCGUG
.........((((((....(((((.......)))))....))))))(((((....((((((....))))))............)))))..... (-25.93 = -24.82 +  -1.10)

alignment

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secondary structure

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Window 7

Location 18,827,127 – 18,827,220
Length 93
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 87.10
Mean single sequence MFE -28.80
Consensus MFE -27.29
Energy contribution -27.63
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -2.63
Structure conservation index 0.95
SVM decision value 2.17
SVM RNA-class probability 0.989555
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18827127 93 - 22224390
CACGCGGCCAAGGAAACGAGGAAACCCAUUUGCGGGCUAAAAUGGCCAGCGAAGAGACUCACUUACACUGCGAGGAAUUUCACCUUUUUUCAU
...((((....(....)(((........(((((.((((.....)))).)))))....))).......))))((((((........)))))).. ( -23.70)
>DroSec_CAF1 63953 86 - 1
CACGCGGCCAAGGAAACGAGGAAACCCAUUUGCGGGCUAAAAUGGCCAGCGAAUGGACUCACUCACACUGCGAGAAAUUUCGCCUA-------
..(((((....(....)(((((...((((((((.((((.....)))).))))))))..)).)))...)))))..............------- ( -31.10)
>DroEre_CAF1 61795 93 - 1
CACGCGGCCAAGGAAACGAGGAAACCCAUUUGCGGGCCAAAAUGGCCAACAAAUGGACUCACUCACACUGCGAGAAACUUUGCCUAUUUUCAU
..(((((....(....)(((((...(((((((..((((.....))))..)))))))..)).)))...)))))..................... ( -31.60)
>consensus
CACGCGGCCAAGGAAACGAGGAAACCCAUUUGCGGGCUAAAAUGGCCAGCGAAUGGACUCACUCACACUGCGAGAAAUUUCGCCUAUUUUCAU
..(((((....(....)(((((...((((((((.((((.....)))).))))))))..)).)))...)))))..................... (-27.29 = -27.63 +   0.34)

alignment

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secondary structure

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Window 8

Location 18,827,220 – 18,827,322
Length 102
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 97.39
Mean single sequence MFE -37.60
Consensus MFE -36.81
Energy contribution -37.03
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.98
SVM decision value 1.54
SVM RNA-class probability 0.962599
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18827220 102 - 22224390
CUUGCGUGCCUCUUGCGGGAAUGGCUGUUGGCGGUUUCGCUUUCAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAAAGCCGGCACCUGCCAGAGAGCA
......(((((((.(((((..(((((.....((((((.(((((((((((...........))).))))))))))))))..)))))...))))).)))).))) ( -40.10)
>DroSec_CAF1 64039 102 - 1
CUUGCGUGCCUCUUGCGGGAAUGGCUGUUGGCGGUUUCGCUUUCAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAAAGCCGGCACCUGCCAGAGAGCA
......(((((((.(((((..(((((.....((((((.(((((((((((...........))).))))))))))))))..)))))...))))).)))).))) ( -40.10)
>DroEre_CAF1 61888 102 - 1
CUUGCGUGCCACUUGCGGCAACGGCUGUUGGCGGUUUCGCUUUUAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAAAGCCGGCACCUGCCAGAGAGCA
....((((((......))).)))(((.((((((((.(((((((((..((((..(((((((...)))))))..)))))))))).))).))).)))))..))). ( -32.60)
>consensus
CUUGCGUGCCUCUUGCGGGAAUGGCUGUUGGCGGUUUCGCUUUCAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAAAGCCGGCACCUGCCAGAGAGCA
......(((((((.(((((..(((((.....((((((.(((((((((((...........))).))))))))))))))..)))))...))))).)))).))) (-36.81 = -37.03 +   0.23)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,827,242 – 18,827,362
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -34.57
Consensus MFE -29.63
Energy contribution -29.63
Covariance contribution 0.01
Combinations/Pair 1.09
Mean z-score -1.70
Structure conservation index 0.86
SVM decision value -0.04
SVM RNA-class probability 0.513170
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18827242 120 - 22224390
CCCCCCCCCCCCAUCAAAUCCAUCAGCCGUCCCUGUCGCACUUGCGUGCCUCUUGCGGGAAUGGCUGUUGGCGGUUUCGCUUUCAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAA
...................(((.(((((((.(((((.((((....)))).....))))).))))))).)))((((((.(((((((((((...........))).)))))))))))))).. ( -40.50)
>DroSec_CAF1 64061 120 - 1
CAAAAGCCCCCCAUCCCAUUCAUCAGCUCUCCCUGUCGCACUUGCGUGCCUCUUGCGGGAAUGGCUGUUGGCGGUUUCGCUUUCAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAA
...................(((.(((((.((((.(..((((....))))..)....))))..))))).)))((((((.(((((((((((...........))).)))))))))))))).. ( -33.70)
>DroEre_CAF1 61910 118 - 1
CAAAAG--CCCCAUCCCAUCCAUCACCUCUCCCUGUCGCUCUUGCGUGCCACUUGCGGCAACGGCUGUUGGCGGUUUCGCUUUUAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAA
((((((--(((((...((.((...............(((....)))((((......))))..)).)).))).))))).(((((((((((...........))).))))))))...))).. ( -29.50)
>consensus
CAAAAGCCCCCCAUCCCAUCCAUCAGCUCUCCCUGUCGCACUUGCGUGCCUCUUGCGGGAAUGGCUGUUGGCGGUUUCGCUUUCAGCGUUUUAUUUCAAUGCGAUUGAAAGCAAAUUGAA
...................(((.(((((.((((...(((....))).((.....))))))..))))).)))((((((.(((((((((((...........))).)))))))))))))).. (-29.63 = -29.63 +   0.01)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:54 2006