Locus 856

Sequence ID X_DroMel_CAF1
Location 2,432,712 – 2,432,886
Length 174
Max. P 0.961456
window1377 window1378 window1379

overview

Window 7

Location 2,432,712 – 2,432,809
Length 97
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 80.00
Mean single sequence MFE -17.03
Consensus MFE -14.49
Energy contribution -14.82
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.85
SVM decision value 0.14
SVM RNA-class probability 0.601725
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2432712 97 + 22224390
--ACAAUCGGACCGGAAAUGAUCCC----AAAGAUAACCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGCAAGCCAGCUGGAAACAGCACA--------------U
--....((((...(((.((((((..----...)))....(((.............)))))).)))..))))................((((....))))...--------------. ( -15.92)
>DroSim_CAF1 43908 96 + 1
--ACA-UCGGACCGGAAAUGCCCCC----AAAGAUAACCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA--------------U
--...-((((...(((.((((....----............................)))).)))..))))................((((....))))...--------------. ( -16.55)
>DroEre_CAF1 80486 116 + 1
UUACA-UCGGACUGGAAAUGCCCCCCAAAAAAGAUAACCCAAAACCCGAUUAAUCCUGCAUCUCCCAUCGACUCACAAAGAAAGCAAGCUGGAGACAGCGCAUACAUAUGUACAUAU
.((((-((((...(((.((((....................................)))).)))..))))............((..((((....)))))).......))))..... ( -18.62)
>consensus
__ACA_UCGGACCGGAAAUGCCCCC____AAAGAUAACCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA______________U
......((((...(((.((((....................................)))).)))..))))................((((....)))).................. (-14.49 = -14.82 +   0.33) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,432,743 – 2,432,846
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.05
Mean single sequence MFE -17.45
Consensus MFE -13.97
Energy contribution -13.97
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.80
SVM decision value 1.53
SVM RNA-class probability 0.961456
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2432743 103 + 22224390
CCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGCAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAAUA-CCCCAACAAAAUAUCGCAGU--UCUUAUA
...(((((.(((.((((..(((....................))).....((((....))))...--------------...........-.........)))))))..))--))).... ( -15.45)
>DroSim_CAF1 43938 103 + 1
CCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAUUA-CCCCAACAAAAUAUCGCAGU--UCUAAUC
...(((((.(((.((((.................................((((....))))((.--------------...))......-.........)))))))..))--))).... ( -14.80)
>DroEre_CAF1 80522 120 + 1
CCCAAAACCCGAUUAAUCCUGCAUCUCCCAUCGACUCACAAAGAAAGCAAGCUGGAGACAGCGCAUACAUAUGUACAUAUAUGUAAAUUUCCCCCAACAAAAUAUUGCAGAUAUCUAAUU
..................(((((.......................((..((((....)))))).((((((((....))))))))....................))))).......... ( -22.10)
>consensus
CCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA______________UAUGUAAAUUA_CCCCAACAAAAUAUCGCAGU__UCUAAUA
..................((((............................((((....))))...................(((............))).......)))).......... (-13.97 = -13.97 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 9

Location 2,432,783 – 2,432,886
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.05
Mean single sequence MFE -20.13
Consensus MFE -14.48
Energy contribution -14.03
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.51
Structure conservation index 0.72
SVM decision value 0.00
SVM RNA-class probability 0.534241
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2432783 103 + 22224390
AAGCAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAAUA-CCCCAACAAAAUAUCGCAGU--UCUUAUACCCAAGAUCAUUUUGAACAGAAAGUAAGCUCAUUGUUUUG
((((((((..((((....))))...--------------...........-......(((((((((...((--......))....))).))))))............)))...))))).. ( -17.20)
>DroSim_CAF1 43978 103 + 1
AAGAAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAUUA-CCCCAACAAAAUAUCGCAGU--UCUAAUCCCCAAGAUCAUUUCGAACAGAAAGUAAGCUCAUUGUUUUG
..........((((....))))...--------------...........-......(((((((..((.(.--(((........))).).((((.....))))....))....))))))) ( -16.40)
>DroEre_CAF1 80562 119 + 1
AAGAAAGCAAGCUGGAGACAGCGCAUACAUAUGUACAUAUAUGUAAAUUUCCCCCAACAAAAUAUUGCAGAUAUCUAAUUCCUAAGAUCAUUUCGAACCGAAAGUAAGCUCAUGGUUUU-
..((((((((((((....))))...((((((((....))))))))...................))))....((((........))))..))))((((((..((....))..)))))).- ( -26.80)
>consensus
AAGAAAGCCAGCUGGAAACAGCACA______________UAUGUAAAUUA_CCCCAACAAAAUAUCGCAGU__UCUAAUACCCAAGAUCAUUUCGAACAGAAAGUAAGCUCAUUGUUUUG
......((..((((....))))...................(((............))).......))..........................((((((..((....))..)))))).. (-14.48 = -14.03 +  -0.44) 

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 09:55:23 2006