Locus 3094

Sequence ID X_DroMel_CAF1
Location 8,258,853 – 8,259,029
Length 176
Max. P 0.838703
window5059 window5060 window5061 window5062

overview

Window 9

Location 8,258,853 – 8,258,949
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -21.53
Consensus MFE -17.69
Energy contribution -17.37
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.82
SVM decision value 0.12
SVM RNA-class probability 0.591464
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8258853 96 + 22224390
CUCACUUUGCUUGUGUUUGUUGGUUUCUGCUGGAAAACGAGCAUAAGCAGUUAAUAAUUGGCAGUGAUUGCAAUAAAUGCAAAUAUGUAUUCUUUU
.(((((.((((((((((((((..((((....))))))))))))))))))((((.....)))))))))(((((.....))))).............. ( -27.40)
>DroSec_CAF1 9115 89 + 1
CUCAGUUUGCUUUUGUU---UGGUUUCUGCUGGAAAACGAGCAUAAGCAGUUAAUAAUUGGCAGUGAUUGCAAUAAAUGCAAAU----GUUCUUUU
....((((((.((((((---(((((.((((..(..(((..((....)).))).....)..)))).))))).)))))).))))))----........ ( -19.90)
>DroYak_CAF1 13714 89 + 1
UUCACUUUGCUUUUGUU---UGGUUUUUGCUGGAAAACGGGCAUAAACAGUUAAUAAUUGGCUAUGAUUGCAAUAAAUGCAAAU----AUUCUUUU
.(((....(((.(((((---..((((.((((.(....).)))).))))....)))))..)))..)))(((((.....)))))..----........ ( -17.30)
>consensus
CUCACUUUGCUUUUGUU___UGGUUUCUGCUGGAAAACGAGCAUAAGCAGUUAAUAAUUGGCAGUGAUUGCAAUAAAUGCAAAU____AUUCUUUU
.(((..(((((..((((.....((((.((((.(....).)))).))))....))))...))))))))(((((.....))))).............. (-17.69 = -17.37 +  -0.33)

alignment

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secondary structure

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Window 0

Location 8,258,869 – 8,258,989
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.10
Mean single sequence MFE -25.81
Consensus MFE -18.66
Energy contribution -18.00
Covariance contribution -0.66
Combinations/Pair 1.10
Mean z-score -2.45
Structure conservation index 0.72
SVM decision value 0.32
SVM RNA-class probability 0.685879
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8258869 120 + 22224390
UUGUUGGUUUCUGCUGGAAAACGAGCAUAAGCAGUUAAUAAUUGGCAGUGAUUGCAAUAAAUGCAAAUAUGUAUUCUUUUUUAAAUGGAGCAUGAAAAAAGAAUAUAAGGGGGAAAAUCA
((((..(((.(((((..............))))).....)))..))))((((((((.....))).....(((((((((((((..(((...))).)))))))))))))........))))) ( -25.04)
>DroSec_CAF1 9131 113 + 1
U---UGGUUUCUGCUGGAAAACGAGCAUAAGCAGUUAAUAAUUGGCAGUGAUUGCAAUAAAUGCAAAU----GUUCUUUUUUAAAUGGAGCAUGCAAAAAGAAUAUAAGGGGAGAAAUCA
.---((((((((.((.........((((..(((((((...........))))))).....))))..((----(((((((((...(((...)))..)))))))))))...)).)))))))) ( -25.60)
>DroYak_CAF1 13730 110 + 1
U---UGGUUUUUGCUGGAAAACGGGCAUAAACAGUUAAUAAUUGGCUAUGAUUGCAAUAAAUGCAAAU----AUUCUUUUUUAAAUGGAGCAUGUAAAAAGAAUAUAGGG---GAAACCA
.---..((((.((((.(....).)))).))))(((((.....)))))....(((((.....)))))((----(((((((((...(((...)))..)))))))))))..((---....)). ( -26.80)
>consensus
U___UGGUUUCUGCUGGAAAACGAGCAUAAGCAGUUAAUAAUUGGCAGUGAUUGCAAUAAAUGCAAAU____AUUCUUUUUUAAAUGGAGCAUGAAAAAAGAAUAUAAGGGG_GAAAUCA
......((((.((((.(....).)))).)))).((((.....)))).....(((((.....)))))......(((((((((...(((...)))..)))))))))................ (-18.66 = -18.00 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,258,869 – 8,258,989
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.10
Mean single sequence MFE -16.51
Consensus MFE -11.94
Energy contribution -11.39
Covariance contribution -0.55
Combinations/Pair 1.11
Mean z-score -2.12
Structure conservation index 0.72
SVM decision value 0.00
SVM RNA-class probability 0.534735
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8258869 120 - 22224390
UGAUUUUCCCCCUUAUAUUCUUUUUUCAUGCUCCAUUUAAAAAAGAAUACAUAUUUGCAUUUAUUGCAAUCACUGCCAAUUAUUAACUGCUUAUGCUCGUUUUCCAGCAGAAACCAACAA
(((............(((((((((((.(........).))))))))))).....(((((.....))))))))((((........(((.((....))..))).....)))).......... ( -17.12)
>DroSec_CAF1 9131 113 - 1
UGAUUUCUCCCCUUAUAUUCUUUUUGCAUGCUCCAUUUAAAAAAGAAC----AUUUGCAUUUAUUGCAAUCACUGCCAAUUAUUAACUGCUUAUGCUCGUUUUCCAGCAGAAACCA---A
(((..............((((((((..(((...)))...)))))))).----..(((((.....))))))))((((........(((.((....))..))).....))))......---. ( -14.92)
>DroYak_CAF1 13730 110 - 1
UGGUUUC---CCCUAUAUUCUUUUUACAUGCUCCAUUUAAAAAAGAAU----AUUUGCAUUUAUUGCAAUCAUAGCCAAUUAUUAACUGUUUAUGCCCGUUUUCCAGCAAAAACCA---A
(((((..---....(((((((((((..(((...)))...)))))))))----))(((((.....)))))....)))))..........((((.(((..........))).))))..---. ( -17.50)
>consensus
UGAUUUC_CCCCUUAUAUUCUUUUUACAUGCUCCAUUUAAAAAAGAAU____AUUUGCAUUUAUUGCAAUCACUGCCAAUUAUUAACUGCUUAUGCUCGUUUUCCAGCAGAAACCA___A
(((((............((((((((..(((...)))...)))))))).........(((.....))))))))((((........(((.((....))..))).....)))).......... (-11.94 = -11.39 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,258,909 – 8,259,029
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.33
Mean single sequence MFE -24.12
Consensus MFE -17.37
Energy contribution -16.93
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -3.25
Structure conservation index 0.72
SVM decision value 0.74
SVM RNA-class probability 0.838703
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8258909 120 + 22224390
AUUGGCAGUGAUUGCAAUAAAUGCAAAUAUGUAUUCUUUUUUAAAUGGAGCAUGAAAAAAGAAUAUAAGGGGGAAAAUCAGCAGAGAUUGCAAAUAAAAACUAUAAACAAACCACGGAGU
.......(((.(((((((...(((.....(((((((((((((..(((...))).)))))))))))))..((......)).)))...)))))))(((.....)))........)))..... ( -21.80)
>DroSec_CAF1 9168 116 + 1
AUUGGCAGUGAUUGCAAUAAAUGCAAAU----GUUCUUUUUUAAAUGGAGCAUGCAAAAAGAAUAUAAGGGGAGAAAUCAGCAGAGAUUGCAAAUAAAAACUAUAAACAAACCACGAAAU
.......(((.(((((((...(((..((----(((((((((...(((...)))..))))))))))).....((....)).)))...)))))))(((.....)))........)))..... ( -23.00)
>DroYak_CAF1 13767 113 + 1
AUUGGCUAUGAUUGCAAUAAAUGCAAAU----AUUCUUUUUUAAAUGGAGCAUGUAAAAAGAAUAUAGGG---GAAACCAGCAGAGAUUGCAAAAAAAAACUAUAAACAAAGCACGAAGU
.((((((.((.(((((((...(((..((----(((((((((...(((...)))..)))))))))))..((---....)).)))...)))))))..............)).))).)))... ( -27.56)
>consensus
AUUGGCAGUGAUUGCAAUAAAUGCAAAU____AUUCUUUUUUAAAUGGAGCAUGAAAAAAGAAUAUAAGGGG_GAAAUCAGCAGAGAUUGCAAAUAAAAACUAUAAACAAACCACGAAGU
...........(((((((...(((........(((((((((...(((...)))..)))))))))....((.......)).)))...)))))))........................... (-17.37 = -16.93 +  -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 10:50:50 2006