Locus 262

Sequence ID X_DroMel_CAF1
Location 866,421 – 866,598
Length 177
Max. P 0.999999
window396 window397 window398 window399 window400 window401

overview

Window 6

Location 866,421 – 866,522
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.16
Mean single sequence MFE -18.41
Consensus MFE -11.13
Energy contribution -11.47
Covariance contribution 0.34
Combinations/Pair 1.14
Mean z-score -1.25
Structure conservation index 0.60
SVM decision value -0.04
SVM RNA-class probability 0.511346
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 866421 101 + 22224390
ACGCACACAGCGAAAUUUUCGUUUUGAGUGAGUUUUU--U-GCAUUCCUACUGAGUUUUACUCUGAUUUUA---------------UUCUGCACAAUAAACUCACUCAC-UUGAGUUUGA
.(((.....))).....((((...(((((((((((..--(-(((........(((.....))).((.....---------------.))))))....))))))))))).-.))))..... ( -25.20)
>DroEre_CAF1 72870 117 + 1
ACGC---CAGCGAAAUAUUUGUUUUGAGUGAGUUUUUGUUAGAUAUUAUACUGAGUUUUACUCUAUUUUUUAUUUCUUUGUUUUUUUUUUGCACCAACAACCCACUCACAUUGAGUUUGA
..((---(((((((((....)))))).((((((..((((((((((.......(((.....))).......)))))...(((.........)))..)))))...)))))).))).)).... ( -15.54)
>DroYak_CAF1 69077 94 + 1
ACGC---CAGCGAAGUAUUUGUUUUGAGUGAGUUUUU--UCACUAUUCAACUGAGUUUUACUCUAUUUUUAAUUUUUU---------------------ACUUACUCACUUUGAGUUUGA
.((.---...))(((((...(((...((((((....)--)))))....))).(((.....)))..............)---------------------))))((((.....)))).... ( -14.50)
>consensus
ACGC___CAGCGAAAUAUUUGUUUUGAGUGAGUUUUU__U_GCUAUUCUACUGAGUUUUACUCUAUUUUUAAUUU_UU________UU_UGCAC_A__AACUCACUCAC_UUGAGUUUGA
.(((.....))).....((((...((((((((((..................(((.....)))((....))...........................))))))))))...))))..... (-11.13 = -11.47 +   0.34)

alignment

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secondary structure

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dotplot

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Window 7

Location 866,421 – 866,522
Length 101
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.16
Mean single sequence MFE -20.27
Consensus MFE -13.37
Energy contribution -13.60
Covariance contribution 0.23
Combinations/Pair 1.12
Mean z-score -2.61
Structure conservation index 0.66
SVM decision value 5.64
SVM RNA-class probability 0.999991
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 866421 101 - 22224390
UCAAACUCAA-GUGAGUGAGUUUAUUGUGCAGAA---------------UAAAAUCAGAGUAAAACUCAGUAGGAAUGC-A--AAAAACUCACUCAAAACGAAAAUUUCGCUGUGUGCGU
..........-.(((((((((((....((((((.---------------.....)).(((.....)))........)))-)--..)))))))))))............(((.....))). ( -25.00)
>DroEre_CAF1 72870 117 - 1
UCAAACUCAAUGUGAGUGGGUUGUUGGUGCAAAAAAAAAACAAAGAAAUAAAAAAUAGAGUAAAACUCAGUAUAAUAUCUAACAAAAACUCACUCAAAACAAAUAUUUCGCUG---GCGU
............(((((((((((((((................(....)........(((.....)))..........))))))...))))))))).................---.... ( -18.10)
>DroYak_CAF1 69077 94 - 1
UCAAACUCAAAGUGAGUAAGU---------------------AAAAAAUUAAAAAUAGAGUAAAACUCAGUUGAAUAGUGA--AAAAACUCACUCAAAACAAAUACUUCGCUG---GCGU
...........((.(((((((---------------------(..............(((.....))).(((....(((((--......)))))...)))...))))).))).---)).. ( -17.70)
>consensus
UCAAACUCAA_GUGAGUGAGUU__U_GUGCA_AA________AA_AAAUUAAAAAUAGAGUAAAACUCAGUAGAAUAGC_A__AAAAACUCACUCAAAACAAAUAUUUCGCUG___GCGU
............((((((((((...................................(((.....))).(........).......))))))))))............(((.....))). (-13.37 = -13.60 +   0.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 866,459 – 866,560
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.74
Mean single sequence MFE -17.40
Consensus MFE -13.88
Energy contribution -14.32
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -2.79
Structure conservation index 0.80
SVM decision value 6.16
SVM RNA-class probability 0.999997
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 866459 101 + 22224390
-GCAUUCCUACUGAGUUUUACUCUGAUUUUA---------------UUCUGCACAAUAAACUCACUCAC-UUGAGUUUGAGUAAGUCCCAAA-AUUUCCCCUUCUU-UUAGGACAAUUUU
-(((........(((.....))).((.....---------------.)))))....((((((((.....-.)))))))).....((((.(((-(..........))-)).))))...... ( -16.30)
>DroEre_CAF1 72907 120 + 1
AGAUAUUAUACUGAGUUUUACUCUAUUUUUUAUUUCUUUGUUUUUUUUUUGCACCAACAACCCACUCACAUUGAGUUUGAGUACGUCCCAAAAAUUUCCCCUCCCUCUUGGGACAAUUUU
..................(((((..............(((((.............)))))...((((.....))))..))))).(((((((................)))))))...... ( -16.91)
>DroYak_CAF1 69112 99 + 1
CACUAUUCAACUGAGUUUUACUCUAUUUUUAAUUUUUU---------------------ACUUACUCACUUUGAGUUUGAGUAAGUCCCAAAAAUUUCCCCUCCUUCUUGGGACAAUUUU
...(((((((..(((.....)))...............---------------------....((((.....))))))))))).(((((((................)))))))...... ( -18.99)
>consensus
_GCUAUUCUACUGAGUUUUACUCUAUUUUUAAUUU_UU________UU_UGCAC_A__AACUCACUCAC_UUGAGUUUGAGUAAGUCCCAAAAAUUUCCCCUCCUUCUUGGGACAAUUUU
............(((.....)))....................................((((((((.....))))..))))..(((((((................)))))))...... (-13.88 = -14.32 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 866,459 – 866,560
Length 101
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.74
Mean single sequence MFE -23.30
Consensus MFE -18.65
Energy contribution -18.77
Covariance contribution 0.12
Combinations/Pair 1.14
Mean z-score -3.03
Structure conservation index 0.80
SVM decision value 6.54
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 866459 101 - 22224390
AAAAUUGUCCUAA-AAGAAGGGGAAAU-UUUGGGACUUACUCAAACUCAA-GUGAGUGAGUUUAUUGUGCAGAA---------------UAAAAUCAGAGUAAAACUCAGUAGGAAUGC-
......(((((((-((..........)-))))))))((((((..((((..-..))))((.((((((......))---------------)))).)).))))))................- ( -22.30)
>DroEre_CAF1 72907 120 - 1
AAAAUUGUCCCAAGAGGGAGGGGAAAUUUUUGGGACGUACUCAAACUCAAUGUGAGUGGGUUGUUGGUGCAAAAAAAAAACAAAGAAAUAAAAAAUAGAGUAAAACUCAGUAUAAUAUCU
......((((((((((..........))))))))))(((((..((((((.......))))))...)))))...........................(((.....)))............ ( -25.90)
>DroYak_CAF1 69112 99 - 1
AAAAUUGUCCCAAGAAGGAGGGGAAAUUUUUGGGACUUACUCAAACUCAAAGUGAGUAAGU---------------------AAAAAAUUAAAAAUAGAGUAAAACUCAGUUGAAUAGUG
......((((((((((..........))))))))))(((((...((((.....)))).)))---------------------))...((((..(((.(((.....))).)))...)))). ( -21.70)
>consensus
AAAAUUGUCCCAAGAAGGAGGGGAAAUUUUUGGGACUUACUCAAACUCAA_GUGAGUGAGUU__U_GUGCA_AA________AA_AAAUUAAAAAUAGAGUAAAACUCAGUAGAAUAGC_
......((((((((((..........))))))))))(((((...((((.....))))........................................(((.....))))))))....... (-18.65 = -18.77 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 866,489 – 866,598
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.28
Mean single sequence MFE -23.73
Consensus MFE -14.42
Energy contribution -14.53
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -2.35
Structure conservation index 0.61
SVM decision value 2.27
SVM RNA-class probability 0.991395
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 866489 109 + 22224390
------UUCUGCACAAUAAACUCACUCAC-UUGAGUUUGAGUAAGUCCCAAA-AUUUCCCCUUCUU-UUAGGACAAUUUUUUUGCAGACGAAACUUAAAACGUUGGGAAAUUCCAGCU--
------.((((((...((((((((.....-.)))))))).....((((.(((-(..........))-)).))))........)))))).............((((((....)))))).-- ( -26.30)
>DroEre_CAF1 72947 120 + 1
UUUUUUUUUUGCACCAACAACCCACUCACAUUGAGUUUGAGUACGUCCCAAAAAUUUCCCCUCCCUCUUGGGACAAUUUUUUUGCAGACACAAAUUAAAACACAGGGAAAUUUCUGCUUU
..........(((....(((...((((.....)))))))............(((((((((.((((....))))...((..((((......))))..))......))))))))).)))... ( -21.30)
>DroYak_CAF1 69150 99 + 1
-------------------ACUUACUCACUUUGAGUUUGAGUAAGUCCCAAAAAUUUCCCCUCCUUCUUGGGACAAUUUUUUGGCGGACGCAAAUGAAAACAUUGGGAAAUUCCUGCU--
-------------------(((((((((.........)))))))))..((..((((((((.((((....))))...(((((..((....))....)))))....))))))))..))..-- ( -23.60)
>consensus
______UU_UGCAC_A__AACUCACUCAC_UUGAGUUUGAGUAAGUCCCAAAAAUUUCCCCUCCUUCUUGGGACAAUUUUUUUGCAGACGCAAAUUAAAACAUUGGGAAAUUCCUGCU__
...................((((((((.....))))..))))..........((((((((.((((....))))(((.....)))....................))))))))........ (-14.42 = -14.53 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 866,489 – 866,598
Length 109
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.28
Mean single sequence MFE -30.30
Consensus MFE -22.08
Energy contribution -23.87
Covariance contribution 1.79
Combinations/Pair 1.13
Mean z-score -2.70
Structure conservation index 0.73
SVM decision value 4.15
SVM RNA-class probability 0.999815
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 866489 109 - 22224390
--AGCUGGAAUUUCCCAACGUUUUAAGUUUCGUCUGCAAAAAAAUUGUCCUAA-AAGAAGGGGAAAU-UUUGGGACUUACUCAAACUCAA-GUGAGUGAGUUUAUUGUGCAGAA------
--.(.(((......))).).............((((((..((((((.((((..-......)))))))-))).(((((((((((.......-.)))))))))))....)))))).------ ( -28.40)
>DroEre_CAF1 72947 120 - 1
AAAGCAGAAAUUUCCCUGUGUUUUAAUUUGUGUCUGCAAAAAAAUUGUCCCAAGAGGGAGGGGAAAUUUUUGGGACGUACUCAAACUCAAUGUGAGUGGGUUGUUGGUGCAAAAAAAAAA
....(((((((((((((.........(((((....))))).......((((....)))))))))))))))))....(((((..((((((.......))))))...))))).......... ( -35.10)
>DroYak_CAF1 69150 99 - 1
--AGCAGGAAUUUCCCAAUGUUUUCAUUUGCGUCCGCCAAAAAAUUGUCCCAAGAAGGAGGGGAAAUUUUUGGGACUUACUCAAACUCAAAGUGAGUAAGU-------------------
--..((((((((((((.............((....))..........(((......))).))))))))))))..(((((((((.........)))))))))------------------- ( -27.40)
>consensus
__AGCAGGAAUUUCCCAAUGUUUUAAUUUGCGUCUGCAAAAAAAUUGUCCCAAGAAGGAGGGGAAAUUUUUGGGACUUACUCAAACUCAA_GUGAGUGAGUU__U_GUGCA_AA______
....((((((((((((...........((((....))))........((((....)))).)))))))))))).((((((((((.........)))))))))).................. (-22.08 = -23.87 +   1.79)

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 09:40:19 2006