Locus 5389

Sequence ID 2L_DroMel_CAF1
Location 15,372,076 – 15,372,258
Length 182
Max. P 0.979334
window8552 window8553 window8554

overview

Window 2

Location 15,372,076 – 15,372,196
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -35.95
Consensus MFE -32.96
Energy contribution -33.59
Covariance contribution 0.63
Combinations/Pair 1.07
Mean z-score -1.33
Structure conservation index 0.92
SVM decision value 0.87
SVM RNA-class probability 0.870941
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15372076 120 + 22407834
AAAUGUGUGUCUAUAUGGCCUGCUUAUUACCUAAUUUCAUUGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAU
((((((.((((...((((((.(((((..............)))))..))).))).)))).))))))((((((((((((.(((((((.....))))))).))).)))).))).....)).. ( -39.24)
>DroSec_CAF1 117899 120 + 1
AAAUGUGUGUCUAUAUGGCCAGCUUAUUACCUAAUUUCAUUGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAU
((((((.((((...((((((.(((((..............)))))..))).))).)))).))))))((((((((((((.(((((((.....))))))).))).)))).))).....)).. ( -39.74)
>DroSim_CAF1 122003 120 + 1
AAAUGUGUGUCUAUAUGGCCAGCUUAUUACCUAAUUUCAUUGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAU
((((((.((((...((((((.(((((..............)))))..))).))).)))).))))))((((((((((((.(((((((.....))))))).))).)))).))).....)).. ( -39.74)
>DroEre_CAF1 124088 120 + 1
AAAUGUGUGUCUAUAUGGCUUGCUUAUUACCUAAUUUCAUUGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAU
((((((.((((...((((((.(((((..............)))))..))).))).)))).))))))((((((((((((.(((((((.....))))))).))).)))).))).....)).. ( -37.24)
>DroYak_CAF1 124049 120 + 1
AAAUGUGUGUCUAUAUGGCUUGCUUAUUACCUAAUUUCAUUGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAU
((((((.((((...((((((.(((((..............)))))..))).))).)))).))))))((((((((((((.(((((((.....))))))).))).)))).))).....)).. ( -37.24)
>DroAna_CAF1 125772 107 + 1
AAAUGUGUUUCUAUAUGGCCUGCUUAUUACCUAAUUUCAUUCGGCCCGUUGCAUUGACAGGCGUUUGCUCAUUCGCCCCGU-------------CGAUUGGCUCGGAUUGACUUUGGCAU
..............................((((..((((((((((......((((((.((((..(....)..))))..))-------------)))).))).)))).)))..))))... ( -22.50)
>consensus
AAAUGUGUGUCUAUAUGGCCUGCUUAUUACCUAAUUUCAUUGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAU
((((((.((((...((((((.(((((..............)))))..))).))).)))).))))))((((((((((((.(((((((.....))))))).))).)))).))).....)).. (-32.96 = -33.59 +   0.63)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,372,116 – 15,372,222
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -35.20
Consensus MFE -35.20
Energy contribution -35.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 1.00
SVM decision value 0.63
SVM RNA-class probability 0.804621
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15372116 106 + 22407834
UGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCUUUUUUGCGGCUUUUG
.(((((....((........))....((((((((((((.(((((((.....))))))).))).)))).)))....(((((.....)))))......)))))))... ( -35.20)
>DroSec_CAF1 117939 106 + 1
UGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCUUUUUUGCGGCUUUUG
.(((((....((........))....((((((((((((.(((((((.....))))))).))).)))).)))....(((((.....)))))......)))))))... ( -35.20)
>DroSim_CAF1 122043 106 + 1
UGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCUUUUUUGCGGCUUUUG
.(((((....((........))....((((((((((((.(((((((.....))))))).))).)))).)))....(((((.....)))))......)))))))... ( -35.20)
>DroEre_CAF1 124128 106 + 1
UGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCUUUUUUGCGGCUUUUG
.(((((....((........))....((((((((((((.(((((((.....))))))).))).)))).)))....(((((.....)))))......)))))))... ( -35.20)
>DroYak_CAF1 124089 106 + 1
UGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCUUUUUUGCGGCUUUUG
.(((((....((........))....((((((((((((.(((((((.....))))))).))).)))).)))....(((((.....)))))......)))))))... ( -35.20)
>consensus
UGGGCCCGGUGCAUUGACAGGCGUUUGCUCAUUCGGCUCGUCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCUUUUUUGCGGCUUUUG
.(((((....((........))....((((((((((((.(((((((.....))))))).))).)))).)))....(((((.....)))))......)))))))... (-35.20 = -35.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,372,156 – 15,372,258
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 89.53
Mean single sequence MFE -36.85
Consensus MFE -30.65
Energy contribution -30.92
Covariance contribution 0.27
Combinations/Pair 1.07
Mean z-score -3.27
Structure conservation index 0.83
SVM decision value 1.83
SVM RNA-class probability 0.979334
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15372156 102 + 22407834
UCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCU------UUUUUGC--------GGCUUUUGGCAUUUGGCCGAG-AGCCAAGGGUUAGAGGAUGUUGU
((((((.....))))))(((((((...........(((((.....))))).------.......--------((((((((((.....))))))-))))..))))))).......... ( -38.80)
>DroSec_CAF1 117979 102 + 1
UCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCU------UUUUUGC--------GGCUUUUGGCAUUUGGCCAAG-AGUCAAGGGUUAGAGGAUGUUGU
((((((.....))))))(((((((...........(((((.....))))).------.......--------((((((((((.....))))))-))))..))))))).......... ( -36.40)
>DroSim_CAF1 122083 102 + 1
UCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCU------UUUUUGC--------GGCUUUUGGCAUUUGGCCAAG-AGCCAAGGGUUAGAGGAUGUUGU
((((((.....))))))(((((((...........(((((.....))))).------.......--------((((((((((.....))))))-))))..))))))).......... ( -39.10)
>DroEre_CAF1 124168 102 + 1
UCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCU------UUUUUGC--------GGCUUUUGGCAUUUGGCCGAG-AGCCAAGGGUUAGAGGAUGUUGU
((((((.....))))))(((((((...........(((((.....))))).------.......--------((((((((((.....))))))-))))..))))))).......... ( -38.80)
>DroYak_CAF1 124129 102 + 1
UCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCU------UUUUUGC--------GGCUUUUGGCAUUUGGCCGAG-AGCCAAGGGUUAGAGGAUGUUGU
((((((.....))))))(((((((...........(((((.....))))).------.......--------((((((((((.....))))))-))))..))))))).......... ( -38.80)
>DroAna_CAF1 125852 104 + 1
U-------------CGAUUGGCUCGGAUUGACUUUGGCAUUUUAAGUGCCUGUUUUUUUUUUGCUGUUGUUUGGCUUUUGCCAUUUGGCCGAGAAGCCAAGGGUUAGAGGAUAUUGU
(-------------(..((((((((((..(((...(((((.....))))).)))..)))...........((((((((((((....)))..))))))))))))))))..))...... ( -29.20)
>consensus
UCGGCCAACUUGGUCGAUUGGCUCGAAUUGACUUUGGCAUUUUAAGUGCCU______UUUUUGC________GGCUUUUGGCAUUUGGCCGAG_AGCCAAGGGUUAGAGGAUGUUGU
((((((.....))))))(((((((...........(((((.....)))))......................((((((((((.....)))))).))))..))))))).......... (-30.65 = -30.92 +   0.27)

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 11:42:56 2006