Locus 1449

Sequence ID 2L_DroMel_CAF1
Location 3,846,068 – 3,846,200
Length 132
Max. P 0.998649
window2356 window2357 window2358 window2359

overview

Window 6

Location 3,846,068 – 3,846,174
Length 106
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 77.30
Mean single sequence MFE -28.08
Consensus MFE -19.91
Energy contribution -20.80
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -2.16
Structure conservation index 0.71
SVM decision value 1.84
SVM RNA-class probability 0.979508
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3846068 106 + 22407834
UUGCCCGCAAACGAAUA------CGCGAAUUUGCGAGCUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCA-UUCGAGUCGAUAGCUCC-
..((.((((((((....------..))..)))))).))....((((((((((((((((....((....))....)))))...)))))))))))..-...((((.....)))).- ( -32.10)
>DroSec_CAF1 34862 106 + 1
UAGCCCACAAUCGAAUA------CGCGAAUUUGCGAGCUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCA-UUCGAGUCGGUAGCUCG-
..(((.((..((((((.------((((....)))).......((((((((((((((((....((....))....)))))...))))))))))).)-))))))).)))......- ( -33.10)
>DroSim_CAF1 34165 106 + 1
UUGCCAACAAUCGAAUA------CGCGAAUUUGCGAGCUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCA-UUCGAGUCGAUAGCUCG-
..((......((((((.------((((....)))).......((((((((((((((((....((....))....)))))...))))))))))).)-))))).......))...- ( -30.72)
>DroWil_CAF1 65436 94 + 1
UUGCCG-GAAUCGAA-------A------GAUUCGA----AACUUCUCAAUUGAAUGCUCUACCUUUUGGCUUUGGGUUUUCCACUUGAGUUGCAAUUUGAUUCAA--ACUCCU
((((..-(((((...-------.------)))))..----.....(((((..(((.((((..((....))....)))).)))...)))))..))))..........--...... ( -21.10)
>DroYak_CAF1 36768 93 + 1
-------------AAUAUCCAAA------UUUGCGAGCUUAACAACUCAACUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCA-UUCGAUGCGGUAGCUCG-
-------------..........------....((((((...((((((((..((((((....((....))....)))))).....)))))))(((-(...)))))..))))))- ( -23.40)
>consensus
UUGCCC_CAAUCGAAUA______CGCGAAUUUGCGAGCUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCA_UUCGAGUCGAUAGCUCG_
..................................(((((...((((((((((((((((....((....))....)))))...)))))))))))....(((...))).))))).. (-19.91 = -20.80 +   0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,846,068 – 3,846,174
Length 106
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 77.30
Mean single sequence MFE -32.02
Consensus MFE -21.37
Energy contribution -22.50
Covariance contribution 1.13
Combinations/Pair 1.04
Mean z-score -2.92
Structure conservation index 0.67
SVM decision value 3.17
SVM RNA-class probability 0.998649
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3846068 106 - 22407834
-GGAGCUAUCGACUCGAA-UGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAGCUCGCAAAUUCGCG------UAUUCGUUUGCGGGCAA
-.((((....).)))...-..(((((((((((((....((...(((....)))...)).)))))))))))))....((((((((....(((------....))))))))))).. ( -38.20)
>DroSec_CAF1 34862 106 - 1
-CGAGCUACCGACUCGAA-UGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAGCUCGCAAAUUCGCG------UAUUCGAUUGUGGGCUA
-(((((....).))))..-..(((((((((((((....((...(((....)))...)).)))))))))))))...(((((((((..(((..------....)))))))))))). ( -38.70)
>DroSim_CAF1 34165 106 - 1
-CGAGCUAUCGACUCGAA-UGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAGCUCGCAAAUUCGCG------UAUUCGAUUGUUGGCAA
-...((((.(((.(((((-(((((((((((((((....((...(((....)))...)).)))))))))))).........((......)))------)))))))))).)))).. ( -38.80)
>DroWil_CAF1 65436 94 - 1
AGGAGU--UUGAAUCAAAUUGCAACUCAAGUGGAAAACCCAAAGCCAAAAGGUAGAGCAUUCAAUUGAGAAGUU----UCGAAUC------U-------UUCGAUUC-CGGCAA
.(((((--(.((.(((((((....(((((.(((.....)))..(((....)))...........))))).))))----).)).))------.-------...)))))-)..... ( -17.40)
>DroYak_CAF1 36768 93 - 1
-CGAGCUACCGCAUCGAA-UGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCAGUUGAGUUGUUAAGCUCGCAAA------UUUGGAUAUU-------------
-((((((...((((...)-)))(((((((.((((....((...(((....)))...)).)))).)))))))....))))))....------..........------------- ( -27.00)
>consensus
_CGAGCUAUCGACUCGAA_UGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAGCUCGCAAAUUCGCG______UAUUCGAUUG_GGGCAA
..(((((..((...)).....(((((((((((((....((...(((....)))...)).)))))))))))))...))))).................................. (-21.37 = -22.50 +   1.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,846,099 – 3,846,200
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 88.71
Mean single sequence MFE -20.79
Consensus MFE -17.26
Energy contribution -18.76
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.83
SVM decision value 2.74
SVM RNA-class probability 0.996708
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3846099 101 + 22407834
CUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCAUUCGAGUCGAUAGCUCCCUCUCUUUCACACCUGUUCUACCUUU
.....((((((((((((((((....((....))....)))))...))))))))))).....((((.....))))........................... ( -23.10)
>DroSec_CAF1 34893 101 + 1
CUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCAUUCGAGUCGGUAGCUCGUUCUCUUUCACACCUGUUCUACCUCU
.....((((((((((((((((....((....))....)))))...)))))))))))..........(((((..((..............))..)))))... ( -25.34)
>DroSim_CAF1 34196 101 + 1
CUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCAUUCGAGUCGAUAGCUCGUUCUCUUUCACACCUGUUCUACCUCU
.....((((((((((((((((....((....))....)))))...)))))))))))....(((((.....))))).......................... ( -25.10)
>DroEre_CAF1 39841 88 + 1
CUCAUCAACUCAACUGAAUGCUCUA-------------CGUUUUCCACUUGAGUUGCAUUCGAUUCGCUAGCUCGUUCUCUUUCACACCUGUUCUACCUUU
.....((((((((..(((.((....-------------.)).)))...))))))))............................................. ( -10.10)
>DroYak_CAF1 36786 101 + 1
CUUAACAACUCAACUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCAUUCGAUGCGGUAGCUCGUACUUUUUCAUACCUGUUCUACCUUU
.....((((((((..((((((....((....))....)))))).....))))))))..........(((((..((((........)))..)..)))))... ( -20.30)
>consensus
CUUAUCAACUCAAGUGAAUGCCCUACCUUUUGGCUUUGCGUUUUCCACUUGAGUUGCAUUCGAGUCGAUAGCUCGUUCUCUUUCACACCUGUUCUACCUUU
.....((((((((((((((((....((....))....)))))...)))))))))))....(((((.....))))).......................... (-17.26 = -18.76 +   1.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,846,099 – 3,846,200
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 88.71
Mean single sequence MFE -25.96
Consensus MFE -21.67
Energy contribution -22.45
Covariance contribution 0.78
Combinations/Pair 1.08
Mean z-score -2.92
Structure conservation index 0.83
SVM decision value 3.16
SVM RNA-class probability 0.998620
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3846099 101 - 22407834
AAAGGUAGAACAGGUGUGAAAGAGAGGGAGCUAUCGACUCGAAUGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAG
...(((((..(.....(....).....)..)))))..........(((((((((((((....((...(((....)))...)).)))))))))))))..... ( -27.00)
>DroSec_CAF1 34893 101 - 1
AGAGGUAGAACAGGUGUGAAAGAGAACGAGCUACCGACUCGAAUGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAG
...(((((......(((........)))..)))))..........(((((((((((((....((...(((....)))...)).)))))))))))))..... ( -30.10)
>DroSim_CAF1 34196 101 - 1
AGAGGUAGAACAGGUGUGAAAGAGAACGAGCUAUCGACUCGAAUGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAG
.(((...((.....(((........))).....))..))).....(((((((((((((....((...(((....)))...)).)))))))))))))..... ( -28.00)
>DroEre_CAF1 39841 88 - 1
AAAGGUAGAACAGGUGUGAAAGAGAACGAGCUAGCGAAUCGAAUGCAACUCAAGUGGAAAACG-------------UAGAGCAUUCAGUUGAGUUGAUGAG
...(.(((......(((........)))..))).)...(((....((((((((.((((.....-------------.......)))).)))))))).))). ( -16.00)
>DroYak_CAF1 36786 101 - 1
AAAGGUAGAACAGGUAUGAAAAAGUACGAGCUACCGCAUCGAAUGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCAGUUGAGUUGUUAAG
...(((((.....((((......))))...))))).........(((((((((.((((....((...(((....)))...)).)))).))))))))).... ( -28.70)
>consensus
AAAGGUAGAACAGGUGUGAAAGAGAACGAGCUACCGACUCGAAUGCAACUCAAGUGGAAAACGCAAAGCCAAAAGGUAGGGCAUUCACUUGAGUUGAUAAG
...(((((........(....)........)))))..........(((((((((((((....((...(((....)))...)).)))))))))))))..... (-21.67 = -22.45 +   0.78)

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 10:02:56 2006