Locus 1032

Sequence ID X_DroMel_CAF1
Location 3,017,291 – 3,017,465
Length 174
Max. P 0.999969
window1668 window1669 window1670 window1671 window1672

overview

Window 8

Location 3,017,291 – 3,017,391
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 95.20
Mean single sequence MFE -24.82
Consensus MFE -24.06
Energy contribution -24.26
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.14
Structure conservation index 0.97
SVM decision value 0.49
SVM RNA-class probability 0.755269
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3017291 100 + 22224390
-GCUUUCUGGCUCAUUAGAAUUUUUGAUUGGUCGCAAUUAAAAGGCCAGACGACGAAUAUAUAGCGAAGCUUAUCAAAUUGUUUUAGCUACCCUCGCUGCA
-((..((((((((....)).((((((((((....))))))))))))))))............(((((((((...(.....)....))))....))))))). ( -24.50)
>DroSec_CAF1 5002 99 + 1
-GCUUUCUGGCUCAUUAGAAUUUUUGAUUGGUCGCAAUUAAAAGGCCAGACGAAG-AUAGAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCA
-((..((((((((....)).((((((((((....))))))))))))))))....(-(..(.(((((((((..........))))).)))))..))...)). ( -25.10)
>DroSim_CAF1 5229 99 + 1
-GCUUUCUGGCUCAUUAGAAUUUUUGAUUGGUCGCAAUUAAAAGGCCAGACGAAG-AUACAGAGCGAAGCUUAUCAAAUUGUUUUUGCUCCCCUCGCUGCA
-((..((((((((....)).((((((((((....)))))))))))))))).....-.....(((((((((..........).))))))))........)). ( -23.90)
>DroEre_CAF1 5255 100 + 1
UGCUUUCUGGCUCAUUAGAAUUUUUGAUUGGACGCAAUUAAAAGGCCAGACGAAG-UUGCAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCA
.((((((((((((....)).((((((((((....))))))))))))))))..)))-)((((..((((((((...(.....)....))))....)))))))) ( -25.60)
>DroYak_CAF1 5182 100 + 1
CGCUUUCUGGCUCAUUAGAAUUUUUGAUUGGACGCAAUUAAAAGGCCAGACGAAG-AUACAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCA
.((..((((((((....)).((((((((((....)))))))))))))))).....-......(((((((((...(.....)....))))....))))))). ( -25.00)
>consensus
_GCUUUCUGGCUCAUUAGAAUUUUUGAUUGGUCGCAAUUAAAAGGCCAGACGAAG_AUACAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCA
.((..((((((((....)).((((((((((....))))))))))))))))............(((((((((...(.....)....))))....))))))). (-24.06 = -24.26 +   0.20)

alignment

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secondary structure

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Window 9

Location 3,017,330 – 3,017,426
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 95.70
Mean single sequence MFE -26.86
Consensus MFE -24.54
Energy contribution -24.22
Covariance contribution -0.32
Combinations/Pair 1.04
Mean z-score -1.29
Structure conservation index 0.91
SVM decision value 0.61
SVM RNA-class probability 0.797619
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3017330 96 + 22224390
AAAGGCCAGACGACGAAUAUAUAGCGAAGCUUAUCAAAUUGUUUUAGCUACCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCG
....((.(.(((((((.....(((((((((..........))))).)))).....((((((.....)))))).......))))))).)))...... ( -26.40)
>DroSec_CAF1 5041 95 + 1
AAAGGCCAGACGAAG-AUAGAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCCUGUAAAUUGUCGUGUGCAAUUCG
....(((((((((..-((((.(((((((((..........))))).)))).....((((((.....))))))))))...))))).)).))...... ( -27.10)
>DroSim_CAF1 5268 95 + 1
AAAGGCCAGACGAAG-AUACAGAGCGAAGCUUAUCAAAUUGUUUUUGCUCCCCUCGCUGCAGUUUGUGCAGCCUGUAAAUUGUCGUGUGCAAUUCG
....(((((((((..-.(((((((((((((..........).)))))))).....((((((.....)))))).))))..))))).)).))...... ( -26.10)
>DroEre_CAF1 5295 95 + 1
AAAGGCCAGACGAAG-UUGCAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCG
....(((((((((..-((((((((((((((..........))))).)))).....((((((.....)))))).))))).))))).)).))...... ( -28.10)
>DroYak_CAF1 5222 95 + 1
AAAGGCCAGACGAAG-AUACAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCG
....(((((((((..-.(((((((((((((..........))))).)))).....((((((.....)))))).))))..))))).)).))...... ( -26.60)
>consensus
AAAGGCCAGACGAAG_AUACAGAGCGAAGCUUAUCAAAUUGUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCG
....(((((((((........(((((((((..........))))).)))).....((((((.....)))))).......))))).)).))...... (-24.54 = -24.22 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,017,330 – 3,017,426
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 95.70
Mean single sequence MFE -27.42
Consensus MFE -24.80
Energy contribution -25.40
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.90
SVM decision value 3.29
SVM RNA-class probability 0.998941
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3017330 96 - 22224390
CGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGUAGCUAAAACAAUUUGAUAAGCUUCGCUAUAUAUUCGUCGUCUGGCCUUU
......((..(((((.........((((((.....))))))(((.(((((.....................)))))...))))))))...)).... ( -23.90)
>DroSec_CAF1 5041 95 - 1
CGAAUUGCACACGACAAUUUACAGGCUGCACAAACUGCAGCGAGGGGAGCUAAAACAAUUUGAUAAGCUUCGCUCUCUAU-CUUCGUCUGGCCUUU
......((.((.(((.........((((((.....))))))(((.((((((..............)))))).))).....-....))))))).... ( -27.24)
>DroSim_CAF1 5268 95 - 1
CGAAUUGCACACGACAAUUUACAGGCUGCACAAACUGCAGCGAGGGGAGCAAAAACAAUUUGAUAAGCUUCGCUCUGUAU-CUUCGUCUGGCCUUU
......((.((.(((((..((((.((((((.....))))))(((.(((((................))))).))))))).-.)).))))))).... ( -27.79)
>DroEre_CAF1 5295 95 - 1
CGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGGAGCUAAAACAAUUUGAUAAGCUUCGCUCUGCAA-CUUCGUCUGGCCUUU
(((((((((...............((((((.....))))))(((.((((((..............)))))).))))))))-.)))).......... ( -28.94)
>DroYak_CAF1 5222 95 - 1
CGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGGAGCUAAAACAAUUUGAUAAGCUUCGCUCUGUAU-CUUCGUCUGGCCUUU
......((.((.(((((..((((.((((((.....))))))(((.((((((..............)))))).))))))).-.)).))))))).... ( -29.24)
>consensus
CGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGGAGCUAAAACAAUUUGAUAAGCUUCGCUCUGUAU_CUUCGUCUGGCCUUU
......((.((.(((.........((((((.....))))))(((.((((((..............)))))).)))..........))))))).... (-24.80 = -25.40 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,017,370 – 3,017,465
Length 95
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 97.07
Mean single sequence MFE -27.32
Consensus MFE -26.70
Energy contribution -26.74
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -3.09
Structure conservation index 0.98
SVM decision value 5.03
SVM RNA-class probability 0.999969
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3017370 95 + 22224390
GUUUUAGCUACCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCGCAUCAAUUGGAAUGAAUUAAUUGAAAAUUGCACACAAA-C
...............((((((.....))))))............((((((((((....((((((((......)))))))).))))))))))...-. ( -26.80)
>DroSec_CAF1 5080 95 + 1
GUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCCUGUAAAUUGUCGUGUGCAAUUCGCAUCAAUUGAAAUGAAUUAAUUGAAAAUUGCACACAAA-C
...............((((((.....))))))............((((((((((....((((((((......)))))))).))))))))))...-. ( -27.70)
>DroSim_CAF1 5307 95 + 1
GUUUUUGCUCCCCUCGCUGCAGUUUGUGCAGCCUGUAAAUUGUCGUGUGCAAUUCGCAUCAAUUGAAAUGAAUUAAUUGAAAAUUGCACACAAA-C
...(((((.......((((((.....))))))..))))).....((((((((((....((((((((......)))))))).))))))))))...-. ( -28.00)
>DroEre_CAF1 5334 96 + 1
GUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCGCAUCAAUUGAAAUGAAUUAAUUGAAAAUUGCACACAAAAC
(((((..........((((((.....))))))............((((((((((....((((((((......)))))))).))))))))))))))) ( -28.90)
>DroYak_CAF1 5261 96 + 1
GUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCGCAUCAAUUGAAAUGAAUUAAUUGAAAAUUGCACAAAAAAC
(((((..........((((((.....)))))).............(((((((((....((((((((......)))))))).))))))))).))))) ( -25.20)
>consensus
GUUUUAGCUCCCCUCGCUGCAGUUUGUGCAGCUUGUAAAUUGUCGUGUGCAAUUCGCAUCAAUUGAAAUGAAUUAAUUGAAAAUUGCACACAAA_C
...............((((((.....))))))............((((((((((....((((((((......)))))))).))))))))))..... (-26.70 = -26.74 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,017,370 – 3,017,465
Length 95
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 97.07
Mean single sequence MFE -29.38
Consensus MFE -28.20
Energy contribution -28.40
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.74
Structure conservation index 0.96
SVM decision value 4.87
SVM RNA-class probability 0.999958
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3017370 95 - 22224390
G-UUUGUGUGCAAUUUUCAAUUAAUUCAUUCCAAUUGAUGCGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGUAGCUAAAAC
.-.(((((((((((((...(((((((......)))))))..)))))))))))))....((((..((((((.....))))))....))))....... ( -30.80)
>DroSec_CAF1 5080 95 - 1
G-UUUGUGUGCAAUUUUCAAUUAAUUCAUUUCAAUUGAUGCGAAUUGCACACGACAAUUUACAGGCUGCACAAACUGCAGCGAGGGGAGCUAAAAC
(-((((((((((((((...(((((((......)))))))..)))))))))))............((((((.....)))))).....))))...... ( -29.40)
>DroSim_CAF1 5307 95 - 1
G-UUUGUGUGCAAUUUUCAAUUAAUUCAUUUCAAUUGAUGCGAAUUGCACACGACAAUUUACAGGCUGCACAAACUGCAGCGAGGGGAGCAAAAAC
(-((((((((((((((...(((((((......)))))))..)))))))))))............((((((.....)))))).....))))...... ( -29.90)
>DroEre_CAF1 5334 96 - 1
GUUUUGUGUGCAAUUUUCAAUUAAUUCAUUUCAAUUGAUGCGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGGAGCUAAAAC
((((((((((((((((...(((((((......)))))))..)))))))))))............((((((.....))))))....)))))...... ( -30.10)
>DroYak_CAF1 5261 96 - 1
GUUUUUUGUGCAAUUUUCAAUUAAUUCAUUUCAAUUGAUGCGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGGAGCUAAAAC
((((((((((((((((...(((((((......)))))))..)))))))))..............((((((.....))))))..)))))))...... ( -26.70)
>consensus
G_UUUGUGUGCAAUUUUCAAUUAAUUCAUUUCAAUUGAUGCGAAUUGCACACGACAAUUUACAAGCUGCACAAACUGCAGCGAGGGGAGCUAAAAC
...(((((((((((((...(((((((......)))))))..)))))))))))))..........((((((.....))))))............... (-28.20 = -28.40 +   0.20)

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 09:59:50 2006