Locus 4310

Sequence ID 3R_DroMel_CAF1
Location 11,434,800 – 11,435,017
Length 217
Max. P 0.999776
window7027 window7028 window7029 window7030 window7031

overview

Window 7

Location 11,434,800 – 11,434,915
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.10
Mean single sequence MFE -31.30
Consensus MFE -27.84
Energy contribution -27.88
Covariance contribution 0.04
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.89
SVM decision value 2.15
SVM RNA-class probability 0.989057
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11434800 115 - 27905053
CUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGCAGCUAUUAAGCGGGGGAAUAGUUCUUCGCUAAGUGGUCGGGCGAAUGCACUUU-----UUCAGAAG
...(((......))).....(((((......)))))((((((..((((((((.(.((((((.(((((((((....))))))))).)))))).).)).)))))).)))-----)))..... ( -34.10)
>DroSec_CAF1 174899 120 - 1
CUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGCAGCUAUUAAGCGGGGGAAUAGUUCUUCGCUAAGUGGUCGGGCGAAUGCACUUAUGGUAUUCAGAAG
.(((((...........((.(((((......))))).)).....((((((((.(.((((((.(((((((((....))))))))).)))))).).)).))))))....)))))........ ( -33.60)
>DroSim_CAF1 169115 115 - 1
CUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUUCAGCUAUUAAGCGGGGGAAUAGUUCUUCGCUAAGUGGUCGGGCGAAUGCACUUA-----UUCAGAAG
............((((.((.(((((......))))).)).....((((((((((.((((((.(((((((((....))))))))).)))))).)))).))))))....-----)))).... ( -34.10)
>DroEre_CAF1 164477 115 - 1
CUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGUAGCUAUUAAGCGGGGGAAUAGUUCCACGCUAAGUGCUCGGUUGAAUGCACUUU-----UUCAGAAG
...(((......))).....(((((......)))))((((((..((((((.((.(((.(((.((((.((((....)))).)))).))))))))....)))))).)))-----)))..... ( -25.70)
>DroYak_CAF1 167229 115 - 1
CUAUCAGCGAAAUGCAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGUAGCUAUUAAGCGGGCGAAUAGUUCUUCGCUAAGUGGUCGGAUGAAUGCACUUA-----UUCAGAAG
......(((.(((((((((.(((((......))))).....))))))))).))).((((((.((((((.((.....)))))))).)))))).((((((......)))-----)))..... ( -29.00)
>consensus
CUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGCAGCUAUUAAGCGGGGGAAUAGUUCUUCGCUAAGUGGUCGGGCGAAUGCACUUA_____UUCAGAAG
........(((......((.(((((......))))).)).....((((((((.(.((((((.(((((((((....))))))))).)))))).).)).)))))).........)))..... (-27.84 = -27.88 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,434,835 – 11,434,955
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.17
Mean single sequence MFE -30.18
Consensus MFE -24.80
Energy contribution -25.84
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.73
Structure conservation index 0.82
SVM decision value 0.57
SVM RNA-class probability 0.785880
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11434835 120 + 27905053
AAGAACUAUUCCCCCGCUUAAUAGCUGCACAAUGCAAUCUUUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGAAGCUGGCGAAGCCAUCAAACUGGCAAA
........(((.((.((((..(((((((.(((((.((....))))))).......................(((.....))))))))))...)))).)).)))((((......))))... ( -30.30)
>DroSec_CAF1 174939 120 + 1
AAGAACUAUUCCCCCGCUUAAUAGCUGCACAAUGCAAUCUUUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGGAGCUGGCGAAGCCAUCAAACUGGCAAA
........(((.((.((((..(((((((.(((((.((....))))))).......................(((.....))))))))))...)))).)).)))((((......))))... ( -30.70)
>DroSim_CAF1 169150 120 + 1
AAGAACUAUUCCCCCGCUUAAUAGCUGAACAAUGCAAUCUUUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGUAGCUGGAGAAGCCAUCAAACUGGCAAA
........(((.((.(((.....(((((....(((.........(((((......)))))...........(((.....)))))).)))))..))).)).)))((((......))))... ( -26.70)
>DroEre_CAF1 164512 120 + 1
UGGAACUAUUCCCCCGCUUAAUAGCUACACAAUGCAAUCUUUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGGAGCUGGCGAAGCCAUCAAACUGGCAAA
........((((((((((.(((.(((((.(((((.((....)))))))..........((((............)))).))))).))))))))....)).)))((((......))))... ( -27.50)
>DroYak_CAF1 167264 120 + 1
AAGAACUAUUCGCCCGCUUAAUAGCUACACAAUGCAAUCUUUUCAUUGGCAUUUUCCAAUCAAUUGCAUUUCGCUGAUAGUGGCAGUUAGCGAAGCUGGCGUUGCCAUCAAACUGGCAAA
..........((((.((((....((((.((((((((((......(((((......)))))..))))))))..(((......))).)))))).)))).))))((((((......)))))). ( -35.70)
>consensus
AAGAACUAUUCCCCCGCUUAAUAGCUGCACAAUGCAAUCUUUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGAAGCUGGCGAAGCCAUCAAACUGGCAAA
........(((.((.((((..(((((((.(((((.((....))))))).......................(((.....))))))))))...)))).)).)))((((......))))... (-24.80 = -25.84 +   1.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,434,835 – 11,434,955
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.17
Mean single sequence MFE -32.78
Consensus MFE -28.34
Energy contribution -28.94
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.86
SVM decision value 0.07
SVM RNA-class probability 0.570567
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11434835 120 - 27905053
UUUGCCAGUUUGAUGGCUUCGCCAGCUUCGCUAACUGCCACUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGCAGCUAUUAAGCGGGGGAAUAGUUCUU
(((.((.(((((((((((.(((..((((((((.............))))))......((.(((((......))))).))......))...))).))))))))))).)).)))........ ( -33.02)
>DroSec_CAF1 174939 120 - 1
UUUGCCAGUUUGAUGGCUUCGCCAGCUCCGCUAACUGCCACUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGCAGCUAUUAAGCGGGGGAAUAGUUCUU
(((.((.(((((((((((.(((..((..((((.............))))........((.(((((......))))).))......))...))).))))))))))).)).)))........ ( -30.72)
>DroSim_CAF1 169150 120 - 1
UUUGCCAGUUUGAUGGCUUCUCCAGCUACGCUAACUGCCACUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUUCAGCUAUUAAGCGGGGGAAUAGUUCUU
...((((......))))((((((.(((.((((.............))))............(((((.(((((.(((......)))))))).)))))......))).))))))........ ( -27.32)
>DroEre_CAF1 164512 120 - 1
UUUGCCAGUUUGAUGGCUUCGCCAGCUCCGCUAACUGCCACUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGUAGCUAUUAAGCGGGGGAAUAGUUCCA
....((.(((((((((((.(((..((..((((.............))))........((.(((((......))))).))......))...))).))))))))))).))(((.....))). ( -31.02)
>DroYak_CAF1 167264 120 - 1
UUUGCCAGUUUGAUGGCAACGCCAGCUUCGCUAACUGCCACUAUCAGCGAAAUGCAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGUAGCUAUUAAGCGGGCGAAUAGUUCUU
((((((.((((((((((.((((.....(((((.............)))))(((((((((.(((((......))))).....))))))))))))).)))))))))).))))))........ ( -41.82)
>consensus
UUUGCCAGUUUGAUGGCUUCGCCAGCUCCGCUAACUGCCACUAUCAGCGAAAUGAAAUUGAUUGGAAAAUGCCAAUGAAAAGAUUGCAUUGUGCAGCUAUUAAGCGGGGGAAUAGUUCUU
(((.((.(((((((((((.(((..((..((((.............))))........((.(((((......))))).))......))...))).))))))))))).)).)))........ (-28.34 = -28.94 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,434,875 – 11,434,995
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.50
Mean single sequence MFE -37.70
Consensus MFE -35.10
Energy contribution -35.34
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.83
Structure conservation index 0.93
SVM decision value 4.05
SVM RNA-class probability 0.999776
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11434875 120 + 27905053
UUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGAAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUG
.....(((((......................((((((((((.(((((.....))))).)...((((......))))..))))))))).......((((.....)))).)))))...... ( -38.20)
>DroSec_CAF1 174979 120 + 1
UUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGGAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUG
.....(((((......................((((((((((.(((((.....))))).)...((((......))))..))))))))).......((((.....)))).)))))...... ( -38.30)
>DroSim_CAF1 169190 120 + 1
UUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGUAGCUGGAGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUG
.....(((((......................(((((((((..((((((...)))))).....((((......))))..))))))))).......((((.....)))).)))))...... ( -36.10)
>DroEre_CAF1 164552 120 + 1
UUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGGAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAACCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUG
....(((((......))))).........(((((((((.......)))))))))((((((...((((......))))..................((((.....)))).))))))..... ( -36.90)
>DroYak_CAF1 167304 120 + 1
UUUCAUUGGCAUUUUCCAAUCAAUUGCAUUUCGCUGAUAGUGGCAGUUAGCGAAGCUGGCGUUGCCAUCAAACUGGCAAACUAUCAACCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUG
....(((((......))))).........(((((((((.......)))))))))((((((.((((((......))))))................((((.....)))).))))))..... ( -39.00)
>consensus
UUUCAUUGGCAUUUUCCAAUCAAUUUCAUUUCGCUGAUAGUGGCAGUUAGCGAAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUG
....(((((......))))).........(((((((((.......)))))))))((((((...((((......))))..................((((.....)))).))))))..... (-35.10 = -35.34 +   0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,434,915 – 11,435,017
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.85
Mean single sequence MFE -37.18
Consensus MFE -33.06
Energy contribution -33.10
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.89
SVM decision value 1.40
SVM RNA-class probability 0.950787
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11434915 102 + 27905053
UGGCAGUUAGCGAAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUGCGACUGUUCCCGGUAACGGC---------GA---------
..((((((.(((..((((((...((((......))))..................((((.....)))).))))))...)))))))))(((((....))).---------))--------- ( -36.80)
>DroSec_CAF1 175019 102 + 1
UGGCAGUUAGCGGAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUGCGACUGUGCCCGGCGAUGGC---------GA---------
..((((((.(((..((((((...((((......))))..................((((.....)))).))))))...)))))))))(((.......)))---------..--------- ( -37.70)
>DroSim_CAF1 169230 102 + 1
UGGCAGUUAGCGUAGCUGGAGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUGCGACUGUUCCCGGUGAUGGC---------GA---------
..((((((.((((((((((....((((......))))..................((((.....))))..))))).)))))))))))(((((....))).---------))--------- ( -34.30)
>DroEre_CAF1 164592 111 + 1
UGGCAGUUAGCGGAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAACCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUGCGACUGUUCCCGCUGAUGGC---------GAAAAUGGUGA
..((.((((((((.((((((...((((......))))..................((((.....)))).))))))......((....)))))))))).))---------........... ( -38.80)
>DroYak_CAF1 167344 120 + 1
UGGCAGUUAGCGAAGCUGGCGUUGCCAUCAAACUGGCAAACUAUCAACCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUGCGACUGUUCCCGGUGAUGGCAAAAUUGGUGAAAAUGGUGA
..((((((.(((..((((((.((((((......))))))................((((.....)))).))))))...)))))))))(((((((.........))))).))......... ( -38.30)
>consensus
UGGCAGUUAGCGAAGCUGGCGAAGCCAUCAAACUGGCAAACUAUCAGCCACCCAAGCGGCAAAUCCGCAGCCAGCAUAUGCGACUGUUCCCGGUGAUGGC_________GA_________
..((((((.(((..((((((...((((......))))..................((((.....)))).))))))...)))))))))..(((....)))..................... (-33.06 = -33.10 +   0.04)

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 11:25:39 2006