Locus 5722

Sequence ID 3R_DroMel_CAF1
Location 14,940,408 – 14,940,646
Length 238
Max. P 0.928012
window9362 window9363 window9364 window9365

overview

Window 2

Location 14,940,408 – 14,940,526
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.55
Mean single sequence MFE -27.10
Consensus MFE -19.29
Energy contribution -20.85
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -2.00
Structure conservation index 0.71
SVM decision value 0.79
SVM RNA-class probability 0.851377
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14940408 118 - 27905053
ACAA-AAGUAUAGUGUAUAUAUUUAUGUAUAAGCCGAAUUCCAGAAAACAAAUUCUCCGUCAAAUGGAUGCGAUGUUCGAGGGGAAGGGGAGG-GGGAUUCGAGCGAUGAAUGCGGCAAC
(((.-(((((((.....))))))).)))....((((((((((......(...(((((((((.....))).((.....)).))))))..)....-)))))))..(((.....))))))... ( -30.00)
>DroSec_CAF1 76231 108 - 1
ACAAAAAGUAUAG--UAUAUAUUUAUGUAAAAGCCGAAUUCCAGAAAACAAAUUCUCCGUCAAAUGGACGGGAUG----------AGGGAAGGGGGGAUUCGAGCGAUGAGUGCGGCAAC
(((..(((((((.--..))))))).)))....((((((((((......(....((.(((((.....)))))))..----------..)......)))))))..(((.....))))))... ( -27.20)
>DroSim_CAF1 69052 107 - 1
ACAAAAAGUAUAG--UAUAUAUUUAUGUAUAAGCCGAAUUCCAGAAAACAAAUUCUCCGUCAAAUGGAUGGGAUG----------AGGGGAUG-GUGAUUCGAGCGAUGAGUGCGGCAAC
.......((((.(--(((((....))))))..(((((((((((.....(....((.(((((.....)))))))..----------..)...))-).)))))).)).....))))...... ( -23.50)
>DroYak_CAF1 73298 94 - 1
ACAAAAAGUAUAA--UAUAU--------AUAAGCCGAAUUCCAGAAAACAAAUUCUCCGUCAAAUGGAUG-GAUG----------UU----GG-GGGAUUCGAGCGCUGAGUGCGGCAAC
.............--.....--------....((((((((((....((((.....((((((.....))))-))))----------))----..-)))))))).))((((....))))... ( -27.70)
>consensus
ACAAAAAGUAUAG__UAUAUAUUUAUGUAUAAGCCGAAUUCCAGAAAACAAAUUCUCCGUCAAAUGGAUGGGAUG__________AGGGGAGG_GGGAUUCGAGCGAUGAGUGCGGCAAC
.....(((((((.....)))))))........((((((((((.(((......)))((((((.....))))))......................)))))))..(((.....))))))... (-19.29 = -20.85 +   1.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,940,487 – 14,940,606
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.92
Mean single sequence MFE -28.27
Consensus MFE -21.39
Energy contribution -23.20
Covariance contribution 1.81
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.76
SVM decision value 0.36
SVM RNA-class probability 0.702460
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14940487 119 - 27905053
AUGCAACAUUUACGAGCUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCCCCUGCGAGUGGGAGUCUCGGCGAAAAAAUAAGACAA-AAGUAUAGUGUAUAUAUUUAUGUAUAAGCCGAAUU
............((.(((((((((((...(((((..((((((((.....))).)))))..))))))))))).........(((.-(((((((.....))))))).))).))))))).... ( -36.10)
>DroSec_CAF1 76301 118 - 1
AUGCAACAUUUACGAGAUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCAGCCGCGAGUGGGAGUCUCGGCGAAAAAAAAAGACAAAAAGUAUAG--UAUAUAUUUAUGUAAAAGCCGAAUU
........((((((......((((((...(((((..((((((.(.....).).)))))..)))))))))))..............(((((((.--..))))))).))))))......... ( -24.90)
>DroSim_CAF1 69121 117 - 1
AUGCAACAUUUACGAGCUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCACCCGCGAGUGGGAGUCUCGGCGAAAA-AAAAGACAAAAAGUAUAG--UAUAUAUUUAUGUAUAAGCCGAAUU
............((.(((((((((((...(((((..((((((.........).)))))..)))))))))))...-.....(((..(((((((.--..))))))).))).))))))).... ( -27.70)
>DroYak_CAF1 73362 107 - 1
AUGCAACAUUUACGAGCUUGUCGCUGCGAAGAUUUUCAUUCCAGUUCCCC--CGAGUGGGAGUCUCAGGCAGAA-AAAAGACAAAAAGUAUAA--UAUAU--------AUAAGCCGAAUU
............((.(((((((.((((..(((((..(((((.........--.)))))..)))))...))))..-....))).....(((((.--..)))--------)))))))).... ( -24.40)
>consensus
AUGCAACAUUUACGAGCUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCACCCGCGAGUGGGAGUCUCGGCGAAAA_AAAAGACAAAAAGUAUAG__UAUAUAUUUAUGUAUAAGCCGAAUU
............((.(((((((((((...(((((..(((((............)))))..)))))))))))..............(((((((.....))))))).....))))))).... (-21.39 = -23.20 +   1.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,940,526 – 14,940,646
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -35.20
Consensus MFE -31.04
Energy contribution -32.10
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -2.17
Structure conservation index 0.88
SVM decision value 1.19
SVM RNA-class probability 0.928012
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14940526 120 + 27905053
CUUAUUUUUUCGCCGAGACUCCCACUCGCAGGGGAACUGGAAUGAAAAUCUUUGCAGCGACAAGCUCGUAAAUGUUGCAUGCCACACCGCACAAUUCCAUUCCGUUCCCCAGGUGACAUG
.........((((((((.......)))...(((((((.((((((..(((.((((((((.....))).))))).)))...(((......)))......))))))))))))).))))).... ( -39.40)
>DroSec_CAF1 76339 120 + 1
CUUUUUUUUUCGCCGAGACUCCCACUCGCGGCUGAACUGGAAUGAAAAUCUUUGCAGCGACAAUCUCGUAAAUGUUGCAUGCCACACCGCACAAUUCCAUUCCGUUCCCCAGGUGACAUG
.........((((((((.......)))..((..((((.((((((........(((((((((......))...)))))))(((......)))......)))))))))).)).))))).... ( -30.40)
>DroSim_CAF1 69159 119 + 1
CUUUU-UUUUCGCCGAGACUCCCACUCGCGGGUGAACUGGAAUGAAAAUCUUUGCAGCGACAAGCUCGUAAAUGUUGCAUGCCACACCGCACAAUUCCAUUCCGUUCCCCAGGUGACAUG
.....-...((((((((.......)))..(((.((((.((((((..(((.((((((((.....))).))))).)))...(((......)))......))))))))))))).))))).... ( -35.70)
>DroYak_CAF1 73392 117 + 1
CUUUU-UUCUGCCUGAGACUCCCACUCG--GGGGAACUGGAAUGAAAAUCUUCGCAGCGACAAGCUCGUAAAUGUUGCAUGCCACACCGCACAAUUCCAUUCCGUUCCCCAGGUGACAUG
.....-....(((((((.......))).--(((((((.((((((............((((((..........)))))).(((......)))......)))))))))))))))))...... ( -35.30)
>consensus
CUUUU_UUUUCGCCGAGACUCCCACUCGCGGGGGAACUGGAAUGAAAAUCUUUGCAGCGACAAGCUCGUAAAUGUUGCAUGCCACACCGCACAAUUCCAUUCCGUUCCCCAGGUGACAUG
.........((((((((.......)))...(((((((.((((((............((((((..........)))))).(((......)))......))))))))))))).))))).... (-31.04 = -32.10 +   1.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,940,526 – 14,940,646
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -39.60
Consensus MFE -33.79
Energy contribution -34.98
Covariance contribution 1.19
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.85
SVM decision value -0.04
SVM RNA-class probability 0.512127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14940526 120 - 27905053
CAUGUCACCUGGGGAACGGAAUGGAAUUGUGCGGUGUGGCAUGCAACAUUUACGAGCUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCCCCUGCGAGUGGGAGUCUCGGCGAAAAAAUAAG
....((.((.((((((((((((((((...((((((..((((.((...........)).)))))))))).....))))))))).)))))))...(((.......))))).))......... ( -42.90)
>DroSec_CAF1 76339 120 - 1
CAUGUCACCUGGGGAACGGAAUGGAAUUGUGCGGUGUGGCAUGCAACAUUUACGAGAUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCAGCCGCGAGUGGGAGUCUCGGCGAAAAAAAAAG
(((((((((((.(.((..........)).).))).)))))))).................((((((...(((((..((((((.(.....).).)))))..)))))))))))......... ( -33.60)
>DroSim_CAF1 69159 119 - 1
CAUGUCACCUGGGGAACGGAAUGGAAUUGUGCGGUGUGGCAUGCAACAUUUACGAGCUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCACCCGCGAGUGGGAGUCUCGGCGAAAA-AAAAG
....((.((.((((((((((((((((...((((((..((((.((...........)).)))))))))).....))))))))).)))).)))..(((.......))))).))...-..... ( -39.60)
>DroYak_CAF1 73392 117 - 1
CAUGUCACCUGGGGAACGGAAUGGAAUUGUGCGGUGUGGCAUGCAACAUUUACGAGCUUGUCGCUGCGAAGAUUUUCAUUCCAGUUCCCC--CGAGUGGGAGUCUCAGGCAGAA-AAAAG
..((((....((((((((((((((((...((((((..((((.((...........)).)))))))))).....))))))))).)))))))--.(((.......))).))))...-..... ( -42.30)
>consensus
CAUGUCACCUGGGGAACGGAAUGGAAUUGUGCGGUGUGGCAUGCAACAUUUACGAGCUUGUCGCUGCAAAGAUUUUCAUUCCAGUUCACCCGCGAGUGGGAGUCUCGGCGAAAA_AAAAG
..........((((((((((((((((...((((((..((((.((...........)).)))))))))).....))))))))).)))))))((((((.......))).))).......... (-33.79 = -34.98 +   1.19)

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 12:02:52 2006