Locus 6963

Sequence ID 3R_DroMel_CAF1
Location 18,334,796 – 18,334,928
Length 132
Max. P 0.999339
window11289 window11290 window11291 window11292

overview

Window 9

Location 18,334,796 – 18,334,915
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.66
Mean single sequence MFE -50.90
Consensus MFE -45.74
Energy contribution -46.74
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.90
SVM decision value 3.52
SVM RNA-class probability 0.999339
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18334796 119 + 27905053
AAGGUGUUUAUGGGCUUAACUCCG-GCCCUGAUUCCGCCUACUUGGCUGCCUCGCCUCACAGAUUUGGAUUUGCAUGUGCCACGAUUUGGGGCAUGCGGCUGAGAAGGCGGCUGAGCAGG
..((.(((...(((((.......)-)))).))).)).(((.((..((((((((((((((......)))....((((((.(((.....))).)))))))))...).)))))))..)).))) ( -48.60)
>DroSec_CAF1 20947 119 + 1
AAGGUGUUUAUGGGCUUAACUCCG-GCCCUGAUUCCGCCUACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAAAAGGCGGCUGAGCAGG
..((.(((...(((((.......)-)))).))).)).(((.((..(((((((.(((..((......))....((((((((((.....))))))))))))).....)))))))..)).))) ( -51.80)
>DroSim_CAF1 21410 119 + 1
AAGGUGUUUAUGGGCUUAACUCCG-GCCCUGAUUCCGCCUACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAAAAGGCGGCUGAGCAGG
..((.(((...(((((.......)-)))).))).)).(((.((..(((((((.(((..((......))....((((((((((.....))))))))))))).....)))))))..)).))) ( -51.80)
>DroEre_CAF1 21326 120 + 1
AAGGUGUUUAUGGGCUUAACUCCGGGCCCUGAUUCCGCCUACUUGGCUGCCUCGCCUUCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAGAAGGCGACUGAACAGG
....((((((.((((((......))))))......(((((.((..(((((...(((..(((((((((((.........)))).))))))))))..)))))..)).)))))..)))))).. ( -50.30)
>DroYak_CAF1 22910 120 + 1
AAGGUGUUUAUGGGCUUAACUCCGGGCCCUGAUUCCGCCUACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUGCCACGAUUUGGGGCAUGCGGCUGACAAGGCGGCUGAGAAGG
.(((((.(((.((((((......)))))))))...))))).((..(((((((.(((..((......))....((((((.(((.....))).))))))))).....)))))))..)).... ( -52.00)
>consensus
AAGGUGUUUAUGGGCUUAACUCCG_GCCCUGAUUCCGCCUACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAAAAGGCGGCUGAGCAGG
..((.(((...((((..........)))).))).)).(((.((..(((((((.(((..((......))....((((((((((.....))))))))))))).....)))))))..)).))) (-45.74 = -46.74 +   1.00)

alignment

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secondary structure

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Window 0

Location 18,334,796 – 18,334,915
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.66
Mean single sequence MFE -40.18
Consensus MFE -38.18
Energy contribution -38.10
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -1.54
Structure conservation index 0.95
SVM decision value 1.65
SVM RNA-class probability 0.970167
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18334796 119 - 27905053
CCUGCUCAGCCGCCUUCUCAGCCGCAUGCCCCAAAUCGUGGCACAUGCAAAUCCAAAUCUGUGAGGCGAGGCAGCCAAGUAGGCGGAAUCAGGGC-CGGAGUUAAGCCCAUAAACACCUU
((((((..((.(((((....((((((((..(((.....)))..)))))...((((....)).)))))))))).))..))))))........((((-.........))))........... ( -38.70)
>DroSec_CAF1 20947 119 - 1
CCUGCUCAGCCGCCUUUUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGUAGGCGGAAUCAGGGC-CGGAGUUAAGCCCAUAAACACCUU
((((((..((.(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).))..))))))........((((-.........))))........... ( -41.70)
>DroSim_CAF1 21410 119 - 1
CCUGCUCAGCCGCCUUUUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGUAGGCGGAAUCAGGGC-CGGAGUUAAGCCCAUAAACACCUU
((((((..((.(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).))..))))))........((((-.........))))........... ( -41.70)
>DroEre_CAF1 21326 120 - 1
CCUGUUCAGUCGCCUUCUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGAAGGCGAGGCAGCCAAGUAGGCGGAAUCAGGGCCCGGAGUUAAGCCCAUAAACACCUU
(((((((....(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).(((.....))).))).))))....((.(((.........))).)).. ( -38.90)
>DroYak_CAF1 22910 120 - 1
CCUUCUCAGCCGCCUUGUCAGCCGCAUGCCCCAAAUCGUGGCACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGUAGGCGGAAUCAGGGCCCGGAGUUAAGCCCAUAAACACCUU
.........((((((((((....(((((..(((.....)))..)))))...((((....)))).)))))))).(((.....))))).....((((..........))))........... ( -39.90)
>consensus
CCUGCUCAGCCGCCUUCUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGUAGGCGGAAUCAGGGC_CGGAGUUAAGCCCAUAAACACCUU
((((((..((.(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).))..))))))........((((..........))))........... (-38.18 = -38.10 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,334,835 – 18,334,928
Length 93
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -36.92
Consensus MFE -32.56
Energy contribution -33.56
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.88
SVM decision value 2.92
SVM RNA-class probability 0.997714
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18334835 93 + 27905053
ACUUGGCUGCCUCGCCUCACAGAUUUGGAUUUGCAUGUGCCACGAUUUGGGGCAUGCGGCUGAGAAGGCGGCUGAGCAGGCG-----GAUAGAAGACA
.((..((((((((((((((......)))....((((((.(((.....))).)))))))))...).)))))))..))......-----........... ( -33.90)
>DroSec_CAF1 20986 93 + 1
ACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAAAAGGCGGCUGAGCAGGCG-----GAUAGAAGACA
.((..(((((((.(((..((......))....((((((((((.....))))))))))))).....)))))))..))......-----........... ( -37.10)
>DroSim_CAF1 21449 93 + 1
ACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAAAAGGCGGCUGAGCAGGCG-----GAUAGAAGACA
.((..(((((((.(((..((......))....((((((((((.....))))))))))))).....)))))))..))......-----........... ( -37.10)
>DroEre_CAF1 21366 93 + 1
ACUUGGCUGCCUCGCCUUCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAGAAGGCGACUGAACAGGCA-----GAUAGAAGACA
.((...((((((((((((((((........((((((((((((.....))))))))))))))).)))))))).......))))-----)..))...... ( -38.81)
>DroYak_CAF1 22950 98 + 1
ACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUGCCACGAUUUGGGGCAUGCGGCUGACAAGGCGGCUGAGAAGGCGACUGGGAUAGAAGACA
.((..(((((((.(((..((......))....((((((.(((.....))).))))))))).....)))))))..)).((....))............. ( -37.70)
>consensus
ACUUGGCUGCCUCGCCUCCCAGAUUUGGAUUUGCAUGUUCCACGAUUUGGGGCAUGCGGCUGAAAAGGCGGCUGAGCAGGCG_____GAUAGAAGACA
.((..(((((((.(((..((......))....((((((((((.....))))))))))))).....)))))))..))...................... (-32.56 = -33.56 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,334,835 – 18,334,928
Length 93
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -27.94
Consensus MFE -25.44
Energy contribution -25.36
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -1.21
Structure conservation index 0.91
SVM decision value 0.39
SVM RNA-class probability 0.717487
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18334835 93 - 27905053
UGUCUUCUAUC-----CGCCUGCUCAGCCGCCUUCUCAGCCGCAUGCCCCAAAUCGUGGCACAUGCAAAUCCAAAUCUGUGAGGCGAGGCAGCCAAGU
...........-----.....(((..((.(((((....((((((((..(((.....)))..)))))...((((....)).)))))))))).))..))) ( -25.10)
>DroSec_CAF1 20986 93 - 1
UGUCUUCUAUC-----CGCCUGCUCAGCCGCCUUUUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGU
...........-----.....(((..((.(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).))..))) ( -28.10)
>DroSim_CAF1 21449 93 - 1
UGUCUUCUAUC-----CGCCUGCUCAGCCGCCUUUUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGU
...........-----.....(((..((.(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).))..))) ( -28.10)
>DroEre_CAF1 21366 93 - 1
UGUCUUCUAUC-----UGCCUGUUCAGUCGCCUUCUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGAAGGCGAGGCAGCCAAGU
..........(-----((((.......((((((((.(((..(((((..(((.....)))..)))))..........))))))))))))))))...... ( -29.11)
>DroYak_CAF1 22950 98 - 1
UGUCUUCUAUCCCAGUCGCCUUCUCAGCCGCCUUGUCAGCCGCAUGCCCCAAAUCGUGGCACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGU
......................((..((.((((((((....(((((..(((.....)))..)))))...((((....)))).)))))))).))..)). ( -29.30)
>consensus
UGUCUUCUAUC_____CGCCUGCUCAGCCGCCUUCUCAGCCGCAUGCCCCAAAUCGUGGAACAUGCAAAUCCAAAUCUGGGAGGCGAGGCAGCCAAGU
.....................(((..((.(((((....((((((((..(((.....)))..)))))...((((....)))).)))))))).))..))) (-25.44 = -25.36 +  -0.08)

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 12:34:19 2006