Locus 876

Sequence ID 2R_DroMel_CAF1
Location 4,030,055 – 4,030,215
Length 160
Max. P 0.894482
window1517 window1518 window1519

overview

Window 7

Location 4,030,055 – 4,030,175
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -28.20
Consensus MFE -22.16
Energy contribution -22.76
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.79
SVM decision value 0.98
SVM RNA-class probability 0.894482
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4030055 120 + 20766785
AAACUCAAGUGAAAGCCCAACCGAAAUGGGAAUGAAUAUAAUUCCCUGCUAAGCCAGCUUAAAGGAACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCAAGCCAGAAAUCCUGGUU
........((....))...........((((((.......))))))((((..(((.(.((((...........)))).).)))..((....))......))))((((((.....)))))) ( -24.20)
>DroSec_CAF1 12778 120 + 1
AAACUCGAGUGAAAGCCCAGCCGAAAUGGGAAUGAACAUAAUUCCCCGCUUAGCCAGCUUAGAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGAAAGCCAGAAAUCCUGGUU
......(.((....)).).(((.....((((((.......))))))......(((........)))..............)))..((....))..........((((((.....)))))) ( -27.80)
>DroSim_CAF1 14862 120 + 1
AAACUCGAGUGAAAGCCCAGCCGAAAUGGGAAUGAACAUAAUUCCCCGCUUAGCCAGCUUAGAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCAAGCCAGAAAUCCUGGUU
..............((...(((.....((((((.......))))))......(((........)))..............)))..((....)).......)).((((((.....)))))) ( -28.10)
>DroEre_CAF1 11984 120 + 1
AAACUCGAGUGAAAACCCAGCCGAAAUGGGAAUGAAUAUAAUUCCCUGCUUAGCCAGCUUAAAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCUCGCCAGAAAUCCUGGUU
......((((.........(((.....((((((.......))))))......(((........)))..............)))..((....)).......))))(((((.....))))). ( -31.20)
>DroYak_CAF1 15067 120 + 1
AAACUGGAGUGAAGACCUAGCCGAAAUGGGAAUGAAUAUAAUUCCCUGCUUAGCCAGCUUAAAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCACGGCAGAAAUCCUGGUU
.(((((((((....))...((((....((((((.......))))))(((((.(((........)))...................((....)).....))))))))).....))).)))) ( -29.70)
>consensus
AAACUCGAGUGAAAGCCCAGCCGAAAUGGGAAUGAAUAUAAUUCCCUGCUUAGCCAGCUUAAAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCAAGCCAGAAAUCCUGGUU
........((.........(((.....((((((.......))))))......(((........)))..............)))..((....))..)).......(((((.....))))). (-22.16 = -22.76 +   0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,030,055 – 4,030,175
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.17
Mean single sequence MFE -31.36
Consensus MFE -27.62
Energy contribution -27.54
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -1.43
Structure conservation index 0.88
SVM decision value 0.84
SVM RNA-class probability 0.864586
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4030055 120 - 20766785
AACCAGGAUUUCUGGCUUGCUUUGUCUAGUUUCCUGUGCCUGUUUAAUUUGUGUUCCUUUAAGCUGGCUUAGCAGGGAAUUAUAUUCAUUCCCAUUUCGGUUGGGCUUUCACUUGAGUUU
..((((.....))))...((((.((.((((((((((((((.((((((...........)))))).)))...)))))))))))........((((.......)))).....))..)))).. ( -30.10)
>DroSec_CAF1 12778 120 - 1
AACCAGGAUUUCUGGCUUUCUUUGUCUAGUUUCCUGUGCCUGUUUAAUUUGUGUGCCUCUAAGCUGGCUAAGCGGGGAAUUAUGUUCAUUCCCAUUUCGGCUGGGCUUUCACUCGAGUUU
...(((((...(((((.......).))))..))))).........((((((.(((.....((((..(((.....((((((.......)))))).....)))..).))).))).)))))). ( -31.50)
>DroSim_CAF1 14862 120 - 1
AACCAGGAUUUCUGGCUUGCUUUGUCUAGUUUCCUGUGCCUGUUUAAUUUGUGUGCCUCUAAGCUGGCUAAGCGGGGAAUUAUGUUCAUUCCCAUUUCGGCUGGGCUUUCACUCGAGUUU
...(((((...(((((.......).))))..))))).........((((((.(((.....((((..(((.....((((((.......)))))).....)))..).))).))).)))))). ( -31.50)
>DroEre_CAF1 11984 120 - 1
AACCAGGAUUUCUGGCGAGCUUUGUCUAGUUUCCUGUGCCUGUUUAAUUUGUGUGCCUUUAAGCUGGCUAAGCAGGGAAUUAUAUUCAUUCCCAUUUCGGCUGGGUUUUCACUCGAGUUU
..((((.....))))((((.......((((((((((((((.((((((...........)))))).)))...)))))))))))........((((.......))))......))))..... ( -32.80)
>DroYak_CAF1 15067 120 - 1
AACCAGGAUUUCUGCCGUGCUUUGUCUAGUUUCCUGUGCCUGUUUAAUUUGUGUGCCUUUAAGCUGGCUAAGCAGGGAAUUAUAUUCAUUCCCAUUUCGGCUAGGUCUUCACUCCAGUUU
....(((((((..(((((((((.(.(((((((...(..((..........).)..)....)))))))).)))))((((((.......))))))....)))).)))))))........... ( -30.90)
>consensus
AACCAGGAUUUCUGGCUUGCUUUGUCUAGUUUCCUGUGCCUGUUUAAUUUGUGUGCCUUUAAGCUGGCUAAGCAGGGAAUUAUAUUCAUUCCCAUUUCGGCUGGGCUUUCACUCGAGUUU
...(((((...(((((.......).))))..)))))..............(((.((((...(((((((...)).((((((.......))))))....)))))))))...)))........ (-27.62 = -27.54 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,030,095 – 4,030,215
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.17
Mean single sequence MFE -24.10
Consensus MFE -20.50
Energy contribution -21.30
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.85
SVM decision value 0.20
SVM RNA-class probability 0.631188
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4030095 120 + 20766785
AUUCCCUGCUAAGCCAGCUUAAAGGAACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCAAGCCAGAAAUCCUGGUUAAAAGUCAUAACACACAGGCACGCACAAAGCCGCAUUUGU
....(((..((((....)))).)))...((((((......(((..((....)).......((.((((((.....))))))....(((..........)))..)).....)))..)))))) ( -25.90)
>DroSec_CAF1 12818 120 + 1
AUUCCCCGCUUAGCCAGCUUAGAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGAAAGCCAGAAAUCCUGGUUAAAAGUCAAAACACACAGGCACGCACAAAGCCGCAUAUGU
.......((...(((........)))..............(((..((....)).(((......((((((.....))))))....)))......................)))))...... ( -23.90)
>DroSim_CAF1 14902 120 + 1
AUUCCCCGCUUAGCCAGCUUAGAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCAAGCCAGAAAUCCUGGUUAAAAGUCAAAACACACAGGCACGCACAAAGCCGCAUAUGU
.......((...(((........)))..............(((..((....)).......((.((((((.....))))))....(((..........)))..)).....)))))...... ( -25.70)
>DroEre_CAF1 12024 120 + 1
AUUCCCUGCUUAGCCAGCUUAAAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCUCGCCAGAAAUCCUGGUUAAAAGUCAAAACACACAGGCACGCACAAAGCCGCAUAUGU
......(((...(((........)))..............(((..((....)).......((..(((((.....))))).....(((..........)))..)).....))))))..... ( -24.30)
>DroYak_CAF1 15107 120 + 1
AUUCCCUGCUUAGCCAGCUUAAAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCACGGCAGAAAUCCUGGUUAAAAGUCAAAACACACAGGCACGCACAAAGCCGCAUAUGU
......(((...(((........)))..............(((..((....)).(((..(((.(((.(....).))))))....)))......................))))))..... ( -20.70)
>consensus
AUUCCCUGCUUAGCCAGCUUAAAGGCACACAAAUUAAACAGGCACAGGAAACUAGACAAAGCAAGCCAGAAAUCCUGGUUAAAAGUCAAAACACACAGGCACGCACAAAGCCGCAUAUGU
.......((...(((........)))..............(((..((....)).(((......((((((.....))))))....)))......................)))))...... (-20.50 = -21.30 +   0.80)

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 09:49:38 2006