Locus 6047

Sequence ID 3L_DroMel_CAF1
Location 16,117,521 – 16,117,748
Length 227
Max. P 0.889768
window9679 window9680 window9681 window9682

overview

Window 9

Location 16,117,521 – 16,117,628
Length 107
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.48
Mean single sequence MFE -23.70
Consensus MFE -20.34
Energy contribution -20.23
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.76
Structure conservation index 0.86
SVM decision value 0.15
SVM RNA-class probability 0.609798
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16117521 107 + 23771897
GCUGGCGCACAACAAAAGUUAUUAAUUCAAUGAUUAUGAUCAACGCGCUAAUGACAGUCAAGUGCAGCACUUGAUC-------------CGCAUAGAGAAAAGUGGCGAAAAAAAAAAAA
((((((((..(((....)))..........((((....))))..))))).(((...((((((((...)))))))).-------------..)))..........)))............. ( -22.30)
>DroSec_CAF1 3340 116 + 1
GCUGGCACACAACAAAAGUUAUUAAUUCAAUGAUUAUGAUCAACGCGCUAAUGACAGUCAAGUGCAGCACUUGAUCCCACCCACCUACUCGCAUAGAGAAAAGUGCCGAAAAA----AAA
..((((((.........(((((((......((((....))))......))))))).((((((((...))))))))............(((.....)))....)))))).....----... ( -25.90)
>DroSim_CAF1 2678 116 + 1
GCUGGUGCACAACAAAAGUUAUUAAUUCAAUGAUUAUGAUCAACGCGCUAAUGACAGUCAAGUGCAGCACUUGAUCCCACCCACCUCCUCGCAUAGAGAAAAGUGCCGAAAAA----AAA
..(((..(.........(((((((......((((....))))......))))))).((((((((...))))))))............(((.....)))....)..))).....----... ( -22.90)
>consensus
GCUGGCGCACAACAAAAGUUAUUAAUUCAAUGAUUAUGAUCAACGCGCUAAUGACAGUCAAGUGCAGCACUUGAUCCCACCCACCU_CUCGCAUAGAGAAAAGUGCCGAAAAA____AAA
..((((((.........(((((((......((((....))))......))))))).((((((((...))))))))...........................))))))............ (-20.34 = -20.23 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,117,597 – 16,117,708
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.73
Mean single sequence MFE -38.63
Consensus MFE -33.85
Energy contribution -33.97
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.88
SVM decision value 0.73
SVM RNA-class probability 0.835314
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16117597 111 + 23771897
---------CGCAUAGAGAAAAGUGGCGAAAAAAAAAAAAGAUUCGGAGGCAAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUU
---------.((((.........((((((....................(((..(((.((((((((......)).)))))))))..)))((((......))))....)))))).)))).. ( -34.00)
>DroSec_CAF1 3420 116 + 1
CCACCUACUCGCAUAGAGAAAAGUGCCGAAAAA----AAACAUUCGGAGGCAAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUU
.(((((.(((((((........))))((((...----.....)))))))(((..(((.((((((((......)).)))))))))..)))((((((((......)))))))).)))))... ( -41.00)
>DroSim_CAF1 2758 116 + 1
CCACCUCCUCGCAUAGAGAAAAGUGCCGAAAAA----AAACAUUCGGAGGCGAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUU
.....(((((((.............(((((...----.....)))))..(((..(((.((((((((......)).)))))))))..)))))))))).....((((((.....)))))).. ( -40.90)
>consensus
CCACCU_CUCGCAUAGAGAAAAGUGCCGAAAAA____AAACAUUCGGAGGCAAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUU
..........((((.(((((.....(((((............)))))..(((..(((.((((((((......)).)))))))))..)))((((......)))).))))).....)))).. (-33.85 = -33.97 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,117,628 – 16,117,748
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -39.00
Consensus MFE -38.29
Energy contribution -38.07
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.98
SVM decision value 0.91
SVM RNA-class probability 0.880187
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16117628 120 + 23771897
GAUUCGGAGGCAAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUUAAACUAACUAAGGCCAUUAUCAUAAGCUCCCAGCAAUCAU
((((..((((((..(((.((((((((......)).)))))))))..)))((((......))))...)))((.(((.(((((.....................))))).))).)))))).. ( -39.70)
>DroSec_CAF1 3456 120 + 1
CAUUCGGAGGCAAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUUAAACUAACUAAGGCCAUUAUCAUAAGCUCCCAGCAAUCAU
......((((((..(((.((((((((......)).)))))))))..)))((((......))))...)))((.(((.(((((.....................))))).))).))...... ( -38.30)
>DroSim_CAF1 2794 120 + 1
CAUUCGGAGGCGAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUUAAACUAACUGAGGCCAUUAUCAUAAGCUCCCAGCAAUCAU
......((((((..(((.((((((((......)).)))))))))..)))((((......))))...)))((.(((.(((((.......(((........)))))))).))).))...... ( -39.01)
>consensus
CAUUCGGAGGCAAUGCCAUUGACACCUUGAUUGGAUGUCAAGGUUGUGCGCGAGGAUCAUCGCAUUCUCGCCGGGUGCUUAAACUAACUAAGGCCAUUAUCAUAAGCUCCCAGCAAUCAU
......((((((..(((.((((((((......)).)))))))))..)))((((......))))...)))((.(((.(((((.....................))))).))).))...... (-38.29 = -38.07 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,117,628 – 16,117,748
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -39.40
Consensus MFE -38.70
Energy contribution -39.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.98
SVM decision value 0.96
SVM RNA-class probability 0.889768
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16117628 120 - 23771897
AUGAUUGCUGGGAGCUUAUGAUAAUGGCCUUAGUUAGUUUAAGCACCCGGCGAGAAUGCGAUGAUCCUCGCGCACAACCUUGACAUCCAAUCAAGGUGUCAAUGGCAUUGCCUCCGAAUC
..((((((((((.(((((...((((.......))))...))))).))))))(((...((((......))))(((...((((((((((.......)))))))).))...))))))..)))) ( -40.20)
>DroSec_CAF1 3456 120 - 1
AUGAUUGCUGGGAGCUUAUGAUAAUGGCCUUAGUUAGUUUAAGCACCCGGCGAGAAUGCGAUGAUCCUCGCGCACAACCUUGACAUCCAAUCAAGGUGUCAAUGGCAUUGCCUCCGAAUG
......((((((.(((((...((((.......))))...))))).))))))(((...((((......))))(((...((((((((((.......)))))))).))...))))))...... ( -39.80)
>DroSim_CAF1 2794 120 - 1
AUGAUUGCUGGGAGCUUAUGAUAAUGGCCUCAGUUAGUUUAAGCACCCGGCGAGAAUGCGAUGAUCCUCGCGCACAACCUUGACAUCCAAUCAAGGUGUCAAUGGCAUCGCCUCCGAAUG
((..((((((((.(((((...((((.......))))...))))).))))))))..))((((((..((....(.(((.((((((.......))))))))))...))))))))......... ( -38.20)
>consensus
AUGAUUGCUGGGAGCUUAUGAUAAUGGCCUUAGUUAGUUUAAGCACCCGGCGAGAAUGCGAUGAUCCUCGCGCACAACCUUGACAUCCAAUCAAGGUGUCAAUGGCAUUGCCUCCGAAUG
......((((((.(((((...((((.......))))...))))).))))))(((...((((......))))(((...((((((((((.......)))))))).))...))))))...... (-38.70 = -39.03 +   0.33)

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 12:07:56 2006