Locus 7221

Sequence ID X_DroMel_CAF1
Location 18,063,922 – 18,064,122
Length 200
Max. P 0.989899
window11802 window11803 window11804 window11805 window11806

overview

Window 2

Location 18,063,922 – 18,064,042
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -46.40
Consensus MFE -46.00
Energy contribution -46.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.01
Structure conservation index 0.99
SVM decision value 2.01
SVM RNA-class probability 0.985497
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18063922 120 + 22224390
UGUUUCGUAACUUGAGUUGUUUAAUGCACUUUUGCCUGGUGACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCU
.......((((....))))....(((((....((((.(....).)))).......((((((((((((....))))))))))))((((.......))))(((....)))...))))).... ( -46.40)
>DroSec_CAF1 1822 120 + 1
UGUUUCGUAACUUGAGUUGUUUAAUGCACUUUUGCCUGGUGACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCU
.......((((....))))....(((((....((((.(....).)))).......((((((((((((....))))))))))))((((.......))))(((....)))...))))).... ( -46.40)
>DroSim_CAF1 4916 120 + 1
UGUUUCGUAACUUGAGUUGUUUAAUGCACUUUUGCCUGGUGACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCU
.......((((....))))....(((((....((((.(....).)))).......((((((((((((....))))))))))))((((.......))))(((....)))...))))).... ( -46.40)
>consensus
UGUUUCGUAACUUGAGUUGUUUAAUGCACUUUUGCCUGGUGACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCU
.......((((....))))....(((((.....((((((.(((.((((....)).((((((((((((....))))))))))))...)).)))))))))(((....)))...))))).... (-46.00 = -46.00 +   0.00)

alignment

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secondary structure

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Window 3

Location 18,063,922 – 18,064,042
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -40.20
Consensus MFE -40.20
Energy contribution -40.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.00
Structure conservation index 1.00
SVM decision value 2.07
SVM RNA-class probability 0.987316
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18063922 120 - 22224390
AGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUCACCAGGCAAAAGUGCAUUAAACAACUCAAGUUACGAAACA
....(((((..((((((((...((((.......))))((((((((((........))))))))))...........)))).)))).......)))))....................... ( -40.20)
>DroSec_CAF1 1822 120 - 1
AGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUCACCAGGCAAAAGUGCAUUAAACAACUCAAGUUACGAAACA
....(((((..((((((((...((((.......))))((((((((((........))))))))))...........)))).)))).......)))))....................... ( -40.20)
>DroSim_CAF1 4916 120 - 1
AGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUCACCAGGCAAAAGUGCAUUAAACAACUCAAGUUACGAAACA
....(((((..((((((((...((((.......))))((((((((((........))))))))))...........)))).)))).......)))))....................... ( -40.20)
>consensus
AGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUCACCAGGCAAAAGUGCAUUAAACAACUCAAGUUACGAAACA
....(((((..((((((((...((((.......))))((((((((((........))))))))))...........)))).)))).......)))))....................... (-40.20 = -40.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,063,962 – 18,064,082
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -46.10
Consensus MFE -46.10
Energy contribution -46.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.76
Structure conservation index 1.00
SVM decision value 2.19
SVM RNA-class probability 0.989899
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18063962 120 + 22224390
GACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCUGAUGAACAUGCAAAAUAAUUGAAAUGCAUUCAAAAGUUUU
((((((.(((((...((((((((((((....))))))))))))((((.......)))).))))).))))))(((((.((....))..)))))......(((((.....)))))....... ( -46.10)
>DroSec_CAF1 1862 120 + 1
GACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCUGAUGAACAUGCAAAAUAAUUGAAAUGCAUUCAAAAGUUUU
((((((.(((((...((((((((((((....))))))))))))((((.......)))).))))).))))))(((((.((....))..)))))......(((((.....)))))....... ( -46.10)
>DroSim_CAF1 4956 120 + 1
GACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCUGAUGAACAUGCAAAAUAAUUGAAAUGCAUUCAAAAGUUUU
((((((.(((((...((((((((((((....))))))))))))((((.......)))).))))).))))))(((((.((....))..)))))......(((((.....)))))....... ( -46.10)
>consensus
GACUGGCAUUUUUGAGAUGCUCCCCGCGUCGGUGGGGAGCAUCGCCCCCGUUCCGGGCUGGAAUCCCAGUUUGCAUAUCUGAUGAACAUGCAAAAUAAUUGAAAUGCAUUCAAAAGUUUU
((((((.(((((...((((((((((((....))))))))))))((((.......)))).))))).))))))(((((.((....))..)))))......(((((.....)))))....... (-46.10 = -46.10 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,063,962 – 18,064,082
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -46.80
Consensus MFE -46.80
Energy contribution -46.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.52
Structure conservation index 1.00
SVM decision value 1.82
SVM RNA-class probability 0.978830
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18063962 120 - 22224390
AAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUC
.......(((((.....))))).....(((((((((.....)))))))))(((((.(((...((((.......))))((((((((((........)))))))))).....))).))))). ( -46.80)
>DroSec_CAF1 1862 120 - 1
AAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUC
.......(((((.....))))).....(((((((((.....)))))))))(((((.(((...((((.......))))((((((((((........)))))))))).....))).))))). ( -46.80)
>DroSim_CAF1 4956 120 - 1
AAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUC
.......(((((.....))))).....(((((((((.....)))))))))(((((.(((...((((.......))))((((((((((........)))))))))).....))).))))). ( -46.80)
>consensus
AAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAUGCUCCCCACCGACGCGGGGAGCAUCUCAAAAAUGCCAGUC
.......(((((.....))))).....(((((((((.....)))))))))(((((.(((...((((.......))))((((((((((........)))))))))).....))).))))). (-46.80 = -46.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,064,002 – 18,064,122
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -41.37
Consensus MFE -39.87
Energy contribution -40.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.60
Structure conservation index 0.96
SVM decision value 1.50
SVM RNA-class probability 0.959535
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18064002 120 - 22224390
AGGAAUGCACUGCCAAGGCUGCUCCUUUCGGGGCAUUUGGAAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAU
......((.((....))))((((((((((((((((((..((.....))..)))))...........((((((((((.....))))))))))((((....))))))))))..))))))).. ( -41.80)
>DroSec_CAF1 1902 120 - 1
AGGAAUGCACUGCCAAGGCUGCUGCUUUCGGGGCAUUUGGAAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAU
.((.........))...(((.(((.((((((((((((..((.....))..)))))...........((((((((((.....))))))))))((((....)))))))))))))).)))... ( -40.50)
>DroSim_CAF1 4996 120 - 1
AGGAAUGCACUGCCAAGGCUGCUCCUUUCGGGGCAUUUGGAAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAU
......((.((....))))((((((((((((((((((..((.....))..)))))...........((((((((((.....))))))))))((((....))))))))))..))))))).. ( -41.80)
>consensus
AGGAAUGCACUGCCAAGGCUGCUCCUUUCGGGGCAUUUGGAAAACUUUUGAAUGCAUUUCAAUUAUUUUGCAUGUUCAUCAGAUAUGCAAACUGGGAUUCCAGCCCGGAACGGGGGCGAU
......((.((....))))((((((((((((((((((..((.....))..)))))...........((((((((((.....))))))))))((((....))))))))))..))))))).. (-39.87 = -40.20 +   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 12:33:16 2006