Locus 3990

Sequence ID 3L_DroMel_CAF1
Location 11,625,506 – 11,625,706
Length 200
Max. P 0.993949
window6215 window6216 window6217 window6218 window6219 window6220

overview

Window 5

Location 11,625,506 – 11,625,626
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.06
Mean single sequence MFE -39.83
Consensus MFE -34.35
Energy contribution -34.48
Covariance contribution 0.13
Combinations/Pair 1.16
Mean z-score -2.39
Structure conservation index 0.86
SVM decision value 1.79
SVM RNA-class probability 0.977392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11625506 120 + 23771897
UGCCACGCGUAGCAUGCAGUCAUCUUUAGCUUGGAUUCCCUUGUUCACUCUGCUCCUUGGCCACCAGGUUUCAGCCAAGCUUUUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAACAG
..(((.((..((.(((....)))))...)).))).......((((((....(((((((((((((.(((.((((.((((....)))).)))).))))))).....))))))))))))))). ( -43.40)
>DroSec_CAF1 438 112 + 1
--------GUAGAAUGCAGUCAUCUUUAGUUUGGAUUCCCUUGUUCACUCUGCUCCUUGGCCAGCAGGUUUCAGCCAAGCUUUUGGAUGAAUCCUGUGGAAAUUCUAAGGAGCUGAGCAG
--------...((((.(((...........))).))))...((((((....((((((((((((.((((.((((.((((....)))).)))).))))))).....))))))))))))))). ( -38.10)
>DroSim_CAF1 561 120 + 1
UGCCACGCGUAGAAUGCAGUCAUCUUUAGCUUGGAUUUCCUUGUUCACUCUUCUCCUUGGCCACCAGGUUUCAGCCAAGCUUCUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAGCAG
..(((.((..(((.((....)))))...)).))).......((((((.....((((((((((((.(((.((((.(((......))).)))).))))))).....)))))))).)))))). ( -39.40)
>DroYak_CAF1 547 120 + 1
GGCCACGCGCAGAAUGCAGUCAUCUUUAGCUUGGAUUCCCUUGUUCACCCUGCUCCUUGGCCACCAGGUUUCAUCUCAAUUUUUGGAUGAGUCCUGUGGAAAAUUCCAGGAGCAGAGCAG
(((...(((.....))).))).......((((((((......)))))..((((((((.((((((.(((.(((((((........))))))).)))))))......))))))))))))).. ( -38.40)
>consensus
UGCCACGCGUAGAAUGCAGUCAUCUUUAGCUUGGAUUCCCUUGUUCACUCUGCUCCUUGGCCACCAGGUUUCAGCCAAGCUUUUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAGCAG
...........((((.(((.(.......).))).))))...((((((....((((((((((((.((((.((((.(((......))).)))).))))))).....))))))))))))))). (-34.35 = -34.48 +   0.13)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,625,506 – 11,625,626
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -39.58
Consensus MFE -31.24
Energy contribution -32.92
Covariance contribution 1.69
Combinations/Pair 1.06
Mean z-score -2.61
Structure conservation index 0.79
SVM decision value 1.59
SVM RNA-class probability 0.965923
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11625506 120 - 23771897
CUGUUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAAAAGCUUGGCUGAAACCUGGUGGCCAAGGAGCAGAGUGAACAAGGGAAUCCAAGCUAAAGAUGACUGCAUGCUACGCGUGGCA
.(((((((((((((((.....(((((((.((((.((((....)))).)))).))).)))))))))))))....)))))).((..(((.........)))..))...(((((....))))) ( -43.20)
>DroSec_CAF1 438 112 - 1
CUGCUCAGCUCCUUAGAAUUUCCACAGGAUUCAUCCAAAAGCUUGGCUGAAACCUGCUGGCCAAGGAGCAGAGUGAACAAGGGAAUCCAAACUAAAGAUGACUGCAUUCUAC--------
..((((.(((((((.(.....(((((((.((((.((((....)))).)))).)))).)))).))))))).))))(((...((..(((.........)))..))...)))...-------- ( -34.40)
>DroSim_CAF1 561 120 - 1
CUGCUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAGAAGCUUGGCUGAAACCUGGUGGCCAAGGAGAAGAGUGAACAAGGAAAUCCAAGCUAAAGAUGACUGCAUUCUACGCGUGGCA
..((((..((((((((.....(((((((.((((.((((....)))).)))).))).))))))))))))..))))............(((.((....((((....))))....)).))).. ( -40.00)
>DroYak_CAF1 547 120 - 1
CUGCUCUGCUCCUGGAAUUUUCCACAGGACUCAUCCAAAAAUUGAGAUGAAACCUGGUGGCCAAGGAGCAGGGUGAACAAGGGAAUCCAAGCUAAAGAUGACUGCAUUCUGCGCGUGGCC
..(((((((((((((......(((((((..(((((((.....)).)))))..))).)))))).)))))))))))............(((.((...(((((....)).)))..)).))).. ( -40.70)
>consensus
CUGCUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAAAAGCUUGGCUGAAACCUGGUGGCCAAGGAGCAGAGUGAACAAGGGAAUCCAAGCUAAAGAUGACUGCAUUCUACGCGUGGCA
.......(((((((((.....(((((((.((((.((((....)))).)))).)))).))))))))))))((((((.....((..(((.........)))..)).)))))).......... (-31.24 = -32.92 +   1.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,625,546 – 11,625,666
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.53
Mean single sequence MFE -48.50
Consensus MFE -42.84
Energy contribution -42.65
Covariance contribution -0.19
Combinations/Pair 1.15
Mean z-score -3.37
Structure conservation index 0.88
SVM decision value 2.44
SVM RNA-class probability 0.993949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11625546 120 + 23771897
UUGUUCACUCUGCUCCUUGGCCACCAGGUUUCAGCCAAGCUUUUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAACAGGGCAGGACUACAGGCAGCUGCUUGGAUGACAGCCAUCAGU
(((((((....(((((((((((((.(((.((((.((((....)))).)))).))))))).....))))))))))))))))(((.(.....(((((....))))).....).)))...... ( -48.60)
>DroSec_CAF1 470 120 + 1
UUGUUCACUCUGCUCCUUGGCCAGCAGGUUUCAGCCAAGCUUUUGGAUGAAUCCUGUGGAAAUUCUAAGGAGCUGAGCAGGGCAGGAUUACAGGCAGCUGCUUGGAUGACAGCUGUCAGU
((((((.(((.((((((((((((.((((.((((.((((....)))).)))).))))))).....))))))))).)))..)))))).......(((((((((......).))))))))... ( -51.80)
>DroSim_CAF1 601 120 + 1
UUGUUCACUCUUCUCCUUGGCCACCAGGUUUCAGCCAAGCUUCUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAGCAGGGCAGGAUUACAGGCCGCUGCUUGGAUGACAGCUGUCAGU
............((((((((((((.(((.((((.(((......))).)))).))))))).....))))))))(..((((((((..(....)..))).)))))..).((((....)))).. ( -48.20)
>DroYak_CAF1 587 120 + 1
UUGUUCACCCUGCUCCUUGGCCACCAGGUUUCAUCUCAAUUUUUGGAUGAGUCCUGUGGAAAAUUCCAGGAGCAGAGCAGGGCAGGAUUACAGGCAGCUGCUUGGAUGACAGCCGUCAGU
..((((.(((((((((((((((((.(((.(((((((........))))))).)))))))......)))))....))))))))..))))..(((((....)))))..((((....)))).. ( -45.40)
>consensus
UUGUUCACUCUGCUCCUUGGCCACCAGGUUUCAGCCAAGCUUUUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAGCAGGGCAGGAUUACAGGCAGCUGCUUGGAUGACAGCCGUCAGU
(((((((....((((((((((((.((((.((((.(((......))).)))).))))))).....))))))))))))))))(((.(.....(((((....))))).....).)))...... (-42.84 = -42.65 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,625,546 – 11,625,666
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.53
Mean single sequence MFE -43.83
Consensus MFE -37.47
Energy contribution -38.60
Covariance contribution 1.13
Combinations/Pair 1.13
Mean z-score -3.20
Structure conservation index 0.86
SVM decision value 2.12
SVM RNA-class probability 0.988450
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11625546 120 - 23771897
ACUGAUGGCUGUCAUCCAAGCAGCUGCCUGUAGUCCUGCCCUGUUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAAAAGCUUGGCUGAAACCUGGUGGCCAAGGAGCAGAGUGAACAA
((.(..((((((.......))))))..).))..........(((((((((((((((.....(((((((.((((.((((....)))).)))).))).)))))))))))))....)))))). ( -45.50)
>DroSec_CAF1 470 120 - 1
ACUGACAGCUGUCAUCCAAGCAGCUGCCUGUAAUCCUGCCCUGCUCAGCUCCUUAGAAUUUCCACAGGAUUCAUCCAAAAGCUUGGCUGAAACCUGCUGGCCAAGGAGCAGAGUGAACAA
((.(.(((((((.......))))))).).))...........((((.(((((((.(.....(((((((.((((.((((....)))).)))).)))).)))).))))))).))))...... ( -41.30)
>DroSim_CAF1 601 120 - 1
ACUGACAGCUGUCAUCCAAGCAGCGGCCUGUAAUCCUGCCCUGCUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAGAAGCUUGGCUGAAACCUGGUGGCCAAGGAGAAGAGUGAACAA
.......(((((.......)))))(((..(....)..)))..((((..((((((((.....(((((((.((((.((((....)))).)))).))).))))))))))))..))))...... ( -43.20)
>DroYak_CAF1 587 120 - 1
ACUGACGGCUGUCAUCCAAGCAGCUGCCUGUAAUCCUGCCCUGCUCUGCUCCUGGAAUUUUCCACAGGACUCAUCCAAAAAUUGAGAUGAAACCUGGUGGCCAAGGAGCAGGGUGAACAA
((.(.(((((((.......))))))).).))......((((((((((((..(((((....))))((((..(((((((.....)).)))))..)))))..))...))))))))))...... ( -45.30)
>consensus
ACUGACAGCUGUCAUCCAAGCAGCUGCCUGUAAUCCUGCCCUGCUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAAAAGCUUGGCUGAAACCUGGUGGCCAAGGAGCAGAGUGAACAA
((.(.(((((((.......))))))).).))...........((((.(((((((((.....(((((((.((((.((((....)))).)))).)))).)))))))))))).))))...... (-37.47 = -38.60 +   1.13)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,625,586 – 11,625,706
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.81
Mean single sequence MFE -43.15
Consensus MFE -32.04
Energy contribution -31.35
Covariance contribution -0.69
Combinations/Pair 1.17
Mean z-score -1.82
Structure conservation index 0.74
SVM decision value 0.05
SVM RNA-class probability 0.556877
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11625586 120 + 23771897
UUUUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAACAGGGCAGGACUACAGGCAGCUGCUUGGAUGACAGCCAUCAGUAAUGCCUCGCAUUUCCUGUGCGGUGGCACGCUGAUUCACA
....(((....))).(((((...((((((.(((((....((......)).....))))).)))))).........(((((..((((((((((.....)))))).)))).)))))))))). ( -43.60)
>DroSec_CAF1 510 120 + 1
UUUUGGAUGAAUCCUGUGGAAAUUCUAAGGAGCUGAGCAGGGCAGGAUUACAGGCAGCUGCUUGGAUGACAGCUGUCAGUAAUGCCACGCAUUUCCUGUGCGGUGGCACGCUGAUUCACG
.......((((((((((...(.(((....))).)..))))(((...(((((.(((((((((......).)))))))).)))))(((((((((.....)))).)))))..))))))))).. ( -43.60)
>DroSim_CAF1 641 120 + 1
UUCUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAGCAGGGCAGGAUUACAGGCCGCUGCUUGGAUGACAGCUGUCAGUAAUGCCACGCAUUUCCUGUGCGGUGGCACGCUGAUUCAUA
..(((......((((.(((.....))))))).(..((((((((..(....)..))).)))))..)....)))..((((((..((((((((((.....)))).)))))).))))))..... ( -46.50)
>DroYak_CAF1 627 120 + 1
UUUUGGAUGAGUCCUGUGGAAAAUUCCAGGAGCAGAGCAGGGCAGGAUUACAGGCAGCUGCUUGGAUGACAGCCGUCAGUAAUGCCUCGGAUUUUCUGUGCGGUGGCACUCUUAUUCACA
...(((((((((((((.(((...))))))))((...(((.((.((((((..(((((..((((..((((.....)))))))).)))))..)))))))).)))....))...)))))))).. ( -38.90)
>consensus
UUUUGGAUGAAUCCUGUGGAAAUUCCAAGGAGCUGAGCAGGGCAGGAUUACAGGCAGCUGCUUGGAUGACAGCCGUCAGUAAUGCCACGCAUUUCCUGUGCGGUGGCACGCUGAUUCACA
....(((....)))((((((.......(((((....((..((((..(((.(((((....)))))((((.....)))))))..))))..))..)))))((((....)))).....)))))) (-32.04 = -31.35 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,625,586 – 11,625,706
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.81
Mean single sequence MFE -37.53
Consensus MFE -30.65
Energy contribution -31.03
Covariance contribution 0.38
Combinations/Pair 1.18
Mean z-score -2.18
Structure conservation index 0.82
SVM decision value 0.98
SVM RNA-class probability 0.894561
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11625586 120 - 23771897
UGUGAAUCAGCGUGCCACCGCACAGGAAAUGCGAGGCAUUACUGAUGGCUGUCAUCCAAGCAGCUGCCUGUAGUCCUGCCCUGUUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAAAA
.(((((((...(((((..((((.......)))).)))))..(((.(((..((..((((((.(((((...(((....)))......))))).))))))))..)))))))))))))...... ( -38.10)
>DroSec_CAF1 510 120 - 1
CGUGAAUCAGCGUGCCACCGCACAGGAAAUGCGUGGCAUUACUGACAGCUGUCAUCCAAGCAGCUGCCUGUAAUCCUGCCCUGCUCAGCUCCUUAGAAUUUCCACAGGAUUCAUCCAAAA
.(((((((...((((....)))).(((((((((.((((((((.(.(((((((.......))))))).).))))...)))).))).....((....))))))))....)))))))...... ( -38.60)
>DroSim_CAF1 641 120 - 1
UAUGAAUCAGCGUGCCACCGCACAGGAAAUGCGUGGCAUUACUGACAGCUGUCAUCCAAGCAGCGGCCUGUAAUCCUGCCCUGCUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAGAA
.(((((((...(((((((.(((.......))))))))))..(((..(((((.......(((((.(((..(....)..)))))))))))))...(((.....)))))))))))))...... ( -39.61)
>DroYak_CAF1 627 120 - 1
UGUGAAUAAGAGUGCCACCGCACAGAAAAUCCGAGGCAUUACUGACGGCUGUCAUCCAAGCAGCUGCCUGUAAUCCUGCCCUGCUCUGCUCCUGGAAUUUUCCACAGGACUCAUCCAAAA
((((.......((((....)))).((((((((((((.(((((.(.(((((((.......))))))).).))))))))((........))...))).))))))))))(((....))).... ( -33.80)
>consensus
UGUGAAUCAGCGUGCCACCGCACAGGAAAUGCGAGGCAUUACUGACAGCUGUCAUCCAAGCAGCUGCCUGUAAUCCUGCCCUGCUCAGCUCCUUGGAAUUUCCACAGGAUUCAUCCAAAA
.(((((((...((((....)))).(((((((((.((((((((.(.(((((((.......))))))).).))))...)))).)))((((....)))).))))))....)))))))...... (-30.65 = -31.03 +   0.38)

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 11:11:53 2006