Locus 4828

Sequence ID 3L_DroMel_CAF1
Location 13,548,339 – 13,548,504
Length 165
Max. P 0.999562
window7612 window7613 window7614 window7615 window7616

overview

Window 2

Location 13,548,339 – 13,548,429
Length 90
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 87.85
Mean single sequence MFE -29.02
Consensus MFE -21.76
Energy contribution -22.96
Covariance contribution 1.20
Combinations/Pair 1.07
Mean z-score -1.85
Structure conservation index 0.75
SVM decision value 0.47
SVM RNA-class probability 0.750693
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13548339 90 - 23771897
UAAAAAAAAUGGCGCCCAACGUGGGGCAAAGCUGAGGCUGCUGUUUUCUAUAUGAA-------GGUAUGGGAGAACCGGGAGUUUCUUCUUAACGCU
..........(((((((......)))).(((..((((((.(((((((((((((...-------.))))))))))..))).))))))..)))...))) ( -29.40)
>DroSec_CAF1 35520 90 - 1
UAAAAAAAAUGGCGCCCAACGUGGGACAGAGCUGAGGCUGCUGUUUUCUAUAUGAA-------GGUAUGAGAGAACCGGCAGUUUCUUCUUAACGCU
..........(((((((.....)))...(((..((((((((((((((((((((...-------.)))).)))))).))))))))))..)))..)))) ( -30.40)
>DroSim_CAF1 21618 89 - 1
UAAAA-AAAUGGCGCCCAACAUGGGGCAAAGCUGAGGCUGCUGUUUUCUAUAUGAA-------GGUGUGGGAGAACCGGGAGUUUCUUCUUAACGCU
.....-....(((((((......)))).(((..((((((.(((((((((((((...-------.))))))))))..))).))))))..)))...))) ( -29.40)
>DroEre_CAF1 36079 88 - 1
CAAAA-AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUGCUGUUUUCUAUAUG-------GGGGAAUGGG-GCACCGGCAGUUUCUUCUUAACGCU
.....-....(((((((......)))).(((..((((((((((((..((.....-------))..)))((.-...)))))))))))..)))...))) ( -30.90)
>DroYak_CAF1 37566 94 - 1
CGAA--AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUGCUGUUUUCUAUAUGAAGGUACGGGGUAUGGG-GUAACGAGAGUUUCUUCUUAACGCU
.(((--((.((((((((......))))..(((....)))))))))))).............((.((..(((-(.(((....))).))))...)).)) ( -25.00)
>consensus
UAAAA_AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUGCUGUUUUCUAUAUGAA_______GGUAUGGGAGAACCGGGAGUUUCUUCUUAACGCU
..........(((((((......)))).(((..((((((.(((((((((((((...........))))))))))..))).))))))..)))...))) (-21.76 = -22.96 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,548,373 – 13,548,466
Length 93
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 90.12
Mean single sequence MFE -28.96
Consensus MFE -23.92
Energy contribution -24.04
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -2.96
Structure conservation index 0.83
SVM decision value 3.14
SVM RNA-class probability 0.998565
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13548373 93 + 23771897
----UUCAUAUAGAAAACAGCAGCCUCAGCUUUGCCCCACGUUGGGCGCCAUUUUUUUUAUACGGCACACCA--GUGCCCAACGUUGGGCGCCAUUUUU
----........(((((..(((((....)))..((((.((((((((((((.............)))((....--))))))))))).))))))..))))) ( -33.22)
>DroSec_CAF1 35554 93 + 1
----UUCAUAUAGAAAACAGCAGCCUCAGCUCUGUCCCACGUUGGGCGCCAUUUUUUUUAUACGGCACACCA--UUGCCCCACCUUGGGCGCCAUUUUU
----............((((.(((....))))))).........((((((.............((((.....--.)))).(.....)))))))...... ( -22.90)
>DroSim_CAF1 21652 92 + 1
----UUCAUAUAGAAAACAGCAGCCUCAGCUUUGCCCCAUGUUGGGCGCCAUUU-UUUUAUACGGCACACCA--UUGCCGCACGUUGGGCGCCAUUUUU
----........(((((..((.(((.((((...((((......)))).......-.......(((((.....--.)))))...)))))))))..))))) ( -26.40)
>DroEre_CAF1 36114 92 + 1
------CAUAUAGAAAACAGCAGCCUCAGCUCUGCCCCACGUUGGGCGCCAUUU-UUUUGUAUGGCACACCACGUUGCCCCACGUUGGGCGCCAUUUUU
------......(((((..(((((....)))..((((.((((.(((((((((..-......)))))((.....)).)))).)))).))))))..))))) ( -32.20)
>DroYak_CAF1 37602 95 + 1
UACCUUCAUAUAGAAAACAGCAGCCUCAGCUCUGCCCCACGUUGGGCGCCAUUU--UUCGUAUGGCUCACCA--GUGCCCCACGUUGGGCGCCAUUUUU
............(((((..(((((....)))..((((.((((.(((((((((..--.....)))))......--..)))).)))).))))))..))))) ( -30.10)
>consensus
____UUCAUAUAGAAAACAGCAGCCUCAGCUCUGCCCCACGUUGGGCGCCAUUU_UUUUAUACGGCACACCA__UUGCCCCACGUUGGGCGCCAUUUUU
............(((((..(((((....)))..((((.((((.(((((((.............)))..........)))).)))).))))))..))))) (-23.92 = -24.04 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,548,373 – 13,548,466
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 90.12
Mean single sequence MFE -35.56
Consensus MFE -29.50
Energy contribution -30.06
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -3.59
Structure conservation index 0.83
SVM decision value 3.73
SVM RNA-class probability 0.999562
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13548373 93 - 23771897
AAAAAUGGCGCCCAACGUUGGGCAC--UGGUGUGCCGUAUAAAAAAAAUGGCGCCCAACGUGGGGCAAAGCUGAGGCUGCUGUUUUCUAUAUGAA----
.((((((((((((.(((((((((((--....))(((((.........)))))))))))))).))))..(((....))))))))))).........---- ( -41.00)
>DroSec_CAF1 35554 93 - 1
AAAAAUGGCGCCCAAGGUGGGGCAA--UGGUGUGCCGUAUAAAAAAAAUGGCGCCCAACGUGGGACAGAGCUGAGGCUGCUGUUUUCUAUAUGAA----
.........((((......))))..--(((.(((((((.........))))))))))..((((((((((((....))).)))))..)))).....---- ( -30.70)
>DroSim_CAF1 21652 92 - 1
AAAAAUGGCGCCCAACGUGCGGCAA--UGGUGUGCCGUAUAAAA-AAAUGGCGCCCAACAUGGGGCAAAGCUGAGGCUGCUGUUUUCUAUAUGAA----
.(((((((((((((.(((((((((.--.....))))))))....-.......((((......))))...).)).))).)))))))).........---- ( -31.80)
>DroEre_CAF1 36114 92 - 1
AAAAAUGGCGCCCAACGUGGGGCAACGUGGUGUGCCAUACAAAA-AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUGCUGUUUUCUAUAUG------
.((((((((((((.((((.((((.((.....))(((((......-..))))))))).)))).))))..(((....))))))))))).......------ ( -37.30)
>DroYak_CAF1 37602 95 - 1
AAAAAUGGCGCCCAACGUGGGGCAC--UGGUGAGCCAUACGAA--AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUGCUGUUUUCUAUAUGAAGGUA
.((((((((((((.((((.((((.(--....).(((((.....--..))))))))).)))).))))..(((....)))))))))))............. ( -37.00)
>consensus
AAAAAUGGCGCCCAACGUGGGGCAA__UGGUGUGCCGUAUAAAA_AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUGCUGUUUUCUAUAUGAA____
.((((((((((((.((((.((((..........(((((.........))))))))).)))).))))..(((....)))))))))))............. (-29.50 = -30.06 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,548,389 – 13,548,504
Length 115
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 93.94
Mean single sequence MFE -36.05
Consensus MFE -31.12
Energy contribution -31.24
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.42
Structure conservation index 0.86
SVM decision value 0.65
SVM RNA-class probability 0.810944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13548389 115 + 23771897
CAGCCUCAGCUUUGCCCCACGUUGGGCGCCAUUUUUUUUAUACGGCACACCA--GUGCCCAACGUUGGGCGCCAUUUUUGUCAAGUCGCAUUAAGGCAGCGCGCUCAUUCGACUUGU
.(((....)))..((((.((((((((((((.............)))((....--))))))))))).))))...........(((((((.((...(((.....))).)).))))))). ( -40.42)
>DroSec_CAF1 35570 115 + 1
CAGCCUCAGCUCUGUCCCACGUUGGGCGCCAUUUUUUUUAUACGGCACACCA--UUGCCCCACCUUGGGCGCCAUUUUUGUCAAGUCGCAUUAAGGCAGCGCGCUCAUUCGACUUGU
..(((.((((..........)))))))(((.............)))......--..((((......))))...........(((((((.((...(((.....))).)).))))))). ( -28.82)
>DroSim_CAF1 21668 114 + 1
CAGCCUCAGCUUUGCCCCAUGUUGGGCGCCAUUU-UUUUAUACGGCACACCA--UUGCCGCACGUUGGGCGCCAUUUUUGUCAAGUCGCAUUAAGGCAGCGCGCUCAUUCGACUUGU
..(((.((((...((((......)))).......-.......(((((.....--.)))))...)))))))...........(((((((.((...(((.....))).)).))))))). ( -34.30)
>DroEre_CAF1 36128 116 + 1
CAGCCUCAGCUCUGCCCCACGUUGGGCGCCAUUU-UUUUGUAUGGCACACCACGUUGCCCCACGUUGGGCGCCAUUUUUGUCAAGUCGCAUUAAGGCAGCGCGCUCAUUCGACUUGU
.(((....)))..((((.((((.(((((((((..-......)))))((.....)).)))).)))).))))...........(((((((.((...(((.....))).)).))))))). ( -39.40)
>DroYak_CAF1 37622 113 + 1
CAGCCUCAGCUCUGCCCCACGUUGGGCGCCAUUU--UUCGUAUGGCUCACCA--GUGCCCCACGUUGGGCGCCAUUUUUGUCAAGUCGCAUUAAGGCAGCGCGCUCAUUCGACUUGU
.(((....)))..((((.((((.(((((((((..--.....)))))......--..)))).)))).))))...........(((((((.((...(((.....))).)).))))))). ( -37.30)
>consensus
CAGCCUCAGCUCUGCCCCACGUUGGGCGCCAUUU_UUUUAUACGGCACACCA__UUGCCCCACGUUGGGCGCCAUUUUUGUCAAGUCGCAUUAAGGCAGCGCGCUCAUUCGACUUGU
.(((....)))..((((.((((.(((((((.............)))..........)))).)))).))))...........(((((((.((...(((.....))).)).))))))). (-31.12 = -31.24 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,548,389 – 13,548,504
Length 115
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 93.94
Mean single sequence MFE -42.62
Consensus MFE -36.60
Energy contribution -37.16
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.50
Structure conservation index 0.86
SVM decision value 3.08
SVM RNA-class probability 0.998358
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13548389 115 - 23771897
ACAAGUCGAAUGAGCGCGCUGCCUUAAUGCGACUUGACAAAAAUGGCGCCCAACGUUGGGCAC--UGGUGUGCCGUAUAAAAAAAAUGGCGCCCAACGUGGGGCAAAGCUGAGGCUG
.(((((((..((((.((...))))))...)))))))...........((((.(((((((((((--....))(((((.........)))))))))))))).))))..(((....))). ( -48.10)
>DroSec_CAF1 35570 115 - 1
ACAAGUCGAAUGAGCGCGCUGCCUUAAUGCGACUUGACAAAAAUGGCGCCCAAGGUGGGGCAA--UGGUGUGCCGUAUAAAAAAAAUGGCGCCCAACGUGGGACAGAGCUGAGGCUG
.(((((((..((((.((...))))))...)))))))........(((((((......))))..--(((.(((((((.........))))))))))............)))....... ( -37.60)
>DroSim_CAF1 21668 114 - 1
ACAAGUCGAAUGAGCGCGCUGCCUUAAUGCGACUUGACAAAAAUGGCGCCCAACGUGCGGCAA--UGGUGUGCCGUAUAAAA-AAAUGGCGCCCAACAUGGGGCAAAGCUGAGGCUG
.(((((((..((((.((...))))))...)))))))........((((((....((((((((.--.....))))))))....-....)))((((......))))...)))....... ( -38.90)
>DroEre_CAF1 36128 116 - 1
ACAAGUCGAAUGAGCGCGCUGCCUUAAUGCGACUUGACAAAAAUGGCGCCCAACGUGGGGCAACGUGGUGUGCCAUACAAAA-AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUG
.(((((((..((((.((...))))))...)))))))...........((((.((((.((((.((.....))(((((......-..))))))))).)))).))))..(((....))). ( -44.40)
>DroYak_CAF1 37622 113 - 1
ACAAGUCGAAUGAGCGCGCUGCCUUAAUGCGACUUGACAAAAAUGGCGCCCAACGUGGGGCAC--UGGUGAGCCAUACGAA--AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUG
.(((((((..((((.((...))))))...)))))))...........((((.((((.((((.(--....).(((((.....--..))))))))).)))).))))..(((....))). ( -44.10)
>consensus
ACAAGUCGAAUGAGCGCGCUGCCUUAAUGCGACUUGACAAAAAUGGCGCCCAACGUGGGGCAA__UGGUGUGCCGUAUAAAA_AAAUGGCGCCCAACGUGGGGCAGAGCUGAGGCUG
.(((((((..((((.((...))))))...)))))))...........((((.((((.((((..........(((((.........))))))))).)))).))))..(((....))). (-36.60 = -37.16 +   0.56)

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 11:34:36 2006