Locus 6485

Sequence ID 3L_DroMel_CAF1
Location 17,253,863 – 17,254,085
Length 222
Max. P 0.994889
window10457 window10458 window10459 window10460 window10461

overview

Window 7

Location 17,253,863 – 17,253,965
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.65
Mean single sequence MFE -33.46
Consensus MFE -25.26
Energy contribution -25.66
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.24
Structure conservation index 0.75
SVM decision value 2.52
SVM RNA-class probability 0.994889
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17253863 102 + 23771897
UAUAUAUGUAUGCGGGAGCUGCGGCUGUGGCACGUAUUUGUUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC------------------AGUCUCA
.............((((.(((.(((((.(((..((...(((((((....((((((((...))))))))..)))))))...))..))).))))).)------------------)))))). ( -34.30)
>DroSec_CAF1 137661 96 + 1
------UAUAUGCGGGAGCUGCGGCUGUGGCACGUAUUUGUUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC------------------AGUCUCA
------.......((((.(((.(((((.(((..((...(((((((....((((((((...))))))))..)))))))...))..))).))))).)------------------)))))). ( -34.30)
>DroSim_CAF1 132490 96 + 1
------UAUAUGCGGGAGCUGCGGCUGUGGCACGUAUUUGUUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC------------------AGUCUCA
------.......((((.(((.(((((.(((..((...(((((((....((((((((...))))))))..)))))))...))..))).))))).)------------------)))))). ( -34.30)
>DroEre_CAF1 140795 90 + 1
------UAUAUGCGGGAGCUGCGGCUGUUGCACGUAUUUGUUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCACA------------------------
------.....((((...))))(((((..((..((...(((((((....((((((((...))))))))..)))))))...))..))..)))))...------------------------ ( -24.40)
>DroYak_CAF1 144610 112 + 1
-------AUAUGCG-GAGCUGUGGCUGUUGCACGUAUUUGUUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCUCAGUCACAGCCACAGCCACAGUCUCA
-------.......-(((((((((((((.((........((((((....((((((((...))))))))..))))))..((((((((....))))..))))..)).)))))))))).))). ( -40.00)
>consensus
______UAUAUGCGGGAGCUGCGGCUGUGGCACGUAUUUGUUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC__________________AGUCUCA
...........((....))...(((((.(((..((...(((((((....((((((((...))))))))..)))))))...))..))).)))))........................... (-25.26 = -25.66 +   0.40)

alignment

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secondary structure

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Window 8

Location 17,253,863 – 17,253,965
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.65
Mean single sequence MFE -30.03
Consensus MFE -20.91
Energy contribution -21.51
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -3.44
Structure conservation index 0.70
SVM decision value 2.13
SVM RNA-class probability 0.988733
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17253863 102 - 23771897
UGAGACU------------------GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAACAAAUACGUGCCACAGCCGCAGCUCCCGCAUACAUAUAUA
.(((.((------------------(((((((.(((.((.............((((((((...))))))))...............)).))).))))))))))))............... ( -30.19)
>DroSec_CAF1 137661 96 - 1
UGAGACU------------------GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAACAAAUACGUGCCACAGCCGCAGCUCCCGCAUAUA------
.(((.((------------------(((((((.(((.((.............((((((((...))))))))...............)).))).)))))))))))).........------ ( -30.19)
>DroSim_CAF1 132490 96 - 1
UGAGACU------------------GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAACAAAUACGUGCCACAGCCGCAGCUCCCGCAUAUA------
.(((.((------------------(((((((.(((.((.............((((((((...))))))))...............)).))).)))))))))))).........------ ( -30.19)
>DroEre_CAF1 140795 90 - 1
------------------------UGUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAACAAAUACGUGCAACAGCCGCAGCUCCCGCAUAUA------
------------------------((((((((..((.((.............((((((((...))))))))...............)).))..))))))))((....)).....------ ( -21.69)
>DroYak_CAF1 144610 112 - 1
UGAGACUGUGGCUGUGGCUGUGACUGAGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAACAAAUACGUGCAACAGCCACAGCUC-CGCAUAU-------
.(((.((((((((((.((((((..((((((....))))..............((((((((...)))))))).........))..)))).)).)))))))))))))-.......------- ( -37.90)
>consensus
UGAGACU__________________GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAACAAAUACGUGCCACAGCCGCAGCUCCCGCAUAUA______
.........................(((((((.(((.((.............((((((((...))))))))...............)).))).))))))).((....))........... (-20.91 = -21.51 +   0.60)

alignment

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secondary structure

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Window 9

Location 17,253,903 – 17,254,005
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.49
Mean single sequence MFE -25.08
Consensus MFE -21.70
Energy contribution -21.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.87
SVM decision value 0.25
SVM RNA-class probability 0.653661
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17253903 102 + 23771897
UUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC------------------AGUCUCAGUCUCAGUCAGCCAUCCUGCUACAAGGACCUCCAUUUCGG
.........((((((((...))))))))..(((((((.((((.(((....)))..------------------.(.((.......)).).))))((((......))))....))))))). ( -23.90)
>DroSec_CAF1 137695 102 + 1
UUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC------------------AGUCUCAGUCGCAGUGAGCCAUCCUGCUACAAGGACCUCCAUUUCGG
.........((((((((...))))))))..(((((((.((((........)))).------------------.((((..((.((((.((....)))))).))..))))...))))))). ( -27.60)
>DroSim_CAF1 132524 102 + 1
UUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC------------------AGUCUCAGUCGCAGUCAGCCAUCCUGCUACAAGGACCUCCAUUUCGG
.........((((((((...))))))))..(((((((.((((........)))).------------------.((((..((.((((.........)))).))..))))...))))))). ( -24.80)
>DroEre_CAF1 140829 96 + 1
UUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCACA------------------------CUCCCAGUCAGCCAUCCUGCCACAAGGACCUCCAUUUCGG
.........((((((((...))))))))..(((((((.((((.(((....)))..(------------------------(.....))..))))((((......))))....))))))). ( -23.20)
>DroYak_CAF1 144642 120 + 1
UUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCUCAGUCACAGCCACAGCCACAGUCUCAGUCUCAGUCAGCCAUCCUGCUACAAGGACCUCCAUUUCGG
.........((((((((...))))))))..(((((((.((((((((....))))..((.......)).))))........((((..((.(((......)))))..))))...))))))). ( -25.90)
>consensus
UUUUAAUAAAAGUUUUGCAGCAAAACUUAAUGAAAUGUUGGCAGGCCUCAGCCAC__________________AGUCUCAGUCGCAGUCAGCCAUCCUGCUACAAGGACCUCCAUUUCGG
.........((((((((...))))))))..(((((((..((..(((....))).........................................((((......))))))..))))))). (-21.70 = -21.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,253,903 – 17,254,005
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.49
Mean single sequence MFE -31.78
Consensus MFE -23.87
Energy contribution -24.11
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.75
SVM decision value 0.26
SVM RNA-class probability 0.657830
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17253903 102 - 23771897
CCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGAGACUGAGACU------------------GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAA
....(((((((((..((((((((((((((((.....)).))((((.(------------------(((((........))).))))))).....)))))))))))).))))))))).... ( -29.10)
>DroSec_CAF1 137695 102 - 1
CCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUCACUGCGACUGAGACU------------------GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAA
....(((((((((..((((((((((((.((.....))...(((((.(------------------(((((........))).))))))))....)))))))))))).))))))))).... ( -31.90)
>DroSim_CAF1 132524 102 - 1
CCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGCGACUGAGACU------------------GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAA
....(((((((((..((((((((((((.((.....))...(((((.(------------------(((((........))).))))))))....)))))))))))).))))))))).... ( -31.90)
>DroEre_CAF1 140829 96 - 1
CCGAAAUGGAGGUCCUUGUGGCAGGAUGGCUGACUGGGAG------------------------UGUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAA
....(((((((((..(((..(((((((...(((...((((------------------------((((((........))).))))))).))).)))))))..))).))))))))).... ( -31.20)
>DroYak_CAF1 144642 120 - 1
CCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGAGACUGAGACUGUGGCUGUGGCUGUGACUGAGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAA
....(((((((((..((((((((((((((((.....)).))((((.((((((...((((..(.(....))...)))).))).))))))).....)))))))))))).))))))))).... ( -34.80)
>consensus
CCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGAGACUGAGACU__________________GUGGCUGAGGCCUGCCAACAUUUCAUUAAGUUUUGCUGCAAAACUUUUAUUAAAA
....(((((((((..(((((((((((((((...((.......)).......................(((....))).)))).............))))))))))).))))))))).... (-23.87 = -24.11 +   0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,253,965 – 17,254,085
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -42.02
Consensus MFE -36.30
Energy contribution -37.70
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.86
SVM decision value 1.01
SVM RNA-class probability 0.899309
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17253965 120 - 23771897
CAUUUGCACACACAUAACUUUGCAGCAGUCGCAGUCGGAACAUGUUCAUGUCUUGGGCCUGUCUGGGAAACAAGCUAGGCCCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGAGAC
...(((((............)))))..(((.(((((((......(((((...(((((((((.((.(....).)).))))))))).))))).(((((......)))))..))))))).))) ( -42.60)
>DroSec_CAF1 137757 120 - 1
CAUUUGCACACACAUAACUUUGCAGCAGUCGCAGUCGGAACAUGUUCAUGUCUUGGGCCUGUCUGGGAAACAAGCUAGGCCCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUCACUGCGAC
...(((((............)))))..((((((((.((......(((((...(((((((((.((.(....).)).))))))))).))))).(((((......)))))..)).)))))))) ( -42.80)
>DroSim_CAF1 132586 120 - 1
CAUUUGCACACACAUAACUUUGCAGCAAUCGCAGUCGGAACAUGUUCCUGUCUUGGGCCUGUCUGGGAAACAAGCUAGGCCCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGCGAC
...(((((............)))))...((((((((((.......((((((.(((((((((.((.(....).)).)))))))))...((....)).....))))))...)))))))))). ( -47.20)
>DroEre_CAF1 140885 120 - 1
CAUUUGCACACACAUAACUUUGCAGCAGUCGCAGUCGGAACGUGUUCAUGUCUUGGUCCUGUCUGGGAAACAAGCUAGGCCCGAAAUGGAGGUCCUUGUGGCAGGAUGGCUGACUGGGAG
...(((((............)))))...((.(((((((.((((....))))....((((((((..(....)..((.(((.((........)).))).))))))))))..))))))).)). ( -36.80)
>DroYak_CAF1 144722 120 - 1
CAUUUGCACACACAUAAGUAAGCAGCAGUCGGAGUCGGAACAUGUUCAUGUCUUGGGCCUGUCUGGGAAACAAGCUAGGCCCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGAGAC
...((((..((......))..))))..(((..((((((......(((((...(((((((((.((.(....).)).))))))))).))))).(((((......)))))..))))))..))) ( -40.70)
>consensus
CAUUUGCACACACAUAACUUUGCAGCAGUCGCAGUCGGAACAUGUUCAUGUCUUGGGCCUGUCUGGGAAACAAGCUAGGCCCGAAAUGGAGGUCCUUGUAGCAGGAUGGCUGACUGAGAC
...(((((............)))))..(((.(((((((......(((((...(((((((((.((.(....).)).))))))))).))))).(((((......)))))..))))))).))) (-36.30 = -37.70 +   1.40)

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 12:20:51 2006