Locus 4430

Sequence ID 2L_DroMel_CAF1
Location 12,748,302 – 12,748,515
Length 213
Max. P 0.772846
window6968 window6969 window6970

overview

Window 8

Location 12,748,302 – 12,748,404
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.17
Mean single sequence MFE -45.43
Consensus MFE -29.68
Energy contribution -29.99
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.65
SVM decision value 0.16
SVM RNA-class probability 0.611778
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12748302 102 + 22407834
CGAGGGAAAG----GGGGUUGCUUCCGAAG-----GGGGUCUGGAGAGCCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCCGGGGGAG---------CCCCA
..........----((((((.((((((...-----(((.((....)).)))(((((((....)))))))..((((((........)))))).......))))))))---------)))). ( -46.40)
>DroSec_CAF1 25263 106 + 1
CGAUGGAAAG----CGGGUU-CUUCCAAAGGAGGGGGGGUCUGGAGUGCCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCCGGGGGAG---------CCCCA
.........(----.(((((-(((((...((.((..((((.......))))(((((((....)))))))..((((((........)))))).))...)))))))))---------)))). ( -42.70)
>DroSim_CAF1 25641 102 + 1
CGAUGGAAAG----GGGGUU-CUUCCAAAG----GGAGGUCUGGAGUGCCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCCGGGGGAG---------CCCCA
..........----((((((-(((((....----((.((((.((.....))(((((((....)))))))...(((((........)))))))))...)))))))))---------)))). ( -45.90)
>DroEre_CAF1 26795 108 + 1
CGACGGCGAG----GGGG---AUUCCGAAG----G-GGGUCUGGAGAGGCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCUGGGGGAGCUGGGGCAGCCCCA
...((((..(----(.((---(((((....----)-))))))((.....))(((((((....)))))))..((((((........)))))).))..)))).(((.((((...))))))). ( -47.00)
>DroYak_CAF1 25786 113 + 1
AGGUGGGAAGGGGGGGGG---GUUCCAAAG----GGGGGUAUGGAGAGCCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCCGGGGGAGCCGGGGGAUCCCCA
..............((((---(((((....----((((((.......))))(((((((....)))))))..((((((........)))))).))...((((.....))))))))))))). ( -48.00)
>DroAna_CAF1 24711 100 + 1
CUUGAGGAUG----GCGG---GUGCCGGCU----G-G----CGGAGAACCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCCGAGGAAGCCGGG----CCCCA
..........----..((---(..((((((----(-(----(..((.....(((((((....)))))))..((((((........)))))).))..))).....)))))).----.))). ( -42.60)
>consensus
CGAUGGAAAG____GGGG___CUUCCAAAG____GGGGGUCUGGAGAGCCCGGCGCGUGACAAUGCGCCAAUGUGUGGUCAAGUGCGCACGACUGAGCCGGGGGAG_________CCCCA
..............((((....(((((..............)))))..((((((((((......))))...((((((........)))))).....)))))).............)))). (-29.68 = -29.99 +   0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,748,373 – 12,748,476
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.96
Mean single sequence MFE -33.13
Consensus MFE -22.64
Energy contribution -24.08
Covariance contribution 1.45
Combinations/Pair 1.12
Mean z-score -1.08
Structure conservation index 0.68
SVM decision value -0.01
SVM RNA-class probability 0.529690
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12748373 103 - 22407834
AACUGGUGCUCGCACCCACAC--------CUCCAAUCCUGCUCCAUGCUCCAUCUGGGAACAAAUUGAUGGAGUCUCCUUUGGGG---------CUCCCCCGGCUCAGUCGUGCGCACUU
....(((((..((((......--------..........((((((.((((((((((....))....))))))))......)))))---------)......(((...)))))))))))). ( -31.70)
>DroSec_CAF1 25338 103 - 1
AACUGGUGCUCGAACCCACAC--------CUCCAAUCCUGCUCCACGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUUUGGGG---------CUCCCCCGGCUCAGUCGUGCGCACUU
.....((((.(((........--------........(((..((..((((((((((....))....)))))))).......((((---------...))))))..)))))).)))).... ( -33.59)
>DroSim_CAF1 25712 103 - 1
AACUGGUGCUCGCACCCACAC--------CUCCAAUCCUGCUCCACGCUCCAUCUGGGAACAAAUUGAUGGAGCCUCCUUUGGGG---------CUCCCCCGGCUCAGUCGUGCGCACUU
....((((....)))).....--------.........(((..((((((....(((((..(.....)..((((((((....))))---------)))))))))...)).)))).)))... ( -32.70)
>DroEre_CAF1 26863 110 - 1
UACGGGUGCCCGCCUCCACAC--------CUCCAAUCCUGC--CGUGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUUUGGGGCUGCCCCAGCUCCCCCAGCUCAGUCGUGCGCACUU
...((((((.(((..(.....--------............--.(.((((((((((....))....)))))))))....((((((..((....))..))))))....)..))).)))))) ( -36.90)
>DroYak_CAF1 25859 118 - 1
UACGGGUGCCCGCCCCCACACCUCCAUACCUCCAAUCCUGC--CGUGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUUUGGGGAUCCCCCGGCUCCCCCGGCUCAGUCGUGCGCACUU
(((((((....))))........................((--((.((((((((((....))....)))))))).......(((((.((...)).)))))))))......)))....... ( -38.00)
>DroAna_CAF1 24775 92 - 1
-----ACCCCCGGCCCCAUAGA-------------------CACACACACACUCGGGGGACAAAUUGAUGGAGCCUCCUUUGGGG----CCCGGCUUCCUCGGCUCAGUCGUGCGCACUU
-----...((.(((((((..((-------------------...........))(((((.((......))...)))))..)))))----)).))........((.((....)).)).... ( -25.90)
>consensus
AACUGGUGCCCGCACCCACAC________CUCCAAUCCUGCUCCACGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUUUGGGG_________CUCCCCCGGCUCAGUCGUGCGCACUU
....(((((.(((.................................((((((((((....))....)))))))).....((((((............)))))).......))).))))). (-22.64 = -24.08 +   1.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,748,404 – 12,748,515
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.50
Mean single sequence MFE -22.92
Consensus MFE -16.66
Energy contribution -17.50
Covariance contribution 0.84
Combinations/Pair 1.21
Mean z-score -1.74
Structure conservation index 0.73
SVM decision value 0.53
SVM RNA-class probability 0.772846
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12748404 111 - 22407834
ACGUUAACUUUUGCUCCAUACCUCCCCCCGUCCCCCAGC-AACUGGUGCUCGCACCCACAC--------CUCCAAUCCUGCUCCAUGCUCCAUCUGGGAACAAAUUGAUGGAGUCUCCUU
............(((((((..............(((((.-....((((....)))).....--------..........((.....)).....)))))..(.....))))))))...... ( -21.40)
>DroSec_CAF1 25369 107 - 1
ACGUUAACUUUUGCUCCAUACCGCCCUCC--CC--UUGC-AACUGGUGCUCGAACCCACAC--------CUCCAAUCCUGCUCCACGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUU
............(((((((.......(((--((--.((.-...(((.((..((........--------......))..)).))).....))...))))).......)))))))...... ( -25.18)
>DroSim_CAF1 25743 109 - 1
ACGUUAACUUUUGCUUCAUCCAACCCACC--CCCUCUGC-AACUGGUGCUCGCACCCACAC--------CUCCAAUCCUGCUCCACGCUCCAUCUGGGAACAAAUUGAUGGAGCCUCCUU
..........((((...............--......))-))..((((....)))).....--------.................((((((((((....))....))))))))...... ( -20.70)
>DroEre_CAF1 26903 98 - 1
ACGUUAACUUUUGCUCCAUCCCC------------CUGCUUACGGGUGCCCGCCUCCACAC--------CUCCAAUCCUGC--CGUGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUU
............((((((((...------------........(((((..........)))--------))..........--.((.((((....)))))).....))))))))...... ( -23.90)
>DroYak_CAF1 25899 102 - 1
ACGUUAACUUUUGCUCCAUUCCU------------C----UACGGGUGCCCGCCCCCACACCUCCAUACCUCCAAUCCUGC--CGUGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUU
............((((((((...------------.----...((((....))))..........................--.((.((((....)))))).....))))))))...... ( -23.40)
>consensus
ACGUUAACUUUUGCUCCAUACCUCCC_CC__CC__CUGC_AACUGGUGCUCGCACCCACAC________CUCCAAUCCUGCUCCAUGCUCCAUCUGGGGACAAAUUGAUGGAGCCUCCUU
............((((((((........................((((....)))).............(((((.....((.....))......))))).......))))))))...... (-16.66 = -17.50 +   0.84)

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 11:17:34 2006