Locus 1759

Sequence ID 2L_DroMel_CAF1
Location 4,810,599 – 4,810,729
Length 130
Max. P 0.880924
window2824 window2825 window2826

overview

Window 4

Location 4,810,599 – 4,810,704
Length 105
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 90.06
Mean single sequence MFE -25.18
Consensus MFE -21.13
Energy contribution -21.80
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.84
SVM decision value 0.92
SVM RNA-class probability 0.880924
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4810599 105 + 22407834
-----CCAAUUACAAUUGUGAUUGCCAAUAGGCUCGGGACCUAUCAUCAUCGAUUGCAAUGGCCAAACAAUGGCCAAUGCCACAUGAAGAACGAACUCCACCCACAUAAU
-----.........((((((...(((....)))..(((.....((.((((.(...(((.((((((.....)))))).)))..))))).))..(.....).))).)))))) ( -26.80)
>DroSec_CAF1 13247 105 + 1
-----CCAAUUACAAGUGUGAUUGCCAAUAGGCUCGGGACCUAUCAUCAUCGAUUGCAGUGGCCAAACAAUGGCCAAUGCCACAUGAAGCACGAACUCCACCCACAUAAU
-----..((((((....))))))(((....)))..(((....(((......))).(((.((((((.....)))))).)))....................)))....... ( -25.50)
>DroSim_CAF1 10744 105 + 1
-----CCAAUUACAAUUGUGAUUGCCAAUAGGCCCGGGACCUAUCAUCAUCGAUUGCAGUGGCCAAACAAUGGCCAAUGCCACAUGAAGCACGAACUCCACCCACAUAAU
-----.........((((((...(((....)))..(((....(((......))).(((.((((((.....)))))).)))....................))).)))))) ( -25.20)
>DroEre_CAF1 13329 105 + 1
-----CCAAUUACAAUUGUGAUUGCCAAUAGGCUCGGGACCUAUCAUCAUCGAAUGCAAUGGCCAAACAAUGGCCAAUGCCACAUGAAGCACGAACUCCACCCACCUAAU
-----.(((((((....)))))))....((((...(((........((((.(...(((.((((((.....)))))).)))..))))).....(.....).))).)))).. ( -26.50)
>DroYak_CAF1 13815 110 + 1
CGCCGCCAAUUACAAUUGUGAUUGCCAAUAGGCCCGGGACCUAUCAUCAUCGAAUGCUAUGGCCAAACAAUGGCCAAUGCCACAUGAUGCACGAACUCCACCCACAUAAU
.(((..(((((((....)))))))......)))..(((......((((((.(...((..((((((.....))))))..))..)))))))...(.....).)))....... ( -28.30)
>DroAna_CAF1 14265 94 + 1
-----CCAAUUACAGAUGUGAUUGCCAAUAGGCCCG-AACCUAUC---AUCGAAUGCAGUGACCAAACAAUGGCCAAUGCUGCAU-------GAACUCCACCCACAUAAU
-----..........(((((.(((...(((((....-..))))).---..)))((((((((.(((.....))).)...)))))))-------..........)))))... ( -18.80)
>consensus
_____CCAAUUACAAUUGUGAUUGCCAAUAGGCCCGGGACCUAUCAUCAUCGAAUGCAAUGGCCAAACAAUGGCCAAUGCCACAUGAAGCACGAACUCCACCCACAUAAU
.......((((((....))))))(((....)))..(((.....((......))..(((.((((((.....)))))).)))....................)))....... (-21.13 = -21.80 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,810,599 – 4,810,704
Length 105
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 90.06
Mean single sequence MFE -33.38
Consensus MFE -28.84
Energy contribution -29.73
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.86
SVM decision value 0.49
SVM RNA-class probability 0.755114
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4810599 105 - 22407834
AUUAUGUGGGUGGAGUUCGUUCUUCAUGUGGCAUUGGCCAUUGUUUGGCCAUUGCAAUCGAUGAUGAUAGGUCCCGAGCCUAUUGGCAAUCACAAUUGUAAUUGG-----
....(((((((((((......))))))...(((.((((((.....)))))).)))......((..(((((((.....)))))))..)).)))))...........----- ( -32.80)
>DroSec_CAF1 13247 105 - 1
AUUAUGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCACUGCAAUCGAUGAUGAUAGGUCCCGAGCCUAUUGGCAAUCACACUUGUAAUUGG-----
....((..((((((.....(((((((((..(((.((((((.....)))))).)))...).)))).(((((((.....))))))))))).)).))))..)).....----- ( -35.80)
>DroSim_CAF1 10744 105 - 1
AUUAUGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCACUGCAAUCGAUGAUGAUAGGUCCCGGGCCUAUUGGCAAUCACAAUUGUAAUUGG-----
....((((((((((((....)))))))...(((.((((((.....)))))).)))......((..(((((((.....)))))))..)).)))))...........----- ( -35.40)
>DroEre_CAF1 13329 105 - 1
AUUAGGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCAUUGCAUUCGAUGAUGAUAGGUCCCGAGCCUAUUGGCAAUCACAAUUGUAAUUGG-----
.....(((((((((((....)))))))...(((.((((((.....)))))).)))......((..(((((((.....)))))))..)).))))............----- ( -33.40)
>DroYak_CAF1 13815 110 - 1
AUUAUGUGGGUGGAGUUCGUGCAUCAUGUGGCAUUGGCCAUUGUUUGGCCAUAGCAUUCGAUGAUGAUAGGUCCCGGGCCUAUUGGCAAUCACAAUUGUAAUUGGCGGCG
.....((((((((..(..((.(((((((..((..((((((.....))))))..))...).))))))))..)..))..))))))((.((((.((....)).)))).))... ( -33.30)
>DroAna_CAF1 14265 94 - 1
AUUAUGUGGGUGGAGUUC-------AUGCAGCAUUGGCCAUUGUUUGGUCACUGCAUUCGAU---GAUAGGUU-CGGGCCUAUUGGCAAUCACAUCUGUAAUUGG-----
....((..((((((....-------.(((.(((.((((((.....)))))).))).......---(((((((.-...))))))).))).)).))))..)).....----- ( -29.60)
>consensus
AUUAUGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCACUGCAAUCGAUGAUGAUAGGUCCCGAGCCUAUUGGCAAUCACAAUUGUAAUUGG_____
....(((((((((((......))))))((.(((.((((((.....)))))).)))..........(((((((.....))))))).))..)))))................ (-28.84 = -29.73 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,810,634 – 4,810,729
Length 95
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 86.33
Mean single sequence MFE -29.68
Consensus MFE -21.22
Energy contribution -22.02
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.71
SVM decision value 0.14
SVM RNA-class probability 0.603526
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4810634 95 - 22407834
UGCUU--CUGCUCGUUCUGCUGCUGCAAUUAUGUGGGUGGAGUUCGUUCUUCAUGUGGCAUUGGCCAUUGUUUGGCCAUUGCAAUCGAUGAUGAUAG
...((--(..((((...(((....)))......))))..))).....((.(((((..(((.((((((.....)))))).)))...).)))).))... ( -28.20)
>DroSec_CAF1 13282 80 - 1
UGCU-----------------GCUGCAAUUAUGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCACUGCAAUCGAUGAUGAUAG
(((.-----------------...)))(((((.((((((((((....)))))))...(((.((((((.....)))))).)))..))))))))..... ( -25.50)
>DroSim_CAF1 10779 95 - 1
UGCUG--CUGCUCGUUCUGCUGCUGCAAUUAUGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCACUGCAAUCGAUGAUGAUAG
(((.(--(.((.......)).)).)))(((((.((((((((((....)))))))...(((.((((((.....)))))).)))..))))))))..... ( -31.20)
>DroEre_CAF1 13364 94 - 1
UGCCGCGCUCCUCGUUCAU---CUGCAAUUAGGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCAUUGCAUUCGAUGAUGAUAG
.((((.(((((..(..(((---(((....))))))..)))))).)).)).(((((..(((.((((((.....)))))).)))...).))))...... ( -35.90)
>DroYak_CAF1 13855 92 - 1
UGCCG--CUCCUCGUUCUU---CAGCAAUUAUGUGGGUGGAGUUCGUGCAUCAUGUGGCAUUGGCCAUUGUUUGGCCAUAGCAUUCGAUGAUGAUAG
..(((--(.((.(((....---........))).))))))........(((((((..((..((((((.....))))))..))...).)))))).... ( -27.60)
>consensus
UGCUG__CUCCUCGUUCUG__GCUGCAAUUAUGUGGGUGGAGUUCGUGCUUCAUGUGGCAUUGGCCAUUGUUUGGCCAUUGCAAUCGAUGAUGAUAG
......................((((......))))(((((((....)))))))...(((.((((((.....)))))).)))............... (-21.22 = -22.02 +   0.80)

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 10:10:27 2006