Locus 2328

Sequence ID 2R_DroMel_CAF1
Location 8,534,240 – 8,534,432
Length 192
Max. P 0.996366
window3834 window3835 window3836 window3837 window3838 window3839

overview

Window 4

Location 8,534,240 – 8,534,360
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.24
Mean single sequence MFE -33.15
Consensus MFE -22.64
Energy contribution -23.27
Covariance contribution 0.63
Combinations/Pair 1.03
Mean z-score -2.71
Structure conservation index 0.68
SVM decision value 0.79
SVM RNA-class probability 0.851138
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534240 120 + 20766785
AUGAAUAAACCAGGCACAACAACGCAUUUGAUUGAGUGUGUGUGUGUGUGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAUAUAUUCAGGCAAACUCGAAGGCCAUCAAAGGCC
.((((((...(((((((((((((((((((....)))))))).))).))))).)))...((((.((((((((....)))))))))))).))))))............((((......)))) ( -35.50)
>DroSec_CAF1 9746 111 + 1
AUGAAUAAACCAGGCACA---CCGCUUAUGAUUGAGUGUGU----GUGCGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAU--AUUCAGGCAAACUCGAAGGCCAACUGAGGCC
.(((.........(((((---(((((((....)))))).))----))))((.(((...((((.((((((((....))))))))))))--...)))))....)))..((((......)))) ( -34.90)
>DroSim_CAF1 13210 113 + 1
AUGAAUAAGCCAGGCACA---CCGCUUUUGAUUGAGUGUGUG--UGUGUGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAU--AUUCAGGCAAACUCGAAGGCCAAAUGAGGCC
.(((((((((((.(((((---(.((((......)))))))))--).)).)))....(((....((((((((....))))))))))))--)))))............((((......)))) ( -32.70)
>DroYak_CAF1 12983 105 + 1
AUGAAUAAACCAGGCA-----CCGCUUGUGAUUGAGUGU--------GUGCUCUGCUCAUUACAUUCAUUAAGUUUAAUGAAUUGAU--AUUCAGGCAAACUCGAAGGCCAUCCGAGGCC
.((((((...((((((-----((((((......))))).--------)))).))).(((....((((((((....))))))))))))--)))))............((((......)))) ( -29.50)
>consensus
AUGAAUAAACCAGGCACA___CCGCUUUUGAUUGAGUGUGU____GUGUGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAU__AUUCAGGCAAACUCGAAGGCCAACUGAGGCC
............(((........((((((((..(((((..(....)..)))))((((......((((((((....))))))))(((.....)))))))...))))))))........))) (-22.64 = -23.27 +   0.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,534,240 – 8,534,360
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.24
Mean single sequence MFE -30.16
Consensus MFE -24.15
Energy contribution -24.09
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -2.01
Structure conservation index 0.80
SVM decision value 0.91
SVM RNA-class probability 0.879998
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534240 120 - 20766785
GGCCUUUGAUGGCCUUCGAGUUUGCCUGAAUAUAUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCACACACACACACACUCAAUCAAAUGCGUUGUUGUGCCUGGUUUAUUCAU
((((......))))...((((..(((...........((((((((....)))))))).........((.(((((.(((.((.((..........)).)))))))))))))))..)))).. ( -29.20)
>DroSec_CAF1 9746 111 - 1
GGCCUCAGUUGGCCUUCGAGUUUGCCUGAAU--AUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCGCAC----ACACACUCAAUCAUAAGCGG---UGUGCCUGGUUUAUUCAU
((((......))))...((((..(((((..(--((..((((((((....))))))))...)))..)).((.((((----((.(.((........)).))---))))))))))..)))).. ( -32.10)
>DroSim_CAF1 13210 113 - 1
GGCCUCAUUUGGCCUUCGAGUUUGCCUGAAU--AUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCACACA--CACACACUCAAUCAAAAGCGG---UGUGCCUGGCUUAUUCAU
((((......))))...((((..(((.....--....((((((((....)))))))).........((.((((((.--(.(..............).))---))))))))))..)))).. ( -30.84)
>DroYak_CAF1 12983 105 - 1
GGCCUCGGAUGGCCUUCGAGUUUGCCUGAAU--AUCAAUUCAUUAAACUUAAUGAAUGUAAUGAGCAGAGCAC--------ACACUCAAUCACAAGCGG-----UGCCUGGUUUAUUCAU
((((......))))...(((((((..(((((--....))))).))))))).(((((((....((.(((.((((--------.(.((........)).))-----)))))).))))))))) ( -28.50)
>consensus
GGCCUCAGAUGGCCUUCGAGUUUGCCUGAAU__AUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCACAC____ACACACUCAAUCAAAAGCGG___UGUGCCUGGUUUAUUCAU
((((......))))...((((..(((...........((((((((....)))))))).........((.(((((............................))))))))))..)))).. (-24.15 = -24.09 +  -0.06)

alignment

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secondary structure

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Window 6

Location 8,534,280 – 8,534,395
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.82
Mean single sequence MFE -32.25
Consensus MFE -22.40
Energy contribution -22.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.35
Structure conservation index 0.69
SVM decision value 1.83
SVM RNA-class probability 0.979256
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534280 115 + 20766785
UGUGUGUGUGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAUAUAUUCAGGCAAACUCGAAGGCCAUCAAAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGUAUAAUA-----
....((((..(.(.(((.((((.((((((((....))))))))))))((((((((..((..(((.(((((......))))).))).))..)))))))).))).).)..))))...----- ( -34.00)
>DroSec_CAF1 9783 109 + 1
U----GUGCGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAU--AUUCAGGCAAACUCGAAGGCCAACUGAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGCUUAAUA-----
.----(..(((...(((......((((((((....)))))))).(((--((((((..((..(((.(((((......))))).))).))..)))))))))))).)))..)......----- ( -36.20)
>DroSim_CAF1 13247 111 + 1
UG--UGUGUGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAU--AUUCAGGCAAACUCGAAGGCCAAAUGAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGUAUAGUA-----
..--((((..(.(.(((......((((((((....)))))))).(((--((((((..((..(((.(((((......))))).))).))..)))))))))))).).)..))))...----- ( -34.80)
>DroYak_CAF1 13017 109 + 1
-------GUGCUCUGCUCAUUACAUUCAUUAAGUUUAAUGAAUUGAU--AUUCAGGCAAACUCGAAGGCCAUCCGAGGCCUACGACUUAUAAAAAAAGUG--UAUGUGUAUAAUAAUUAC
-------.(((.(((...((((.((((((((....))))))))))))--...))))))...(((.(((((......))))).)))...............--.................. ( -24.00)
>consensus
U____GUGUGCUCUGCUCAUUACAUUCAUUAACUUUAAUGAAUUGAU__AUUCAGGCAAACUCGAAGGCCAACUGAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGUAUAAUA_____
.........((.(((...((((.((((((((....)))))))))))).....)))))....(((.(((((......))))).)))................................... (-22.40 = -22.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,534,280 – 8,534,395
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.82
Mean single sequence MFE -29.93
Consensus MFE -25.34
Energy contribution -25.16
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -3.18
Structure conservation index 0.85
SVM decision value 2.69
SVM RNA-class probability 0.996366
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534280 115 - 20766785
-----UAUUAUACACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUUUGAUGGCCUUCGAGUUUGCCUGAAUAUAUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCACACACACA
-----.............((((((((((((.(((((((.(((((......))))).))).)))).))))))))....((((((((....))))))))....)).)).............. ( -30.80)
>DroSec_CAF1 9783 109 - 1
-----UAUUAAGCACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUCAGUUGGCCUUCGAGUUUGCCUGAAU--AUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCGCAC----A
-----......((.(.(.((((((((((((.(((((((.(((((......))))).))).)))).))))))--))..((((((((....))))))))....)).)).).).))..----. ( -32.50)
>DroSim_CAF1 13247 111 - 1
-----UACUAUACACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUCAUUUGGCCUUCGAGUUUGCCUGAAU--AUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCACACA--CA
-----.............((((((((((((.(((((((.(((((......))))).))).)))).))))))--))..((((((((....))))))))....)).))..........--.. ( -30.20)
>DroYak_CAF1 13017 109 - 1
GUAAUUAUUAUACACAUA--CACUUUUUUUAUAAGUCGUAGGCCUCGGAUGGCCUUCGAGUUUGCCUGAAU--AUCAAUUCAUUAAACUUAAUGAAUGUAAUGAGCAGAGCAC-------
..................--............((.(((.(((((......))))).))).))((((((..(--((..((((((((....))))))))...)))..))).))).------- ( -26.20)
>consensus
_____UAUUAUACACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUCAGAUGGCCUUCGAGUUUGCCUGAAU__AUCAAUUCAUUAAAGUUAAUGAAUGUAAUGAGCAGAGCACAC____A
................................((.(((.(((((......))))).))).))((((((.........((((((((....))))))))........))).)))........ (-25.34 = -25.16 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,534,320 – 8,534,432
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.78
Mean single sequence MFE -30.48
Consensus MFE -21.23
Energy contribution -22.23
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -2.39
Structure conservation index 0.70
SVM decision value 1.19
SVM RNA-class probability 0.927850
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534320 112 + 20766785
AAUUGAUAUAUUCAGGCAAACUCGAAGGCCAUCAAAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGUAUAAUA--------AUUACAGUGUCAAUUUCCUGGGCGAGGCAUUUAGUAA
(((((((((((((((..((..(((.(((((......))))).))).))..))))))))..((((((.........--------..))))))))))))).(((.....))).......... ( -30.70)
>DroSec_CAF1 9819 110 + 1
AAUUGAU--AUUCAGGCAAACUCGAAGGCCAACUGAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGCUUAAUA--------GCAACAGUGUCAAUUUCCUAGGCGAGACAUUUAGCAA
(((((((--((((((..((..(((.(((((......))))).))).))..))))))....(((((.((((....)--------)))))))))))))))......((..........)).. ( -33.10)
>DroSim_CAF1 13285 110 + 1
AAUUGAU--AUUCAGGCAAACUCGAAGGCCAAAUGAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGUAUAGUA--------AUUACAGUGUCAAUUUCCUAGGCGAGGCAUUUAGCAA
....(((--((((((..((..(((.(((((......))))).))).))..))))))))).((((.((((...((.--------.....(((....)))......))...)))).)))).. ( -31.70)
>DroYak_CAF1 13050 116 + 1
AAUUGAU--AUUCAGGCAAACUCGAAGGCCAUCCGAGGCCUACGACUUAUAAAAAAAGUG--UAUGUGUAUAAUAAUUACAUAAUUACAGUGUCAAUUUCCUACGCGAGGCUAUUAGCAA
(((((((--(((.........(((.(((((......))))).)))............(((--..((((((.......))))))..))))))))))))).....(....)((.....)).. ( -26.40)
>consensus
AAUUGAU__AUUCAGGCAAACUCGAAGGCCAACUGAGGCCUACGACUUAUCUGAAUAUUGGCUGUGUGUAUAAUA________AUUACAGUGUCAAUUUCCUAGGCGAGGCAUUUAGCAA
..((((.....))))((....(((.(((((......))))).)))((..((((...((((((..((((.................))))..))))))....))))..)).......)).. (-21.23 = -22.23 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,534,320 – 8,534,432
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.78
Mean single sequence MFE -26.48
Consensus MFE -20.87
Energy contribution -20.69
Covariance contribution -0.19
Combinations/Pair 1.13
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.43
SVM RNA-class probability 0.731845
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8534320 112 - 20766785
UUACUAAAUGCCUCGCCCAGGAAAUUGACACUGUAAU--------UAUUAUACACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUUUGAUGGCCUUCGAGUUUGCCUGAAUAUAUCAAUU
..........(((.....))).((((((..((((...--------..........))))...((((((((.(((((((.(((((......))))).))).)))).)))))))).)))))) ( -27.82)
>DroSec_CAF1 9819 110 - 1
UUGCUAAAUGUCUCGCCUAGGAAAUUGACACUGUUGC--------UAUUAAGCACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUCAGUUGGCCUUCGAGUUUGCCUGAAU--AUCAAUU
........((((...(....).....))))(((((((--------(....)))).))))...((((((((.(((((((.(((((......))))).))).)))).))))))--))..... ( -32.00)
>DroSim_CAF1 13285 110 - 1
UUGCUAAAUGCCUCGCCUAGGAAAUUGACACUGUAAU--------UACUAUACACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUCAUUUGGCCUUCGAGUUUGCCUGAAU--AUCAAUU
..........(((.....))).((((((..((((...--------..........))))....(((((((.(((((((.(((((......))))).))).)))).))))))--))))))) ( -26.52)
>DroYak_CAF1 13050 116 - 1
UUGCUAAUAGCCUCGCGUAGGAAAUUGACACUGUAAUUAUGUAAUUAUUAUACACAUA--CACUUUUUUUAUAAGUCGUAGGCCUCGGAUGGCCUUCGAGUUUGCCUGAAU--AUCAAUU
..((.....))......((((.....(((..((((....((((.......))))..))--)).............(((.(((((......))))).))))))..))))...--....... ( -19.60)
>consensus
UUGCUAAAUGCCUCGCCUAGGAAAUUGACACUGUAAU________UAUUAUACACACAGCCAAUAUUCAGAUAAGUCGUAGGCCUCAGAUGGCCUUCGAGUUUGCCUGAAU__AUCAAUU
..........(((.....))).((((((...((((...............))))..........((((((.(((((((.(((((......))))).))).)))).))))))...)))))) (-20.87 = -20.69 +  -0.19)

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 10:27:03 2006