Locus 3104

Sequence ID 2R_DroMel_CAF1
Location 10,621,910 – 10,622,042
Length 132
Max. P 0.879721
window5121 window5122 window5123

overview

Window 1

Location 10,621,910 – 10,622,003
Length 93
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 78.01
Mean single sequence MFE -27.28
Consensus MFE -12.76
Energy contribution -13.09
Covariance contribution 0.33
Combinations/Pair 1.13
Mean z-score -2.45
Structure conservation index 0.47
SVM decision value 0.91
SVM RNA-class probability 0.879721
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10621910 93 - 20766785
GAAA--AAAUA--UGAAGACGGCGCAGGCAA-AAUGCAAAGUUGGCA----AGAGCGCGAGUUGCUCGCAAGGAAAUCGUGGGCCUCGAAAGUAGGCCAAAA
....--...((--(((...((((....((..-...))...))))((.----...))(((((...))))).......)))))((((((....).))))).... ( -27.30)
>DroPse_CAF1 90751 90 - 1
UCUAAAAAAUAAUGGAAGCCAGAGC----CG-AAUGCAAACUUGGCA----GGCGCUGGAUUCUCUGGCAGGGAUAUCG--GGCC-UGAAAGUAGGCCAAAA
(((..............(((...((----((-(........))))).----)))((..(.....)..))..))).....--((((-((....)))))).... ( -26.40)
>DroSec_CAF1 64106 95 - 1
GAAAAAAAAUA--UGAAGACGGCGCAGGCAA-AAUGCAAAGUUGGCA----AGAGCGCGAGUUGCUCGCAAGGAAAUCGUGGGCCUCGAAUGUAGGCCAAAA
.........((--(((...((((....((..-...))...))))((.----...))(((((...))))).......)))))(((((.......))))).... ( -23.20)
>DroEre_CAF1 64406 92 - 1
GGAA--AAAUA--UGUAGACGGCGCAGGCAA-AAUGCAAACUUGGCA----AGAGCGCGAGUUGCU-GCAAGGAAAUCGUGGGCCUCGAAAGUAGGCCAAAA
....--.....--....(.(((((((.....-..))).((((((((.----...)).)))))))))-))............((((((....).))))).... ( -27.40)
>DroYak_CAF1 71323 98 - 1
GGAA--AAAUG--UGUAGACGGCGCUGGCAAAAAUGCAAACUUGGCAGAAGAGCGCGCGAGUUGCUCGCAAGGCAAUCGUGGGCCACGAAAGUAGGCCAAAA
....--.....--........(((((.(((....)))...(((.....))))))))((((.((((.(....))))))))).((((((....)).)))).... ( -33.00)
>DroPer_CAF1 91948 90 - 1
UCUAAAAAAUAAUGGAAGCCAGAGC----CG-AAUGCAAACUUGGCA----GGCGCUGGAUUCUCUGGCAGGGAUAUCG--GGCC-UGAAAGUAGGCCAAAA
(((..............(((...((----((-(........))))).----)))((..(.....)..))..))).....--((((-((....)))))).... ( -26.40)
>consensus
GAAA__AAAUA__UGAAGACGGCGCAGGCAA_AAUGCAAACUUGGCA____AGAGCGCGAGUUGCUCGCAAGGAAAUCGUGGGCCUCGAAAGUAGGCCAAAA
..............((((...((((.........(((.......))).......))))...))))................((((.........)))).... (-12.76 = -13.09 +   0.33)

alignment

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secondary structure

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Window 2

Location 10,621,948 – 10,622,042
Length 94
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 82.47
Mean single sequence MFE -21.82
Consensus MFE -14.47
Energy contribution -14.39
Covariance contribution -0.08
Combinations/Pair 1.14
Mean z-score -2.44
Structure conservation index 0.66
SVM decision value 0.56
SVM RNA-class probability 0.782100
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10621948 94 + 20766785
CAACUCGCGCUCU----UGCCAACUUUGCAUU-UUGCCUGCGCCGUCUUCA--UAUUU-----UUUCUUCC-AAAUCCCCAAGCCUCUUGGCUUUGGCAAGUUUCGU
......(((..((----(((((.....(((..-.....)))..........--.....-----........-........(((((....))))))))))))...))) ( -20.50)
>DroSec_CAF1 64144 96 + 1
CAACUCGCGCUCU----UGCCAACUUUGCAUU-UUGCCUGCGCCGUCUUCA--UAUUUU---UUUUCUUCU-AAAUCCCCAAGCCUCUUGGCUUUGGCAAGUUUCGU
......(((..((----(((((.....(((..-.....)))..........--......---.........-........(((((....))))))))))))...))) ( -20.50)
>DroSim_CAF1 64716 99 + 1
CAACUCGCGCUCU----UGCCAACUUUGCAUU-UUGCCUGCGCCGUCUUCA--UAUUUUUUUUUUUCUUCU-AAAUCCCCAAGCCUCUUGGCUUUGGCAAGUUUCGU
......(((..((----(((((.....(((..-.....)))..........--..................-........(((((....))))))))))))...))) ( -20.50)
>DroEre_CAF1 64443 94 + 1
CAACUCGCGCUCU----UGCCAAGUUUGCAUU-UUGCCUGCGCCGUCUACA--UAUUU-----UUCCUUCU-AAAUCCCCAAGCCUCUUGGCUUUGGCAAGUUUCGC
......(((..((----((((((((..((...-..))..))..........--.....-----........-.........((((....))))))))))))...))) ( -23.10)
>DroYak_CAF1 71361 99 + 1
CAACUCGCGCGCUCUUCUGCCAAGUUUGCAUUUUUGCCAGCGCCGUCUACA--CAUUU-----UUCCUUCU-AAAUCCCCAAGCCUCUUGGCUUUGGCAAGUUUCGU
.((((.((((((......)).......(((....)))..))))........--.....-----........-.....((.(((((....))))).))..)))).... ( -19.90)
>DroPer_CAF1 91983 95 + 1
AGAAUCCAGCGCC----UGCCAAGUUUGCAUU-CG----GCUCUGGCUUCCAUUAUUUU---UUAGAUGCUGCAAGCUGCAAGCCCCUUGGCUUUGGCAAGUUUUCC
.(((..(...(((----.((((((...((...-((----(((...((...((((.....---...))))..)).)))))...))..))))))...)))..)..))). ( -26.40)
>consensus
CAACUCGCGCUCU____UGCCAACUUUGCAUU_UUGCCUGCGCCGUCUUCA__UAUUU_____UUUCUUCU_AAAUCCCCAAGCCUCUUGGCUUUGGCAAGUUUCGU
......((((.......(((.......))).........))))..................................((.(((((....))))).)).......... (-14.47 = -14.39 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,621,948 – 10,622,042
Length 94
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 82.47
Mean single sequence MFE -25.30
Consensus MFE -16.60
Energy contribution -17.16
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.22
Structure conservation index 0.66
SVM decision value 0.39
SVM RNA-class probability 0.718480
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10621948 94 - 20766785
ACGAAACUUGCCAAAGCCAAGAGGCUUGGGGAUUU-GGAAGAAA-----AAAUA--UGAAGACGGCGCAGGCAA-AAUGCAAAGUUGGCA----AGAGCGCGAGUUG
......((((((((.(((......(((.(..((((-........-----)))).--).)))..)))(((.....-..)))....))))))----))(((....))). ( -23.40)
>DroSec_CAF1 64144 96 - 1
ACGAAACUUGCCAAAGCCAAGAGGCUUGGGGAUUU-AGAAGAAAA---AAAAUA--UGAAGACGGCGCAGGCAA-AAUGCAAAGUUGGCA----AGAGCGCGAGUUG
......((((((.(((((....)))))........-.........---......--....(((...(((.....-..)))...)))))))----))(((....))). ( -23.20)
>DroSim_CAF1 64716 99 - 1
ACGAAACUUGCCAAAGCCAAGAGGCUUGGGGAUUU-AGAAGAAAAAAAAAAAUA--UGAAGACGGCGCAGGCAA-AAUGCAAAGUUGGCA----AGAGCGCGAGUUG
......((((((.(((((....)))))........-..................--....(((...(((.....-..)))...)))))))----))(((....))). ( -23.20)
>DroEre_CAF1 64443 94 - 1
GCGAAACUUGCCAAAGCCAAGAGGCUUGGGGAUUU-AGAAGGAA-----AAAUA--UGUAGACGGCGCAGGCAA-AAUGCAAACUUGGCA----AGAGCGCGAGUUG
(((...((((((((((((....)))))........-........-----.....--((((....((....))..-..))))....)))))----))..)))...... ( -27.00)
>DroYak_CAF1 71361 99 - 1
ACGAAACUUGCCAAAGCCAAGAGGCUUGGGGAUUU-AGAAGGAA-----AAAUG--UGUAGACGGCGCUGGCAAAAAUGCAAACUUGGCAGAAGAGCGCGCGAGUUG
....(((((((..(((((....)))))........-........-----.....--........(((((.(((....)))...(((.....))))))))))))))). ( -25.00)
>DroPer_CAF1 91983 95 - 1
GGAAAACUUGCCAAAGCCAAGGGGCUUGCAGCUUGCAGCAUCUAA---AAAAUAAUGGAAGCCAGAGC----CG-AAUGCAAACUUGGCA----GGCGCUGGAUUCU
((((..(.((((...((((((..((...(.((((...((.((((.---.......)))).))..))))----.)-...))...)))))).----))))..)..)))) ( -30.00)
>consensus
ACGAAACUUGCCAAAGCCAAGAGGCUUGGGGAUUU_AGAAGAAA_____AAAUA__UGAAGACGGCGCAGGCAA_AAUGCAAACUUGGCA____AGAGCGCGAGUUG
....(((((.((.(((((....))))).))..................................((((.........(((.......))).......))))))))). (-16.60 = -17.16 +   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 10:47:37 2006