Locus 5531

Sequence ID 2R_DroMel_CAF1
Location 17,667,454 – 17,667,609
Length 155
Max. P 0.884586
window8875 window8876 window8877 window8878

overview

Window 5

Location 17,667,454 – 17,667,569
Length 115
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 89.80
Mean single sequence MFE -40.77
Consensus MFE -29.46
Energy contribution -29.79
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.72
SVM decision value 0.12
SVM RNA-class probability 0.592387
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17667454 115 + 20766785
AUGCGAUGCGGCAUCAGCGUCGGCAACAUUCCAGCCAUGAGUCACUGCAGCAGAAGCAACAGCAGCAGC----ACACUUGCUGCGCCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUA
.((((((((.......))))).)))....(((..(((((......((((((((..((....)).(((((----(....))))))....)))))))).))))))))..(((.....))). ( -40.30)
>DroSec_CAF1 20852 119 + 1
AUGCGAUGCGGCAUCAGCGUCGGCAACAUUCCAGCCAUGAGUCACUGCAGCAGAAGCAACAUCAGCAGCAGCAACACUUGCUGCGCCGCUUCUGCGACAUGGGGAUAAUCACAUUGAUA
.((((((((.......))))).)))....(((..(((((.((....)).((((((((.......(((((((......)))))))...))))))))..))))))))..(((.....))). ( -40.80)
>DroEre_CAF1 21303 107 + 1
AUGCGAUGCGGCAUCAGCUUCGGCAACAUUCCAGCCAUGAGUCACAGCAGCAGA---AGCAGCA---------ACACUUGCUGCACCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUA
...(((((.((.....((....)).....(((..((((..(((.(((((((.(.---.((((((---------.....))))))..)))))))).))))))))))...)).)))))... ( -41.20)
>consensus
AUGCGAUGCGGCAUCAGCGUCGGCAACAUUCCAGCCAUGAGUCACUGCAGCAGAAGCAACAGCAGCAGC____ACACUUGCUGCGCCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUA
.((((((((.......))))).)))....(((..(((((.......(((((((........................)))))))..(((....))).))))))))..(((.....))). (-29.46 = -29.79 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,667,454 – 17,667,569
Length 115
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 89.80
Mean single sequence MFE -45.93
Consensus MFE -34.09
Energy contribution -34.54
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.75
Structure conservation index 0.74
SVM decision value 0.48
SVM RNA-class probability 0.751237
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17667454 115 - 20766785
UAUCAAUGUGAUUAUCCCCAUGUCGCAGCAGCGGCGCAGCAAGUGU----GCUGCUGCUGUUGCUUCUGCUGCAGUGACUCAUGGCUGGAAUGUUGCCGACGCUGAUGCCGCAUCGCAU
.....((((((...((((((((((((((((((((((((.....)))----)))))))))((.((....)).)).)))))..))))..)))....(((....((....)).))))))))) ( -43.90)
>DroSec_CAF1 20852 119 - 1
UAUCAAUGUGAUUAUCCCCAUGUCGCAGAAGCGGCGCAGCAAGUGUUGCUGCUGCUGAUGUUGCUUCUGCUGCAGUGACUCAUGGCUGGAAUGUUGCCGACGCUGAUGCCGCAUCGCAU
......((((((.........))))))((.((((((((((..(.((..((((.((.((.......)).)).))))..)).).((((.........))))..)))).)))))).)).... ( -46.00)
>DroEre_CAF1 21303 107 - 1
UAUCAAUGUGAUUAUCCCCAUGUCGCAGCAGCGGUGCAGCAAGUGU---------UGCUGCU---UCUGCUGCUGUGACUCAUGGCUGGAAUGUUGCCGAAGCUGAUGCCGCAUCGCAU
.....((((((...((((((((((((((((((((.((((((.....---------)))))).---.)))))))))))))..))))..)))....(((....((....)).))))))))) ( -47.90)
>consensus
UAUCAAUGUGAUUAUCCCCAUGUCGCAGCAGCGGCGCAGCAAGUGU____GCUGCUGCUGUUGCUUCUGCUGCAGUGACUCAUGGCUGGAAUGUUGCCGACGCUGAUGCCGCAUCGCAU
.....((((((...((((((((((((.(((((((.((((((..............)))))).....))))))).)))))..))))..)))....(((....((....)).))))))))) (-34.09 = -34.54 +   0.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,667,494 – 17,667,609
Length 115
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 89.24
Mean single sequence MFE -41.87
Consensus MFE -30.50
Energy contribution -31.50
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.46
Structure conservation index 0.73
SVM decision value 0.90
SVM RNA-class probability 0.878044
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17667494 115 + 20766785
GUCACUGCAGCAGAAGCAACAGCAGCAGC----ACACUUGCUGCGCCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACCACUGCCUAACUGGCC
(((.(((..((((..(((.((((.(((((----(....))))))...)))).)))....((((.(((.((.....))))).)))).....))))..))).)))....(((.....))). ( -43.40)
>DroSec_CAF1 20892 119 + 1
GUCACUGCAGCAGAAGCAACAUCAGCAGCAGCAACACUUGCUGCGCCGCUUCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACCACUGCCUAACUGGCC
(((..((..((((((((.......(((((((......)))))))...))))))))..))((((.(((.((.....))))).))))....((((...)))))))....(((.....))). ( -40.60)
>DroEre_CAF1 21343 107 + 1
GUCACAGCAGCAGA---AGCAGCA---------ACACUUGCUGCACCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACUACUGCCUAACUGGCU
(((.(((((((.(.---.((((((---------.....))))))..)))))))).))).((((.(((.((.....))))).))))....((((...)))).......(((.....))). ( -41.60)
>consensus
GUCACUGCAGCAGAAGCAACAGCAGCAGC____ACACUUGCUGCGCCGCUGCUGCGACAUGGGGAUAAUCACAUUGAUAUGCCUAAUUAGCUGCAACAGCGACCACUGCCUAACUGGCC
(((...(((((((......((((((............)))))).....)))))))....((((.(((.((.....))))).))))....((((...)))))))....(((.....))). (-30.50 = -31.50 +   1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,667,494 – 17,667,609
Length 115
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 89.24
Mean single sequence MFE -49.77
Consensus MFE -35.53
Energy contribution -37.98
Covariance contribution 2.45
Combinations/Pair 1.03
Mean z-score -3.88
Structure conservation index 0.71
SVM decision value 0.93
SVM RNA-class probability 0.884586
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17667494 115 - 20766785
GGCCAGUUAGGCAGUGGUCGCUGUUGCAGCUAAUUAGGCAUAUCAAUGUGAUUAUCCCCAUGUCGCAGCAGCGGCGCAGCAAGUGU----GCUGCUGCUGUUGCUUCUGCUGCAGUGAC
.(((.....)))....((((((((.((((.......((...(((.....)))...))....((.((((((((((((((.....)))----))))))))))).))..)))).)))))))) ( -51.10)
>DroSec_CAF1 20892 119 - 1
GGCCAGUUAGGCAGUGGUCGCUGUUGCAGCUAAUUAGGCAUAUCAAUGUGAUUAUCCCCAUGUCGCAGAAGCGGCGCAGCAAGUGUUGCUGCUGCUGAUGUUGCUUCUGCUGCAGUGAC
.(((.....)))....((((((((.((((......(((((((((..((((((.........))))))..(((((((((((....))))).)))))))))).))))))))).)))))))) ( -49.60)
>DroEre_CAF1 21343 107 - 1
AGCCAGUUAGGCAGUAGUCGCUGUUGCAGCUAAUUAGGCAUAUCAAUGUGAUUAUCCCCAUGUCGCAGCAGCGGUGCAGCAAGUGU---------UGCUGCU---UCUGCUGCUGUGAC
.(((.....))).((((((((.((((..(((.....)))....))))))))))))......(((((((((((((.((((((.....---------)))))).---.))))))))))))) ( -48.60)
>consensus
GGCCAGUUAGGCAGUGGUCGCUGUUGCAGCUAAUUAGGCAUAUCAAUGUGAUUAUCCCCAUGUCGCAGCAGCGGCGCAGCAAGUGU____GCUGCUGCUGUUGCUUCUGCUGCAGUGAC
.(((.....)))....((((((((.((((.......((((((((.....))).......)))))(((((((((((...((....))....))))))))))).....)))).)))))))) (-35.53 = -37.98 +   2.45)

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 11:48:06 2006