Locus 1859

Sequence ID 2R_DroMel_CAF1
Location 6,985,201 – 6,985,294
Length 93
Max. P 0.985234
window3086 window3087

overview

Window 6

Location 6,985,201 – 6,985,294
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.25
Mean single sequence MFE -25.43
Consensus MFE -13.58
Energy contribution -14.92
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.53
SVM decision value 0.47
SVM RNA-class probability 0.749408
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6985201 93 + 20766785
AGGG---GG------------------AAUGGGUAAAUUGCAUGCGAUUGAA------AUUGAAUGGUUUAAACGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
....---((------------------..((..(((((((((.((.((((((------((.((.((.......)).)))))))))).))))))))))).))..))............... ( -26.90)
>DroVir_CAF1 19034 117 + 1
GGGG---GGGGGGGGUUGCAGCAAAAGGGGCAGCAAAUUGCAUGCGAUUGAAAUUGAAAUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUUAUUG
.((.---..(..((((((((((.......(((((.....)).))).((((((((.((.(((..........)))..)))))))))).))))))))))..)...))............... ( -29.30)
>DroGri_CAF1 21544 93 + 1
AGGA---GC------------------GAGGAGUAAAUGGCAUGCGAUUGAA------AUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
..(.---((------------------..(...(((((.(((.((.((((((------((.((.(.((....)).))))))))))).))))).))))).)..)))............... ( -18.60)
>DroWil_CAF1 23878 93 + 1
AGGG---GG------------------GUUGGUUAAAUUGCAUGCUAUUGAA------AUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
....---.(------------------(((.(((((((((((.(((((((((------((.((.(.((....)).))))))))))))))))))))))))).))))............... ( -31.80)
>DroMoj_CAF1 22496 97 + 1
AGGC---GCAGG--------GCACAAG-GGCAG-----UGCAUGCGAUGGAA------AUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
...(---(((..--------((((...-....)-----))).)))).....(------((((((((((((((((((((((....))))))...))))))...)))))..))))))..... ( -22.90)
>DroAna_CAF1 18936 96 + 1
AGGGGCAGG------------------AGGAGCUAAAUUGCAUGCGAUUGAA------AUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCGUAAUUAGUUGAUUG
...(((.(.------------------.....)(((((((((.((.((((((------((.((.(.((....)).))))))))))).)))))))))))....)))............... ( -23.10)
>consensus
AGGG___GG__________________GGGGAGUAAAUUGCAUGCGAUUGAA______AUUGAAUGGUUUAAAUGGUCAUUUCAAUGGCUGCAAUUUAACAAGCCAUAAUUAGUUGAUUG
.................................(((((((((.((.((((((...........(((..(.....)..))))))))).)))))))))))...................... (-13.58 = -14.92 +   1.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,985,201 – 6,985,294
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.25
Mean single sequence MFE -20.08
Consensus MFE -11.08
Energy contribution -12.00
Covariance contribution 0.92
Combinations/Pair 1.09
Mean z-score -4.00
Structure conservation index 0.55
SVM decision value 2.00
SVM RNA-class probability 0.985234
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6985201 93 - 20766785
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCGUUUAAACCAUUCAAU------UUCAAUCGCAUGCAAUUUACCCAUU------------------CC---CCCU
...............((..((.(((((((((((.((((((((((..((....))...)).))------)))))).)).)))))))))..))..------------------))---.... ( -20.00)
>DroVir_CAF1 19034 117 - 1
CAAUAAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAUUUCAAUUUCAAUCGCAUGCAAUUUGCUGCCCCUUUUGCUGCAACCCCCCCC---CCCC
...............(((..((.((((((((((.((((((((........................)))))))).)).)))))))))).))).....................---.... ( -21.36)
>DroGri_CAF1 21544 93 - 1
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAU------UUCAAUCGCAUGCCAUUUACUCCUC------------------GC---UCCU
.............(((((.(((......)))((.((((((((..................))------)))))).))..))))).........------------------..---.... ( -14.67)
>DroWil_CAF1 23878 93 - 1
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAU------UUCAAUAGCAUGCAAUUUAACCAAC------------------CC---CCCU
...............((.(((((((((((((((.((((((((..................))------)))))).)).)))))))))).))).------------------))---.... ( -22.27)
>DroMoj_CAF1 22496 97 - 1
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAU------UUCCAUCGCAUGCA-----CUGCC-CUUGUGC--------CCUGC---GCCU
...(((.......((((((.((......)))))))).....)))..................------......((((.(((-----(....-...))))--------..)))---)... ( -17.80)
>DroAna_CAF1 18936 96 - 1
CAAUCAACUAAUUACGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAU------UUCAAUCGCAUGCAAUUUAGCUCCU------------------CCUGCCCCU
...............(((..(((((((((((((.((((((((..................))------)))))).)).)))))))))))....------------------...)))... ( -24.37)
>consensus
CAAUCAACUAAUUAUGGCUUGUUAAAUUGCAGCCAUUGAAAUGACCAUUUAAACCAUUCAAU______UUCAAUCGCAUGCAAUUUACCCCCC__________________CC___CCCU
......................(((((((((((.((((((......(((.((....)).)))......)))))).)).)))))))))................................. (-11.08 = -12.00 +   0.92)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:58 2006