Locus 2370

Sequence ID 2R_DroMel_CAF1
Location 8,608,577 – 8,608,722
Length 145
Max. P 0.967294
window3913 window3914

overview

Window 3

Location 8,608,577 – 8,608,682
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.76
Mean single sequence MFE -28.84
Consensus MFE -16.72
Energy contribution -17.52
Covariance contribution 0.80
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.58
SVM decision value -0.01
SVM RNA-class probability 0.530542
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8608577 105 + 20766785
UAUCGAUUGAAGUCGAAAAAUGAGUCAAUCUUCGAUCGGCUUUAAUGGCAACUG-------CAUAGCGG-AAA----UCUGUGCACUCAAUCUGCAUGCAUGCUUCU---AUAUUUGCCA
....((((((((..((........))...))))))))(((..((..((((..((-------(((.((((-(..----..((......)).))))))))))))))..)---).....))). ( -27.90)
>DroSec_CAF1 9538 108 + 1
UAUCGAUUGAAGGCGAAAAAUGAGUCAAUCUUCGAUCGGCUUUAAUGGCAACUGACUGCAUCAUAGUGG-GAA----UCUGUGCACUCAAUCUGGU----UGCUUCU---AUAUUUGCCA
....(((((((((.((........))..)))))))))(((..((..(((((((((.((...(((((...-...----.)))))....)).)).)))----))))..)---).....))). ( -27.00)
>DroSim_CAF1 6382 109 + 1
UAUCGAUUGAAGGCGAAAAAUGAGUCAAUCUUCGAUCGGCUUUAAUGGCAACUGACUGCAUCAUAGUAGUGAA----UCUGUGCACUCAAUCUGCG----UGCUUCU---AUAUUUGCCA
..(((((((((((.((........))..)))))))))))......((((((.(.(((((......))))).).----.....((((.(.....).)----)))....---....)))))) ( -28.30)
>DroEre_CAF1 8974 93 + 1
UAUCGAUUGAAGGCAGAAAA-GAGUCAAUCUUCGAUCGGCUUUACUGGCAACUG-------CAUAG---------------UGCACUCAAUCUGCA----UGCCUCUGCCAUAUUUGCCA
....(((((((((..((...-...))..)))))))))(((.....(((((...(-------((...---------------((((.......))))----)))...))))).....))). ( -28.20)
>DroYak_CAF1 4000 105 + 1
---CGAUUGAAGGCGAAAAAGGAGUCAAUCUUCGAUCGGCUUUAAUGGCAACUG----UGGCACAGUGG-GAAUCUAUCUGUGCACUCAGUCUGCA----UGCUUCU---AUAUUUGCCA
---........((((((...((((((.(((...))).))))))....(((((((----.((((((((((-....))).)))))).).)))).))).----.......---...)))))). ( -32.80)
>consensus
UAUCGAUUGAAGGCGAAAAAUGAGUCAAUCUUCGAUCGGCUUUAAUGGCAACUG_______CAUAGUGG_GAA____UCUGUGCACUCAAUCUGCA____UGCUUCU___AUAUUUGCCA
...(((((((((..((........))...))))))))).......((((((..........(((((............)))))..........(((....)))...........)))))) (-16.72 = -17.52 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,608,617 – 8,608,722
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.65
Mean single sequence MFE -33.28
Consensus MFE -19.02
Energy contribution -20.32
Covariance contribution 1.30
Combinations/Pair 1.00
Mean z-score -3.32
Structure conservation index 0.57
SVM decision value 1.61
SVM RNA-class probability 0.967294
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8608617 105 - 20766785
GGCGGGCUUUUAAUUAAAAGGCCGAAUGGGCCAAAAAUGUUGGCAAAUAU---AGAAGCAUGCAUGCAGAUUGAGUGCACAGA----UUU-CCGCUAUG-------CAGUUGCCAUUAAA
..(((.(((((....))))).)))((((((((((.....)))))......---...(((.(((((((.(((((......))).----..)-).)).)))-------))))).)))))... ( -28.30)
>DroSec_CAF1 9578 108 - 1
GGCGUGCUUUUAAUUAAAAGGCCGAAUGGGCCAAAAAUGUUGGCAAAUAU---AGAAGCA----ACCAGAUUGAGUGCACAGA----UUC-CCACUAUGAUGCAGUCAGUUGCCAUUAAA
(((.((((((((.......((((.....)))).....((((....)))))---)))))))----....((((((.((((((..----...-......)).)))).)))))))))...... ( -32.40)
>DroSim_CAF1 6422 109 - 1
GGCGUGCUUUUAAUUAAAAGGCCGAAUGGGCCAAAAAUGUUGGCAAAUAU---AGAAGCA----CGCAGAUUGAGUGCACAGA----UUCACUACUAUGAUGCAGUCAGUUGCCAUUAAA
.(((((((((((.......((((.....)))).....((((....)))))---)))))))----))).((((((.((((((..----..........)).)))).))))))......... ( -36.00)
>DroEre_CAF1 9013 94 - 1
GGCGGGCUUUUAAUUAAAAGGCCGAAUGGGCCAAAAAUGCUGGCAAAUAUGGCAGAGGCA----UGCAGAUUGAGUGCA---------------CUAUG-------CAGUUGCCAGUAAA
(((.(((((((.....)))))))......))).....(((((((((.....(((.(((((----(.(.....).)))).---------------)).))-------)..))))))))).. ( -33.00)
>DroYak_CAF1 4037 108 - 1
GGCGUGCUUUUAAUUAAAAGGCCGAAUGGGCCAAAAAUGUUGGCAAAUAU---AGAAGCA----UGCAGACUGAGUGCACAGAUAGAUUC-CCACUGUGCCA----CAGUUGCCAUUAAA
.(((((((((((.......((((.....)))).....((((....)))))---)))))))----))).(((((.(.((((((........-...))))))).----)))))......... ( -36.70)
>consensus
GGCGUGCUUUUAAUUAAAAGGCCGAAUGGGCCAAAAAUGUUGGCAAAUAU___AGAAGCA____UGCAGAUUGAGUGCACAGA____UUC_CCACUAUG_______CAGUUGCCAUUAAA
(((((((.(((((((....((((.....)))).........................((......)).))))))).)))).................(((.....)))...)))...... (-19.02 = -20.32 +   1.30)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:14 2006