Locus 1230

Sequence ID 2R_DroMel_CAF1
Location 4,841,464 – 4,841,559
Length 95
Max. P 0.999831
window2136 window2137

overview

Window 6

Location 4,841,464 – 4,841,559
Length 95
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 74.75
Mean single sequence MFE -22.20
Consensus MFE -13.24
Energy contribution -14.80
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.60
SVM decision value 2.47
SVM RNA-class probability 0.994366
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4841464 95 + 20766785
---CACCA------CAUGUGCUCUCACACAUCCCACAUCCAUCCAAUCUGGGCGUCAAGUUGGA-AAUGUAAUUUGAGCUCAAAUUACAUUUGAGUGCGGAAUUA
---.....------..((((......))))((((((.....(((((..((.....))..)))))-(((((((((((....)))))))))))...))).))).... ( -26.60)
>DroVir_CAF1 11193 73 + 1
---CA-----------------------------ACACAAAUGUAAUCUGAGCGGCAAGUUGGAAAAUGUAAUUUGAGCGAAAAUUUCAUUUGAGUAGAAAAUUA
---..-----------------------------((.((((((.(((.(..((..(((((((.......))))))).))..).))).)))))).))......... ( -12.90)
>DroSim_CAF1 2119 93 + 1
---AACCA------CAUGUGCUCUCA--CAUCCCACAUCCAUCCAAUCUCGGCGUCAAGUUGGA-AAUGUAAUUUGAGCUCAAAUUACAUUUGAGUGCGGAAUUA
---.....------..((((....))--))((((((............(((((.....)))))(-(((((((((((....))))))))))))..))).))).... ( -23.50)
>DroYak_CAF1 2468 102 + 1
AAGCACCACAUGCCCAUGUGCUCUUA--CAUCCCACAUCCAUCCAAUCUCGGCGUCAAGUUGGA-AAUGUAAUUUGAGCUCAAAUUACAUUUGAGUGCGGAAUUA
(((...(((((....)))))..))).--..((((((............(((((.....)))))(-(((((((((((....))))))))))))..))).))).... ( -25.80)
>consensus
___CACCA______CAUGUGCUCUCA__CAUCCCACAUCCAUCCAAUCUCGGCGUCAAGUUGGA_AAUGUAAUUUGAGCUCAAAUUACAUUUGAGUGCGGAAUUA
..............................((((((.....(((((.((........))))))).(((((((((((....)))))))))))...))).))).... (-13.24 = -14.80 +   1.56)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 4,841,464 – 4,841,559
Length 95
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 74.75
Mean single sequence MFE -27.94
Consensus MFE -17.15
Energy contribution -20.03
Covariance contribution 2.88
Combinations/Pair 1.07
Mean z-score -3.12
Structure conservation index 0.61
SVM decision value 4.19
SVM RNA-class probability 0.999831
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4841464 95 - 20766785
UAAUUCCGCACUCAAAUGUAAUUUGAGCUCAAAUUACAUU-UCCAACUUGACGCCCAGAUUGGAUGGAUGUGGGAUGUGUGAGAGCACAUG------UGGUG---
..((((((((..(((((((((((((....)))))))))))-(((((.(((.....))).)))))))..))))))))((((....))))...------.....--- ( -34.70)
>DroVir_CAF1 11193 73 - 1
UAAUUUUCUACUCAAAUGAAAUUUUCGCUCAAAUUACAUUUUCCAACUUGCCGCUCAGAUUACAUUUGUGU-----------------------------UG---
.........((.((((((.(((((..((.(((...............)))..))..))))).)))))).))-----------------------------..--- (  -7.86)
>DroSim_CAF1 2119 93 - 1
UAAUUCCGCACUCAAAUGUAAUUUGAGCUCAAAUUACAUU-UCCAACUUGACGCCGAGAUUGGAUGGAUGUGGGAUG--UGAGAGCACAUG------UGGUU---
..((((((((..(((((((((((((....)))))))))))-(((((((((....)))).)))))))..))))))))(--(....)).....------.....--- ( -32.60)
>DroYak_CAF1 2468 102 - 1
UAAUUCCGCACUCAAAUGUAAUUUGAGCUCAAAUUACAUU-UCCAACUUGACGCCGAGAUUGGAUGGAUGUGGGAUG--UAAGAGCACAUGGGCAUGUGGUGCUU
..((((((((..(((((((((((((....)))))))))))-(((((((((....)))).)))))))..)))))))).--...((((((((......)).)))))) ( -36.60)
>consensus
UAAUUCCGCACUCAAAUGUAAUUUGAGCUCAAAUUACAUU_UCCAACUUGACGCCCAGAUUGGAUGGAUGUGGGAUG__UGAGAGCACAUG______UGGUG___
..((((((((..(((((((((((((....))))))))))).(((((((((....)))).)))))))..))))))))............................. (-17.15 = -20.03 +   2.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:34 2006