Locus 3429

Sequence ID	3R_DroMel_CAF1
Location	9,305,194 – 9,305,287
Length	93
Max. P	0.658565

overview

Window 4

Location	9,305,194 – 9,305,287
Length	93
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.07
Mean single sequence MFE	-26.98
Consensus MFE	-18.27
Energy contribution	-19.33
Covariance contribution	1.06
Combinations/Pair	1.25
Mean z-score	-1.40
Structure conservation index	0.68
SVM decision value	0.09
SVM RNA-class probability	0.576328
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9305194 93 + 27905053
---UGAGCAGGCAA---UCC-----GGAUACCCUACGGAAUUGUGGGAGCCUGCUUCGGCAGGAUACAUAUGUCUCUAUGUAUAUUC---------AUGAGCAAUAUAUUUUA
---...((..((((---(((-----(.........))).))))).(((.(((((....)))))(((((((......))))))).)))---------....))........... ( -26.60)
>DroPse_CAF1 73687 99 + 1
CGAAGAGCAGAGAAGAGAGC-----CGAGCCCCUUGGGGGUUAAGGAAGCGUGAGCCAGCAGCAUACAUAUGCCUAUAUGUAUAUUC---------AUGAGCAAUAUAUUUUA
.(((..((...........(-----(.((((((...))))))..))..((....))..))...((((((((....)))))))).)))---------................. ( -22.60)
>DroSim_CAF1 77705 93 + 1
---UGAGCAGGCAA---UCC-----GGAUACCCUACGGAAUUGUGGGAGCCUGCUCCGGCAGGAUACAUAUGUCUCUAUGUAUAUUC---------AUGAGCAAUAUAUUUUA
---.((((((((..---...-----(....)((((((....)))))).))))))))....((((((.((.((.(((.(((......)---------))))))))).)))))). ( -26.20)
>DroEre_CAF1 77187 102 + 1
---UGAGCGGGCAA---GCC-----GGAUACCCUACGGAAUUGUGGGAGCCUGCUCCGGCAGGAUACAUAUGUCUCUAUGUAUAUUCAUGAGAUUCAUGAGCAAUAUAUUUUA
---.((((((((..---...-----(....)((((((....)))))).))))))))..((...(((((((......)))))))..(((((.....)))))))........... ( -31.60)
>DroYak_CAF1 77187 93 + 1
---UGAGCAGGCAA---UCC-----GGAUACCCUACGGAAUUGUGGGAGCCUGCUCCGGCAGGAUACAUAUGUCUCUAUGUAUAUUC---------AUGAGCAAUAUAUUUUA
---.((((((((..---...-----(....)((((((....)))))).))))))))....((((((.((.((.(((.(((......)---------))))))))).)))))). ( -26.20)
>DroAna_CAF1 75184 97 + 1
---UGAGCACUCG----UCUGGAAAGGAAGCCCGGCGGGAUUGCAGGAGCGUGCUCCGGCAGGAUACAUAUGUCUAUAUGUAUAUUC---------AUGAGCAAUAUAUUUUA
---...((.((((----((.((........)).)))))).((((.((((....)))).)))).((((((((....))))))))....---------....))........... ( -28.70)
>consensus
___UGAGCAGGCAA___UCC_____GGAUACCCUACGGAAUUGUGGGAGCCUGCUCCGGCAGGAUACAUAUGUCUCUAUGUAUAUUC_________AUGAGCAAUAUAUUUUA
....((((((((.....(((.....)))...((((((....)))))).)))))))).......(((((((......))))))).............................. (-18.27 = -19.33 +   1.06)

alignment

secondary structure

dotplot

Window 5

Location	9,305,194 – 9,305,287
Length	93
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.07
Mean single sequence MFE	-23.78
Consensus MFE	-16.03
Energy contribution	-16.26
Covariance contribution	0.23
Combinations/Pair	1.30
Mean z-score	-1.58
Structure conservation index	0.67
SVM decision value	0.26
SVM RNA-class probability	0.658565
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9305194 93 - 27905053
UAAAAUAUAUUGCUCAU---------GAAUAUACAUAGAGACAUAUGUAUCCUGCCGAAGCAGGCUCCCACAAUUCCGUAGGGUAUCC-----GGA---UUGCCUGCUCA---
....((((((..(((((---------(......))).)))..))))))........((.((((((.(((((......)).))).....-----...---..)))))))).--- ( -22.40)
>DroPse_CAF1 73687 99 - 1
UAAAAUAUAUUGCUCAU---------GAAUAUACAUAUAGGCAUAUGUAUGCUGCUGGCUCACGCUUCCUUAACCCCCAAGGGGCUCG-----GCUCUCUUCUCUGCUCUUCG
...........((....---------((((((((((((....)))))))))..((((((....))........((((...))))..))-----))....)))...))...... ( -18.80)
>DroSim_CAF1 77705 93 - 1
UAAAAUAUAUUGCUCAU---------GAAUAUACAUAGAGACAUAUGUAUCCUGCCGGAGCAGGCUCCCACAAUUCCGUAGGGUAUCC-----GGA---UUGCCUGCUCA---
....((((((..(((((---------(......))).)))..)))))).........((((((((.(((((......)).))).....-----...---..)))))))).--- ( -25.90)
>DroEre_CAF1 77187 102 - 1
UAAAAUAUAUUGCUCAUGAAUCUCAUGAAUAUACAUAGAGACAUAUGUAUCCUGCCGGAGCAGGCUCCCACAAUUCCGUAGGGUAUCC-----GGC---UUGCCCGCUCA---
...........(((((((.....)))))..(((((((......)))))))...))(((.((((((((((((......)).))).....-----)))---)))))))....--- ( -28.30)
>DroYak_CAF1 77187 93 - 1
UAAAAUAUAUUGCUCAU---------GAAUAUACAUAGAGACAUAUGUAUCCUGCCGGAGCAGGCUCCCACAAUUCCGUAGGGUAUCC-----GGA---UUGCCUGCUCA---
....((((((..(((((---------(......))).)))..)))))).........((((((((.(((((......)).))).....-----...---..)))))))).--- ( -25.90)
>DroAna_CAF1 75184 97 - 1
UAAAAUAUAUUGCUCAU---------GAAUAUACAUAUAGACAUAUGUAUCCUGCCGGAGCACGCUCCUGCAAUCCCGCCGGGCUUCCUUUCCAGA----CGAGUGCUCA---
...........((....---------....((((((((....))))))))..(((.((((....)))).))).....)).(((((((.((....))----.))).)))).--- ( -21.40)
>consensus
UAAAAUAUAUUGCUCAU_________GAAUAUACAUAGAGACAUAUGUAUCCUGCCGGAGCAGGCUCCCACAAUUCCGUAGGGUAUCC_____GGA___UUGCCUGCUCA___
..............................(((((((......))))))).......((((((((.(((((......)).)))..................)))))))).... (-16.03 = -16.26 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:48 2006