Locus 10231

Sequence ID	3R_DroMel_CAF1
Location	27,422,605 – 27,422,753
Length	148
Max. P	0.992807

overview

Window 0

Location	27,422,605 – 27,422,713
Length	108
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	82.76
Mean single sequence MFE	-18.63
Consensus MFE	-11.00
Energy contribution	-12.00
Covariance contribution	1.00
Combinations/Pair	1.12
Mean z-score	-2.44
Structure conservation index	0.59
SVM decision value	0.22
SVM RNA-class probability	0.641651
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27422605 108 + 27905053
CCUAA-AGUGUAAACCUCAACCGAAUAUAAGCUCAAAACUUGACGAUGGGCAAUUGCCCACCAUCAUUGUUAUCAUGAAUAAAAGUAGUCGUCAAAUAAAAACUAAAUA-----------
.....-.................................((((((((((((....))))....((((.......)))).........))))))))..............----------- ( -18.40)
>DroSim_CAF1 257 108 + 1
CCUAA-AAUGUAAACCUCAACCGAAUAUAAGCUCAAAACUUGACGAUGGGCGAUUGCCCACCAUCAUUGUUAGCAUCAAUAAAAGUAGUCGUCAAAUAAAAACUAAAUA-----------
.....-.................................((((((((((((....))))......((((.......)))).......))))))))..............----------- ( -17.50)
>DroYak_CAF1 361 118 + 1
CCUAAAAAUGUAAACCUCAACCGAAUAUAAGCUCAAAACUUGCCGAUGGUGGAUUAACCAUC--CAUCAUCAGCAUCAAUAAAACUAGUCAUCAAAUAAAAACUAAUUAUGCAUACACUU
.......(((((............................(((.((((((((((.....)))--))))))).)))..........((((............))))....)))))...... ( -20.00)
>consensus
CCUAA_AAUGUAAACCUCAACCGAAUAUAAGCUCAAAACUUGACGAUGGGCGAUUGCCCACCAUCAUUGUUAGCAUCAAUAAAAGUAGUCGUCAAAUAAAAACUAAAUA___________
.......................................((((((((((((....)))).......(((((......))))).....))))))))......................... (-11.00 = -12.00 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	27,422,605 – 27,422,713
Length	108
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.76
Mean single sequence MFE	-28.30
Consensus MFE	-20.33
Energy contribution	-20.67
Covariance contribution	0.34
Combinations/Pair	1.08
Mean z-score	-2.37
Structure conservation index	0.72
SVM decision value	1.06
SVM RNA-class probability	0.908185
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27422605 108 - 27905053
-----------UAUUUAGUUUUUAUUUGACGACUACUUUUAUUCAUGAUAACAAUGAUGGUGGGCAAUUGCCCAUCGUCAAGUUUUGAGCUUAUAUUCGGUUGAGGUUUACACU-UUAGG
-----------.....(((((..(((((((............((((.......)))).(((((((....))))))))))))))...))))).........(((((((....)))-)))). ( -28.10)
>DroSim_CAF1 257 108 - 1
-----------UAUUUAGUUUUUAUUUGACGACUACUUUUAUUGAUGCUAACAAUGAUGGUGGGCAAUCGCCCAUCGUCAAGUUUUGAGCUUAUAUUCGGUUGAGGUUUACAUU-UUAGG
-----------.....(((((..(((((((((..(((.((((((.......)))))).)))((((....)))).)))))))))...))))).........(((((((....)))-)))). ( -26.70)
>DroYak_CAF1 361 118 - 1
AAGUGUAUGCAUAAUUAGUUUUUAUUUGAUGACUAGUUUUAUUGAUGCUGAUGAUG--GAUGGUUAAUCCACCAUCGGCAAGUUUUGAGCUUAUAUUCGGUUGAGGUUUACAUUUUUAGG
(((((((.((..((((((((.((....)).))))))))..(((((.(((((((.((--(((.....))))).)))))))((((.....))))....)))))....)).)))))))..... ( -30.10)
>consensus
___________UAUUUAGUUUUUAUUUGACGACUACUUUUAUUGAUGCUAACAAUGAUGGUGGGCAAUCGCCCAUCGUCAAGUUUUGAGCUUAUAUUCGGUUGAGGUUUACAUU_UUAGG
...............(((((.((....)).)))))...................(((((((((((....))))))))))).((...((.((((........)))).)).))......... (-20.33 = -20.67 +   0.34)

alignment

secondary structure

dotplot

Window 2

Location	27,422,644 – 27,422,753
Length	109
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	82.23
Mean single sequence MFE	-22.22
Consensus MFE	-15.12
Energy contribution	-15.57
Covariance contribution	0.45
Combinations/Pair	1.12
Mean z-score	-1.73
Structure conservation index	0.68
SVM decision value	0.06
SVM RNA-class probability	0.564085
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27422644 109 + 27905053
UGACGAUGGGCAAUUGCCCACCAUCAUUGUUAUCAUGAAUAAAAGUAGUCGUCAAAUAAAAACUAAAUA-----------UACAAUAAUUGAGAUUUUCAUUCAUGUUUUUGAUGUUGAU
(((((((((((....))))....((((.......)))).........)))))))...............-----------..(((((.(..(((.............)))..)))))).. ( -20.82)
>DroSim_CAF1 296 109 + 1
UGACGAUGGGCGAUUGCCCACCAUCAUUGUUAGCAUCAAUAAAAGUAGUCGUCAAAUAAAAACUAAAUA-----------UACAAUAAUUGAGAUUUUCAUUCAUGUUUUUGAUGUUGAU
(((.(.(((((....))))).).)))..(((((((((((......((((..(......)..))))....-----------............((.......))......))))))))))) ( -20.10)
>DroYak_CAF1 401 118 + 1
UGCCGAUGGUGGAUUAACCAUC--CAUCAUCAGCAUCAAUAAAACUAGUCAUCAAAUAAAAACUAAUUAUGCAUACACUUUACAAUAAUUGAGAUUUUUCUUCACGUUUUUGAUGUUGAU
....((((((((.....))).)--))))(((((((((((..((((...................((((((..............))))))((((....))))...))))))))))))))) ( -25.74)
>consensus
UGACGAUGGGCGAUUGCCCACCAUCAUUGUUAGCAUCAAUAAAAGUAGUCGUCAAAUAAAAACUAAAUA___________UACAAUAAUUGAGAUUUUCAUUCAUGUUUUUGAUGUUGAU
(((.(.(((((....))))).).)))..(((((((((((......((((............))))...........................((.......))......))))))))))) (-15.12 = -15.57 +   0.45)

alignment

secondary structure

dotplot

Window 3

Location	27,422,644 – 27,422,753
Length	109
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.23
Mean single sequence MFE	-27.90
Consensus MFE	-19.85
Energy contribution	-20.97
Covariance contribution	1.12
Combinations/Pair	1.09
Mean z-score	-3.40
Structure conservation index	0.71
SVM decision value	2.35
SVM RNA-class probability	0.992807
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27422644 109 - 27905053
AUCAACAUCAAAAACAUGAAUGAAAAUCUCAAUUAUUGUA-----------UAUUUAGUUUUUAUUUGACGACUACUUUUAUUCAUGAUAACAAUGAUGGUGGGCAAUUGCCCAUCGUCA
..............(((((((((((.((((((..((((..-----------....))))......)))).))....))))))))))).......(((((((((((....))))))))))) ( -29.50)
>DroSim_CAF1 296 109 - 1
AUCAACAUCAAAAACAUGAAUGAAAAUCUCAAUUAUUGUA-----------UAUUUAGUUUUUAUUUGACGACUACUUUUAUUGAUGCUAACAAUGAUGGUGGGCAAUCGCCCAUCGUCA
.....((((((..((((((.(((.....))).))).))).-----------....(((((.((....)).)))))......)))))).......(((((((((((....))))))))))) ( -27.20)
>DroYak_CAF1 401 118 - 1
AUCAACAUCAAAAACGUGAAGAAAAAUCUCAAUUAUUGUAAAGUGUAUGCAUAAUUAGUUUUUAUUUGAUGACUAGUUUUAUUGAUGCUGAUGAUG--GAUGGUUAAUCCACCAUCGGCA
.....(((((((..(.....)(((((.((.((((((.(((.......)))))))))))))))).)))))))..............((((((((.((--(((.....))))).)))))))) ( -27.00)
>consensus
AUCAACAUCAAAAACAUGAAUGAAAAUCUCAAUUAUUGUA___________UAUUUAGUUUUUAUUUGACGACUACUUUUAUUGAUGCUAACAAUGAUGGUGGGCAAUCGCCCAUCGUCA
.....((((((..((((((.(((.....))).))).)))................(((((.((....)).)))))......)))))).......(((((((((((....))))))))))) (-19.85 = -20.97 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:08 2006