Locus 3537

Sequence ID	X_DroMel_CAF1
Location	9,480,671 – 9,480,851
Length	180
Max. P	0.908370

overview

Window 1

Location	9,480,671 – 9,480,775
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.97
Mean single sequence MFE	-23.48
Consensus MFE	-18.24
Energy contribution	-19.08
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.37
Structure conservation index	0.78
SVM decision value	0.64
SVM RNA-class probability	0.809669
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9480671 104 + 22224390
AUUAU--U---------UAAAACACCCAGUUAAGUAACAUUCCUUGAAUUACGCGAUCGGACGUCGAUUU-----UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAU
.((((--(---------(((.........)))))))).................(((((.....))))).-----..((((((((((((((......)))))).)))))..)))...... ( -23.00)
>DroSec_CAF1 23877 115 + 1
AUUUUAAUCAAAAAUAAAAAAACACCCAAUUAAGUAACAUCCCUUGAAUUACGCGAUCGGACGUCGAUUU-----UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUUU
..............(((((..((..((.(((..((((((.....))..))))..))).))..))...)))-----))((((((((((((((......)))))).)))))..)))...... ( -23.10)
>DroSim_CAF1 23891 87 + 1
----------------------------AUUAAGUAACAUCCCUUGAAUUACGCGAUCGGACGUCGAUUU-----UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAU
----------------------------.(((((........))))).......(((((.....))))).-----..((((((((((((((......)))))).)))))..)))...... ( -22.80)
>DroEre_CAF1 23953 117 + 1
AGUUCUUACAU---UAAAAAACCACCGAAUUAAGUAAGAUCCCUUUAAUUCGGCGUUCGAAAGUAGAUUUACAUGUAGCCACGCCUUUUGGAAAUACCCGAAAUGACGUAUGGCACAUAU
......(((((---((((....(.((((((((((.........)))))))))).)..(....)....)))).)))))(((((((.((((((......)))))).).)))..)))...... ( -25.00)
>DroYak_CAF1 23899 114 + 1
AUUUCUUUCAC-----AAAAACCACCCAAUUAAGUAAAAUCCCUUGAAUUCCGCGAUCGGAAGACGAUUUACACGUGGUCACGCCU-UUGGAAAUUCCCGAAAUGGCGUAUGGCACAUUU
...........-----....(((((....(((((........))))).(((((....)))))............))))).((((((-((((......)))))..)))))........... ( -23.50)
>consensus
AUUUC__UCA______AAAAAACACCCAAUUAAGUAACAUCCCUUGAAUUACGCGAUCGGACGUCGAUUU_____UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAU
.............................(((((........))))).......(((((.....)))))........((((((((((((((......)))))).)))))..)))...... (-18.24 = -19.08 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	9,480,700 – 9,480,815
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.44
Mean single sequence MFE	-29.06
Consensus MFE	-24.82
Energy contribution	-25.62
Covariance contribution	0.80
Combinations/Pair	1.12
Mean z-score	-1.46
Structure conservation index	0.85
SVM decision value	0.33
SVM RNA-class probability	0.690630
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9480700 115 + 22224390
UCCUUGAAUUACGCGAUCGGACGUCGAUUU-----UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAUUCCAAUGAAUCCAUGCAAUGGCAUUUAAUUGCAAUCUAUA
............(((((((.....))))).-----..((((.(((((((((......)))))).)))((((((..(((......)))...))))))..))))........))........ ( -30.50)
>DroSec_CAF1 23917 115 + 1
CCCUUGAAUUACGCGAUCGGACGUCGAUUU-----UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUUUUCGAAUGAAUCCGUGCAAUGGCAUUUAAUUGCAAUCUAUA
..............(((((((..((((...-----..((((((((((((((......)))))).)))))..)))......)))).....))))((((((........))))))))).... ( -32.00)
>DroSim_CAF1 23903 115 + 1
CCCUUGAAUUACGCGAUCGGACGUCGAUUU-----UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAUUCCAAUGAAUCCAUGCAAUGGCAUUUAAUUGCAAUCUAUA
............(((((((.....))))).-----..((((.(((((((((......)))))).)))((((((..(((......)))...))))))..))))........))........ ( -30.50)
>DroEre_CAF1 23990 120 + 1
CCCUUUAAUUCGGCGUUCGAAAGUAGAUUUACAUGUAGCCACGCCUUUUGGAAAUACCCGAAAUGACGUAUGGCACAUAUUCCAUUGAAUCAAUGAGAUGACAUUUAAUUGCAAUCUAUA
........((((.....)))).(((((((....(((.(((((((.((((((......)))))).).)))..))))))(((..(((((...)))))..)))............))))))). ( -24.50)
>DroYak_CAF1 23934 119 + 1
CCCUUGAAUUCCGCGAUCGGAAGACGAUUUACACGUGGUCACGCCU-UUGGAAAUUCCCGAAAUGGCGUAUGGCACAUUUUCCAUUGAAUCCAUGAGAUGACAUUUAAUUGCAAUCUAGA
...(((..(((((....)))))..)))......(((((((((((((-((((......)))))..)))))((((........)))).))..)))))((((..((......))..))))... ( -27.80)
>consensus
CCCUUGAAUUACGCGAUCGGACGUCGAUUU_____UAGCCACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAUUCCAAUGAAUCCAUGCAAUGGCAUUUAAUUGCAAUCUAUA
............(((((..((.((((...........((((((((((((((......)))))).)))))..))).(((((((....))))..)))...)))).))..)))))........ (-24.82 = -25.62 +   0.80)

alignment

secondary structure

dotplot

Window 3

Location	9,480,735 – 9,480,851
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.65
Mean single sequence MFE	-30.39
Consensus MFE	-23.12
Energy contribution	-23.68
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.37
Structure conservation index	0.76
SVM decision value	1.06
SVM RNA-class probability	0.908370
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9480735 116 + 22224390
ACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAUUCCAAUGAAUCCAUGCAAUGGCAUUUAAUUGCAAUCUAUACAAAUGUCAAGGGGGAACU----CACAAGGAACCCAAUUA
(((((((((((......)))))).))))).((((((((......)))......((((((........))))))...........)))))..(((...((----....))...)))..... ( -29.30)
>DroSec_CAF1 23952 115 + 1
ACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUUUUCGAAUGAAUCCGUGCAAUGGCAUUUAAUUGCAAUCUAUACAAAUGUCAAGGGGG-ACU----CACAAGGAAGCCAAUUA
(((((((((((......)))))).))))).((((.((((....))))..(((.((((((........))))))...........(((...((...-.))----.))).))).)))).... ( -33.20)
>DroSim_CAF1 23938 115 + 1
ACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAUUCCAAUGAAUCCAUGCAAUGGCAUUUAAUUGCAAUCUAUACAAAUGUCAAGGGGG-ACU----CACAAGGAAGCCAAUUA
(((((((((((......)))))).))))).((((.....((((..(((.(((.((((((........)))))).(((..((....))..))).))-).)----))...)))))))).... ( -33.30)
>DroEre_CAF1 24030 115 + 1
ACGCCUUUUGGAAAUACCCGAAAUGACGUAUGGCACAUAUUCCAUUGAAUCAAUGAGAUGACAUUUAAUUGCAAUCUAUACAAAUGUCAAGGGGG-ACU----CACAAGGAAGCCAAUUA
((((.((((((......)))))).).))).((((.....((((.(((...........((((((((...............)))))))).((...-.))----..))))))))))).... ( -24.46)
>DroYak_CAF1 23974 118 + 1
ACGCCU-UUGGAAAUUCCCGAAAUGGCGUAUGGCACAUUUUCCAUUGAAUCCAUGAGAUGACAUUUAAUUGCAAUCUAGACAAAUGUCAAGUGGG-ACUCACUCACAAGGAAGCCAAUUA
((((((-((((......)))))..))))).((((.((........))..(((......((((((((..(((.....)))..)))))))).(((((-.....)))))..))).)))).... ( -31.70)
>consensus
ACGCCUUUUGGAAAUUCCCGAAAUGGCGUAUGGCACAUAUUCCAAUGAAUCCAUGCAAUGGCAUUUAAUUGCAAUCUAUACAAAUGUCAAGGGGG_ACU____CACAAGGAAGCCAAUUA
(((((((((((......)))))).))))).((((.....(((....)))(((.((...((((((((...............))))))))((......))......)).))).)))).... (-23.12 = -23.68 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:54 2006