Locus 8728

Sequence ID	3R_DroMel_CAF1
Location	23,310,677 – 23,310,835
Length	158
Max. P	0.997637

overview

Window 5

Location	23,310,677 – 23,310,769
Length	92
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.47
Mean single sequence MFE	-34.77
Consensus MFE	-14.44
Energy contribution	-14.20
Covariance contribution	-0.25
Combinations/Pair	1.28
Mean z-score	-2.31
Structure conservation index	0.42
SVM decision value	0.89
SVM RNA-class probability	0.876387
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23310677 92 - 27905053
GGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAG----GCUGCAAAAUGGCC-AGAAUGAAUGGCC-------------GU--GCC-CGAGGC
.(((....(((.(.((((........((((.......))))..(((...)))..----)))))...((((((-(.......)))))-------------))--)))-...))) ( -30.60)
>DroSec_CAF1 108128 91 - 1
GGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAG----GCUGCAAAAUGGCC-GGAAUGAAUGUC--------------UU--GCC-CCGGGC
(.((((..((((((((...((.((.(((((.....((..((..(((...)))..----))..))...)))))-.)).))..))))--------------.)--)))-)))).) ( -37.20)
>DroSim_CAF1 112313 91 - 1
GGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAG----GCUGCAAAAUGGCC-GGAAUGAAUGUC--------------CU--GCC-CCGGGC
(.((((..((((((((...((.((.(((((.....((..((..(((...)))..----))..))...)))))-.)).))..))).--------------))--)))-)))).) ( -37.20)
>DroEre_CAF1 114394 88 - 1
---UGGAUGGCAGACAGCGCAAUUAGGCCAGCAAAUGUGGCGAGCGAAACGCGC----GCUGCGAAAUGGCC-GAAAUGAAUGUC--------------CU--GCC-CCGGGC
---.((..((((((((...((.((.(((((.....((..(((.(((...))).)----))..))...)))))-.)).))..))).--------------))--)))-)).... ( -35.70)
>DroYak_CAF1 119080 80 - 1
---UGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGC---------GCAA----GCUGCGAAAUGGCC-AAAAUGAAUGUC--------------CU--GCCCCCAGGC
---(((..((((((((...((.((.(((((.....((..((---------....----))..))...)))))-.)).))..))).--------------))--))).)))... ( -34.00)
>DroPer_CAF1 111699 112 - 1
GGCCAACUGGCAGACGGCGCAAUUAGGCCGUCAAAUGUGGCGAGCAAAGGACAGCGACUCUGUAUAGUCGCCCAAAAUGAAUGUCGACAAAGGGCAAUCCUCUCCU-UUCAGC
.((((.......((((((........)))))).....))))..(.((((((..((((((......)))))).......((.((((.......)))).))...))))-)))... ( -33.90)
>consensus
GGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAG____GCUGCAAAAUGGCC_AAAAUGAAUGUC______________CU__GCC_CCGGGC
............((((...((....(((((.....((..((.................))..))...))))).....))..))))..................(((....))) (-14.44 = -14.20 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	23,310,700 – 23,310,808
Length	108
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.06
Mean single sequence MFE	-37.45
Consensus MFE	-24.99
Energy contribution	-26.30
Covariance contribution	1.31
Combinations/Pair	1.20
Mean z-score	-2.07
Structure conservation index	0.67
SVM decision value	1.14
SVM RNA-class probability	0.921588
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23310700 108 - 27905053
C-GAUUUCUUCCUUUGCGCUUUUUAUUCCGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAGGCUGCAAAAUGGCCA-----
.-...........(((((((......((.((((((..(....)..)))))).)).)))))))...(((((.....((..((..(((...)))..))..))...))))).----- ( -41.40)
>DroSec_CAF1 108150 108 - 1
C-GAUUUCGUCCUUUGCGUUUUUUAUUUUGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAGGCUGCAAAAUGGCCG-----
.-...........(((((((......(((((((((..(....)..))))))))).)))))))...(((((.....((..((..(((...)))..))..))...))))).----- ( -41.00)
>DroSim_CAF1 112335 108 - 1
C-GAUUUCGUCCUUUGCGCUUUUUAUUUCGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAGGCUGCAAAAUGGCCG-----
.-...........(((((((.(((.....((((((..(....)..))))))))).)))))))...(((((.....((..((..(((...)))..))..))...))))).----- ( -41.20)
>DroEre_CAF1 114416 104 - 1
C-GAUUUCUUACUUUGCGCUUUUUAUUUCGCCAUUUGGC----UGGAUGGCAGACAGCGCAAUUAGGCCAGCAAAUGUGGCGAGCGAAACGCGCGCUGCGAAAUGGCCG-----
.-...........(((((((.(((.....(((((((...----.)))))))))).)))))))...(((((.....((..(((.(((...))).)))..))...))))).----- ( -39.30)
>DroYak_CAF1 119103 95 - 1
C-GAUUUCUUACUUGGCGCUUUUUAUUUUGCCAUUUGGC----UGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGC---------GCAAGCUGCGAAAUGGCCA-----
.-.............(((((......((((((((((...----.)))))))))).))))).....(((((.....((..((---------....))..))...))))).----- ( -36.90)
>DroAna_CAF1 102768 100 - 1
AGGGUUUUCUGCUUUUUGGGUUUCAUUCCGUUGUUU-------UGGCCGCCAGACGUCGCAAUUAGGCCAGCAAAUGUGGCGAGCAAAAG-------CCGAAAUUGCCAUUGGC
..(((((((.((((((.(((......))).......-------..(((((((.(.((.((......))..))...).))))).)))))))-------).))))..)))...... ( -24.90)
>consensus
C_GAUUUCUUCCUUUGCGCUUUUUAUUUCGCCAUUUGGC____UGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUGGCGAGCGAAACGCAGGCUGCAAAAUGGCCA_____
.............(((((((.(((.....(((((((........)))))))))).)))))))...(((((.....((((((..((.....))..))))))...)))))...... (-24.99 = -26.30 +   1.31)

alignment

secondary structure

dotplot

Window 7

Location	23,310,730 – 23,310,835
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-27.28
Consensus MFE	-23.22
Energy contribution	-23.06
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.14
Structure conservation index	0.85
SVM decision value	2.27
SVM RNA-class probability	0.991460
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23310730 105 + 27905053
CACAUUUACUGGCCUAAUUGCGCUGUCUGCCAUCCAGCCAGCCAAAUGGCGGAAUAAAAAGCGCAAAGGAAGAAAUCGAAAGGCAAACACGCAAACAGCGAGCUG
...........((((..(((((((.((((((((...(....)...))))))))......)))))))..((.....))...)))).....(((.....)))..... ( -29.40)
>DroSec_CAF1 108180 105 + 1
CACAUUUACUGGCCUAAUUGCGCUGUCUGCCAUCCAGCCAGCCAAAUGGCAAAAUAAAAAACGCAAAGGACGAAAUCGAAAGGCAAACACGCAAACAGCGAGCUG
........((.((....(((((.(((.((((.....((((......))))....................((....))...)))).))))))))...)).))... ( -26.80)
>DroSim_CAF1 112365 105 + 1
CACAUUUACUGGCCUAAUUGCGCUGUCUGCCAUCCAGCCAGCCAAAUGGCGAAAUAAAAAGCGCAAAGGACGAAAUCGAAAGGCAAACACGCAAACAGCGAGCUG
........((.((....(((((.(((.((((.(((.((((......))))(..........).....)))((....))...)))).))))))))...)).))... ( -26.90)
>DroEre_CAF1 114446 101 + 1
CACAUUUGCUGGCCUAAUUGCGCUGUCUGCCAUCCA----GCCAAAUGGCGAAAUAAAAAGCGCAAAGUAAGAAAUCGAAAGGCAAGCACGCAAACAGCGAGCUG
......((((.((((..(((((((.((.(((((...----.....))))))).......))))))).....(....)...)))).))))(((.....)))..... ( -29.00)
>DroYak_CAF1 119124 101 + 1
CACAUUUACUGGCCUAAUUGCGCUGUCUGCCAUCCA----GCCAAAUGGCAAAAUAAAAAGCGCCAAGUAAGAAAUCGAAAGGCAAACACGCAAACAGCGAGCUG
........((.((....(((((.(((.((((.....----(((....)))..........((.....))............)))).))))))))...)).))... ( -24.30)
>consensus
CACAUUUACUGGCCUAAUUGCGCUGUCUGCCAUCCAGCCAGCCAAAUGGCGAAAUAAAAAGCGCAAAGGAAGAAAUCGAAAGGCAAACACGCAAACAGCGAGCUG
........((.((....(((((.(((.((((.........(((....))).....................(....)....)))).))))))))...)).))... (-23.22 = -23.06 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	23,310,730 – 23,310,835
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	94.07
Mean single sequence MFE	-32.54
Consensus MFE	-30.32
Energy contribution	-30.36
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.90
Structure conservation index	0.93
SVM decision value	2.90
SVM RNA-class probability	0.997637
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23310730 105 - 27905053
CAGCUCGCUGUUUGCGUGUUUGCCUUUCGAUUUCUUCCUUUGCGCUUUUUAUUCCGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUG
..(((.(((..(((((((((((((....((.....))...............(((((((......)))).))).)))))))).)))))...))).)))....... ( -33.70)
>DroSec_CAF1 108180 105 - 1
CAGCUCGCUGUUUGCGUGUUUGCCUUUCGAUUUCGUCCUUUGCGUUUUUUAUUUUGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUG
..(((.(((..(((((((((((((.((((....(((.....)))...........((((......)))))))).)))))))).)))))...))).)))....... ( -33.60)
>DroSim_CAF1 112365 105 - 1
CAGCUCGCUGUUUGCGUGUUUGCCUUUCGAUUUCGUCCUUUGCGCUUUUUAUUUCGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUG
..(((.(((..(((((((((((((.((((....(((.....)))...........((((......)))))))).)))))))).)))))...))).)))....... ( -33.70)
>DroEre_CAF1 114446 101 - 1
CAGCUCGCUGUUUGCGUGCUUGCCUUUCGAUUUCUUACUUUGCGCUUUUUAUUUCGCCAUUUGGC----UGGAUGGCAGACAGCGCAAUUAGGCCAGCAAAUGUG
.....(((.....)))((((.((((..............(((((((.(((.....(((((((...----.)))))))))).)))))))..)))).))))...... ( -29.49)
>DroYak_CAF1 119124 101 - 1
CAGCUCGCUGUUUGCGUGUUUGCCUUUCGAUUUCUUACUUGGCGCUUUUUAUUUUGCCAUUUGGC----UGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUG
..(((.(((..(((((((((((((.((((....((....(((((..........)))))...)).----)))).)))))))).)))))...))).)))....... ( -32.20)
>consensus
CAGCUCGCUGUUUGCGUGUUUGCCUUUCGAUUUCUUCCUUUGCGCUUUUUAUUUCGCCAUUUGGCUGGCUGGAUGGCAGACAGCGCAAUUAGGCCAGUAAAUGUG
..(((.(((..(((((((((((((.((((....).....................(((....))).....))).)))))))).)))))...))).)))....... (-30.32 = -30.36 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:16 2006