Locus 5515

Sequence ID	3R_DroMel_CAF1
Location	14,515,084 – 14,515,232
Length	148
Max. P	0.992209

overview

Window 8

Location	14,515,084 – 14,515,200
Length	116
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	69.20
Mean single sequence MFE	-38.62
Consensus MFE	-13.06
Energy contribution	-14.04
Covariance contribution	0.97
Combinations/Pair	1.21
Mean z-score	-2.06
Structure conservation index	0.34
SVM decision value	0.70
SVM RNA-class probability	0.827407
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14515084 116 + 27905053
GCUCCGUAGGAGGAAGAUGGCGGGGCGGGUGCUCCAUAAGACUUGGAAGGAGCAGCAGGAGCUCCAUACGAAGAAGAUGGAGGAGCAGGGGCUCCAUAAGAUUUGGAUGGUGGUGC
(((((((............))))))).(.((((((.............)))))).)....((.((((.((((....((((((.........))))))....))))....)))).)) ( -38.52)
>DroPse_CAF1 11699 116 + 1
GCUCCAUAAGAUGAUGAUGGCUGCGGGGGUGCACCAUACGAUUUGGAUGGUGGUGCAGGAGCUCCAUAAGAUGAUGAUGGCUGCUGGGGGGCACCAUACGAUUUCGAUGGUGGUGC
(((((...((..........))...)))))(((((((.(((..(.(((((((.(.(((.((((.(((......)))..)))).)))...).)))))).).)..)))...))))))) ( -38.60)
>DroSec_CAF1 12035 98 + 1
------------------GGCGGGGCGGGUGCUCCAUAAGACUUAGAAGGAGCAGCAGGUGCUCCAUACGAAGAAGAUGGAGGAGCAGGGGCUCCGUAAGAUUUGGAUGGUGGUGC
------------------.(((((((.(.((((((.............)))))).).(.(.((((((.(......))))))).).)....)))))))................... ( -33.92)
>DroEre_CAF1 11393 116 + 1
GCUCCGUAGGAGGAAGAUGGUGGUGCAGGUGCUCCGUAGGAGGAAGACGGUGGGGCAGGUGCUCCAUAAGACUUGGAAGGAGCAGCAGGCGCUCCAUACGAAGAAGAUGGAGGAGC
.((((((.........((((.(((((.(.((((((....(((.......(((((((....)))))))....)))....)))))).)..))))))))).........)))))).... ( -44.97)
>DroYak_CAF1 11211 97 + 1
GCUCCAUAGGAGGAAGAUGGUGGGGCCGGUGCUCCAUAAGACUUGGAAGGAGCAGCGGGGGUUCCAUACGAAGAAGAGGGAGGAGCUGGGACUCCAU-------------------
.((((...)))).......(((((((((.((((((.............)))))).))).((((((...(........)...))))))....))))))------------------- ( -33.62)
>DroAna_CAF1 11104 116 + 1
GCACCAUAGGAGGGUGAUGGCGGGGCAGGUGCUCCAUAAGACUUAGAUGGCGCUGGAGGUGCUCCAUAUGAUGGAGAAGGAGCGGCAGGUGCCCCAUAUGAUUGGGAUGGUGGGGC
.((((((.....(((.(((..(((((((.((((((..............((((.....))))(((((...)))))...)))))).)...)))))).))).)))...)))))).... ( -42.10)
>consensus
GCUCCAUAGGAGGAAGAUGGCGGGGCGGGUGCUCCAUAAGACUUAGAAGGAGCAGCAGGUGCUCCAUACGAAGAAGAUGGAGGAGCAGGGGCUCCAUAAGAUUUGGAUGGUGGUGC
...........................(.((((((.............)))))).).((.(((((......................))))).))..................... (-13.06 = -14.04 +   0.97)

alignment

secondary structure

dotplot

Window 9

Location	14,515,084 – 14,515,200
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	69.20
Mean single sequence MFE	-28.81
Consensus MFE	-9.58
Energy contribution	-10.64
Covariance contribution	1.06
Combinations/Pair	1.29
Mean z-score	-2.56
Structure conservation index	0.33
SVM decision value	1.92
SVM RNA-class probability	0.982606
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14515084 116 - 27905053
GCACCACCAUCCAAAUCUUAUGGAGCCCCUGCUCCUCCAUCUUCUUCGUAUGGAGCUCCUGCUGCUCCUUCCAAGUCUUAUGGAGCACCCGCCCCGCCAUCUUCCUCCUACGGAGC
.....................(((((....)))))........(((((((.((((.......((((((.............))))))...((...)).......))))))))))). ( -28.52)
>DroPse_CAF1 11699 116 - 1
GCACCACCAUCGAAAUCGUAUGGUGCCCCCCAGCAGCCAUCAUCAUCUUAUGGAGCUCCUGCACCACCAUCCAAAUCGUAUGGUGCACCCCCGCAGCCAUCAUCAUCUUAUGGAGC
((((((....(((....(.((((((.....(((.(((..((((......)))).))).)))...)))))))....)))..))))))......((..((((.........)))).)) ( -26.40)
>DroSec_CAF1 12035 98 - 1
GCACCACCAUCCAAAUCUUACGGAGCCCCUGCUCCUCCAUCUUCUUCGUAUGGAGCACCUGCUGCUCCUUCUAAGUCUUAUGGAGCACCCGCCCCGCC------------------
....................(((.((...((((((........(((.(...((((((.....))))))..).)))......))))))...)).)))..------------------ ( -26.74)
>DroEre_CAF1 11393 116 - 1
GCUCCUCCAUCUUCUUCGUAUGGAGCGCCUGCUGCUCCUUCCAAGUCUUAUGGAGCACCUGCCCCACCGUCUUCCUCCUACGGAGCACCUGCACCACCAUCUUCCUCCUACGGAGC
((((((((((...(((.(...((((((.....))))))..).)))....)))))(((..(((....((((.........)))).)))..)))...................))))) ( -31.80)
>DroYak_CAF1 11211 97 - 1
-------------------AUGGAGUCCCAGCUCCUCCCUCUUCUUCGUAUGGAACCCCCGCUGCUCCUUCCAAGUCUUAUGGAGCACCGGCCCCACCAUCUUCCUCCUAUGGAGC
-------------------..(((((....)))))............(.((((.....(((.((((((.............)))))).))).....)))))((((......)))). ( -26.32)
>DroAna_CAF1 11104 116 - 1
GCCCCACCAUCCCAAUCAUAUGGGGCACCUGCCGCUCCUUCUCCAUCAUAUGGAGCACCUCCAGCGCCAUCUAAGUCUUAUGGAGCACCUGCCCCGCCAUCACCCUCCUAUGGUGC
((((((..............)))))).......(((((.............))))).......(((((((...((..(.((((.((....))....)))).)..))...))))))) ( -33.06)
>consensus
GCACCACCAUCCAAAUCGUAUGGAGCCCCUGCUCCUCCAUCUUCUUCGUAUGGAGCACCUGCUGCUCCUUCCAAGUCUUAUGGAGCACCCGCCCCGCCAUCUUCCUCCUAUGGAGC
.....................(((((....)))))..............((((..........(((((.............)))))..........))))................ ( -9.58 = -10.64 +   1.06)

alignment

secondary structure

dotplot

Window 0

Location	14,515,124 – 14,515,232
Length	108
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	67.75
Mean single sequence MFE	-34.44
Consensus MFE	-13.34
Energy contribution	-14.18
Covariance contribution	0.84
Combinations/Pair	1.19
Mean z-score	-1.76
Structure conservation index	0.39
SVM decision value	0.13
SVM RNA-class probability	0.600282
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14515124 108 + 27905053
ACUUGGAAGGAGCAGCAGGAGCUCCAUACGAAGAAGAUGGAGGAGCAGGGGCUCCAUAAGAUUUGGAUGGUGGUGCUG---GGGCUCCGUAAGAUGGGGAUGGCGGUGCAG-----
.((((...(((((..(((.(.(.((((.((((....((((((.........))))))....)))).)))).).).)))---..))))).))))..................----- ( -34.50)
>DroPse_CAF1 11739 113 + 1
AUUUGGAUGGUGGUGCAGGAGCUCCAUAAGAUGAUGAUGGCUGCUGGGGGGCACCAUACGAUUUCGAUGGUGGUGCAG---GUGCUCCAUAAGAAGAGGAAGGUGCUGCUGGUCUU
....((((((..(..(((.((((.(((......)))..)))).))..((((((((.(((.(((.....))).)))..)---)))))))..............)..)..)).)))). ( -34.70)
>DroSec_CAF1 12057 95 + 1
ACUUAGAAGGAGCAGCAGGUGCUCCAUACGAAGAAGAUGGAGGAGCAGGGGCUCCGUAAGAUUUGGAUGGUGGUGCUG---GGGCUCCGUAAGAUGGG------------------
.((((...(((((....((..((((((.((((....((((((.........))))))....)))).)))).))..)).---..))))).)))).....------------------ ( -33.50)
>DroEre_CAF1 11433 108 + 1
AGGAAGACGGUGGGGCAGGUGCUCCAUAAGACUUGGAAGGAGCAGCAGGCGCUCCAUACGAAGAAGAUGGAGGAGCAG---GGGCUCCAUAAGAUUUUGAUGGCGGUGCGG-----
......((.(((((((....))))).(((((((((...(((((..(..((.((((((.(......)))))))..))..---).))))).)))).)))))...)).))....----- ( -35.50)
>DroAna_CAF1 11144 103 + 1
ACUUAGAUGGCGCUGGAGGUGCUCCAUAUGAUGGAGAAGGAGCGGCAGGUGCCCCAUAUGAUUGGGAUGGUGGGGCGGGAGGAGCUCCGUAUGACUUCGAUGG-------------
...............(((((.((((((...))))))..(((((......((((((((............))))))))......))))).....))))).....------------- ( -34.00)
>consensus
ACUUAGAAGGAGCAGCAGGUGCUCCAUAAGAAGAAGAUGGAGGAGCAGGGGCUCCAUAAGAUUUGGAUGGUGGUGCAG___GGGCUCCGUAAGAUGGGGAUGG_G_UGC_G_____
.................((.(((((((.........))))).........(((((((............))))))).......)).))............................ (-13.34 = -14.18 +   0.84)

alignment

secondary structure

dotplot

Window 1

Location	14,515,124 – 14,515,232
Length	108
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	67.75
Mean single sequence MFE	-24.46
Consensus MFE	-10.68
Energy contribution	-11.64
Covariance contribution	0.96
Combinations/Pair	1.15
Mean z-score	-2.40
Structure conservation index	0.44
SVM decision value	2.31
SVM RNA-class probability	0.992209
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14515124 108 - 27905053
-----CUGCACCGCCAUCCCCAUCUUACGGAGCCC---CAGCACCACCAUCCAAAUCUUAUGGAGCCCCUGCUCCUCCAUCUUCUUCGUAUGGAGCUCCUGCUGCUCCUUCCAAGU
-----.......................(((((..---.((((..................(((((....)))))((((((......).))))).....)))))))))........ ( -23.60)
>DroPse_CAF1 11739 113 - 1
AAGACCAGCAGCACCUUCCUCUUCUUAUGGAGCAC---CUGCACCACCAUCGAAAUCGUAUGGUGCCCCCCAGCAGCCAUCAUCAUCUUAUGGAGCUCCUGCACCACCAUCCAAAU
((((...((((....((((.........))))...---))))..((((((((....)).))))))....................)))).(((.((....)).))).......... ( -23.40)
>DroSec_CAF1 12057 95 - 1
------------------CCCAUCUUACGGAGCCC---CAGCACCACCAUCCAAAUCUUACGGAGCCCCUGCUCCUCCAUCUUCUUCGUAUGGAGCACCUGCUGCUCCUUCUAAGU
------------------.....((((.(((((..---.((((..................(((((....)))))((((((......).))))).....)))))))))...)))). ( -24.00)
>DroEre_CAF1 11433 108 - 1
-----CCGCACCGCCAUCAAAAUCUUAUGGAGCCC---CUGCUCCUCCAUCUUCUUCGUAUGGAGCGCCUGCUGCUCCUUCCAAGUCUUAUGGAGCACCUGCCCCACCGUCUUCCU
-----..(((.(((..............(((((..---..)))))((((((......).))))))))..)))((((((.............))))))................... ( -26.02)
>DroAna_CAF1 11144 103 - 1
-------------CCAUCGAAGUCAUACGGAGCUCCUCCCGCCCCACCAUCCCAAUCAUAUGGGGCACCUGCCGCUCCUUCUCCAUCAUAUGGAGCACCUCCAGCGCCAUCUAAGU
-------------...............((.(((......((((((..............)))))).......(((((.............)))))......))).))........ ( -25.26)
>consensus
_____C_GCA_C_CCAUCCACAUCUUACGGAGCCC___CAGCACCACCAUCCAAAUCGUAUGGAGCCCCUGCUCCUCCAUCUUCAUCGUAUGGAGCACCUGCAGCACCAUCUAAGU
............................((((........(((((................)))))........)))).............((.((.......)).))........ (-10.68 = -11.64 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:05 2006