Locus 7535

Sequence ID	2L_DroMel_CAF1
Location	20,917,518 – 20,917,756
Length	238
Max. P	0.999120

overview

Window 0

Location	20,917,518 – 20,917,638
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.75
Mean single sequence MFE	-38.69
Consensus MFE	-34.38
Energy contribution	-34.26
Covariance contribution	-0.12
Combinations/Pair	1.12
Mean z-score	-1.20
Structure conservation index	0.89
SVM decision value	0.14
SVM RNA-class probability	0.600855
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917518 120 + 22407834
UGCGGUAGCCUCGUCCAUCACAAGGAUGCGGUUCUCGCGGAGAAUCGCCCUGGCCAAGCAGACCAACUGCCUCUGACCUACACUGUAGUUGGAUCCGCCCUCGGCAACCACACUUUCCAG
.(((..((((.(((((.......))))).))))..)))(((((.........(((..((.((((((((((...((.....))..)))))))).)).))....)))........))))).. ( -40.53)
>DroSec_CAF1 2876 120 + 1
UGCGGUAGCCUCGUCCAUCACAAGGAUGCGGUUCUCGCGGAGAAUCGCCCUGGCCAAGCAGACCAGCUGCCUCUGACCUACACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAG
.(((..((((.(((((.......))))).))))..)))(((((.........(((..((.((((((((((...((.....))..)))))))).)).))....)))........))))).. ( -40.53)
>DroSim_CAF1 2136 120 + 1
UGCGGUAGUCUCGUCCAUCACCAGGAUGCGGUUCUCGCGGAGAAUCGCCCUGGCCAAGCAGACCAACUGCCUCUGACCUACACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAG
((.(((.(((..........(((((..(((((((((...))))))))))))))....((.((((((((((...((.....))..)))))))).)).))....))).))).))........ ( -41.00)
>DroEre_CAF1 1927 120 + 1
GGCAGUAGCCUCGUCCAUGACAAGGAUGCGGUUCUCGCGGAGGAUCGCCCUGGCCAAGCAGACCAAUUGCCUCUGACCUACACUGUAGUUGGCUCCGCCUUCUGCAACCACACUUUCCAA
.((((.((((.(((((.......))))).))))...((((((....((....))........((((((((...((.....))..))))))))))))))...))))............... ( -36.40)
>DroYak_CAF1 1931 120 + 1
CGCGGUAGCCUCGUCCAUCACAAGGAUACGGUUCUCGCGGAGAAUCGCCCUGGCCAAGCAGACCAAUUGCCUCUGACCUACACUGUAGUUGGCUCCACCCUCUGCAACCACACUUUCCAG
.(((..((((..((((.......))))..))))..)))(((((...((....))...(((((((((((((...((.....))..))))))))........)))))........))))).. ( -35.00)
>consensus
UGCGGUAGCCUCGUCCAUCACAAGGAUGCGGUUCUCGCGGAGAAUCGCCCUGGCCAAGCAGACCAACUGCCUCUGACCUACACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAG
.((((.((((.(((((.......))))).)))).))))(((((...((....))...((.((((((((((...((.....))..)))))))).)).))...............))))).. (-34.38 = -34.26 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	20,917,558 – 20,917,678
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.00
Mean single sequence MFE	-36.96
Consensus MFE	-33.42
Energy contribution	-33.22
Covariance contribution	-0.20
Combinations/Pair	1.14
Mean z-score	-2.24
Structure conservation index	0.90
SVM decision value	3.38
SVM RNA-class probability	0.999120
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917558 120 + 22407834
AGAAUCGCCCUGGCCAAGCAGACCAACUGCCUCUGACCUACACUGUAGUUGGAUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUCGGCAGCUCGGAUACCUCAUCUUUGAGGUGCACC
......(((.(((((..((.((((((((((...((.....))..)))))))).)).))....(....)...........)))))...))).....(..(((((((....)))))))..). ( -38.40)
>DroSec_CAF1 2916 120 + 1
AGAAUCGCCCUGGCCAAGCAGACCAGCUGCCUCUGACCUACACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUUGGCAGCUUCGACACCUCAUCUUUGAGGUGAACC
.(((.((((.(((((..(.((.((((((((...((.....))..)))))))))).)(((...)))..............)))))...))).).)))..(((((((....))))))).... ( -40.90)
>DroSim_CAF1 2176 120 + 1
AGAAUCGCCCUGGCCAAGCAGACCAACUGCCUCUGACCUACACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUUGGCAGCUCCGACACCUCAUCUUUGAGGUGAACC
......(((.(((((..(.((.((((((((...((.....))..)))))))))).)(((...)))..............)))))...)))........(((((((....))))))).... ( -40.20)
>DroEre_CAF1 1967 120 + 1
AGGAUCGCCCUGGCCAAGCAGACCAAUUGCCUCUGACCUACACUGUAGUUGGCUCCGCCUUCUGCAACCACACUUUCCAAGCCAUUUGGCAGCUCGGAUACCUCAUCCUUGAGGUGAACC
.((.((..((.(((...(((((((((((((...((.....))..))))))))........)))))...............(((....))).))).))..((((((....)))))))).)) ( -33.30)
>DroYak_CAF1 1971 120 + 1
AGAAUCGCCCUGGCCAAGCAGACCAAUUGCCUCUGACCUACACUGUAGUUGGCUCCACCCUCUGCAACCACACUUUCCAGGCCUUUUGGCAGCUCGGACACUUCAUCUUUGAGGUGAACC
........((.(((...(((((((((((((...((.....))..))))))))........)))))...............(((....))).))).)).(((((((....))))))).... ( -32.00)
>consensus
AGAAUCGCCCUGGCCAAGCAGACCAACUGCCUCUGACCUACACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUUGGCAGCUCGGACACCUCAUCUUUGAGGUGAACC
......(((.(((((.....((((((((((...((.....))..)))))))).)).((.....))..............)))))...)))........(((((((....))))))).... (-33.42 = -33.22 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	20,917,558 – 20,917,678
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.00
Mean single sequence MFE	-47.02
Consensus MFE	-42.16
Energy contribution	-43.08
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-2.02
Structure conservation index	0.90
SVM decision value	2.73
SVM RNA-class probability	0.996669
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917558 120 - 22407834
GGUGCACCUCAAAGAUGAGGUAUCCGAGCUGCCGAAUGGCCUGGAAAGUGUGGUUGCCGAGGGCGGAUCCAACUACAGUGUAGGUCAGAGGCAGUUGGUCUGCUUGGCCAGGGCGAUUCU
..(((((((((....))))))..((.(((((((...(((((((.(...(((((((((((....)))...)))))))).).)))))))..)))))))((((.....)))).)))))..... ( -51.60)
>DroSec_CAF1 2916 120 - 1
GGUUCACCUCAAAGAUGAGGUGUCGAAGCUGCCAAAUGGCCUGGAAAGUGUGGUUGCCGAGGGCGGAGCCAACUACAGUGUAGGUCAGAGGCAGCUGGUCUGCUUGGCCAGGGCGAUUCU
....(((((((....)))))))(((.(((((((...(((((((.(...(((((((((((....)))...)))))))).).)))))))..)))))))((((.....))))....))).... ( -52.50)
>DroSim_CAF1 2176 120 - 1
GGUUCACCUCAAAGAUGAGGUGUCGGAGCUGCCAAAUGGCCUGGAAAGUGUGGUUGCCGAGGGCGGAGCCAACUACAGUGUAGGUCAGAGGCAGUUGGUCUGCUUGGCCAGGGCGAUUCU
....(((((((....)))))))(((.(((((((...(((((((.(...(((((((((((....)))...)))))))).).)))))))..)))))))((((.....))))....))).... ( -50.40)
>DroEre_CAF1 1967 120 - 1
GGUUCACCUCAAGGAUGAGGUAUCCGAGCUGCCAAAUGGCUUGGAAAGUGUGGUUGCAGAAGGCGGAGCCAACUACAGUGUAGGUCAGAGGCAAUUGGUCUGCUUGGCCAGGGCGAUCCU
((.((((((((....))))))......((((((...(((((((.(...(((((((((..........).)))))))).).)))))))..)))..((((((.....))))))))))).)). ( -41.90)
>DroYak_CAF1 1971 120 - 1
GGUUCACCUCAAAGAUGAAGUGUCCGAGCUGCCAAAAGGCCUGGAAAGUGUGGUUGCAGAGGGUGGAGCCAACUACAGUGUAGGUCAGAGGCAAUUGGUCUGCUUGGCCAGGGCGAUUCU
((..(((.(((....))).))).))(((.((((....((((((.(..((((((((.((.....)).)))))..)))..).))))))........((((((.....)))))))))).))). ( -38.70)
>consensus
GGUUCACCUCAAAGAUGAGGUGUCCGAGCUGCCAAAUGGCCUGGAAAGUGUGGUUGCCGAGGGCGGAGCCAACUACAGUGUAGGUCAGAGGCAGUUGGUCUGCUUGGCCAGGGCGAUUCU
.((((((((((....)))))).....(((((((...(((((((.(...(((((((((((....)))...)))))))).).)))))))..)))))))((((.....)))).))))...... (-42.16 = -43.08 +   0.92)

alignment

secondary structure

dotplot

Window 3

Location	20,917,598 – 20,917,716
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.15
Mean single sequence MFE	-37.70
Consensus MFE	-27.12
Energy contribution	-29.08
Covariance contribution	1.96
Combinations/Pair	1.16
Mean z-score	-2.11
Structure conservation index	0.72
SVM decision value	0.75
SVM RNA-class probability	0.840876
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917598 118 + 22407834
CACUGUAGUUGGAUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUCGGCAGCUCGGAUACCUCAUCUUUGAGGUGCACCUGGCGAGGGAAAAUGGUUUAAUUAUAGUU--AUGAUUGUC
.((((((((((((((..((((((.((.........((((((((....)))..)).)))(((((((....)))))))....)).)))))).....)))))))))))))).--......... ( -42.50)
>DroSec_CAF1 2956 115 + 1
CACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUUGGCAGCUUCGACACCUCAUCUUUGAGGUGAACCUGGCGAGAAAAGGGUGAUUAGUUAUAGUU--AUG---GUU
.(((((((.(((((.((((((.(....)....(((.(((((((....)))........(((((((....)))))))...)))).)))...))))))...)))))...))--)))---)). ( -39.10)
>DroSim_CAF1 2216 115 + 1
CACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUUGGCAGCUCCGACACCUCAUCUUUGAGGUGAACCUGGCGAGGAAAGGGUGAUUAGUUAUAGUU--AUG---GUC
.(((((((.(((((.((((((.(....)....(((.(((((((....)))........(((((((....)))))))...)))).)))...))))))...)))))...))--)))---)). ( -39.30)
>DroEre_CAF1 2007 118 + 1
CACUGUAGUUGGCUCCGCCUUCUGCAACCACACUUUCCAAGCCAUUUGGCAGCUCGGAUACCUCAUCCUUGAGGUGAACCUGACGAAGAAAGAGUGUUCAUUUAUAAUU--AUAGCUUUU
...(((((..(((...)))..)))))..(((.(((((...(((....))).(.((((.(((((((....)))))))...)))))...))))).))).............--......... ( -32.20)
>DroYak_CAF1 2011 119 + 1
CACUGUAGUUGGCUCCACCCUCUGCAACCACACUUUCCAGGCCUUUUGGCAGCUCGGACACUUCAUCUUUGAGGUGAACCUGGCGAAGGAAGAGUGUUUAUUUG-AAUUAAAUAACUUUU
...(((((..((.....))..)))))...(((((((((..(((....))).(((.((.(((((((....)))))))..)).)))...)).)))))))(((((((-...)))))))..... ( -35.40)
>consensus
CACUGUAGUUGGCUCCGCCCUCGGCAACCACACUUUCCAGGCCAUUUGGCAGCUCGGACACCUCAUCUUUGAGGUGAACCUGGCGAGGAAAGAGUGUUUAGUUAUAGUU__AUG__UGUU
.(((((((((((....((.....))...(((.((((((..(((....))).(((.((.(((((((....)))))))..)).)))..)))))).))).)))))))))))............ (-27.12 = -29.08 +   1.96)

alignment

secondary structure

dotplot

Window 4

Location	20,917,638 – 20,917,756
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.39
Mean single sequence MFE	-36.26
Consensus MFE	-23.40
Energy contribution	-22.44
Covariance contribution	-0.96
Combinations/Pair	1.39
Mean z-score	-2.44
Structure conservation index	0.65
SVM decision value	1.82
SVM RNA-class probability	0.978805
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917638 118 + 22407834
GCCAUUCGGCAGCUCGGAUACCUCAUCUUUGAGGUGCACCUGGCGAGGGAAAAUGGUUUAAUUAUAGUU--AUGAUUGUCAGGUUUGGUAAUUACUCACCUCUUCUAAGGCCUCCCACAA
(((....))).(((.((.(((((((....)))))))..)).)))..((((....(((((((((((....--))))))...((((..(((....))).))))......))))))))).... ( -32.90)
>DroSec_CAF1 2996 114 + 1
GCCAUUUGGCAGCUUCGACACCUCAUCUUUGAGGUGAACCUGGCGAGAAAAGGGUGAUUAGUUAUAGUU--AUG---GUUAGGUUU-GUAAUUACUCACCUCUUCUAAGGCCUUCCACAA
(((....)))........(((((((....))))))).....(((.((((..((((((.(((((((((..--...---.......))-))))))).)))))).))))...)))........ ( -36.40)
>DroSim_CAF1 2256 114 + 1
GCCAUUUGGCAGCUCCGACACCUCAUCUUUGAGGUGAACCUGGCGAGGAAAGGGUGAUUAGUUAUAGUU--AUG---GUCAGGUUU-GUAAUUUCUCACCUCUUCUAAGGCCUUCCACAA
(((....)))........(((((((....))))))).....(((..((((..(((((..((((((((..--...---.......))-))))))..)))))..))))...)))........ ( -37.00)
>DroEre_CAF1 2047 117 + 1
GCCAUUUGGCAGCUCGGAUACCUCAUCCUUGAGGUGAACCUGACGAAGAAAGAGUGUUCAUUUAUAAUU--AUAGCUUUUGGACGU-GGAGACUCUCACUUCUUCCAGGGCCUCCCACAA
(((....))).....((((((((((....)))))))..((((..(((((((((((.(((((...(((..--.......)))...))-))).)))))...))))))))))...)))..... ( -37.00)
>DroYak_CAF1 2051 116 + 1
GCCUUUUGGCAGCUCGGACACUUCAUCUUUGAGGUGAACCUGGCGAAGGAAGAGUGUUUAUUUG-AAUUAAAUAACUUUUGG--GU-AAAAACUCUCACUUCUUCUAGUGCCUCCCACAA
(((....))).(((.((.(((((((....)))))))..)).)))((((..(((((.((((((..-((..........))..)--))-))).)))))..)))).....(((.....))).. ( -38.00)
>consensus
GCCAUUUGGCAGCUCGGACACCUCAUCUUUGAGGUGAACCUGGCGAGGAAAGAGUGUUUAGUUAUAGUU__AUG__UGUUAGGUUU_GUAAUUUCUCACCUCUUCUAAGGCCUCCCACAA
(((.((((.(((......(((((((....)))))))...))).))))(((.(((((...((((((.......((.....))......))))))...))))).)))...)))......... (-23.40 = -22.44 +  -0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:14 2006