Locus 4817

Sequence ID	2L_DroMel_CAF1
Location	13,739,258 – 13,739,461
Length	203
Max. P	0.998053

overview

Window 2

Location	13,739,258 – 13,739,361
Length	103
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	85.26
Mean single sequence MFE	-18.60
Consensus MFE	-14.82
Energy contribution	-15.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.80
SVM decision value	-0.05
SVM RNA-class probability	0.508307
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739258 103 - 22407834
AAAAAUACGUUAAGAAAAUAAAAAAAA-AAGGAAAAACUAAGGAUCUACCUGACGCCAUUCGAAUGGCAGUUAAGGCAGGUGUGUGCACUAUUUACACUCGAGA
.............((............-...............((((.(((((((((((....))))).))).))).))))(((((.......))))))).... ( -16.90)
>DroSec_CAF1 3086 100 - 1
A--AAAACCUUAAGAAAAUAAAAAAAA-GGGGAAAAACUAAAAAUCUACCUGACGCCAUUCG-AUGGCAGUUAAGGCAGGUGUGUGCACUAUUUACACUCGAGA
.--....((((..............))-)).............((((.(((((((((((...-))))).))).))).))))(((((.......)))))...... ( -17.54)
>DroSim_CAF1 4751 99 - 1
---AAAACCUUAAGAAAAUAAAAAAAA-G-GAAAAAACUAAAAAUCUACCUGACGCCAUUCGAAUGGCAGUUAAGGCAGGUGUGUGCACUAUUUACACUCGAGA
---....((((..............))-)-)............((((.(((((((((((....))))).))).))).))))(((((.......)))))...... ( -18.24)
>DroEre_CAF1 4629 92 - 1
---AAUACUUAA--------AAAAAAAAAACGAAA-AAUAGGAAUGUACCUGACGCCAUUCGAAUGGCAGUUAAGGCAGGUGUGUGCACUAUUUACACUCGAGA
---.........--------..........(((.(-(((((..(..(((((((((((((....))))).)).....))))))..)...))))))....)))... ( -20.90)
>DroYak_CAF1 4784 92 - 1
---AAUACGUUA--------AAAUAAA-AACGAAAAGCUAGGAAUGUACCUGACGCCAUUCGAAUGGCAGUUAAGGCAGGUGUGUGCACUAUUUACACUCGAGA
---....((((.--------.......-)))).....((..((.(((((((((((((((....))))).))).)))..((((....))))...)))).)).)). ( -19.40)
>consensus
___AAUACCUUAAGAAAAUAAAAAAAA_AAGGAAAAACUAAGAAUCUACCUGACGCCAUUCGAAUGGCAGUUAAGGCAGGUGUGUGCACUAUUUACACUCGAGA
...........................................((((.(((((((((((....))))).))).))).))))(((((.......)))))...... (-14.82 = -15.22 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	13,739,287 – 13,739,401
Length	114
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	78.03
Mean single sequence MFE	-21.50
Consensus MFE	-13.70
Energy contribution	-13.92
Covariance contribution	0.22
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.64
SVM decision value	1.98
SVM RNA-class probability	0.984761
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739287 114 + 22407834
CUUAACUGCCAUUCGAAUGGCGUCAGGUAGAUCCUUAGUUUUUCCUU-UUUUUUUUAUUUUCUUAACGUAUUUUUUUUUAGCCAUUUUUGGCGGCAUGCACCUGGCAUUAUUUGC
.......(((((....)))))(((((((..((((...(((.......-................))).............((((....)))))).))..)))))))......... ( -24.40)
>DroSec_CAF1 3115 98 + 1
CUUAACUGCCAU-CGAAUGGCGUCAGGUAGAUUUUUAGUUUUUCCCC-UUUUUUUUAUUUUCUUAAGGUUUU--UUUUUA-------------GCAUGCACCUGGCAUUAUUUGC
.......(((((-...)))))(((((((.(....((((.......((-((..............))))....--...)))-------------)....))))))))......... ( -17.38)
>DroSim_CAF1 4780 97 + 1
CUUAACUGCCAUUCGAAUGGCGUCAGGUAGAUUUUUAGUUUUUUC-C-UUUUUUUUAUUUUCUUAAGGUUUU---UUUUA-------------GCAUGCACCUGGCAUUAUUUGC
.......(((((....)))))(((((((.(....((((......(-(-((..............))))....---..)))-------------)....))))))))......... ( -19.14)
>DroEre_CAF1 4658 101 + 1
CUUAACUGCCAUUCGAAUGGCGUCAGGUACAUUCCUAUU-UUUCGUUUUUUUUUU--------UUAAGUAUU-----UUACCUAUUUUUGGCGGCAUGCACCUGGCAUUAUUUGC
.......(((((....)))))(((((((.(((.((((((-(..............--------..)))))..-----...((.......)).)).))).)))))))......... ( -21.69)
>DroYak_CAF1 4813 101 + 1
CUUAACUGCCAUUCGAAUGGCGUCAGGUACAUUCCUAGCUUUUCGUU-UUUAUUU--------UAACGUAUU-----UUACCUAUUUUUGGCGGCAUGCACCUGGCAUUAUUUGC
.......(((((....)))))(((((((.(((.((........((((-.......--------.))))....-----...((.......)).)).))).)))))))......... ( -24.90)
>consensus
CUUAACUGCCAUUCGAAUGGCGUCAGGUAGAUUCUUAGUUUUUCCUU_UUUUUUUUAUUUUCUUAACGUAUU___UUUUA_C_AUUUUUGGCGGCAUGCACCUGGCAUUAUUUGC
.......(((((....)))))(((((((.....................................................(((....)))..(....))))))))......... (-13.70 = -13.92 +   0.22)

alignment

secondary structure

dotplot

Window 4

Location	13,739,287 – 13,739,401
Length	114
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	78.03
Mean single sequence MFE	-21.25
Consensus MFE	-11.81
Energy contribution	-11.81
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.00
Structure conservation index	0.56
SVM decision value	2.99
SVM RNA-class probability	0.998053
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739287 114 - 22407834
GCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAUGGCUAAAAAAAAAUACGUUAAGAAAAUAAAAAAAA-AAGGAAAAACUAAGGAUCUACCUGACGCCAUUCGAAUGGCAGUUAAG
(((.....)))((((((.((.((((((....))))................................-.((......))..)))).))))))..(((((....)))))....... ( -22.90)
>DroSec_CAF1 3115 98 - 1
GCAAAUAAUGCCAGGUGCAUGC-------------UAAAAA--AAAACCUUAAGAAAAUAAAAAAAA-GGGGAAAAACUAAAAAUCUACCUGACGCCAUUCG-AUGGCAGUUAAG
(((.....)))((((((.((..-------------......--....((((...............)-)))............)).))))))..(((((...-)))))....... ( -15.81)
>DroSim_CAF1 4780 97 - 1
GCAAAUAAUGCCAGGUGCAUGC-------------UAAAA---AAAACCUUAAGAAAAUAAAAAAAA-G-GAAAAAACUAAAAAUCUACCUGACGCCAUUCGAAUGGCAGUUAAG
(((.....)))((((((.((..-------------.....---....((((..............))-)-)............)).))))))..(((((....)))))....... ( -15.54)
>DroEre_CAF1 4658 101 - 1
GCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAUAGGUAA-----AAUACUUAA--------AAAAAAAAAACGAAA-AAUAGGAAUGUACCUGACGCCAUUCGAAUGGCAGUUAAG
(((.....)))(((((((((.(((((.......)))..-----.....((..--------....)).........-....)).)))))))))..(((((....)))))....... ( -23.20)
>DroYak_CAF1 4813 101 - 1
GCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAUAGGUAA-----AAUACGUUA--------AAAUAAA-AACGAAAAGCUAGGAAUGUACCUGACGCCAUUCGAAUGGCAGUUAAG
(((.....)))(((((((((.(((((.......)))..-----....((((.--------.......-))))........)).)))))))))..(((((....)))))....... ( -28.80)
>consensus
GCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAU_G_UAAAA___AAUACCUUAAGAAAAUAAAAAAAA_AAGGAAAAACUAAGAAUCUACCUGACGCCAUUCGAAUGGCAGUUAAG
(((.....)))((((((.((...............................................................)).))))))..(((((....)))))....... (-11.81 = -11.81 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	13,739,361 – 13,739,461
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	89.64
Mean single sequence MFE	-27.66
Consensus MFE	-23.28
Energy contribution	-23.88
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.45
Structure conservation index	0.84
SVM decision value	2.62
SVM RNA-class probability	0.995823
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13739361 100 - 22407834
UGGUAAGCACUUGAAGGACGGGCGCCUUAACUCAGUUCUGUUUUUCAUCUUUUAUCUUAUGCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAUGGCUAAAA
.((((.(((((((((((((((((...........).))))))))))..............(((.....))).)))))).))))((((....))))..... ( -28.60)
>DroSec_CAF1 3186 87 - 1
UGGUAAGCACUUGAAGGACGGGCGCCUUAACUCAGGUCUGUUUUUCAUCUUUUAUCUUAUGCAAAUAAUGCCAGGUGCAUGC-------------UAAAA
(((((.(((((((((((((((..((((......)))))))))))))..............(((.....))).)))))).)))-------------))... ( -25.50)
>DroSim_CAF1 4850 87 - 1
UGGUAAGCACUUGAAGGACGGGCGCCUUAACUCAGGUCUGUUUUUCAUCUUUUAUCUUAUGCAAAUAAUGCCAGGUGCAUGC-------------UAAAA
(((((.(((((((((((((((..((((......)))))))))))))..............(((.....))).)))))).)))-------------))... ( -25.50)
>DroEre_CAF1 4721 98 - 1
UGGUAAGCACUUGAAGGACGGGCGCCUUAACUCAGGUCUGUUUUUCAUCUUUUAUCUUAUGCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAUAGGUAA--
.((((.(((((((((((((((..((((......)))))))))))))..............(((.....))).)))))).))))(((.......)))..-- ( -29.00)
>DroYak_CAF1 4876 98 - 1
UGGUAAGCACUUGAAGGACGGGCGCCUUAACUUAGGUCUGUUUUUCAUCUUUUAUCUUAUGCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAUAGGUAA--
.((((.(((((((((((((((..((((......)))))))))))))..............(((.....))).)))))).))))(((.......)))..-- ( -29.70)
>consensus
UGGUAAGCACUUGAAGGACGGGCGCCUUAACUCAGGUCUGUUUUUCAUCUUUUAUCUUAUGCAAAUAAUGCCAGGUGCAUGCCGCCAAAAAU_G_UAAAA
.((((.(((((((((((((((..((((......)))))))))))))..............(((.....))).)))))).))))................. (-23.28 = -23.88 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:11 2006