Locus 3318

Sequence ID	3L_DroMel_CAF1
Location	9,723,858 – 9,723,988
Length	130
Max. P	0.964485

overview

Window 7

Location	9,723,858 – 9,723,962
Length	104
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	74.37
Mean single sequence MFE	-21.34
Consensus MFE	-11.14
Energy contribution	-12.06
Covariance contribution	0.92
Combinations/Pair	1.20
Mean z-score	-1.70
Structure conservation index	0.52
SVM decision value	0.08
SVM RNA-class probability	0.573373
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9723858 104 + 23771897
CUUCUACACUUCCCCCAAUUAGAGAAA-AUAAACCAAAUGCUCUUUUAUGAAAUAAGGGUGGCUAAGUCACAAUGGUACUUAACCACCCGGUUAGUAAAAUUUGC
.......(((..((.((...((((...-((.......)).))))....))......((((((.(((((.((....))))))).))))))))..)))......... ( -22.80)
>DroSec_CAF1 19122 104 + 1
CUUCUACACUUUCCCCAAUUAGAGAAA-AUAAACCAAAUGCUCUUUUAUAAAAUAAGGGUGGCUAAGUCACAAUGGUAUUUAACCACCCGGUUAGUAAUAUGUGC
.......(((..((......((((...-((.......)).))))............((((((.(((((.((....))))))).))))))))..)))......... ( -19.90)
>DroSim_CAF1 19632 104 + 1
CUUCUACACUUUCCCCAAUUAGAGAAA-AUAAACUAAAUGCUCUUUUAUGAAAUAAGGGUGGCUAAGUCACACUGGUAUUUAACCACCCGGUUAGUAAAAUUUGC
.......(((..((.((...((((...-((.......)).))))....))......((((((.(((((.((....))))))).))))))))..)))......... ( -20.20)
>DroEre_CAF1 18372 98 + 1
CCUUUA------CCCCAGUUGGAGUAAACUAAACCAAAUGCUC-UUUAUGAAAUAAGGGUGGCUUAGUGAUAUUGGCACUUAAGCACCUUGUUAGUAAGCCGUGC
((((((------...((...((((((............)))))-)...))...)))))).((((((.(((((..(((......)).)..))))).)))))).... ( -26.10)
>DroYak_CAF1 27758 79 + 1
--UUUC------UACCAAUUAAAG------AAAGCAAAAGCUGUUUUAUGAAAUAAGGGUGGUGU------------UUUCAACCACCUGGUUAGUGAACCUUGC
--.(((------.(((.....(((------(.(((....))).)))).........(((((((..------------.....))))))))))....)))...... ( -17.70)
>consensus
CUUCUACACUU_CCCCAAUUAGAGAAA_AUAAACCAAAUGCUCUUUUAUGAAAUAAGGGUGGCUAAGUCACAAUGGUAUUUAACCACCCGGUUAGUAAAAUUUGC
.......................................((...(((((.((....((((((.(((((.........))))).))))))..)).)))))....)) (-11.14 = -12.06 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	9,723,858 – 9,723,962
Length	104
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	74.37
Mean single sequence MFE	-25.34
Consensus MFE	-11.17
Energy contribution	-13.12
Covariance contribution	1.95
Combinations/Pair	1.24
Mean z-score	-2.20
Structure conservation index	0.44
SVM decision value	1.57
SVM RNA-class probability	0.964485
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9723858 104 - 23771897
GCAAAUUUUACUAACCGGGUGGUUAAGUACCAUUGUGACUUAGCCACCCUUAUUUCAUAAAAGAGCAUUUGGUUUAU-UUUCUCUAAUUGGGGGAAGUGUAGAAG
.....((((((.((((((((((((((((((....)).))))))))))))....(((......))).....)))).((-(((((((....))))))))))))))). ( -33.00)
>DroSec_CAF1 19122 104 - 1
GCACAUAUUACUAACCGGGUGGUUAAAUACCAUUGUGACUUAGCCACCCUUAUUUUAUAAAAGAGCAUUUGGUUUAU-UUUCUCUAAUUGGGGAAAGUGUAGAAG
((((........((((((((((((((.(((....)))..))))))))))...((((....))))......))))...-(((((((....)))))))))))..... ( -26.90)
>DroSim_CAF1 19632 104 - 1
GCAAAUUUUACUAACCGGGUGGUUAAAUACCAGUGUGACUUAGCCACCCUUAUUUCAUAAAAGAGCAUUUAGUUUAU-UUUCUCUAAUUGGGGAAAGUGUAGAAG
.....((((((.....((((((((((.(((....)))..)))))))))).............((((.....))))((-(((((((....))))))))))))))). ( -26.80)
>DroEre_CAF1 18372 98 - 1
GCACGGCUUACUAACAAGGUGCUUAAGUGCCAAUAUCACUAAGCCACCCUUAUUUCAUAAA-GAGCAUUUGGUUUAGUUUACUCCAACUGGGG------UAAAGG
(((((((...((....))..)))...)))).......(((((((((..(((.((....)).-)))....)))))))))(((((((....))))------)))... ( -23.80)
>DroYak_CAF1 27758 79 - 1
GCAAGGUUCACUAACCAGGUGGUUGAAA------------ACACCACCCUUAUUUCAUAAAACAGCUUUUGCUUU------CUUUAAUUGGUA------GAAA--
((..((((....)))).(((((((....------------).))))))................))(((((((..------........))))------))).-- ( -16.20)
>consensus
GCAAAUUUUACUAACCGGGUGGUUAAAUACCAUUGUGACUUAGCCACCCUUAUUUCAUAAAAGAGCAUUUGGUUUAU_UUUCUCUAAUUGGGG_AAGUGUAGAAG
................((((((((((.............)))))))))).......................(((((..((((((....))))))...))))).. (-11.17 = -13.12 +   1.95)

alignment

secondary structure

dotplot

Window 9

Location	9,723,883 – 9,723,988
Length	105
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	80.83
Mean single sequence MFE	-22.66
Consensus MFE	-12.96
Energy contribution	-14.08
Covariance contribution	1.12
Combinations/Pair	1.19
Mean z-score	-1.98
Structure conservation index	0.57
SVM decision value	0.31
SVM RNA-class probability	0.683089
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9723883 105 + 23771897
AA-AUAAACCAAAUGCUCUUUUAUGAAAUAAGGGUGGCUAAGUCACAAUGGUACUUAACCACCCGGUUAGUAAAAUUUGCAAUUAUUAUUACCAAGAAAACCGUGC
..-..........(((..((((((.......((((((.(((((.((....))))))).)))))).....))))))...)))......................... ( -22.10)
>DroSec_CAF1 19147 105 + 1
AA-AUAAACCAAAUGCUCUUUUAUAAAAUAAGGGUGGCUAAGUCACAAUGGUAUUUAACCACCCGGUUAGUAAUAUGUGCAAUUAUUAUUACCAAGAAAAUGGUGC
..-....((((.....((((...........((((((.(((((.((....))))))).))))))(((.(((((((........))))))))))))))...)))).. ( -25.90)
>DroSim_CAF1 19657 105 + 1
AA-AUAAACUAAAUGCUCUUUUAUGAAAUAAGGGUGGCUAAGUCACACUGGUAUUUAACCACCCGGUUAGUAAAAUUUGCAAUUAUUAUUACCAAGAAAAUGGUGC
..-......(((.(((..((((((.......((((((.(((((.((....))))))).)))))).....))))))...))).)))....(((((......))))). ( -23.60)
>DroEre_CAF1 18391 105 + 1
AAACUAAACCAAAUGCUC-UUUAUGAAAUAAGGGUGGCUUAGUGAUAUUGGCACUUAAGCACCUUGUUAGUAAGCCGUGCAAUUAUUAUUACCAAGAAUACUGUGC
..............((((-((........))))))((((((.(((((..(((......)).)..))))).))))))(..((..((((.........)))).))..) ( -21.60)
>DroYak_CAF1 27774 89 + 1
-----AAAGCAAAAGCUGUUUUAUGAAAUAAGGGUGGUGU------------UUUCAACCACCUGGUUAGUGAACCUUGCAAUUAUUAUUACCAAGAAAACUGCGC
-----.........((.(((((..(.((((((((((((..------------.....)))))))((((....)))).........))))).)....))))).)).. ( -20.10)
>consensus
AA_AUAAACCAAAUGCUCUUUUAUGAAAUAAGGGUGGCUAAGUCACAAUGGUAUUUAACCACCCGGUUAGUAAAAUUUGCAAUUAUUAUUACCAAGAAAACGGUGC
.............(((...(((((.((....((((((.(((((.........))))).))))))..)).)))))....)))......................... (-12.96 = -14.08 +   1.12)

alignment

secondary structure

dotplot

Window 0

Location	9,723,883 – 9,723,988
Length	105
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	80.83
Mean single sequence MFE	-22.80
Consensus MFE	-13.72
Energy contribution	-14.96
Covariance contribution	1.24
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.60
SVM decision value	0.36
SVM RNA-class probability	0.705073
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9723883 105 - 23771897
GCACGGUUUUCUUGGUAAUAAUAAUUGCAAAUUUUACUAACCGGGUGGUUAAGUACCAUUGUGACUUAGCCACCCUUAUUUCAUAAAAGAGCAUUUGGUUUAU-UU
((..((((......(((((....)))))..........))))((((((((((((((....)).))))))))))))...............))...........-.. ( -27.49)
>DroSec_CAF1 19147 105 - 1
GCACCAUUUUCUUGGUAAUAAUAAUUGCACAUAUUACUAACCGGGUGGUUAAAUACCAUUGUGACUUAGCCACCCUUAUUUUAUAAAAGAGCAUUUGGUUUAU-UU
..((((..((((((((((((...........)))))))....((((((((((.(((....)))..))))))))))...........)))))....))))....-.. ( -24.40)
>DroSim_CAF1 19657 105 - 1
GCACCAUUUUCUUGGUAAUAAUAAUUGCAAAUUUUACUAACCGGGUGGUUAAAUACCAGUGUGACUUAGCCACCCUUAUUUCAUAAAAGAGCAUUUAGUUUAU-UU
..((((......)))).....(((.(((..............((((((((((.(((....)))..)))))))))).....((......))))).)))......-.. ( -22.90)
>DroEre_CAF1 18391 105 - 1
GCACAGUAUUCUUGGUAAUAAUAAUUGCACGGCUUACUAACAAGGUGCUUAAGUGCCAAUAUCACUAAGCCACCCUUAUUUCAUAAA-GAGCAUUUGGUUUAGUUU
(((((((((.(((((((((....)))))..(.....)...)))))))))...)))).......(((((((((..(((.((....)).-)))....))))))))).. ( -21.20)
>DroYak_CAF1 27774 89 - 1
GCGCAGUUUUCUUGGUAAUAAUAAUUGCAAGGUUCACUAACCAGGUGGUUGAAA------------ACACCACCCUUAUUUCAUAAAACAGCUUUUGCUUU-----
..((.(((((..(((.(((((.........((((....)))).(((((((....------------).)))))).)))))))).))))).)).........----- ( -18.00)
>consensus
GCACAGUUUUCUUGGUAAUAAUAAUUGCAAAUUUUACUAACCGGGUGGUUAAAUACCAUUGUGACUUAGCCACCCUUAUUUCAUAAAAGAGCAUUUGGUUUAU_UU
((............(((((....)))))..............((((((((((.............))))))))))...............)).............. (-13.72 = -14.96 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:43 2006