Locus 5406

Sequence ID	3L_DroMel_CAF1
Location	14,821,218 – 14,821,396
Length	178
Max. P	0.997205

overview

Window 2

Location	14,821,218 – 14,821,316
Length	98
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	95.43
Mean single sequence MFE	-25.34
Consensus MFE	-21.38
Energy contribution	-21.98
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.84
SVM decision value	0.66
SVM RNA-class probability	0.813219
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14821218 98 + 23771897
GGCGGCGACGCCUUCAGGCCUCACUUUUAUCCUCAUGCCAGGACUCAGUUUCGGAUGCACCGCCUCCACUU-UGGCAUUACUGCCGCAAAACUCUUUGC
.(((((((.(((....))).))............(((((((((......)))(((.((...)).)))....-))))))....)))))............ ( -29.00)
>DroSec_CAF1 56029 98 + 1
GGCGGCGACGCCUUCAGGCCUCACUUUUAUCCUCAUGCCAGGACUCAGUUUCGGAUGCACCGCCUCCACUU-UGGCAUUACUGCCGCAAAACUCUUUGC
.(((((((.(((....))).))............(((((((((......)))(((.((...)).)))....-))))))....)))))............ ( -29.00)
>DroSim_CAF1 49218 99 + 1
GGCGGCGACGCCUUCAGGCCUCACUUUUAUCCUCAUGCCAGGACUCAGUUUCGGAUGCACCGCCUCCACUUUUGGCAUUACUGCCACAAAACUCUUUGC
(((((.((.(((....))).))............(((((((((......)))(((.((...)).))).....))))))..))))).............. ( -25.90)
>DroEre_CAF1 56459 98 + 1
GGCGGCAACGCCUCCAGGCCUCACUUUUAUCCUCAUUGCAGGACUCAGUUUCGGAUACACCGCCUCCACUU-UGCCAUUACUGCCGCAAAACUCUUUGC
((((....))))....(((..........((((......))))........(((.....))).........-.))).........(((((....))))) ( -21.40)
>DroYak_CAF1 59302 98 + 1
GGCGGCAACGCCUCCAGGCCUCACUUUUAUCCUCAUUUCAGGACUCAGUUUCGGAUACACCGCCUCCACUU-UGCCAUUACUGCCGCAAAACUCUUUGC
((((....))))....(((..........((((......))))........(((.....))).........-.))).........(((((....))))) ( -21.40)
>consensus
GGCGGCGACGCCUUCAGGCCUCACUUUUAUCCUCAUGCCAGGACUCAGUUUCGGAUGCACCGCCUCCACUU_UGGCAUUACUGCCGCAAAACUCUUUGC
((((....))))...((((..........((((......)))).........((.....))))))........((((....))))(((((....))))) (-21.38 = -21.98 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	14,821,218 – 14,821,316
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	95.43
Mean single sequence MFE	-33.24
Consensus MFE	-32.38
Energy contribution	-32.38
Covariance contribution	-0.00
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.97
SVM decision value	2.82
SVM RNA-class probability	0.997205
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14821218 98 - 23771897
GCAAAGAGUUUUGCGGCAGUAAUGCCA-AAGUGGAGGCGGUGCAUCCGAAACUGAGUCCUGGCAUGAGGAUAAAAGUGAGGCCUGAAGGCGUCGCCGCC
(((((....)))))((((....)))).-.......((((((.........(((..(((((......)))))...)))((.(((....))).)))))))) ( -36.60)
>DroSec_CAF1 56029 98 - 1
GCAAAGAGUUUUGCGGCAGUAAUGCCA-AAGUGGAGGCGGUGCAUCCGAAACUGAGUCCUGGCAUGAGGAUAAAAGUGAGGCCUGAAGGCGUCGCCGCC
(((((....)))))((((....)))).-.......((((((.........(((..(((((......)))))...)))((.(((....))).)))))))) ( -36.60)
>DroSim_CAF1 49218 99 - 1
GCAAAGAGUUUUGUGGCAGUAAUGCCAAAAGUGGAGGCGGUGCAUCCGAAACUGAGUCCUGGCAUGAGGAUAAAAGUGAGGCCUGAAGGCGUCGCCGCC
.............(((((....)))))........((((((.........(((..(((((......)))))...)))((.(((....))).)))))))) ( -34.00)
>DroEre_CAF1 56459 98 - 1
GCAAAGAGUUUUGCGGCAGUAAUGGCA-AAGUGGAGGCGGUGUAUCCGAAACUGAGUCCUGCAAUGAGGAUAAAAGUGAGGCCUGGAGGCGUUGCCGCC
(((((....)))))(.((....)).).-.......((((((.........(((..(((((......)))))...)))((.(((....))).)))))))) ( -29.50)
>DroYak_CAF1 59302 98 - 1
GCAAAGAGUUUUGCGGCAGUAAUGGCA-AAGUGGAGGCGGUGUAUCCGAAACUGAGUCCUGAAAUGAGGAUAAAAGUGAGGCCUGGAGGCGUUGCCGCC
(((((....)))))(.((....)).).-.......((((((.........(((..(((((......)))))...)))((.(((....))).)))))))) ( -29.50)
>consensus
GCAAAGAGUUUUGCGGCAGUAAUGCCA_AAGUGGAGGCGGUGCAUCCGAAACUGAGUCCUGGCAUGAGGAUAAAAGUGAGGCCUGAAGGCGUCGCCGCC
(((((....)))))((((....)))).........((((((.........(((..(((((......)))))...)))((.(((....))).)))))))) (-32.38 = -32.38 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	14,821,258 – 14,821,356
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	97.56
Mean single sequence MFE	-29.24
Consensus MFE	-27.22
Energy contribution	-27.38
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.84
Structure conservation index	0.93
SVM decision value	2.17
SVM RNA-class probability	0.989564
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14821258 98 - 23771897
AGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGCCA-AAGUGGAGGCGGUGCAUCCGAAACUGAGUCC
.(((((...(((((((....((((((((..((((....))))...)))))))).((((....)))).-.)))))))..)))))................ ( -31.00)
>DroSec_CAF1 56069 98 - 1
AGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGCCA-AAGUGGAGGCGGUGCAUCCGAAACUGAGUCC
.(((((...(((((((....((((((((..((((....))))...)))))))).((((....)))).-.)))))))..)))))................ ( -31.00)
>DroSim_CAF1 49258 99 - 1
AGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGUGGCAGUAAUGCCAAAAGUGGAGGCGGUGCAUCCGAAACUGAGUCC
.(((((...(((((((...(((((((((..((((....))))...)))))))))((((....))))...)))))))..)))))................ ( -32.50)
>DroEre_CAF1 56499 98 - 1
AGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGGCA-AAGUGGAGGCGGUGUAUCCGAAACUGAGUCC
...((((......(((((..((((((((..((((....))))...))))))))..)))))..)))).-....(((..((((.........))))..))) ( -25.40)
>DroYak_CAF1 59342 98 - 1
AGCGCUAAACUUCAUUGCUACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGGCA-AAGUGGAGGCGGUGUAUCCGAAACUGAGUCC
...((((......(((((..((((((((..((((....))))...))))))))..)))))..)))).-....(((..((((.........))))..))) ( -26.30)
>consensus
AGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGCCA_AAGUGGAGGCGGUGCAUCCGAAACUGAGUCC
.(((((...(((((((....((((((((..((((....))))...)))))))).((((....))))...)))))))..)))))................ (-27.22 = -27.38 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	14,821,291 – 14,821,396
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	93.15
Mean single sequence MFE	-31.25
Consensus MFE	-26.88
Energy contribution	-26.97
Covariance contribution	0.09
Combinations/Pair	1.10
Mean z-score	-2.03
Structure conservation index	0.86
SVM decision value	1.08
SVM RNA-class probability	0.912608
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14821291 105 + 23771897
---------------GCAUUACUGCCGCAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUUGCAAUGAAGUUUAGCGCUGAGUGCAUGUUGCUCUUGAGCAAAAUUAAUGUAAUUGCUC
---------------(((((((...............(((((.(..((((..((((((..(....)..)))))).))))..))))))..(((((....))))).......)))).))).. ( -29.50)
>DroSec_CAF1 56102 105 + 1
---------------GCAUUACUGCCGCAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUUGCAAUGAAGUUUAGCGCUGAGUGCAUGUUGCUCUUGAGCAAAAUUAAUGUAAUUGCUC
---------------(((((((...............(((((.(..((((..((((((..(....)..)))))).))))..))))))..(((((....))))).......)))).))).. ( -29.50)
>DroSim_CAF1 49292 105 + 1
---------------GCAUUACUGCCACAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUUGCAAUGAAGUUUAGCGCUGAGUGCAUGUUGCUCUUGAGCAAAAUUAAUGUAAUUGCUC
---------------(((((((...............(((((.(..((((..((((((..(....)..)))))).))))..))))))..(((((....))))).......)))).))).. ( -29.50)
>DroEre_CAF1 56532 105 + 1
---------------CCAUUACUGCCGCAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUUGCAAUGAAGUUUAGCGCUGAGUGCAUGUUGCUCUUGAGCAAAAUUAAUGUAAUUGCUC
---------------...........((((.......(((((.(..((((..((((((..(....)..)))))).))))..))))))..(((((....)))))...........)))).. ( -28.40)
>DroYak_CAF1 59375 105 + 1
---------------CCAUUACUGCCGCAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUAGCAAUGAAGUUUAGCGCUGAGUGCAUGUUGCUCUUGAGCAAAAUUAAUGUAAUUGCUC
---------------...........((((.......(((((.(..((((..((((((..(....)..)))))).))))..))))))..(((((....)))))...........)))).. ( -28.60)
>DroAna_CAF1 53562 120 + 1
GCAAGCGGUAGCGCGGCGUUACUGCCGCAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUUGCAAUGAAGUUUAGCGCCGAGUGCAUGUUGCACUUGAGUAAAAUUAAUGUAAUUGCUC
(((((((((((((...))))))))).(((((....)))))((((((((((..((((((..(....)..)))))).)))))((((((.....))))))..........)))))..)))).. ( -42.00)
>consensus
_______________GCAUUACUGCCGCAAAACUCUUUGCACAUUGGUGCGGAAAUUUUGUUGCAAUGAAGUUUAGCGCUGAGUGCAUGUUGCUCUUGAGCAAAAUUAAUGUAAUUGCUC
...............(((((((...............(((((.(((((((..((((((..(....)..)))))).))))))))))))..(((((....))))).......)))).))).. (-26.88 = -26.97 +   0.09)

alignment

secondary structure

dotplot

Window 6

Location	14,821,291 – 14,821,396
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.15
Mean single sequence MFE	-27.66
Consensus MFE	-23.88
Energy contribution	-24.05
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.36
Structure conservation index	0.86
SVM decision value	1.70
SVM RNA-class probability	0.972981
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14821291 105 - 23771897
GAGCAAUUACAUUAAUUUUGCUCAAGAGCAACAUGCACUCAGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGC---------------
((((((...........))))))....(((....((.....))..........(((((..((((((((..((((....))))...))))))))..)))))..)))--------------- ( -26.50)
>DroSec_CAF1 56102 105 - 1
GAGCAAUUACAUUAAUUUUGCUCAAGAGCAACAUGCACUCAGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGC---------------
((((((...........))))))....(((....((.....))..........(((((..((((((((..((((....))))...))))))))..)))))..)))--------------- ( -26.50)
>DroSim_CAF1 49292 105 - 1
GAGCAAUUACAUUAAUUUUGCUCAAGAGCAACAUGCACUCAGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGUGGCAGUAAUGC---------------
((((((...........))))))....(((....((.....))..........(((((.(((((((((..((((....))))...))))))))).)))))..)))--------------- ( -26.90)
>DroEre_CAF1 56532 105 - 1
GAGCAAUUACAUUAAUUUUGCUCAAGAGCAACAUGCACUCAGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGG---------------
((((((...........))))))........(((((.....))..........(((((..((((((((..((((....))))...))))))))..))))).))).--------------- ( -25.70)
>DroYak_CAF1 59375 105 - 1
GAGCAAUUACAUUAAUUUUGCUCAAGAGCAACAUGCACUCAGCGCUAAACUUCAUUGCUACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGG---------------
((((((...........))))))........(((((.....))..........(((((..((((((((..((((....))))...))))))))..))))).))).--------------- ( -26.60)
>DroAna_CAF1 53562 120 - 1
GAGCAAUUACAUUAAUUUUACUCAAGUGCAACAUGCACUCGGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAACGCCGCGCUACCGCUUGC
((((....................(((((.....))))).(((((........(((((..((((((((..((((....))))...))))))))..)))))......)))))...)))).. ( -33.74)
>consensus
GAGCAAUUACAUUAAUUUUGCUCAAGAGCAACAUGCACUCAGCGCUAAACUUCAUUGCAACAAAAUUUCCGCACCAAUGUGCAAAGAGUUUUGCGGCAGUAAUGC_______________
((((((...........))))))....((.....)).................(((((..((((((((..((((....))))...))))))))..))))).................... (-23.88 = -24.05 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:35 2006