Locus 4297

Sequence ID	2L_DroMel_CAF1
Location	12,296,640 – 12,296,776
Length	136
Max. P	0.567655

overview

Window 3

Location	12,296,640 – 12,296,752
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.17
Mean single sequence MFE	-30.79
Consensus MFE	-19.74
Energy contribution	-19.83
Covariance contribution	0.09
Combinations/Pair	1.19
Mean z-score	-1.94
Structure conservation index	0.64
SVM decision value	-0.03
SVM RNA-class probability	0.515793
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12296640 112 + 22407834
UUCUGCUAGGAUUAUGAUAAUAUAGCUCAAGUGCAGUUAGUCGAUGUCGCUGCUACUGCUGCUGCUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA--
....((((..((((((((.((..((((((((((((((.((.((....)))))))...(((((....))))).))))))).))))....)).)))))))).....)))).------...-- ( -32.80)
>DroSim_CAF1 123117 108 + 1
UUCUGCUAG-AUUAUGAUAAUAUAGCUCAAGUGCAGUUAGUCGAUGUCGCUGCUGCU---GCUGCUGCAUUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA--
....((((.-((((((((.((..((((((((((((.......(((((.((.((....---)).)).))))))))))))).))))....)).)))))))).....)))).------...-- ( -31.41)
>DroEre_CAF1 117496 100 + 1
UUCUGCUAGGAUUAUGAUAAUAUAGCUCAAGUGCAGUUAGUCGAUGUCGCUG------------CUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA--
....((((..((((((((......((......))..........((((((.(------------((((((......)))))))..)))))))))))))).....)))).------...-- ( -27.80)
>DroYak_CAF1 123788 100 + 1
UUCUGCUAGGAUUAUGAUAAUAUAGCUCAAGUGCAGUUAGUCGAUGUCGCUG------------CUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA--
....((((..((((((((......((......))..........((((((.(------------((((((......)))))))..)))))))))))))).....)))).------...-- ( -27.80)
>DroAna_CAF1 108148 111 + 1
UUCUGCCAGGAUUAUGAUAAUGUAGCUCAAGUGCAGUUAGUCGAUGUCGCUGCU------GCAGUUGCACUUGCUCCUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUGGUG---CUGGA
..(..(((..((((((((......((......))..........((((((.(((------((((..((....))..)))))))..)))))))))))))).....)))..)..---..... ( -38.40)
>DroPer_CAF1 186781 113 + 1
--CUGCGGGGAUUAUGAUAAUAUAGCUCAAGUGCAGUUAGUUGAUGUCGUUGGCGUU---GCCUUUGCUGUUCCCGUUGCAGUUUGCGAUAAUCAUAAUAAUAAUAUCUGUGCUGCUC--
--..(((((((.(((....)))((((..(((.((((...((..((...))..)).))---))))).))))))))))).(((((..((((((.............)))).)))))))..-- ( -26.52)
>consensus
UUCUGCUAGGAUUAUGAUAAUAUAGCUCAAGUGCAGUUAGUCGAUGUCGCUGCU______GC_GCUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG______CAA__
....((((..((((((((......((......))..........((((((..............((((((......))))))...)))))))))))))).....))))............ (-19.74 = -19.83 +   0.09)

alignment

secondary structure

dotplot

Window 4

Location	12,296,680 – 12,296,776
Length	96
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	72.50
Mean single sequence MFE	-26.12
Consensus MFE	-10.32
Energy contribution	-10.46
Covariance contribution	0.14
Combinations/Pair	1.14
Mean z-score	-1.86
Structure conservation index	0.40
SVM decision value	0.07
SVM RNA-class probability	0.567655
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12296680 96 + 22407834
UCGAUGUCGCUGCUACUGCUGCUGCUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA---GUGCUCCGCCGCCGC--C------CCAUCUCC
..((((..((.((....(((((....))))).((((((((.(....)....(((((.......))))))------)))---))))......)).))--.------.))))... ( -30.60)
>DroSim_CAF1 123156 90 + 1
UCGAUGUCGCUGCUGCU---GCUGCUGCAUUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA---GUGCUCCUC---CGC--C------CCAUCUCC
..((((..(((((.((.---...)).)))...((((((((.(....)....(((((.......))))))------)))---)))).....---.))--.------.))))... ( -26.40)
>DroEre_CAF1 117536 81 + 1
UCGAUGUCGCUG------------CUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA---GUGCUCCUC---CGC--C------CCAUCUCC
..((((..((.(------------..(((.((((((((((.....))))....(((.......))))))------)))---.)))..)..---.))--.------.))))... ( -22.80)
>DroYak_CAF1 123828 81 + 1
UCGAUGUCGCUG------------CUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG------CAA---GUGCUCCUC---CGC--C------CCAUCUCC
..((((..((.(------------..(((.((((((((((.....))))....(((.......))))))------)))---.)))..)..---.))--.------.))))... ( -22.80)
>DroAna_CAF1 108188 101 + 1
UCGAUGUCGCUGCU------GCAGUUGCACUUGCUCCUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUGGUG---CUGGAGCCGCUCCUC---CCACUCCCACUCCCACUCCC
..((((((((.(((------((((..((....))..)))))))..))))).)))..........(((..(((---..((((...))))..---.)))..)))........... ( -36.20)
>DroPer_CAF1 186819 93 + 1
UUGAUGUCGUUGGCGUU---GCCUUUGCUGUUCCCGUUGCAGUUUGCGAUAAUCAUAAUAAUAAUAUCUGUGCUGCUC---GUGGCCCUG---GGA--U------G---CUUC
..(((((.....)))))---......((...(((((((((.....))))).....................((((...---.))))...)---)))--.------)---)... ( -17.90)
>consensus
UCGAUGUCGCUGCU______GC_GCUGCAGUUGCACUUGCAGUUUGCGAUAAUCAUAAUAAUAAUGGUG______CAA___GUGCUCCUC___CGC__C______CCAUCUCC
..((((((((..............((((((......))))))...))))).)))........................................................... (-10.32 = -10.46 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:26 2006