Locus 4663

Sequence ID	2L_DroMel_CAF1
Location	13,365,174 – 13,365,331
Length	157
Max. P	0.730636

overview

Window 3

Location	13,365,174 – 13,365,291
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.55
Mean single sequence MFE	-34.65
Consensus MFE	-26.22
Energy contribution	-26.70
Covariance contribution	0.48
Combinations/Pair	1.18
Mean z-score	-1.79
Structure conservation index	0.76
SVM decision value	0.42
SVM RNA-class probability	0.730636
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13365174 117 + 22407834
GGCUGCUCCUCCUCGGCGUUGACCUCGUCAUCC---UCCUCGUCAAAUCCAGAAUCUAGUUUCUCAAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUU
.((((........)))).(((((..........---.....)))))....((((......))))(((((((.....(((((((((((((....)))).))))))))))))))))...... ( -37.26)
>DroSec_CAF1 6055 116 + 1
GGCUGCUCCUCCUCGGCGUUGACCUCGUCAUCC---UCCUCGUCA-AUCCAGAAUCUAGUUUCUCGAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUU
.((((........))))((((((..........---.....))))-))..((((......))))(((((((.....(((((((((((((....)))).))))))))))))))))...... ( -37.76)
>DroSim_CAF1 5210 117 + 1
GGCUGCUCCUCCUCGGCGUUGACCUCGUCAUCC---UCCUCGUCAAAUCCAGAAUCUAGUUUCUCGAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUU
.(((..........(((.(((((..........---.....)))))(((.((((......)))).)))))).....(((((((((((((....)))).)))))))))))).......... ( -37.16)
>DroWil_CAF1 36733 120 + 1
GAUGACUUCUUUUCUUCGUCCUCUUCGUCAUCCAUUUCCUCGUCGAAACCAGAAUCCAGUUUUUCGACAUCAUCUAUCGAGGCAGUGGGAAAGCCCAUUUCUUUCCAAGCUGAGUACUUU
((((((....................)))))).........(((((((.............))))))).(((.((...((((.((((((....)))))).))))...)).)))....... ( -23.77)
>DroYak_CAF1 5751 117 + 1
GGCUGCUCCUCCUCGGCGUUGCCCUCGUCAUCC---UCCUCAUCAAAUCCAGAAUCUAGUUUCUCGAUAUCAUCAAUGGAGGCGGUGGGGAAGCCCAUCAGCUUCCAGGCAUUGUACUUU
(((.((.((.....)).)).)))...(((....---..........(((.((((......)))).)))........(((((((((((((....)))))).)))))))))).......... ( -37.30)
>consensus
GGCUGCUCCUCCUCGGCGUUGACCUCGUCAUCC___UCCUCGUCAAAUCCAGAAUCUAGUUUCUCGAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUU
...((((.......((((.......)))).................(((.((((......)))).)))........(((((((((((((....)))))).)))))))))))......... (-26.22 = -26.70 +   0.48)

alignment

secondary structure

dotplot

Window 4

Location	13,365,211 – 13,365,331
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.11
Mean single sequence MFE	-35.54
Consensus MFE	-23.33
Energy contribution	-24.00
Covariance contribution	0.67
Combinations/Pair	1.35
Mean z-score	-2.09
Structure conservation index	0.66
SVM decision value	0.14
SVM RNA-class probability	0.602437
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13365211 120 + 22407834
CGUCAAAUCCAGAAUCUAGUUUCUCAAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUUUCGCUGUACUGUCGUCCUAAGUCGCUCUGGUACAUCAGAU
.........(((.....(((....(((((((.....(((((((((((((....)))).)))))))))))))))).))).....)))..(((..((((..((...))..)).))..))).. ( -41.00)
>DroVir_CAF1 6967 120 + 1
CAUCGAAGCCUGAGUCCAUCUUUUCGACAUCGUCUAUAGAGGCGCUGGGAAAACCCAUUUCCUUCCAUGCCUUGUACUUCUCGCUGUACUCGCGACCCAAUUCACUCUGAUAAAGCAAAU
..((((((...((.....)).))))))..((((.....((((((..((((((.....))))))....))))))((((........))))..))))......................... ( -23.00)
>DroSec_CAF1 6092 119 + 1
CGUCA-AUCCAGAAUCUAGUUUCUCGAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUUUCGCUGUACUGUCGUCCCAAGUCGCUCUGGUACAUCAGAU
.....-...(((.....(((....(((((((.....(((((((((((((....)))).)))))))))))))))).))).....)))..(((..((.(((........))).))..))).. ( -42.30)
>DroSim_CAF1 5247 120 + 1
CGUCAAAUCCAGAAUCUAGUUUCUCGAUGUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUUUCGCUGUACUGUCGCCCCAAGUCGCUCUGAUAUAUCAGAU
.(((......((((......)))).(((((.((((.(((((((((((((....)))).)))))))))(((((.((((........)))).)).)))...........))))))))).))) ( -42.00)
>DroWil_CAF1 36773 120 + 1
CGUCGAAACCAGAAUCCAGUUUUUCGACAUCAUCUAUCGAGGCAGUGGGAAAGCCCAUUUCUUUCCAAGCUGAGUACUUUUCACUAUAUUCGCGACCCAACUCGCUUUGAUAUAGCAAAU
.(((((((.............)))))))......((((((((((((.((((((.......))))))..((.(((((..........)))))))......))).)))))))))........ ( -28.02)
>DroYak_CAF1 5788 120 + 1
CAUCAAAUCCAGAAUCUAGUUUCUCGAUAUCAUCAAUGGAGGCGGUGGGGAAGCCCAUCAGCUUCCAGGCAUUGUACUUUUCGCUGUACUCUCGUCCCAAGUCGCUCUGGUACAGGAGAU
......(((.((((......)))).)))........(((((((((((((....)))))).)))))))...........((((.(((((((..((.(....).))....))))))))))). ( -36.90)
>consensus
CGUCAAAUCCAGAAUCUAGUUUCUCGAUAUCAUCAAUGGAGGCGGUGGGGAAACCCAUCUGCUUCCAGGCAUUGUACUUUUCGCUGUACUCUCGUCCCAAGUCGCUCUGAUACAGCAGAU
.........((((.......................(((((((((((((....)))))).)))))))(((((.((((........)))).)).))).........))))........... (-23.33 = -24.00 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:02 2006