Locus 5458

Sequence ID	3R_DroMel_CAF1
Location	14,422,005 – 14,422,196
Length	191
Max. P	0.959608

overview

Window 1

Location	14,422,005 – 14,422,104
Length	99
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	75.19
Mean single sequence MFE	-34.37
Consensus MFE	-19.63
Energy contribution	-20.55
Covariance contribution	0.92
Combinations/Pair	1.20
Mean z-score	-2.10
Structure conservation index	0.57
SVM decision value	1.50
SVM RNA-class probability	0.959608
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14422005 99 - 27905053
GCCGUUCGAUGUACAGCAGGAGGCACAGCCAGU-GGGCAACAAAAAGGUGGGCUGAGGAGACUUGACCUGGCCGGCCA--GUGUCUCAUGUAUGUAUGUACA
........((((((((((.(((((((.(((...-.)))........(((.(((((((....))).....)))).))).--))))))).))).)))))))... ( -39.20)
>DroSec_CAF1 200359 98 - 1
GCUAUUCGAUGUACAGCAGGAGGCACAGCCAGU-GGGCAACAAAAUGGUGGGCUGAGGAGACUUGACCUGGCCGGCCA--GUGUCUCAUGUAUGUAUGUAC-
........((((((((((.(((((((.(((...-.))).......((((.(((((((....))).....)))).))))--))))))).))).)))))))..- ( -40.00)
>DroSim_CAF1 192327 98 - 1
GCCAUUCGAUGUACAGCAGGAGGCACAGCCAGU-GGGCAACAAAAUGGUGGGCUGAGGAGACUUGACCUGGCCGGCCA--GUGUCUCAUGUAUGUAUGUAC-
........((((((((((.(((((((.(((...-.))).......((((.(((((((....))).....)))).))))--))))))).))).)))))))..- ( -40.00)
>DroEre_CAF1 208963 81 - 1
GCCGUUCGUUGUACAGCAAGAGGCGCAGCCAGU-GGGCA-----AAGGUGGUUUGGGGAGACUCGACCUGG----CCA--GUGUCUCGUGU--------UC-
..............((((.(((((((.(((...-.))).-----..(((((((.(((....)))))))..)----)).--))))))).)))--------).- ( -30.30)
>DroWil_CAF1 239512 92 - 1
GCAGUUUGAUGUACUGCAUGCGGCACUGCCAAAGGGGCA-----AAAGUGGGCGAAUCAGAUAU-ACCUCUC---UCAUUCUAUCUCACAUAUCU-CGUAUC
(((((.......)))))((((((...((((.....))))-----...(((((.((((.(((...-.....))---).))))...))))).....)-))))). ( -24.30)
>DroYak_CAF1 208102 81 - 1
GCCGUUCGAUGUACAGCAGGAGGCACAGCCAGU-GGGCA-----AAGGUGGGCUGGGGAGACUUGACCUGG----CCA--GUGUCUCAUGU--------AC-
..........(((((....(((((((.(((...-.))).-----......(((..((.........))..)----)).--))))))).)))--------))- ( -32.40)
>consensus
GCCGUUCGAUGUACAGCAGGAGGCACAGCCAGU_GGGCA_____AAGGUGGGCUGAGGAGACUUGACCUGGC___CCA__GUGUCUCAUGUAUGU_UGUAC_
...............(((.(((((((.(((.....)))...........(((.((((....)))).)))...........))))))).)))........... (-19.63 = -20.55 +   0.92)

alignment

secondary structure

dotplot

Window 2

Location	14,422,104 – 14,422,196
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	91.63
Mean single sequence MFE	-23.54
Consensus MFE	-17.08
Energy contribution	-17.96
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-2.16
Structure conservation index	0.73
SVM decision value	0.34
SVM RNA-class probability	0.695023
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14422104 92 - 27905053
CCAUCUCUGAAUCCGGUCGUCCACAUCGUCACCAUCUUUGCAACUGCACUGGUGACGUAAGAUCCAUGACGACAACGAUUGCGACUCCAAUU
.........((((..((((((.....((((((((....(((....))).))))))))..........))))))...))))............ ( -24.36)
>DroSec_CAF1 200457 92 - 1
CCAACUCUGAAUCGGGUCGUCCACAUCGUCACCAUCUUUGCAACUGCACUGGUGACGUAAGAUCCAUGACGACAACGAUUGCGACUCCAAUU
.........(((((.((((((.....((((((((....(((....))).))))))))..........))))))..)))))............ ( -26.26)
>DroSim_CAF1 192425 92 - 1
CCAACUCUGAAUCCGGUCGUCCACAUCGUCACCAUCUUUGCAACUGCACUGGUGACGUAAGAUCCAUGACGACAACGAUUGCGACUCCAAUU
.........((((..((((((.....((((((((....(((....))).))))))))..........))))))...))))............ ( -24.36)
>DroEre_CAF1 209044 92 - 1
CCUACUCUGAAUCCGGUCUUCCACAUAGUCACCAUCUUUGCAACUCCAGAGGUGACGUAAGACCCAUGACGACAGCCAUAGCGACUCCAAUU
........((.((.((((((.......((((((.(((..........)))))))))..))))))..........((....)))).))..... ( -17.20)
>DroYak_CAF1 208183 92 - 1
CCAACUCUGAGUCCAGUCUUCCACAUUGUCACCAUCUUUGCAACUGCAGUGGUGACGUUAGAUCCAUGACGACAACCAUUGCGACUUCGAUU
.....((.(((((((((..........((((((((...(((....)))))))))))((((......)))).......)))).))))).)).. ( -25.50)
>consensus
CCAACUCUGAAUCCGGUCGUCCACAUCGUCACCAUCUUUGCAACUGCACUGGUGACGUAAGAUCCAUGACGACAACGAUUGCGACUCCAAUU
...............((((((.....((((((((....(((....))).))))))))..........))))))................... (-17.08 = -17.96 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:12 2006