Locus 5106

Sequence ID	2R_DroMel_CAF1
Location	16,604,889 – 16,604,999
Length	110
Max. P	0.959336

overview

Window 4

Location	16,604,889 – 16,604,999
Length	110
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	78.71
Mean single sequence MFE	-28.80
Consensus MFE	-14.60
Energy contribution	-16.64
Covariance contribution	2.04
Combinations/Pair	1.11
Mean z-score	-2.44
Structure conservation index	0.51
SVM decision value	1.50
SVM RNA-class probability	0.959336
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16604889 110 + 20766785
UUCAAAUUUCGUUAUCGACUUAUCGAUAGCCACGGCCAUGUGUUUCAGUAUAUACGGUUGUAUAUUAUACGGUCACACUAGGCACAAGGGGCGGAUUUUUUGAAACUUC----U
((((((..((((((((((....))))))))..((.((.(((((((.(((((((((....)))))).....(....)))))))))))..)).))))...)))))).....----. ( -29.00)
>DroSec_CAF1 4852 111 + 1
UUCAAAUUUCGUUAUCGACCUAUCGAUAGCCAUGGCCAUGUGAUUCAGUAUAUACUUUUCGAUAGUAUACGGUCACACCAGGCCUAAUGGGCGCACUUUUUGAAAGUUUU---U
((((((......((((((....))))))(((..((((.((((((...((((((...........)))))).))))))...)))).....)))......))))))......---. ( -30.20)
>DroSim_CAF1 4907 114 + 1
UUCGAAUUUCGUUAUCGACUUAUCGAUAGGCAUGGCCAUGUGAUUCAGUAUAUUCGUUUCGAUAUUAUACGGUCACACCAAGCCUAAUGGGCGCACUUUUUGAACGUUUUUUUU
((((((...((((.((((....))))(((((.(((...((((((...(((((.(((...)))...))))).))))))))).)))))...)))).....)))))).......... ( -28.60)
>DroEre_CAF1 6608 101 + 1
UUCAAAUUUCU--------UUAUCGAUAGCUGUGGCCAUGUGUUUUAGUAUAUACAUUUGCUUACUAUAUGGUCACACUUGACGAAAGAGGCCCACUUUUUGAAAGUA-----U
((((((..(((--------((.(((.(((.(((((((((((((...((((........)))).)).))))))))))).))).))).))))).......))))))....-----. ( -27.50)
>DroYak_CAF1 5012 108 + 1
UUCAAAUUUCUUGAUCGAUUUAUCGAUAGCUGUGGCCAUGUGUUUCAGUAUAUAUGUUUUCUUACUAUACGGUCACACUUGGCCUAAGAGGCGGACUUUUUGAAA-UA-----U
((((((..(((..(((((....))))).(((..(((((.((((..(.(((((((........)).))))).)..)))).))))).....))))))...)))))).-..-----. ( -28.70)
>consensus
UUCAAAUUUCGUUAUCGACUUAUCGAUAGCCAUGGCCAUGUGUUUCAGUAUAUACGUUUCCAUACUAUACGGUCACACUAGGCCUAAGGGGCGCACUUUUUGAAAGUU_____U
((((((......(((((......)))))(((..((((..((((....(((((.............)))))....))))..)))).....)))......)))))).......... (-14.60 = -16.64 +   2.04)

alignment

secondary structure

dotplot

Window 5

Location	16,604,889 – 16,604,999
Length	110
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	78.71
Mean single sequence MFE	-24.22
Consensus MFE	-12.12
Energy contribution	-14.40
Covariance contribution	2.28
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.50
SVM decision value	-0.01
SVM RNA-class probability	0.528263
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16604889 110 - 20766785
A----GAAGUUUCAAAAAAUCCGCCCCUUGUGCCUAGUGUGACCGUAUAAUAUACAACCGUAUAUACUGAAACACAUGGCCGUGGCUAUCGAUAAGUCGAUAACGAAAUUUGAA
.----.(((((((.........(((...((.(((..((((..(.(((((...(((....)))))))).)..))))..))))).)))((((((....))))))..)))))))... ( -27.90)
>DroSec_CAF1 4852 111 - 1
A---AAAACUUUCAAAAAGUGCGCCCAUUAGGCCUGGUGUGACCGUAUACUAUCGAAAAGUAUAUACUGAAUCACAUGGCCAUGGCUAUCGAUAGGUCGAUAACGAAAUUUGAA
.---......((((((......(((.....((((..((((((..(((((((.......)))))))......))))))))))..)))((((((....))))))......)))))) ( -27.60)
>DroSim_CAF1 4907 114 - 1
AAAAAAAACGUUCAAAAAGUGCGCCCAUUAGGCUUGGUGUGACCGUAUAAUAUCGAAACGAAUAUACUGAAUCACAUGGCCAUGCCUAUCGAUAAGUCGAUAACGAAAUUCGAA
........(((.(.....).))).....(((((.(((((((((.(((((...(((...))).))))).)..))))...)))).)))))((((....(((....)))...)))). ( -23.80)
>DroEre_CAF1 6608 101 - 1
A-----UACUUUCAAAAAGUGGGCCUCUUUCGUCAAGUGUGACCAUAUAGUAAGCAAAUGUAUAUACUAAAACACAUGGCCACAGCUAUCGAUAA--------AGAAAUUUGAA
.-----....((((((.(((.((((......((((....))))....(((((.((....))...)))))........))))...))).((.....--------.))..)))))) ( -17.80)
>DroYak_CAF1 5012 108 - 1
A-----UA-UUUCAAAAAGUCCGCCUCUUAGGCCAAGUGUGACCGUAUAGUAAGAAAACAUAUAUACUGAAACACAUGGCCACAGCUAUCGAUAAAUCGAUCAAGAAAUUUGAA
.-----..-.((((((...((.........(((((.((((..(.(((((.............))))).)..)))).)))))......(((((....)))))...))..)))))) ( -24.02)
>consensus
A_____AACUUUCAAAAAGUGCGCCCCUUAGGCCUAGUGUGACCGUAUAAUAUCCAAACGUAUAUACUGAAACACAUGGCCAUGGCUAUCGAUAAGUCGAUAACGAAAUUUGAA
..........((((((..............((((..((((....(((((.............)))))....))))..)))).....((((((....))))))......)))))) (-12.12 = -14.40 +   2.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:41 2006