Locus 404

Sequence ID	3R_DroMel_CAF1
Location	1,503,822 – 1,503,962
Length	140
Max. P	0.942598

overview

Window 1

Location	1,503,822 – 1,503,934
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.54
Mean single sequence MFE	-42.85
Consensus MFE	-26.16
Energy contribution	-26.33
Covariance contribution	0.17
Combinations/Pair	1.34
Mean z-score	-2.08
Structure conservation index	0.61
SVM decision value	0.82
SVM RNA-class probability	0.860243
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1503822 112 + 27905053
AGCAGCGCACGGUGAGCAUUACGAGCGUAAAUGAGGAGGAUGACGAGUCGGCUUCGCUGCUCAGCGAGCGUUGUCGCUACAUAAGCGUAAGCGAGGAGGAUGAGUUGCAUGC--------
.(((((((.((.((((((((((....))))..((((..(((.....)))..))))..)))))).)).)).((.(((((((......)).))))).))......)))))....-------- ( -39.60)
>DroVir_CAF1 5609 117 + 1
AGGAGCGCACGGUGAGCAUCUCUAGCGUUAACGAGGAGGAGGACGAGUCUGCCUCGUUGCUCAGUGAGCGCUGUCGCUACAUCAGCGUUAGUGAGGAGGAUGAAUUGCUGGCGCUUG---
..((((((.(((..(.((((.((.....((((((((....(((....))).))))))))((((.(((.(((((.........)))))))).)))).))))))..)..))))))))).--- ( -48.20)
>DroGri_CAF1 4344 120 + 1
AGGAGCGCACGGUGAGCAUAAGCAGCGUCAACGAGGAGGAGGACGAGUCUGCCUCGUUGCUCAGCGAACGCUGUCGCUACAUUAGCGUAAGUGAGGAAGACGAAUUGCUUGCUGGUGCUU
..((((((.(((..((((.......(((((((((((....(((....))).))))))).((((.(..((((((.........))))))..)))))...))))...))))..))))))))) ( -49.70)
>DroWil_CAF1 4139 112 + 1
AAGAGCGCACAGUGAGCAUAACCAGUGUCAAUGAGGAGGACGAUGAAUCGGCCUCGUUGCUAAGUGAGAGCUGUCGUUACAUAAGUGUCAGUGAGGAGAACGAACUGAUUGC--------
...((((.(((((...(((.......(.((((((((....(((....))).)))))))))...)))...)))))))))........((((((..(.....)..))))))...-------- ( -30.50)
>DroMoj_CAF1 4512 117 + 1
AAGAACGGACGGUGAGCAUCUCUAGCGUAAACGAGGAGGAAGAUGAGUCAGCCUCCUUGCUCAGUGAGCGCUGUCGAUACAUUAGCGUUAGCGAGGAGGAUGAAUUGUUGGCGGUUC---
......((((.((.(((((((((..((....)).)))))........(((.((((((((((.....(((((((.........))))))))))))))))).)))..)))).)).))))--- ( -42.50)
>DroPer_CAF1 4496 112 + 1
AGCAGCGCACUGUGAGCAUCACGAGCGUGAACGAGGAGGACGACGAGUCCGCUUCGUUGCUCAGCGAGCGCUGUCGCUACAUUAGCGUGAGCGAAGAAGAUGAACUGCUUGC--------
.(((((((.(..((((((((((....))))((((((.((((.....)))).))))))))))))..).))))))).((((...))))(..((((............))))..)-------- ( -46.60)
>consensus
AGGAGCGCACGGUGAGCAUCACCAGCGUAAACGAGGAGGACGACGAGUCGGCCUCGUUGCUCAGCGAGCGCUGUCGCUACAUUAGCGUAAGCGAGGAGGAUGAAUUGCUUGC________
...(((((.((.((((((.......((....))..((((.(((....))).))))..)))))).)).))))).(((((((......)).))))).......................... (-26.16 = -26.33 +   0.17)

alignment

secondary structure

dotplot

Window 2

Location	1,503,862 – 1,503,962
Length	100
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.32
Mean single sequence MFE	-40.67
Consensus MFE	-20.53
Energy contribution	-19.93
Covariance contribution	-0.60
Combinations/Pair	1.44
Mean z-score	-2.14
Structure conservation index	0.50
SVM decision value	1.33
SVM RNA-class probability	0.942598
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1503862 100 + 27905053
UGACGAGUCGGCUUCGCUGCUCAGCGAGCGUUGUCGCUACAUAAGCGUAAGCGAGGAGGAUGAGUUGCAUGC---------UGCUG--GUGGCUCAAUGCCGGCAGUAACA
.(((..(((..(((((((((((...)))).....((((.....))))..)))))))..)))..)))...(((---------(((((--(((......)))))))))))... ( -40.40)
>DroVir_CAF1 5649 98 + 1
GGACGAGUCUGCCUCGUUGCUCAGUGAGCGCUGUCGCUACAUCAGCGUUAGUGAGGAGGAUGAAUUGCUGGCGCUUG---CUGCUG--GCGGC--------GGCGGCGGCA
.((((((.....))))))((((...))))(((((((((.....((((((((..(..........)..)))))))).(---(((...--.))))--------))))))))). ( -44.80)
>DroGri_CAF1 4384 101 + 1
GGACGAGUCUGCCUCGUUGCUCAGCGAACGCUGUCGCUACAUUAGCGUAAGUGAGGAAGACGAAUUGCUUGCUGGUGCUUCUGUUG--UCGGU--------GGCAGCAGCA
......((((.(((((((((.((((....))))..((((...)))))))).))))).))))........(((((.((((.(((...--.))).--------)))).))))) ( -39.20)
>DroEre_CAF1 4724 100 + 1
UGACGAGUCGGCUUCGCUGCUCAGCGAGCGUUGUCGCUACAUAAGCGUCAGCGAGGAGGAUGAGUUGCAUGC---------UGCUG--GUGGGAUAGUGCCGGCAGUAACA
.(((..(((..(((((((((((...))))...(.((((.....)))).))))))))..)))..)))...(((---------(((((--((........))))))))))... ( -42.00)
>DroYak_CAF1 3728 100 + 1
UGAUGAGUCGGCAUCGCUGCUCAGCGAGCGUUGUCGCUACAUAAGCGUCAGCGAAGAGGAUGAGUUGCAUGC---------UGCUG--GUGGCUCAGUGCCGGCAGUAACA
......((((((((.((..(.((((...(((((.((((.....)))).)))))...((.(((.....))).)---------)))))--)..))...))))))))....... ( -42.10)
>DroMoj_CAF1 4552 100 + 1
AGAUGAGUCAGCCUCCUUGCUCAGUGAGCGCUGUCGAUACAUUAGCGUUAGCGAGGAGGAUGAAUUGUUGGCGGUUC---CUACUUCUGCUGC--------UGAAGCAACA
.(.((..((((((((((((((.....(((((((.........))))))))))))))))...........(((((...---......)))))))--------)))..)).). ( -35.50)
>consensus
UGACGAGUCGGCCUCGCUGCUCAGCGAGCGCUGUCGCUACAUAAGCGUAAGCGAGGAGGAUGAAUUGCAUGC_________UGCUG__GCGGC________GGCAGCAACA
.(((..(((..((((...((((...))))((((.((((.....)))).))))))))..)))..)))...............(((((.................)))))... (-20.53 = -19.93 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:22 2006