Locus 3165

Sequence ID	3R_DroMel_CAF1
Location	8,392,675 – 8,392,801
Length	126
Max. P	0.976981

overview

Window 8

Location	8,392,675 – 8,392,773
Length	98
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.77
Mean single sequence MFE	-36.95
Consensus MFE	-26.84
Energy contribution	-27.32
Covariance contribution	0.47
Combinations/Pair	1.25
Mean z-score	-2.85
Structure conservation index	0.73
SVM decision value	1.78
SVM RNA-class probability	0.976981
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8392675 98 - 27905053
CUCGCAGAACUUCUGACAGUUUGCUGUCAGAGGCAGCACAAGCUGGAAAUGACAAACGGAAACGGAAGCGAGGCAAGCAGCACUC-CUUCCU------GCAGGCU-----
(((((....((((((((((....))))))))))((((....))))...........((....))...)))))((..((((.....-....))------))..)).----- ( -39.30)
>DroVir_CAF1 69440 92 - 1
CUCGCCAAACUUCUGGCAGUUUGCUGUCAGAAACAGCAAAUGCUG-AAAUCAGAAAC------GGAAGCGGGGCAAGUGGCAGCUCUUUCCU------GGAAACA-----
....(((...(((((((((....))))))))).((((....))))-...........------((((..(((((........))))))))))------)).....----- ( -29.50)
>DroSim_CAF1 53831 98 - 1
CUCGCAGAACUUCUGACAGUUUGCUGUCAGAGGCAGCACAAGCUGGAAAUGACAAACGGAAACGGAAGCGGGGCAAGCAGCACUC-CUUCCU------GCAGGCU-----
(((((....((((((((((....))))))))))((((....))))...........((....))...)))))((..((((.....-....))------))..)).----- ( -38.40)
>DroYak_CAF1 56162 98 - 1
CUCGCAGAACUUCUGACAGUUUGCUGUCAGAGGCAGCACAAGCUGGAAAUGACAAACGGAAACGGAAGCGGGGCAGGCAGCACUC-CUUCCU------GCAGGCU-----
(((((....((((((((((....))))))))))((((....))))...........((....))...)))))(((((.((.....-)).)))------)).....----- ( -40.90)
>DroAna_CAF1 56723 90 - 1
UUCGCCGAACUUCUGACAGUUUGCUGUCAGAGGCAGCGCAGACUGGAAAUGACAAAC------GGAAGCGAGGCAGGCAGCACUA-CGUCCU------GGCGG-------
..(((((..((((((((((....))))))))))(((......)))............------(((....((((.....)).)).-..))))------)))).------- ( -30.50)
>DroPer_CAF1 55855 103 - 1
CUCUGCGAAGUUCUGACAGUUUGCUGUCAGAGGCAGCGAAGGCUGGAAAUGACAAAC------GGAAGCGAGGCAGGCAGCAGCU-CUUCCUCUUCCUGGAAACAGGAAC
.((((.....(((((((((....))))))))).((((....))))...........)------)))...((((.((((....)).-)).))))((((((....)))))). ( -43.10)
>consensus
CUCGCAGAACUUCUGACAGUUUGCUGUCAGAGGCAGCACAAGCUGGAAAUGACAAAC______GGAAGCGAGGCAAGCAGCACUC_CUUCCU______GCAGGCU_____
.........((((((((((....))))))))))((((....))))..................(((((.(((((.....)).))).)))))................... (-26.84 = -27.32 +   0.47)

alignment

secondary structure

dotplot

Window 9

Location	8,392,697 – 8,392,801
Length	104
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	79.49
Mean single sequence MFE	-33.93
Consensus MFE	-18.67
Energy contribution	-18.33
Covariance contribution	-0.33
Combinations/Pair	1.17
Mean z-score	-2.24
Structure conservation index	0.55
SVM decision value	0.71
SVM RNA-class probability	0.829817
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8392697 104 + 27905053
UUGCCUCGCUUCCGUUUCCGUUUGUCAUUUCCAGCUUGUGCUGCCUCUGACAGCAAACUGUCAGAAGUUCUGCGAGCGUUGCG--CUGAUUGACGAACCCACGGAA
..........(((((....((((((((....(((((((((..((.((((((((....)))))))).))..)))))((...)))--)))..))))))))..))))). ( -36.70)
>DroVir_CAF1 69463 97 + 1
UUGCCCCGCUUCC------GUUUCUGAUUU-CAGCAUUUGCUGUUUCUGACAGCAAACUGCCAGAAGUUUGGCGAGCGCAUCG--CUGAUUGACGAACGCACGCUU
(((((..(((((.------.....((....-))((((((((((((...))))))))).)))..)))))..)))))(((..(((--(.....).))).)))...... ( -29.10)
>DroGri_CAF1 62090 97 + 1
UUGGCCUGCUUCC------GUUUGUCAUUU-CAGUAUUUGCUGUUUCUGACAGCAAGCUGCCAGAAGUUUAGCGAACGCAUCU--CUGAUUGACGAAUGUACGCUU
.......((...(------((((((((..(-(((..(((((((((((((.(((....))).))))))..))))))).......--)))).)))))))))...)).. ( -29.70)
>DroEre_CAF1 56361 104 + 1
CUGCCCCACUUCCGUUUCCGUUUGUCAUUUCCAGCUUGCGCUGCCUCUGACAGCAAACUGUCAGAAGUUCUGCGAGCGUUGCG--CUGAUUGACGAACCCACGGAA
..........(((((....((((((((....((((..((((((((((((((((....))))))).))....)).)))))...)--)))..))))))))..))))). ( -39.60)
>DroMoj_CAF1 64924 99 + 1
UUGGCCCGAUUCC------GUUUGUCAUUU-GAGCAUUUGCUGCUUCUGACAGCCAGCUGCCAGAAGUUUGGCGAGCGCGCCAACCUGAUUGACGAACGCACGCUU
..(((.......(------((((((((.((-.(((....)))(((((((.(((....))).)))))))((((((....))))))...)).)))))))))...))). ( -34.00)
>DroAna_CAF1 56743 98 + 1
CUGCCUCGCUUCC------GUUUGUCAUUUCCAGUCUGCGCUGCCUCUGACAGCAAACUGUCAGAAGUUCGGCGAACAUGGCG--CUGAUUGACGAACGCACGGAU
..........(((------((.(((......(((((.(((((...((((((((....)))))))).((((...))))..))))--).)))))....))).))))). ( -34.50)
>consensus
UUGCCCCGCUUCC______GUUUGUCAUUU_CAGCAUGUGCUGCCUCUGACAGCAAACUGCCAGAAGUUCGGCGAGCGCAGCG__CUGAUUGACGAACGCACGCAU
...................((((((((....((((....))))..((((.(((....))).)))).((((...)))).............))))))))........ (-18.67 = -18.33 +  -0.33)

alignment

secondary structure

dotplot

Window 0

Location	8,392,697 – 8,392,801
Length	104
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.49
Mean single sequence MFE	-35.22
Consensus MFE	-22.75
Energy contribution	-22.83
Covariance contribution	0.09
Combinations/Pair	1.25
Mean z-score	-2.46
Structure conservation index	0.65
SVM decision value	1.35
SVM RNA-class probability	0.945059
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8392697 104 - 27905053
UUCCGUGGGUUCGUCAAUCAG--CGCAACGCUCGCAGAACUUCUGACAGUUUGCUGUCAGAGGCAGCACAAGCUGGAAAUGACAAACGGAAACGGAAGCGAGGCAA
....((..((((((......)--)).))).(((((....((((((((((....))))))))))((((....))))...........((....))...))))))).. ( -36.90)
>DroVir_CAF1 69463 97 - 1
AAGCGUGCGUUCGUCAAUCAG--CGAUGCGCUCGCCAAACUUCUGGCAGUUUGCUGUCAGAAACAGCAAAUGCUG-AAAUCAGAAAC------GGAAGCGGGGCAA
..(.((((((.(((......)--)))))))).)(((...((((((...(((((((((.....))))))))).(((-....)))...)------)))))...))).. ( -36.40)
>DroGri_CAF1 62090 97 - 1
AAGCGUACAUUCGUCAAUCAG--AGAUGCGUUCGCUAAACUUCUGGCAGCUUGCUGUCAGAAACAGCAAAUACUG-AAAUGACAAAC------GGAAGCAGGCCAA
..((...(.((.((((.((((--.((.....))(((....(((((((((....)))))))))..))).....)))-)..)))).)).------)...))....... ( -26.00)
>DroEre_CAF1 56361 104 - 1
UUCCGUGGGUUCGUCAAUCAG--CGCAACGCUCGCAGAACUUCUGACAGUUUGCUGUCAGAGGCAGCGCAAGCUGGAAAUGACAAACGGAAACGGAAGUGGGGCAG
((((((..(((..((.....(--((.......)))....((((((((((....))))))))))((((....))))))...)))..))))))((....))....... ( -40.40)
>DroMoj_CAF1 64924 99 - 1
AAGCGUGCGUUCGUCAAUCAGGUUGGCGCGCUCGCCAAACUUCUGGCAGCUGGCUGUCAGAAGCAGCAAAUGCUC-AAAUGACAAAC------GGAAUCGGGCCAA
..((.((((((.((((......((((((....)))))).((((((((((....)))))))))).(((....))).-...)))).)))------)....)).))... ( -34.50)
>DroAna_CAF1 56743 98 - 1
AUCCGUGCGUUCGUCAAUCAG--CGCCAUGUUCGCCGAACUUCUGACAGUUUGCUGUCAGAGGCAGCGCAGACUGGAAAUGACAAAC------GGAAGCGAGGCAG
..((.(((.(((((...(((.--..(((.((..(((...((((((((((....))))))))))..).))..)))))...)))...))------))).))).))... ( -37.10)
>consensus
AACCGUGCGUUCGUCAAUCAG__CGCAACGCUCGCCAAACUUCUGACAGUUUGCUGUCAGAAGCAGCAAAUGCUG_AAAUGACAAAC______GGAAGCGGGGCAA
.............................((((((....((((((((((....))))))))))((((....))))......................))))).).. (-22.75 = -22.83 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:41 2006