Locus 6027

Sequence ID	3R_DroMel_CAF1
Location	15,893,742 – 15,893,890
Length	148
Max. P	0.643816

overview

Window 2

Location	15,893,742 – 15,893,861
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.42
Mean single sequence MFE	-34.83
Consensus MFE	-14.82
Energy contribution	-17.10
Covariance contribution	2.28
Combinations/Pair	1.11
Mean z-score	-2.20
Structure conservation index	0.43
SVM decision value	-0.05
SVM RNA-class probability	0.507619
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15893742 119 + 27905053
AGACGCUACAAAAGCAGGGGAAAUGCCGUGGACCUGGCCACUGAGCUGGCGAGGGC-CAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCGGUGGCUUUUCCGGGAAUUCAGAGAUGGCA
....(((.....)))........((((((((.(((.((((......)))).))).)-)..(..((((.((((..(((((...(((.....)))..)))))..)))).))))..))))))) ( -38.60)
>DroPse_CAF1 7419 101 + 1
UGCUGCUACACUAGU----------------GACUAGCCACUAU---GGAGGGGCCUUAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCAUUGCCUCUCUGGAGAAUCUAGAGAUGGCA
...((((.((.((((----------------(......))))))---)..((((..(((....)))..))))...............)))).(((((((((((.....))))))).)))) ( -28.70)
>DroSec_CAF1 696 119 + 1
AGACGCUACAAAAGCAGGGGAAAUGCCCUGGACCUGGCCACUGAGCUGGCGAGGGC-CAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCGGUGGCUUUUCCGGGAAUUCAGAGAUGGCA
..............(((((......)))))..(((.((((......)))).)))((-((.(..((((.((((..(((((...(((.....)))..)))))..)))).))))..).)))). ( -42.10)
>DroEre_CAF1 704 119 + 1
AGACGCUACAAAAGCAGGGGAAACGCUGUAGACCUGGCCACUGAGCUGGUGAGGGC-CAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCGGUGGCUUUUCCUGGAAUUCAGAGAUGGCA
.............((((.(....).))))...(((.((((......)))).)))((-((.(..((((.(((...(((((...(((.....)))..)))))...))).))))..).)))). ( -37.10)
>DroYak_CAF1 664 119 + 1
AGACGCUACAAAAGCAGGGGAAAUGCUGUGGACCUGGCCACUGAGCUGGUGAGGGC-CAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCGGUGGCUUUUCCGGGAAUUCAGAGAUGGCA
.....(((((...(((.......)))))))).(((.((((......)))).)))((-((.(..((((.((((..(((((...(((.....)))..)))))..)))).))))..).)))). ( -38.00)
>DroPer_CAF1 7451 101 + 1
UGCUGCUACACUAGU----------------GACUAGCCACUAU---GGAGGGGCCUUAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCAUUGCCUCUCGGGAGAAUCUAGAGAUGGCA
...((((.((.((((----------------(......))))))---)..((((..(((....)))..))))...............)))).((((((((.((.....)).)))).)))) ( -24.50)
>consensus
AGACGCUACAAAAGCAGGGGAAAUGC_GUGGACCUGGCCACUGAGCUGGAGAGGGC_CAACAAUGAAAUCCCAUAAAAGAAAAUCAAGGCGGUGGCUUUUCCGGGAAUUCAGAGAUGGCA
....((((........................(((.(((........))).)))......(..((((.((((..(((((...(((.....)))..)))))..)))).))))..).)))). (-14.82 = -17.10 +   2.28)

alignment

secondary structure

dotplot

Window 3

Location	15,893,782 – 15,893,890
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.26
Mean single sequence MFE	-30.56
Consensus MFE	-13.46
Energy contribution	-12.77
Covariance contribution	-0.69
Combinations/Pair	1.30
Mean z-score	-2.40
Structure conservation index	0.44
SVM decision value	0.23
SVM RNA-class probability	0.643816
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15893782 108 - 27905053
-----------UUUGAGCGCCGGCACUCUGUAUAUCACAUUGCCAUCUCUGAAUUCCCGGAAAAGCCACCGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUG-GCCCUCGCCAGCUCAG
-----------..(((((...(((....(((.....)))..((((.(..((((.((((((((((..((......)).)))))).....)))).))))..).))-))....))).))))). ( -31.30)
>DroPse_CAF1 7443 113 - 1
UCACACACCAGUUUGU----AUGGAGUCCGUAUAUCACAUUGCCAUCUCUAGAUUCUCCAGAGAGGCAAUGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUAAGGCCCCUCC---AUAG
...............(----((((((............((((((.(((((.(.....).)))))))))))((((((((..((((....)))).......))))))))..))))---))). ( -32.60)
>DroSim_CAF1 730 108 - 1
-----------UUUGAGCGCCGGCACUCAGUAUAUCACAUUGCCAUCUCUGAAUUCCCGGAAAAGCCACCGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUG-GCCCUCGCCAGCUCAG
-----------..(((((...(((.....((.....))...((((.(..((((.((((((((((..((......)).)))))).....)))).))))..).))-))....))).))))). ( -30.90)
>DroEre_CAF1 744 108 - 1
-----------AUUGAGCGCCGGCACUCAGUAUAUCACAUUGCCAUCUCUGAAUUCCAGGAAAAGCCACCGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUG-GCCCUCACCAGCUCAG
-----------..(((((...((((...............)))).((.(((.....)))))...((((..((..(((..((((.....))))..)))..))))-))........))))). ( -25.56)
>DroYak_CAF1 704 108 - 1
-----------UUUGAGCGCCGACACUCAGUAUAUCACAUUGCCAUCUCUGAAUUCCCGGAAAAGCCACCGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUG-GCCCUCACCAGCUCAG
-----------..((((.(((((((....(((........)))......((((.((((((((((..((......)).)))))).....)))).)))).)))))-)).))))......... ( -27.20)
>DroPer_CAF1 7475 113 - 1
UCAGACACCAGUCUGU----AUGGAGUCCGUAUAUCACAUUGCCAUCUCUAGAUUCUCCCGAGAGGCAAUGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUAAGGCCCCUCC---AUAG
.(((((....)))))(----((((((............((((((.((((..(.....)..))))))))))((((((((..((((....)))).......))))))))..))))---))). ( -35.80)
>consensus
___________UUUGAGCGCCGGCACUCAGUAUAUCACAUUGCCAUCUCUGAAUUCCCGGAAAAGCCACCGCCUUGAUUUUCUUUUAUGGGAUUUCAUUGUUG_GCCCUCACCAGCUCAG
............((((((...........(((........)))......((((.(((((.(((((................))))).))))).)))).................)))))) (-13.46 = -12.77 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:47 2006