Locus 6216

Sequence ID	2L_DroMel_CAF1
Location	17,305,219 – 17,305,358
Length	139
Max. P	0.605378

overview

Window 3

Location	17,305,219 – 17,305,320
Length	101
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.94
Mean single sequence MFE	-28.75
Consensus MFE	-17.53
Energy contribution	-17.78
Covariance contribution	0.25
Combinations/Pair	1.25
Mean z-score	-1.44
Structure conservation index	0.61
SVM decision value	0.09
SVM RNA-class probability	0.579274
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17305219 101 + 22407834
--CG-----UAAUGGGGGCGUGGCAAUGA-----GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGCGAACAC
--((-----(((((...(((((((.....-----..)))))..((((...))))....)).))))...(((.(((((((((((.....))))))))))))))...)))..... ( -25.50)
>DroSec_CAF1 2749 101 + 1
--CG-----UAAUGGGGGCGUGGCAAUGA-----GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGGGAACAC
--..-----(((((...(((((((.....-----..)))))..((((...))))....)).)))))..(((.(((((((((((.....))))))))))))))........... ( -24.90)
>DroSim_CAF1 3058 101 + 1
--CG-----UAAUGGGGGCGUGGCAAUGA-----GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGGGAACAC
--..-----(((((...(((((((.....-----..)))))..((((...))))....)).)))))..(((.(((((((((((.....))))))))))))))........... ( -24.90)
>DroEre_CAF1 5580 101 + 1
--CG-----UAAUGGGGGCGUGGCAAUGA-----GAGCCAUUAGACGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAGGGAAGAACAC
--..-----(((((.....(((((.....-----..)))))...(((((......))))).))))).((((.(((((((((((.....))))))))))))))).......... ( -29.00)
>DroMoj_CAF1 20672 101 + 1
CAUUGCGGCAUUCGCCCGG----------CUGCCUGGCCAUUAGACUGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGUGCGGGCAGCGGCUGCCGCAG--
...(((((((...(((..(----------(((((((..((((((.....(((..(((.(.(((......)))).)))..)))....)))))))))))))))))))))))).-- ( -38.70)
>DroAna_CAF1 14577 95 + 1
--UG-----GCGUGGAGGCGUGGCAAUGA-----GAACCAUUAAAUGGUACAUCAACUGUACAUUAGCUUGUCUGUUUUUGUUUCAUUAGCAAGAACAGCAGGCAGG------
--..-----..(((.((((...))..(((-----..(((((...)))))...))).)).)))....(((((.(((((((((((.....))))))))))))))))...------ ( -29.50)
>consensus
__CG_____UAAUGGGGGCGUGGCAAUGA_____GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGGGAACAC
...................(((((............)))))......(((((.....)))))......(((.(((((((((((.....))))))))))))))........... (-17.53 = -17.78 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	17,305,241 – 17,305,358
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.90
Mean single sequence MFE	-27.66
Consensus MFE	-18.14
Energy contribution	-17.94
Covariance contribution	-0.20
Combinations/Pair	1.23
Mean z-score	-1.52
Structure conservation index	0.66
SVM decision value	0.15
SVM RNA-class probability	0.605378
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17305241 117 + 22407834
-GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGCGAACACUUGGAAAAAAUAGGCCCUGUGAAUCAAAUUC--UUCCAUU
-(((((........(((((.....)))))......(((.(((((((((((.....))))))))))))))..)))...(((..((..........))..)))..))......--....... ( -26.80)
>DroSec_CAF1 2771 119 + 1
-GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGGGAACACUUGGAAAAAAUAUGCCGCAUGAAUCAAAAUUUAUUGCAUU
-...(((..((.(((((((.....))))).((..(((..(((((((((((.....)))))))))))...)))..)).)))))))............((((((((....))))).)))... ( -24.60)
>DroSim_CAF1 3080 117 + 1
-GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGGGAACACUUGGAAAAAAUAGGCCGCUUGAAUCAUAAUC--UUGCAUU
-(.(((........(((((.....))))).((..(((..(((((((((((.....)))))))))))...)))..))................))))((..((.......))--..))... ( -26.00)
>DroEre_CAF1 5602 115 + 1
-GAGCCAUUAGACGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAGGGAAGAACACUUGAAAAAA--AGGCCUCUUGAAUCCUAACC--UUCAAGU
-..(((........(((((.....))))).((..((((.(((((((((((.....)))))))))))))))..))...............--.)))..((((((........--)))))). ( -30.20)
>DroMoj_CAF1 20695 97 + 1
CUGGCCAUUAGACUGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGUGCGGGCAGCGGCUGCCGCAG------CAGCUGUAGCCUCUGCAAA-----------------
............((((((.........(((..(((......)))..))).......))))))((((.((((((.((..------..)).)))))).))))...----------------- ( -30.69)
>consensus
_GAGCCAUUAGAUGGUACAUCAACUGUACAUUAACUUGUCUGUUUUUGUUUCAUUAGCAAGGACAGCAAAAGGCGAACACUUGGAAAAAAUAGGCCCCGUGAAUCAAAAUC__UUCCAUU
...(((........(((((.....)))))......(((.(((((((((((.....)))))))))))))).......................)))......................... (-18.14 = -17.94 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:28 2006