Locus 2683

Sequence ID	2R_DroMel_CAF1
Location	9,470,142 – 9,470,241
Length	99
Max. P	0.841488

overview

Window 5

Location	9,470,142 – 9,470,241
Length	99
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	80.99
Mean single sequence MFE	-29.63
Consensus MFE	-17.02
Energy contribution	-17.00
Covariance contribution	-0.02
Combinations/Pair	1.24
Mean z-score	-2.54
Structure conservation index	0.57
SVM decision value	0.75
SVM RNA-class probability	0.841488
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9470142 99 + 20766785
CGUC----GUAAAUUUUGUGCGGAAAAACCGCAGAGUUUUCAUUGCCGCCGUGAAAAAAACAUAAAUAAUGUCUGUGCCUUUCAGUGGCGCAUUGCGGCGUUC
.((.----((.((..((.(((((.....))))).))..)).)).))(((((..(.....((((.....)))).((((((.......)))))))..)))))... ( -31.10)
>DroPse_CAF1 5910 88 + 1
CGUCGCUCGUAAUUAUUGUU------AAUUCUG--UUUUGCAAUUCCAC---UA--AUUCCUUAA--AAUGUCGGUGCCAUUUAGUGGCACUCUGCGACGUUC
((((((..((....(((((.------((.....--.)).)))))...))---..--.........--......((((((((...))))))))..))))))... ( -22.10)
>DroSec_CAF1 6281 95 + 1
CGUC----GUAAAUUUUGUGCGGAAAAACCGCA--GUUUUCAUUGCCGCCGCUA--AAAACAUAAAUAAUGUCUGUGCCUUUCAGUGGCGCAUUGCGGCGUUC
((((----((((......(((((.....)))))--........(((.(((((((--((..((((.........))))..))).)))))))))))))))))... ( -30.30)
>DroSim_CAF1 6286 97 + 1
CGUC----GUGAAUUUUGUGCGGAAAAACCGCAGAGUUUUUAUUGCCGCCGCUA--AAAACAUAAAUAAUGUCUGUGCCUUUCAGUGGCGCAUUGCGGCGUUC
.((.----(((((..((.(((((.....))))).))..))))).))((((((..--...((((.....)))).((((((.......))))))..))))))... ( -35.20)
>DroEre_CAF1 6262 95 + 1
CGUC----GUAAUUUUUGUGCGGAAAAACCGCA--GUUUUCAUUGGCGCUAAGA--AAAACAUAAAUAAUGUCUGUGCCAUUCAGUGGCGCAUUGCGGCGUUC
((((----(((((.....(((((.....)))))--(((((..(((....)))..--))))).............(((((((...))))))))))))))))... ( -29.70)
>DroYak_CAF1 7957 95 + 1
CGUC----GUAACUUUUGUGCGGAAAAACCGCA--GUUUUUAUUGGCGCUAAGA--AAAACAUAAAUAAUGUCUGUGCCUUUCAGUGGCGCAUUGCGGCGUUC
((((----((((......(((((.....)))))--..........((((((.((--((..((((.........))))..))))..)))))).))))))))... ( -29.40)
>consensus
CGUC____GUAAAUUUUGUGCGGAAAAACCGCA__GUUUUCAUUGCCGCCGAGA__AAAACAUAAAUAAUGUCUGUGCCUUUCAGUGGCGCAUUGCGGCGUUC
((((..............(((((.....))))).....................................((.((((((.......))))))..))))))... (-17.02 = -17.00 +  -0.02)

alignment

secondary structure

dotplot

Window 6

Location	9,470,142 – 9,470,241
Length	99
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	80.99
Mean single sequence MFE	-24.33
Consensus MFE	-16.45
Energy contribution	-18.23
Covariance contribution	1.78
Combinations/Pair	1.11
Mean z-score	-1.54
Structure conservation index	0.68
SVM decision value	0.24
SVM RNA-class probability	0.649826
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9470142 99 - 20766785
GAACGCCGCAAUGCGCCACUGAAAGGCACAGACAUUAUUUAUGUUUUUUUCACGGCGGCAAUGAAAACUCUGCGGUUUUUCCGCACAAAAUUUAC----GACG
....(((((..((.(((.......))).))(((((.....))))).........)))))...........(((((.....)))))..........----.... ( -26.00)
>DroPse_CAF1 5910 88 - 1
GAACGUCGCAGAGUGCCACUAAAUGGCACCGACAUU--UUAAGGAAU--UA---GUGGAAUUGCAAAA--CAGAAUU------AACAAUAAUUACGAGCGACG
...((((((.(.((((((.....)))))))......--....(.(((--((---.((......(....--..)....------..)).))))).)..)))))) ( -20.60)
>DroSec_CAF1 6281 95 - 1
GAACGCCGCAAUGCGCCACUGAAAGGCACAGACAUUAUUUAUGUUUU--UAGCGGCGGCAAUGAAAAC--UGCGGUUUUUCCGCACAAAAUUUAC----GACG
...((((((..((.(((.......))).))(((((.....)))))..--..))))))...........--(((((.....)))))..........----.... ( -28.40)
>DroSim_CAF1 6286 97 - 1
GAACGCCGCAAUGCGCCACUGAAAGGCACAGACAUUAUUUAUGUUUU--UAGCGGCGGCAAUAAAAACUCUGCGGUUUUUCCGCACAAAAUUCAC----GACG
(((((((((..((.(((.......))).))(((((.....)))))..--..)))))).............(((((.....))))).....)))..----.... ( -29.10)
>DroEre_CAF1 6262 95 - 1
GAACGCCGCAAUGCGCCACUGAAUGGCACAGACAUUAUUUAUGUUUU--UCUUAGCGCCAAUGAAAAC--UGCGGUUUUUCCGCACAAAAAUUAC----GACG
....(.(((..((.((((.....)))).))(((((.....)))))..--.....))).).........--(((((.....)))))..........----.... ( -20.10)
>DroYak_CAF1 7957 95 - 1
GAACGCCGCAAUGCGCCACUGAAAGGCACAGACAUUAUUUAUGUUUU--UCUUAGCGCCAAUAAAAAC--UGCGGUUUUUCCGCACAAAAGUUAC----GACG
...((.((.(((((((....((((((((.(((.....))).))))))--))...))))..........--(((((.....))))).....))).)----).)) ( -21.80)
>consensus
GAACGCCGCAAUGCGCCACUGAAAGGCACAGACAUUAUUUAUGUUUU__UAGCGGCGGCAAUGAAAAC__UGCGGUUUUUCCGCACAAAAUUUAC____GACG
....(((((.....(((.......)))..((((((.....))))))........)))))...........(((((.....))))).................. (-16.45 = -18.23 +   1.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:16 2006