Locus 2284

Sequence ID	2R_DroMel_CAF1
Location	8,408,226 – 8,408,318
Length	92
Max. P	0.968478

overview

Window 2

Location	8,408,226 – 8,408,318
Length	92
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	77.06
Mean single sequence MFE	-19.06
Consensus MFE	-10.45
Energy contribution	-11.05
Covariance contribution	0.60
Combinations/Pair	1.12
Mean z-score	-1.77
Structure conservation index	0.55
SVM decision value	0.14
SVM RNA-class probability	0.601322
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8408226 92 + 20766785
UUGUUUACACGCGUUCGUUCGAAACGCUUUAAAGCAAUGAAUU--UUAUUAGUUUUCAUGUGCGUG--UUCAUUGAUAUUGUCAAUGUCAAUGUUU
......((((((((((....).)))))......((((((((..--.........))))).))))))--).(((((((((.....)))))))))... ( -22.10)
>DroSec_CAF1 19722 96 + 1
UUGUUUGCACGUGUUCGUUCGAAACGCUUUAAAGCAAUGCAUUUUUUAUGGGUUUUCAUGUGCGUGUGUUUAUUGAUAUUGUCAAUGUCAAUGUUU
......(((((((............(((....)))(((.(((.....))).)))..))))))).......(((((((((.....)))))))))... ( -20.20)
>DroSim_CAF1 19352 91 + 1
GUGUUUGCACGUGUUCGUUC-----GCUUUAAAACAAUGCAUUUUUUAUGGGUUUUCAUGUGCGUGUUUUCAUUGAUAUUGUCAAUGUCAAUGUUU
......(((((((...(((.-----.......)))(((.(((.....))).)))..))))))).......(((((((((.....)))))))))... ( -19.20)
>DroEre_CAF1 21653 76 + 1
U-GUUUGCACGUGUUC--------------AAGCCAUUGUGUU--UUA-UGCUUUUCAUGUGCGUG--UUCAUUGAUAUUGUCAAUGCCAGUGUUU
.-....(((((((...--------------((((.((......--..)-)))))..)))))))...--..(((((((...)))))))......... ( -17.30)
>DroYak_CAF1 19576 78 + 1
UCGUUUGCACGUGUUC--------------AAAACAUUGUGUU--UUACUGCUUUUCAUGUGCGUG--UUCGUUGAUAUUGUCAAUGACAGAGUUA
......(((((((...--------------(((((.....)))--)).........))))))).((--(.(((((((...))))))))))...... ( -16.50)
>consensus
UUGUUUGCACGUGUUCGUUC_____GCUUUAAAACAAUGCAUU__UUAUUGGUUUUCAUGUGCGUG__UUCAUUGAUAUUGUCAAUGUCAAUGUUU
.....((((((((...........................................))))))))......(((((((((.....)))))))))... (-10.45 = -11.05 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	8,408,226 – 8,408,318
Length	92
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	77.06
Mean single sequence MFE	-14.28
Consensus MFE	-6.11
Energy contribution	-6.19
Covariance contribution	0.08
Combinations/Pair	1.17
Mean z-score	-2.39
Structure conservation index	0.43
SVM decision value	1.63
SVM RNA-class probability	0.968478
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8408226 92 - 20766785
AAACAUUGACAUUGACAAUAUCAAUGAA--CACGCACAUGAAAACUAAUAA--AAUUCAUUGCUUUAAAGCGUUUCGAACGAACGCGUGUAAACAA
.........((((((.....)))))).(--((((((.(((((.........--..))))))))......((((((.....))))))))))...... ( -20.00)
>DroSec_CAF1 19722 96 - 1
AAACAUUGACAUUGACAAUAUCAAUAAACACACGCACAUGAAAACCCAUAAAAAAUGCAUUGCUUUAAAGCGUUUCGAACGAACACGUGCAAACAA
..........(((((.....)))))........(((((((......)))...((((((.((......))))))))...........))))...... ( -11.50)
>DroSim_CAF1 19352 91 - 1
AAACAUUGACAUUGACAAUAUCAAUGAAAACACGCACAUGAAAACCCAUAAAAAAUGCAUUGUUUUAAAGC-----GAACGAACACGUGCAAACAC
.........((((((.....)))))).......(((((((......)))..........((((((......-----))))))....))))...... ( -14.00)
>DroEre_CAF1 21653 76 - 1
AAACACUGGCAUUGACAAUAUCAAUGAA--CACGCACAUGAAAAGCA-UAA--AACACAAUGGCUU--------------GAACACGUGCAAAC-A
.........((((((.....))))))..--...((((.((..((((.-...--.........))))--------------...)).))))....-. ( -14.22)
>DroYak_CAF1 19576 78 - 1
UAACUCUGUCAUUGACAAUAUCAACGAA--CACGCACAUGAAAAGCAGUAA--AACACAAUGUUUU--------------GAACACGUGCAAACGA
......((((.((((.....)))).).)--)).((((.((.((((((....--.......))))))--------------...)).))))...... ( -11.70)
>consensus
AAACAUUGACAUUGACAAUAUCAAUGAA__CACGCACAUGAAAACCAAUAA__AAUACAUUGCUUUAAAGC_____GAACGAACACGUGCAAACAA
.........((((((.....)))))).......((((.((...........................................)).))))...... ( -6.11 =  -6.19 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:41 2006