Locus 102

Sequence ID	3L_DroMel_CAF1
Location	356,836 – 356,931
Length	95
Max. P	0.925246

overview

Window 1

Location	356,836 – 356,931
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.89
Mean single sequence MFE	-27.00
Consensus MFE	-17.11
Energy contribution	-17.58
Covariance contribution	0.47
Combinations/Pair	1.20
Mean z-score	-2.40
Structure conservation index	0.63
SVM decision value	1.16
SVM RNA-class probability	0.924397
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 356836 95 + 23771897
U------------------CGUUUUGGGCUUUUG-------CCGGAUUUGCAUAAAAUAUCGUUAUUAGGCGCAGUUUAUUUUUAUUUGCUGCGCAUGCGCGACCAUUUUGGUCUCCAUU
.------------------.......(((....)-------))(((...((((..((((....))))..(((((((..((....))..)))))))))))..((((.....)))))))... ( -30.00)
>DroSec_CAF1 11011 113 + 1
UCGACAGUAAUUUAGAUUUCGUUUUGGGCUUUUG-------CCGGAUUUGCAUAAAAUAUCGUUAUUAGGCGCAGUUUAUUUUUAUUUGCUGCGCAUGCGCGACCAUUUUGGUCUCCAUU
..........................(((....)-------))(((...((((..((((....))))..(((((((..((....))..)))))))))))..((((.....)))))))... ( -30.00)
>DroSim_CAF1 11646 95 + 1
U------------------CGUUUUGGGCUUUUG-------CCGGAUUUGCAUAAAAUAUCGUUAUUAGGCGCAGUUUAUUUUUAUUUGCUGCGCAUGCGCGACCAUUUUGGUCUCCAUU
.------------------.......(((....)-------))(((...((((..((((....))))..(((((((..((....))..)))))))))))..((((.....)))))))... ( -30.00)
>DroEre_CAF1 12344 113 + 1
UCAACUGUGUUUUAGAUUUCGUUUUGGGCUUUUG-------CCGGAUUUGCAUAAAAUAUCGUUAUUAGGCGCAAUUUAUUUUUAUUUGCUGCGCAUGCGCGACCAUUUCGGUCUCCAGU
..(((.((((((((.....((..((.(((....)-------)).))..))..)))))))).)))....((.((((...........)))).(((....)))((((.....)))).))... ( -25.90)
>DroWil_CAF1 10229 102 + 1
U------------------UUUUUUUGGUUUUUGGUGGGGCCCAUAUUUGCAUAAAAUGUCACUAUUAAAAGCAAUUUAUUUUUAUUUGUUGCGCAUGCGCAGCCAUUUUGAAUUUCGUC
.------------------........((((((((((((((....((((.....))))))).)))))))))))...............((((((....))))))................ ( -20.20)
>DroYak_CAF1 12374 113 + 1
UCAACUGUAUUUUAGAUUUCGUUUUGGGCUUUUG-------CCGGAUUUGCAUAAAAUAUCGUUAUUAGCCGCAAUUUAUUUUUAUUUGCUGCGCAUGCGCGACCAUUUUGGUCUCCACU
..(((.((((((((.....((..((.(((....)-------)).))..))..)))))))).)))....((.((((...........)))).))((....))((((.....))))...... ( -25.90)
>consensus
U__________________CGUUUUGGGCUUUUG_______CCGGAUUUGCAUAAAAUAUCGUUAUUAGGCGCAAUUUAUUUUUAUUUGCUGCGCAUGCGCGACCAUUUUGGUCUCCAUU
........................((((.....................((((..((((....))))..(((((((..((....))..)))))))))))..((((.....)))))))).. (-17.11 = -17.58 +   0.47)

alignment

secondary structure

dotplot

Window 2

Location	356,836 – 356,931
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.89
Mean single sequence MFE	-21.24
Consensus MFE	-15.44
Energy contribution	-14.91
Covariance contribution	-0.52
Combinations/Pair	1.39
Mean z-score	-2.15
Structure conservation index	0.73
SVM decision value	1.17
SVM RNA-class probability	0.925246
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 356836 95 - 23771897
AAUGGAGACCAAAAUGGUCGCGCAUGCGCAGCAAAUAAAAAUAAACUGCGCCUAAUAACGAUAUUUUAUGCAAAUCCGG-------CAAAAGCCCAAAACG------------------A
...(((((((.....))))..((((((((((..............))))))..((((....))))..))))...)))((-------(....))).......------------------. ( -23.74)
>DroSec_CAF1 11011 113 - 1
AAUGGAGACCAAAAUGGUCGCGCAUGCGCAGCAAAUAAAAAUAAACUGCGCCUAAUAACGAUAUUUUAUGCAAAUCCGG-------CAAAAGCCCAAAACGAAAUCUAAAUUACUGUCGA
...(((((((.....))))..((((((((((..............))))))..((((....))))..))))...)))((-------(....))).......................... ( -23.74)
>DroSim_CAF1 11646 95 - 1
AAUGGAGACCAAAAUGGUCGCGCAUGCGCAGCAAAUAAAAAUAAACUGCGCCUAAUAACGAUAUUUUAUGCAAAUCCGG-------CAAAAGCCCAAAACG------------------A
...(((((((.....))))..((((((((((..............))))))..((((....))))..))))...)))((-------(....))).......------------------. ( -23.74)
>DroEre_CAF1 12344 113 - 1
ACUGGAGACCGAAAUGGUCGCGCAUGCGCAGCAAAUAAAAAUAAAUUGCGCCUAAUAACGAUAUUUUAUGCAAAUCCGG-------CAAAAGCCCAAAACGAAAUCUAAAACACAGUUGA
...(((((((.....))))..((((((((((..............))))))..((((....))))..))))...)))((-------(....))).......................... ( -20.54)
>DroWil_CAF1 10229 102 - 1
GACGAAAUUCAAAAUGGCUGCGCAUGCGCAACAAAUAAAAAUAAAUUGCUUUUAAUAGUGACAUUUUAUGCAAAUAUGGGCCCCACCAAAAACCAAAAAAA------------------A
..........(((((((.((((....)))).).............(..((......))..))))))).........(((......))).............------------------. ( -13.60)
>DroYak_CAF1 12374 113 - 1
AGUGGAGACCAAAAUGGUCGCGCAUGCGCAGCAAAUAAAAAUAAAUUGCGGCUAAUAACGAUAUUUUAUGCAAAUCCGG-------CAAAAGCCCAAAACGAAAUCUAAAAUACAGUUGA
...(((((((.....))))(((....)))................(((((...((((....))))...))))).)))((-------(....))).......................... ( -22.10)
>consensus
AAUGGAGACCAAAAUGGUCGCGCAUGCGCAGCAAAUAAAAAUAAACUGCGCCUAAUAACGAUAUUUUAUGCAAAUCCGG_______CAAAAGCCCAAAACG__________________A
..((((((((.....))))..((((((((((..............))))))................))))...)))).......................................... (-15.44 = -14.91 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:27 2006