Locus 6121

Sequence ID	3R_DroMel_CAF1
Location	16,046,832 – 16,046,941
Length	109
Max. P	0.716146

overview

Window 8

Location	16,046,832 – 16,046,941
Length	109
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	87.81
Mean single sequence MFE	-35.40
Consensus MFE	-26.75
Energy contribution	-28.75
Covariance contribution	2.00
Combinations/Pair	1.12
Mean z-score	-1.72
Structure conservation index	0.76
SVM decision value	0.39
SVM RNA-class probability	0.716146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16046832 109 + 27905053
UUAAAUUGCAAAGUUGGCAUUUUGAGGGGCAGAGUGGAUGGAAUGAGCUAGGAGCUAUGUA------UCCACAUUUCCCAUCAUCCCAUUCUGGCCCUGGCAUGACAUUUCCAUU
.((((.(((.......))).))))((((.((((((((((((...(((...(((........------)))....)))...)))).)))))))).))))................. ( -29.90)
>DroSec_CAF1 4324 115 + 1
UUAAAUUGCAAAGUUGGCAUUUUGAGGGGCAGAGUGGGUGGAAUGAGCUAGGAGCUGUGUAUCCGUAUCCACAUCUCCCAUCAUCCCAUUCUGGCCCUGGCAUGACAUUUCCAUU
.((((.(((.......))).))))((((.(((((((((....((((....((((.((((..........)))).))))..))))))))))))).))))................. ( -38.30)
>DroSim_CAF1 4397 115 + 1
UUAAAUUGCAAAGUUGGCAUUUUGAGGGGCAGAGUGGGUGGAAUGAGCUAGGAGCUGUGUAUCCGUAUCCACAUCUCCCAUCAUCCCAUUCUGGCCCUGGCAUGACAUUUCCAUU
.((((.(((.......))).))))((((.(((((((((....((((....((((.((((..........)))).))))..))))))))))))).))))................. ( -38.30)
>DroYak_CAF1 11815 104 + 1
UUAAAUUGCAAAGUUGGCAUUUUGGGGAGGGGAGUGGGUGGAAUGGGCUAGGGGCU------CCGUAUCCACAUCU-----CAACCCAUUCUGUCCCUGGCAUGACAUUUUCAUU
......((.(((((...(((.(..((((.((.((((((((..(((((.((.((...------)).)).)).)))..-----).))))))))).))))..).)))..))))))).. ( -35.10)
>consensus
UUAAAUUGCAAAGUUGGCAUUUUGAGGGGCAGAGUGGGUGGAAUGAGCUAGGAGCUGUGUA_CCGUAUCCACAUCUCCCAUCAUCCCAUUCUGGCCCUGGCAUGACAUUUCCAUU
.((((.(((.......))).))))((((.(((((((((....((((....((((.((((..........)))).))))..))))))))))))).))))................. (-26.75 = -28.75 +   2.00)

alignment

secondary structure

dotplot

Window 9

Location	16,046,832 – 16,046,941
Length	109
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	87.81
Mean single sequence MFE	-32.12
Consensus MFE	-21.85
Energy contribution	-24.85
Covariance contribution	3.00
Combinations/Pair	1.08
Mean z-score	-2.03
Structure conservation index	0.68
SVM decision value	0.37
SVM RNA-class probability	0.707149
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16046832 109 - 27905053
AAUGGAAAUGUCAUGCCAGGGCCAGAAUGGGAUGAUGGGAAAUGUGGA------UACAUAGCUCCUAGCUCAUUCCAUCCACUCUGCCCCUCAAAAUGCCAACUUUGCAAUUUAA
..((.(((((.(((...((((.((((((((((((((((((..((((..------..))))..)))))..)))))))))....)))).))))....))).))..))).))...... ( -33.70)
>DroSec_CAF1 4324 115 - 1
AAUGGAAAUGUCAUGCCAGGGCCAGAAUGGGAUGAUGGGAGAUGUGGAUACGGAUACACAGCUCCUAGCUCAUUCCACCCACUCUGCCCCUCAAAAUGCCAACUUUGCAAUUUAA
..((.(((((.(((...((((.((((.((((((((((((((.((((..........)))).))))))..))))....)))).)))).))))....))).))..))).))...... ( -35.30)
>DroSim_CAF1 4397 115 - 1
AAUGGAAAUGUCAUGCCAGGGCCAGAAUGGGAUGAUGGGAGAUGUGGAUACGGAUACACAGCUCCUAGCUCAUUCCACCCACUCUGCCCCUCAAAAUGCCAACUUUGCAAUUUAA
..((.(((((.(((...((((.((((.((((((((((((((.((((..........)))).))))))..))))....)))).)))).))))....))).))..))).))...... ( -35.30)
>DroYak_CAF1 11815 104 - 1
AAUGAAAAUGUCAUGCCAGGGACAGAAUGGGUUG-----AGAUGUGGAUACGG------AGCCCCUAGCCCAUUCCACCCACUCCCCUCCCCAAAAUGCCAACUUUGCAAUUUAA
........((.(((....((((..((.(((((.(-----..(((.((.((.((------....)))).)))))..)))))).))...))))....))).)).............. ( -24.20)
>consensus
AAUGGAAAUGUCAUGCCAGGGCCAGAAUGGGAUGAUGGGAGAUGUGGAUACGG_UACACAGCUCCUAGCUCAUUCCACCCACUCUGCCCCUCAAAAUGCCAACUUUGCAAUUUAA
..((.(((((.(((...((((.((((.((((((((((((((.((((..........)))).))))))..))))....)))).)))).))))....))).))..))).))...... (-21.85 = -24.85 +   3.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:12 2006