Locus 437

Sequence ID	3R_DroMel_CAF1
Location	1,642,491 – 1,642,602
Length	111
Max. P	0.942280

overview

Window 1

Location	1,642,491 – 1,642,602
Length	111
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	72.05
Mean single sequence MFE	-41.94
Consensus MFE	-21.86
Energy contribution	-22.74
Covariance contribution	0.88
Combinations/Pair	1.20
Mean z-score	-1.99
Structure conservation index	0.52
SVM decision value	1.32
SVM RNA-class probability	0.942280
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1642491 111 + 27905053
CACGUCCACAUCCACACCCACACCCGCACCCACACCAAUAUCCCUGCCCGCGACCCGUUCCC--------GGGCACAGGAUAGGGUUUCUUUCGCCCAGGCGGGUCGGGUGGCUAGGAG
..........(((.(((((..((((((...........(((((.((((((.((.....)).)--------)))))..)))))((((.......))))..)))))).)))))....))). ( -45.60)
>DroSim_CAF1 21900 93 + 1
CACGUCCAC------------------ACCCACACCAAUAUCCCUGCCCGCGACCCGUUCCC--------GGGCACAGGAUAGGGUUUCCUUCGCCCAGGCGGGUCGGGUGGCUAGGGG
.........------------------..............((((((((.(((((((..((.--------((((..((((.......))))..)))).))))))))).).))).)))). ( -43.00)
>DroEre_CAF1 22853 99 + 1
C------ACGCCCACACCCA------UGCCCACACCAAUGUCCCUUUCCUCGACCCGUUCCC--------GGGAACAGGAUAGGGUUUCCUUCGCACAGGCGGGUCGGGUGACUAGGGG
.------...(((.(((((.------.((((..........((((.((((...((((....)--------)))...)))).))))........((....)))))).)))))....))). ( -37.80)
>DroYak_CAF1 20122 105 + 1
CACUUCCACGUCCACACCCA------CACCCACACCAAUCGCCCCUUCCUCCACCCGUUUCC--------GCGAACAGGAUAGGGUUUCCUUCGCACAGGCGGGUCGGGUGGCUAGGGG
....................------...............(((((.(((((((((((((..--------((((..((((.......))))))))..)))))))).))).))..))))) ( -34.60)
>DroAna_CAF1 22044 111 + 1
CACGCCCACACCCACUCGCAC-----CACCCAUUCCACAGGCUA---CUUUGCCCCGGCCCCAACGAGGGGGCGACCGGACAAAGUUUCCUUCGCCCAGGCGGGUCGAGUGGCGAGGGG
....(((....(((((((.((-----(...........(((..(---(((((((.((.((((.....)))).))...)).))))))..))).(((....)))))))))))))....))) ( -48.70)
>consensus
CACGUCCACACCCACACCCA______CACCCACACCAAUAUCCCUGCCCUCGACCCGUUCCC________GGGAACAGGAUAGGGUUUCCUUCGCCCAGGCGGGUCGGGUGGCUAGGGG
............................(((...(((..........((.((((((((((((........)))))).(((.......)))...((....)))))))))))))...))). (-21.86 = -22.74 +   0.88)

alignment

secondary structure

dotplot

Window 2

Location	1,642,491 – 1,642,602
Length	111
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	72.05
Mean single sequence MFE	-49.66
Consensus MFE	-23.08
Energy contribution	-24.00
Covariance contribution	0.92
Combinations/Pair	1.24
Mean z-score	-1.82
Structure conservation index	0.46
SVM decision value	0.55
SVM RNA-class probability	0.778498
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1642491 111 - 27905053
CUCCUAGCCACCCGACCCGCCUGGGCGAAAGAAACCCUAUCCUGUGCCC--------GGGAACGGGUCGCGGGCAGGGAUAUUGGUGUGGGUGCGGGUGUGGGUGUGGAUGUGGACGUG
.(((((.((((((((((((((..(.(....)...((((..(((((((((--------(....)))).)))))).))))...)..).)))))).)))))..)).)).))).......... ( -53.50)
>DroSim_CAF1 21900 93 - 1
CCCCUAGCCACCCGACCCGCCUGGGCGAAGGAAACCCUAUCCUGUGCCC--------GGGAACGGGUCGCGGGCAGGGAUAUUGGUGUGGGU------------------GUGGACGUG
.((((.(((.(.(((((((((((((((.((((.......)))).)))))--------)))..))))))).))))))))..............------------------......... ( -46.00)
>DroEre_CAF1 22853 99 - 1
CCCCUAGUCACCCGACCCGCCUGUGCGAAGGAAACCCUAUCCUGUUCCC--------GGGAACGGGUCGAGGAAAGGGACAUUGGUGUGGGCA------UGGGUGUGGGCGU------G
.(((....((((((.((((((.((((....)...((((.((((...(((--------(....))))...)))).)))).))).)))).))...------)))))).)))...------. ( -45.60)
>DroYak_CAF1 20122 105 - 1
CCCCUAGCCACCCGACCCGCCUGUGCGAAGGAAACCCUAUCCUGUUCGC--------GGAAACGGGUGGAGGAAGGGGCGAUUGGUGUGGGUG------UGGGUGUGGACGUGGAAGUG
..((...((((((.((..(((((..(.((.....((((.((((.(.(.(--------(....)).).).))))))))....)).)..))))))------).)).))))....))..... ( -42.50)
>DroAna_CAF1 22044 111 - 1
CCCCUCGCCACUCGACCCGCCUGGGCGAAGGAAACUUUGUCCGGUCGCCCCCUCGUUGGGGCCGGGGCAAAG---UAGCCUGUGGAAUGGGUG-----GUGCGAGUGGGUGUGGGCGUG
.(((.(((((((((..(((((((..(.((((..(((((((((.(..(((((......)))))).))))))))---)..))).).)..))))))-----)..))))).)))).))).... ( -60.70)
>consensus
CCCCUAGCCACCCGACCCGCCUGGGCGAAGGAAACCCUAUCCUGUGCCC________GGGAACGGGUCGAGGAAAGGGACAUUGGUGUGGGUG______UGGGUGUGGACGUGGACGUG
.(((..(((((((....(((....)))........(((..(((((((((........)))))))))...)))...)))....))))..)))............................ (-23.08 = -24.00 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:10 2006