Locus 8410

Sequence ID	3R_DroMel_CAF1
Location	22,406,084 – 22,406,224
Length	140
Max. P	0.971445

overview

Window 1

Location	22,406,084 – 22,406,184
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	65.40
Mean single sequence MFE	-38.73
Consensus MFE	-21.07
Energy contribution	-21.65
Covariance contribution	0.58
Combinations/Pair	1.19
Mean z-score	-1.29
Structure conservation index	0.54
SVM decision value	0.20
SVM RNA-class probability	0.631587
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22406084 100 - 27905053
UUAUAUUGGAGGUGGCAGCAGGUGGUGUGGGCGACGAGGCGCCAUGCACCAUGGCAGCAGCAGCUGCCAGGACAGAUGGGCCAGUUGGCUGU--UGU----GCAUC
............(((((((..((((((((((((......)))).)))))))).((....)).)))))))(.((((...((((....)))).)--)))----.)... ( -42.20)
>DroPse_CAF1 57566 79 - 1
U------------------GGUGGGUACGGGCGAUGGGGCGCCAUGCACCAGGGCAGCAGCAGCUGCCAGACCCGUCUGACUCGUUGGCUCC---------GCCUC
.------------------(((((((((((((((((((((.....)).....((((((....))))))...)))))).).)))))..)).))---------))).. ( -37.80)
>DroEre_CAF1 37884 100 - 1
UUGUAUUGGAGGUGGCAGCAGGAGGUGUGGGCGACGCAGCGCCGUGCACCAUGGCAGCAGCGGCUGCCAGAACCGAUUGGCCAGUUGGCUGC--UGU----GUGUC
..............(((((((..((((((((((......)))).)))))).(((((((....)))))))...((((((....))))))))))--)))----..... ( -43.70)
>DroWil_CAF1 40631 100 - 1
U--GAUUGGUGUCGGU----GUGGGUGUGGGAGAUGGUGUUCCAUGCACCAAGGCAGCAGCAACAGCCAAGCCGGAUUGGCUAGUUGGUUCUGGUGUGGUAGCAUC
(--(.(((.((((...----.(((((((((((.......)))))))).))).)))).)))))...((((.(((((((..(....)..).)))))).))))...... ( -34.90)
>DroAna_CAF1 43047 82 - 1
U---ACUCGUG------------GGCGUCGGUGAGGCGGCUCCGUGCACCAGGGCAGCAGCAGCUGCCAGGCCAGUUUGGCUCGUUGCC-----UGU----GCAUC
.---...((..------------((((.(((((..(((....))).))))..((((((....)))))).((((.....)))).).))))-----..)----).... ( -36.00)
>DroPer_CAF1 58364 79 - 1
U------------------GGUGGGUACGGGCGAUGGGGCGCCAUGCACCAGGGCAGCAGCAGCUGCCAGACCCGUCUGACUCGUUGGCUCC---------GCCUC
.------------------(((((((((((((((((((((.....)).....((((((....))))))...)))))).).)))))..)).))---------))).. ( -37.80)
>consensus
U___AUUGG_G_________GUGGGUGUGGGCGAUGGGGCGCCAUGCACCAGGGCAGCAGCAGCUGCCAGACCCGAUUGGCUAGUUGGCUCC__UGU____GCAUC
.......................((((((((((......)))).))))))..((((((....))))))...................................... (-21.07 = -21.65 +   0.58)

alignment

secondary structure

dotplot

Window 2

Location	22,406,113 – 22,406,224
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	71.10
Mean single sequence MFE	-34.17
Consensus MFE	-24.38
Energy contribution	-24.68
Covariance contribution	0.31
Combinations/Pair	1.15
Mean z-score	-1.56
Structure conservation index	0.71
SVM decision value	1.68
SVM RNA-class probability	0.971445
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22406113 111 + 27905053
CCUGGCAGCUGCUGCUGCCAUGGUGCAUGGCGCCUCGUCGCCCACACCACCUGCUGCCACCUCCAAUAUAACUCCCUUACCCACAGCCGCGGCAGUAGCAUCUGCUGAUUU
...(((((.((((((((((.(((((...((((......))))..)))))...((((...........................))))...)))))))))).)))))..... ( -42.23)
>DroPse_CAF1 57592 84 + 1
UCUGGCAGCUGCUGCUGCCCUGGUGCAUGGCGCCCCAUCGCCCGUACCCACC------------------AC------ACCUAC-GC--CGCCUGUGGCAGCCGCUGAGUU
.....((((.(((((..(...((((...((((......))))((((......------------------..------...)))-).--)))).)..))))).)))).... ( -30.40)
>DroSec_CAF1 39764 111 + 1
CCUGGCAGCUGCUGCUGCCAUGGUGCAUGGCGCCUCGUCGCCCACACCACCUGCUGCCACCUCCAAUACAACUCCCUUACCCACAGCCGCGCCAGUGGCAUCUGCUGAUUU
..(((((((.((....))..(((((...((((......))))..)))))...)))))))..........................(((((....)))))............ ( -34.70)
>DroEre_CAF1 37913 111 + 1
UCUGGCAGCCGCUGCUGCCAUGGUGCACGGCGCUGCGUCGCCCACACCUCCUGCUGCCACCUCCAAUACAACUCCAUUACCCACAGCCGCGCCAGUGGCAUCUGCUGAUUU
..(((((((.((....))...((((...((((......))))..))))....)))))))..........................(((((....)))))............ ( -33.40)
>DroAna_CAF1 43073 96 + 1
CCUGGCAGCUGCUGCUGCCCUGGUGCACGGAGCCGCCUCACCGACGCC------------CACGAGU---ACACCCAUUCCGACCCCCGUGCCAGUGGCAUCCGCGGACUU
...((((((....))))))..(((.(.(((((((((..(((.......------------...((((---......))))........)))...))))).)))).).))). ( -31.17)
>DroPer_CAF1 58390 84 + 1
UCUGGCAGCUGCUGCUGCCCUGGUGCAUGGCGCCCCAUCGCCCGUACCCACC------------------AC------ACCUAC-GC--CGCCUGCGGCAGCCGCUGACUU
...((((((.((((((((...((((...((((......))))((((......------------------..------...)))-).--)))).)))))))).)))).)). ( -33.10)
>consensus
CCUGGCAGCUGCUGCUGCCAUGGUGCAUGGCGCCCCGUCGCCCACACCACCU________CUCCAAU___ACUCCCUUACCCACAGCCGCGCCAGUGGCAUCCGCUGAUUU
...((((((....))))))..((((...((((......))))..))))...................................((((...((.....))....)))).... (-24.38 = -24.68 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	22,406,113 – 22,406,224
Length	111
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	71.10
Mean single sequence MFE	-42.20
Consensus MFE	-28.22
Energy contribution	-29.05
Covariance contribution	0.83
Combinations/Pair	1.17
Mean z-score	-1.33
Structure conservation index	0.67
SVM decision value	0.96
SVM RNA-class probability	0.890796
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22406113 111 - 27905053
AAAUCAGCAGAUGCUACUGCCGCGGCUGUGGGUAAGGGAGUUAUAUUGGAGGUGGCAGCAGGUGGUGUGGGCGACGAGGCGCCAUGCACCAUGGCAGCAGCAGCUGCCAGG
......((((.((((.(((((((.(((.(.((((.........)))).).))).)).....((((((((((((......)))).))))))))))))).)))).)))).... ( -46.00)
>DroPse_CAF1 57592 84 - 1
AACUCAGCGGCUGCCACAGGCG--GC-GUAGGU------GU------------------GGUGGGUACGGGCGAUGGGGCGCCAUGCACCAGGGCAGCAGCAGCUGCCAGA
.(((..(((.(((((...))))--))-)).)))------.(------------------((((.((...((((......)))))).))))).((((((....))))))... ( -36.00)
>DroSec_CAF1 39764 111 - 1
AAAUCAGCAGAUGCCACUGGCGCGGCUGUGGGUAAGGGAGUUGUAUUGGAGGUGGCAGCAGGUGGUGUGGGCGACGAGGCGCCAUGCACCAUGGCAGCAGCAGCUGCCAGG
......((...(((((((...((((((.(.......).))))))......)))))))))..((((((((((((......)))).))))))))((((((....))))))... ( -45.50)
>DroEre_CAF1 37913 111 - 1
AAAUCAGCAGAUGCCACUGGCGCGGCUGUGGGUAAUGGAGUUGUAUUGGAGGUGGCAGCAGGAGGUGUGGGCGACGCAGCGCCGUGCACCAUGGCAGCAGCGGCUGCCAGA
......((...(((((((...((((((.((.....)).))))))......)))))))))....((((((((((......)))).)))))).(((((((....))))))).. ( -44.80)
>DroAna_CAF1 43073 96 - 1
AAGUCCGCGGAUGCCACUGGCACGGGGGUCGGAAUGGGUGU---ACUCGUG------------GGCGUCGGUGAGGCGGCUCCGUGCACCAGGGCAGCAGCAGCUGCCAGG
..((.((((((.(((.((..(((.((.(((...(((((...---.))))).------------))).)).))).)).))))))))).))...((((((....))))))... ( -44.90)
>DroPer_CAF1 58390 84 - 1
AAGUCAGCGGCUGCCGCAGGCG--GC-GUAGGU------GU------------------GGUGGGUACGGGCGAUGGGGCGCCAUGCACCAGGGCAGCAGCAGCUGCCAGA
......((((...)))).((((--((-((.(.(------((------------------..((((((..((((......)))).))).)))..))).).)).))))))... ( -36.00)
>consensus
AAAUCAGCAGAUGCCACUGGCGCGGCUGUGGGUAAGGGAGU___AUUGGAG________AGGGGGUGUGGGCGACGAGGCGCCAUGCACCAGGGCAGCAGCAGCUGCCAGA
....((((...((((...))))..))))...................................((((((((((......)))).))))))..((((((....))))))... (-28.22 = -29.05 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:49 2006