Locus 6916

Sequence ID	3R_DroMel_CAF1
Location	18,260,479 – 18,260,640
Length	161
Max. P	0.921133

overview

Window 2

Location	18,260,479 – 18,260,569
Length	90
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	72.30
Mean single sequence MFE	-27.83
Consensus MFE	-13.08
Energy contribution	-13.05
Covariance contribution	-0.03
Combinations/Pair	1.17
Mean z-score	-2.03
Structure conservation index	0.47
SVM decision value	1.14
SVM RNA-class probability	0.921133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18260479 90 + 27905053
UUGGCUAAUUUUGGGCUGGAGAAAUCAGCGGC-------CGGCAAGGAAGUCAACGUUU---------------UUUUUU---UUUUUUGCCAACGCAAACA--GAAAUGUGAAA--AA
...((........(((((((....))..))))-------)((((((((((.........---------------.....)---)))))))))...))..(((--....)))....--.. ( -23.14)
>DroPse_CAF1 20687 105 + 1
AUGGCUAAUUUUGGGCUGGUGAAAUCUGCAGGCAGAAAUUGGCAAGGAAGCUGCCGAGCUG--------CAGAG-CUUCU---UUUUUCGCCAAGGCAAACUAGUAAAAGCGAAA--AA
...(((((((((.(.(((..(....)..))).).)))))))))(((((((((((......)--------)..))-)))))---))((((((....((......))....))))))--.. ( -30.90)
>DroSec_CAF1 16504 84 + 1
UUGGCUAAUUUUGGGCUGGAGAAAUCAGCGGC-------CGGCAAGGAAGCCAUCGUUU---------------U---------UUUUUGCCAACGCAAACA--GAAAUGUGUAA--AA
.(((((..((((.(((((((....))..))))-------).).)))..))))).(((((---------------(---------(.(((((....))))).)--)))))).....--.. ( -25.10)
>DroEre_CAF1 17075 87 + 1
UUGGCUAAUUUUGGGCUGGAGAAAUCAGCGGC-------CGGCAAGGAAGCCUCCGUAU---------------UUUUU--------UUGCCAACGCAAACA--GAAAUGUGAAAAAAA
..((((..((((.(((((((....))..))))-------).).)))..))))..(((((---------------(((((--------((((....))))).)--))))))))....... ( -22.80)
>DroYak_CAF1 16814 93 + 1
UUGGCUAAUUUUGGGCUGGAGAAAUCAGCGGC-------CGGCAAGGAAGCCUCUGUUU---------------UUUUUUUGCUUUUUUGCCAACGCAAACA--GAAAUGUGAAA--AA
...((........(((((((....))..))))-------)(((((((((((........---------------.......)))))))))))...))..(((--....)))....--.. ( -27.66)
>DroPer_CAF1 20894 113 + 1
AUGGCUAAUUUUGGGCUGGUGAAAUCUGCAGGCAGAAAUUGGCAAGGAAGCUGCCGAGCUGCAGAGCUGCAGAG-CUUCU---UUUUUCGCCAAGGCAAACUAGUAAAAGCGAAA--AA
..((((.......))))...(((.(((((((((((...((((((.(....))))))).))))....))))))).-.))).---((((((((....((......))....))))))--)) ( -37.40)
>consensus
UUGGCUAAUUUUGGGCUGGAGAAAUCAGCGGC_______CGGCAAGGAAGCCACCGUUU_______________UUUUUU___UUUUUUGCCAACGCAAACA__GAAAUGUGAAA__AA
.((((.........(((((.....)))))...........(((......))).....................................)))).......................... (-13.08 = -13.05 +  -0.03)

alignment

secondary structure

dotplot

Window 3

Location	18,260,536 – 18,260,640
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.25
Mean single sequence MFE	-18.95
Consensus MFE	-16.34
Energy contribution	-15.98
Covariance contribution	-0.36
Combinations/Pair	1.17
Mean z-score	-1.50
Structure conservation index	0.86
SVM decision value	0.09
SVM RNA-class probability	0.576543
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18260536 104 - 27905053
AAAUUUCACUUUUCACCAUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCGUU--------UUC-CUUUU--UUUCACAUUUC--UGUUUGCGUUGGCAAAAAA---A
.........((((..(((.((((.....(((((.(((((((.......)))).))).)))))...--------...-.....--....(((....--))).)))).)))..)))).---. ( -17.30)
>DroPse_CAF1 20757 115 - 1
AAAUUUCACUUUUCACCAUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCGUUACUUUUCUCUCUCCUUU--UUUCGCUUUUACUAGUUUGCCUUGGCGAAAAA---A
.........(((((.(((..(((.....(((((.(((((((.......)))).))).)))))....................--....(((......))).)))..))).))))).---. ( -21.80)
>DroEre_CAF1 17132 101 - 1
AAAUUUCACUUUUCACCAUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCGUU--------UUC-CUUUUUUUUUCACAUUUC--UGUUUGCGUUGGCAA--------
...............(((.((((.....(((((.(((((((.......)))).))).)))))...--------...-...........(((....--))).)))).)))...-------- ( -16.50)
>DroYak_CAF1 16871 107 - 1
AAAUUUCACUUUUCACCAUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCGUU--------UUC-CUUUU--UUUCACAUUUC--UGUUUGCGUUGGCAAAAAAGCAA
........(((((..(((.((((.....(((((.(((((((.......)))).))).)))))...--------...-.....--....(((....--))).)))).)))...)))))... ( -18.30)
>DroAna_CAF1 17128 105 - 1
AAAUUUCACUUUUCACCGUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCACU--------CGCACUUUU--UUUCGCUUUUC--UGUUUGCGUUGGCAAAAAU---A
.........((((..(((.((((....((((((.(((((((.......)))).))).))))))..--------.((......--....)).....--....)))).)))..)))).---. ( -18.00)
>DroPer_CAF1 20972 115 - 1
AAAUUUCACUUUUCACCAUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCGUUACUUUUCUCUCUCCUUU--UUUCGCUUUUACUAGUUUGCCUUGGCGAAAAA---A
.........(((((.(((..(((.....(((((.(((((((.......)))).))).)))))....................--....(((......))).)))..))).))))).---. ( -21.80)
>consensus
AAAUUUCACUUUUCACCAUUGCAUAAUUGCAGUUUGACAAUGCUUAAAAUUGAUUAUGCUGCGUU________CUC_CUUUU__UUUCACAUUUC__UGUUUGCGUUGGCAAAAAA___A
...............(((.((((....((((((.(((((((.......)))).))).)))))).........................(((......))).)))).)))........... (-16.34 = -15.98 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:11 2006