Locus 4980

Sequence ID	2R_DroMel_CAF1
Location	16,233,987 – 16,234,155
Length	168
Max. P	0.895611

overview

Window 3

Location	16,233,987 – 16,234,086
Length	99
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	81.06
Mean single sequence MFE	-27.97
Consensus MFE	-14.64
Energy contribution	-13.96
Covariance contribution	-0.68
Combinations/Pair	1.24
Mean z-score	-1.96
Structure conservation index	0.52
SVM decision value	0.00
SVM RNA-class probability	0.535521
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16233987 99 - 20766785
CAGCCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUGGUUAUUUCUCUAAUUUGUCCUUUAAAUUGAUCACAAUAA--GUUGUUGCGCUAAUGU----------------AAAAAUU
.(((((((((((((((....).))))....)))))))))).......(((((((.....))))))).........(--(((.(((((....)))----------------)).)))) ( -21.90)
>DroSec_CAF1 14680 117 - 1
CAGUCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUGGUUAUUUCUCUCAUUUGUGCUUUAAAUUGAUCACAAUGAGAGUUGUUGCACAAAUGAAACACAAUAAUGUGUAACAAAUU
.(..((((((((((((....).))))....)))))))..)....((((((((.(((.((......)).)))))))))))((((((((((...............))))))))))... ( -36.46)
>DroSim_CAF1 14987 114 - 1
CAGUCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUGGUUAUUUCUCUCAUUUGUGCUUUAAAUUGAUCACAAUGAGAGCUGUUGCACAAAUGAAACACAAUAUUGU---ACAAAUU
.........(((((.(....).((((((((((((.........))(((((((.(((.((......)).))))))))))))))))))))................)))---))..... ( -28.20)
>DroEre_CAF1 19641 112 - 1
CAGUCAGUCGUGCACACGAGCACUGUAGUAGUGAUUGGUUAUUCCUCUAAUUUGUGCUUUAAAUUGGUCACAAUGA--GUUGUUGCACUGAUGGUACACAAUAUUGU---AUAAAUA
..((((((.((((......))))....((((..(((.(((......((((((((.....))))))))....))).)--))..)))))))))).(((((......)))---))..... ( -26.80)
>DroYak_CAF1 26347 112 - 1
CAGUCAGUCGUGCACAGGAACACUGUAGUACCGAUUGGUUUUUCCCUUAAUUUGUGUUUCAAUUUGAUCACAAUGU--GUUGUUGCACUGAUGAAACAUAAUAAUCU---ACAAAUU
.(..(((((((((((((.....)))).))).))))))..)...........((((((((((..(((....))).((--((....))))...))))))))))......---....... ( -26.50)
>consensus
CAGUCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUGGUUAUUUCUCUAAUUUGUGCUUUAAAUUGAUCACAAUGA__GUUGUUGCACUAAUGAAACACAAUAAUGU___ACAAAUU
.(((((((((((((((.......))).))).))))))))).........(((.((((..(((((((....)))).....)))..)))).)))......................... (-14.64 = -13.96 +  -0.68)

alignment

secondary structure

dotplot

Window 4

Location	16,234,049 – 16,234,155
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-33.25
Consensus MFE	-26.38
Energy contribution	-26.14
Covariance contribution	-0.24
Combinations/Pair	1.16
Mean z-score	-1.98
Structure conservation index	0.79
SVM decision value	0.99
SVM RNA-class probability	0.895611
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16234049 106 - 20766785
ACUCGUUGCGGCAGUGUCCUGUCAUAAUUUAACACAUUUUAUUGGCCGUUUUCGCUUGGUCGAUAAGACCAGCCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUG
..((((((((((.((((..............)))).((((((((((((........))))))))))))...))).....((((((....).))))))))))))... ( -35.74)
>DroSec_CAF1 14760 106 - 1
ACUCGUUGCGGCAGUGUCCUGUCAUAAUUUAACACAUUUUAUUAGCCGUUUUCGCUUGGUCGAUAAGACCAGUCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUG
..((((((((((((....)))))........((((.........((((.....(((.((((.....)))))))....)).))..(....).)))).)))))))... ( -32.30)
>DroSim_CAF1 15064 106 - 1
ACUCGUUGCGCCAGUGUCCUGUCAUAAUUUAACACAUUUUAUUAGCCGUUUUCGCUUGGUCGAUAAGACCAGUCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUG
..(((((((..((.(((.(((((((.............((((..((((........))))..))))(((......)))))).))))..))).))..)))))))... ( -27.90)
>DroEre_CAF1 19716 106 - 1
ACUCGCUGCGGCAGUGUCCUGUCAUAAUUUAACACAUUUUAUUAGCCGCUUUCGCCUGGUCGAUAAGACCAGUCAGUCGUGCACACGAGCACUGUAGUAGUGAUUG
..(((((((.((((((..((((((..(((..................((....))((((((.....))))))..)))..)).))).)..)))))).)))))))... ( -34.60)
>DroYak_CAF1 26422 106 - 1
ACUCGUUGCGGCAGUGUCCUGUCAUAAUUUAACACAUUUUAUUAGCCGCUCUCGCUUGGCCGAUAAGACCAGUCAGUCGUGCACAGGAACACUGUAGUACCGAUUG
..(((.(((.(((((((((((((((.............((((..(((((....))..)))..))))(((......)))))).))))).))))))).))).)))... ( -35.70)
>consensus
ACUCGUUGCGGCAGUGUCCUGUCAUAAUUUAACACAUUUUAUUAGCCGUUUUCGCUUGGUCGAUAAGACCAGUCAGUCGUGCACGGAAACAGUGUAGUAGCGAUUG
..(((((((.(((.(((.(((((((.............((((..((((........))))..))))(((......)))))).))))..))).))).)))))))... (-26.38 = -26.14 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:40 2006