Locus 5600

Sequence ID	3R_DroMel_CAF1
Location	14,784,169 – 14,784,365
Length	196
Max. P	0.993171

overview

Window 5

Location	14,784,169 – 14,784,289
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.17
Mean single sequence MFE	-46.12
Consensus MFE	-45.13
Energy contribution	-45.27
Covariance contribution	0.14
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.98
SVM decision value	2.38
SVM RNA-class probability	0.993171
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14784169 120 + 27905053
GGCCGUGGCCAUAUGCUGCAUCCUCGUCCUGCUGGCCGUCUUCAUCGUGAUCAUCAUAGUGGUCGGCCAGACCAUCGAGGAGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUU
.((((.((((....((((..((((((.....(((((((...((((..((.....))..)))).))))))).....))))))........(((.....)))))))..)).))))))..... ( -48.60)
>DroPse_CAF1 40319 120 + 1
GGCUGUGGCCAUCUGCUGCAUCCUCGUCCUGCUGGCGGUGUUCAUCGUGAUCAUCAUUGUGGUCGGCCAGACCAUCGAGGAGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUU
(((....)))...((((...((((((.....(((((.(...((((.(((.....))).)))).).))))).....)))))).((((..((.((.....))))..))))....)))).... ( -41.70)
>DroSec_CAF1 42485 120 + 1
GGCCGUGGCCAUAUGCUGCAUCCUCGUCCUGCUGGCCGUCUUCAUCGUGAUCAUCAUAGUGGUCGGCCAGACCAUCGAGGAGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUU
.((((.((((....((((..((((((.....(((((((...((((..((.....))..)))).))))))).....))))))........(((.....)))))))..)).))))))..... ( -48.60)
>DroSim_CAF1 44483 120 + 1
GGCCGUGGCCAUAUGCUGCAUCCUCGUCCUGCUGGCCGUCUUCAUCGUGAUCAUCAUAGUGGUCGGCCAGACCAUCGAGGAGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUU
.((((.((((....((((..((((((.....(((((((...((((..((.....))..)))).))))))).....))))))........(((.....)))))))..)).))))))..... ( -48.60)
>DroAna_CAF1 44965 120 + 1
GGCCGUGGCCAUUUGCUGCAUCCUCGUCCUGCUGGCCGUCUUCAUUGUGAUCAUCAUUGUGGUGGGCCAGACGAUCGAGGAGCCCAAGUGAGACAUGCUCCAGCUGGGACCUGGCAACUU
.((((.((((....(((((.((((((((...((((((....((((.(((.....))).))))..))))))..)).))))))))....(.(((.....)))))))..)).))))))..... ( -45.30)
>DroPer_CAF1 40449 120 + 1
GGCUGUGGCCAUCUGCUGCAUCCUCGUCCUGCUGGCGGUGUUCAUCGUGAUCAUCAUUGUGGUCGGCCAGACCAUCGAGGAGCCCAAAUGAGACAUGCUCCAGCUGGGACCCGGCAACUU
.((((.((((....((((..((((((.....(((((.(...((((.(((.....))).)))).).))))).....))))))........(((.....)))))))..)).))))))..... ( -43.90)
>consensus
GGCCGUGGCCAUAUGCUGCAUCCUCGUCCUGCUGGCCGUCUUCAUCGUGAUCAUCAUAGUGGUCGGCCAGACCAUCGAGGAGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUU
.((((.((((....((((..((((((.....(((((((...((((.(((.....))).)))).))))))).....))))))........(((.....)))))))..)).))))))..... (-45.13 = -45.27 +   0.14)

alignment

secondary structure

dotplot

Window 6

Location	14,784,249 – 14,784,365
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.91
Mean single sequence MFE	-32.02
Consensus MFE	-19.27
Energy contribution	-19.13
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.61
Structure conservation index	0.60
SVM decision value	0.08
SVM RNA-class probability	0.573027
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14784249 116 + 27905053
AGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUUCCCAGAUGGAUAACAGAGGCCCCCACAAAAUUGUUAGUUUGUUGGGGCCGCCAGCAAAAAUU----UCGUUGCCACCUCA
.((...(((((((..(((((((.((((((...(....).)))))).)))).......((((((.(((((........))))).))))))....)))....))----)))))))....... ( -41.50)
>DroPse_CAF1 40399 96 + 1
AGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUUCCCAGAUGGAUAACAGAGGCCCU---UCAAUUGUUAGUC---------AAUCAGCA-----U----U---CGCACCCGCA
.((........(((....((((.((((((...(....).)))))).))))((((((((....)---))...))))))))---------.....((.-----.----.---.))....)). ( -25.40)
>DroSec_CAF1 42565 116 + 1
AGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUUCCCAGAUGGAUAACAGAGGCCCCCACAAAAUUGUUAGAUUGCUGGGGCCGCCAGCAAAAAUU----UCGUUGCCACCUCA
.((...(((((((..(((((((.((((((...(....).)))))).)))).......((((((..(((..........)))..))))))....)))....))----)))))))....... ( -37.40)
>DroSim_CAF1 44563 116 + 1
AGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUUCCCAGAUGGAUAACAGAGGCCCCCACAAAAUUGUUAGUUUGCUGGGGCCGCCAGCAAAAAUU----UCGUUGCCACCUCA
.((...(((((((..(((((((.((((((...(....).)))))).)))).......((((((..((((........))))..))))))....)))....))----)))))))....... ( -39.20)
>DroAna_CAF1 45045 108 + 1
AGCCCAAGUGAGACAUGCUCCAGCUGGGACCUGGCAACUUCCCAGAUGGAUAACAGAGGCCU---CAAAAUUGUUAGUU-------GCCGCCACCCCCAAUCCCAAUCAUUAUGACCU--
....(((((((.......((((.((((((...(....).)))))).)))).......(((..---(((.........))-------)..)))..............))))).))....-- ( -23.90)
>DroPer_CAF1 40529 96 + 1
AGCCCAAAUGAGACAUGCUCCAGCUGGGACCCGGCAACUUCCCAGAUGGAUAACAGAGGCCCU---UCAAUUGUUAGUC---------AGUCAGCA-----U----U---CGCACCCGCA
.((........(((....((((.((((((...(....).)))))).))))((((((((....)---))...))))))))---------.....((.-----.----.---.))....)). ( -24.70)
>consensus
AGCCCAAAUGAGACAUGCUCCAGCUGGGACCUGGCAACUUCCCAGAUGGAUAACAGAGGCCCC__CAAAAUUGUUAGUU_______GCCGCCAGCAAAAAUU____UCGUUGCCACCUCA
.((((..(((...)))..((((.((((((...(....).)))))).)))).....).)))............................................................ (-19.27 = -19.13 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:04 2006