Locus 9276

Sequence ID	3R_DroMel_CAF1
Location	24,733,923 – 24,734,040
Length	117
Max. P	0.991115

overview

Window 2

Location	24,733,923 – 24,734,040
Length	117
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	68.39
Mean single sequence MFE	-43.03
Consensus MFE	-14.42
Energy contribution	-15.15
Covariance contribution	0.73
Combinations/Pair	1.45
Mean z-score	-2.71
Structure conservation index	0.34
SVM decision value	2.25
SVM RNA-class probability	0.991115
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24733923 117 + 27905053
AGUAGACCUGUUGCUGUGACUGCUGCUCCACCUCCAUCCACCUCGAACGAAAUCAGUUUGGACAAGUUGCUGCAACAGCAGCAGGAGCUAGAGGAGAAAUCCGCGGCAGCCACAAAC
(((((.....)))))(((.(((((((((...((((.......((((((.......))))))......((((((....))))))))))...))(((....)))))))))).))).... ( -42.60)
>DroVir_CAF1 19067 98 + 1
AG----CCGUGUGCAGGCGGCAAAAAU---------------GCUGGGGAAAUCGAUUUGGACAAGCUGCUGCAACAACAGCAACAGCUGGAGGAGAAGUCGGCCGCGGCCACCAGC
.(----((((......)))))......---------------(((((.......(((((...(.(((((.(((.......))).)))))...)...)))))(((....))).))))) ( -35.60)
>DroPse_CAF1 8911 104 + 1
AG----CCGCUUCCUGCUGCUGCUGUUG------CAG---CCUCUGCGGAGAUCAGUCUGGACAAGCUCCUCCAGCAGCAGCAGGAGCUGCAGGAAAAGUCGGCGGCGGCCACGAAC
.(----(((((((((((((((((((..(------(((---...))))((((....((....))...))))..))))))))))))))(((((.......).))))))))))....... ( -53.50)
>DroWil_CAF1 6809 102 + 1
AGCAAACCCGGUGCAGCAUCUGGUGCC---------------CCUGGUGAGAUCAAUCUGGAUAAGCUGUUGCAGCAGCAACAAGAGCUGGAAGAGAAGUCUGCAGCUGCCACGAAU
.....(((.((.(((.(....).))).---------------)).)))........(((((....(((((....)))))......(((((..(((....))).))))).))).)).. ( -29.30)
>DroYak_CAF1 7384 117 + 1
AGUAAACCCGUUGCUGCUGCUGCUGCUUCACUUCCGUCCACCUCAAACGAAAUCAGUUUGGACAAGUUGCUGCAACAGCAGCAGGAGCUGGAGGAGAAAUCCGCGGCAGCCACGAAC
........(((.((((((((......((((.(((((((((.....(((.......))))))))....((((((....)))))))))).))))(((....))))))))))).)))... ( -47.90)
>DroPer_CAF1 8975 104 + 1
AG----CCGCUUCCUGCUGCUGCUUCUG------CGU---CCUCUACGGAGAUCAGUCUGGACAAGCUCCUCCAGCAGCAGCAGGAGCUGCAGGAAAAGUCGGCGGCGGCCACGAAC
.(----(((((((((((((((((..(((------.((---(.((....))))))))..((((........))))))))))))))))(((((.......).))))))))))....... ( -49.30)
>consensus
AG____CCGGUUGCUGCUGCUGCUGCU_______C_U___CCUCUAAGGAAAUCAGUCUGGACAAGCUGCUGCAACAGCAGCAGGAGCUGGAGGAGAAGUCGGCGGCGGCCACGAAC
...............((((((((.........................(....)..(((.....((((.((((.......)))).))))...))).......))))))))....... (-14.42 = -15.15 +   0.73)

alignment

secondary structure

dotplot

Window 3

Location	24,733,923 – 24,734,040
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	68.39
Mean single sequence MFE	-42.85
Consensus MFE	-12.18
Energy contribution	-13.38
Covariance contribution	1.20
Combinations/Pair	1.55
Mean z-score	-2.14
Structure conservation index	0.28
SVM decision value	0.56
SVM RNA-class probability	0.780547
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24733923 117 - 27905053
GUUUGUGGCUGCCGCGGAUUUCUCCUCUAGCUCCUGCUGCUGUUGCAGCAACUUGUCCAAACUGAUUUCGUUCGAGGUGGAUGGAGGUGGAGCAGCAGUCACAGCAACAGGUCUACU
(((.((((((((.(((((....)))((((.((((((((((....))))))....(((((...(((......)))...))))))))).)))))).)))))))))))............ ( -49.20)
>DroVir_CAF1 19067 98 - 1
GCUGGUGGCCGCGGCCGACUUCUCCUCCAGCUGUUGCUGUUGUUGCAGCAGCUUGUCCAAAUCGAUUUCCCCAGC---------------AUUUUUGCCGCCUGCACACGG----CU
(((((.(((....)))(((.........(((((((((.......))))))))).))).............)))))---------------......((((........)))----). ( -35.00)
>DroPse_CAF1 8911 104 - 1
GUUCGUGGCCGCCGCCGACUUUUCCUGCAGCUCCUGCUGCUGCUGGAGGAGCUUGUCCAGACUGAUCUCCGCAGAGG---CUG------CAACAGCAGCAGCAGGAAGCGG----CU
......((((((.((.(.......).))...((((((((((((((..((((...((....))....))))((((...---)))------)..)))))))))))))).))))----)) ( -51.00)
>DroWil_CAF1 6809 102 - 1
AUUCGUGGCAGCUGCAGACUUCUCUUCCAGCUCUUGUUGCUGCUGCAACAGCUUAUCCAGAUUGAUCUCACCAGG---------------GGCACCAGAUGCUGCACCGGGUUUGCU
....(..(((((.(((((((........)).)).))).)))))..)...(((..((((.((......))....((---------------.(((.(....).))).))))))..))) ( -29.80)
>DroYak_CAF1 7384 117 - 1
GUUCGUGGCUGCCGCGGAUUUCUCCUCCAGCUCCUGCUGCUGUUGCAGCAACUUGUCCAAACUGAUUUCGUUUGAGGUGGACGGAAGUGAAGCAGCAGCAGCAGCAACGGGUUUACU
(..((((((((..(.(((....))).)))))).(((((((((((((..((..(((((((..((.(.......).)).)))))))...))..)))))))))))))..)))..)..... ( -45.20)
>DroPer_CAF1 8975 104 - 1
GUUCGUGGCCGCCGCCGACUUUUCCUGCAGCUCCUGCUGCUGCUGGAGGAGCUUGUCCAGACUGAUCUCCGUAGAGG---ACG------CAGAAGCAGCAGCAGGAAGCGG----CU
......((((((.((.(.......).))...((((((((((((((((.(....).)))...(((...(((.....))---)..------))).))))))))))))).))))----)) ( -46.90)
>consensus
GUUCGUGGCCGCCGCCGACUUCUCCUCCAGCUCCUGCUGCUGCUGCAGCAGCUUGUCCAAACUGAUCUCCCCAGAGG___A_G_______AGCAGCAGCAGCAGCAACCGG____CU
....((((...))))..................((((((((((((.........(((......)))(((....)))................))))))))))))............. (-12.18 = -13.38 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:30:31 2006