Locus 6025

Sequence ID	3R_DroMel_CAF1
Location	15,889,904 – 15,890,040
Length	136
Max. P	0.991855

overview

Window 9

Location	15,889,904 – 15,890,023
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.94
Mean single sequence MFE	-29.12
Consensus MFE	-26.40
Energy contribution	-26.18
Covariance contribution	-0.22
Combinations/Pair	1.12
Mean z-score	-2.68
Structure conservation index	0.91
SVM decision value	2.29
SVM RNA-class probability	0.991855
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15889904 119 + 27905053
GGCUGUGACUUUGUGUCGCUGAACGGAAACGGAAAUGCGCCAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU
....(((((((((((.(((....((....)).....))((((...-..))))..).).(((((((((..(........)..)))))))))))))))))))((..(....)..))...... ( -34.60)
>DroVir_CAF1 10413 107 + 1
CU-------------GAGCGCAACGGAAACGGAAAUGCGCCAUUAAACUGGCAAGUUAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU
..-------------..(((((.((....))....)))((((......))))......(((((((((..(........)..))))))))))).....(((((..(....)..)))))... ( -29.90)
>DroGri_CAF1 12300 106 + 1
GU-------------GUAUGGAAUGGAAACGGAAAUGCGCUAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU
((-------------((((....((....))...)))))).....-........((..(((((((((..(........)..))))))))))).....(((((..(....)..)))))... ( -24.50)
>DroEre_CAF1 9293 108 + 1
-----------UGUGUCGCUGAACGGAAACGGAAAUGCGCCAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU
-----------((((((((....((....))....(((((((...-..))))..((..(((((((((..(........)..)))))))))))...........)))...))))))))... ( -29.90)
>DroMoj_CAF1 9798 100 + 1
------------------CGCAAAGGA-ACGGAAGUGCGCCAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUGCCA
------------------......((.-((....))...))....-...((((.(((((((((((((..(........)..)))))))))((((.......)))).....)))).)))). ( -27.70)
>DroAna_CAF1 7174 106 + 1
------G-------AACGGUGAACGGAAACGGAAAUGCGCCAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU
------.-------.........((....))....(((((((...-..))))......(((((((((..(........)..))))))))))))....(((((..(....)..)))))... ( -28.10)
>consensus
_______________GCGCGGAACGGAAACGGAAAUGCGCCAUUA_ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU
.......................((....))....(((((((......))))......(((((((((..(........)..))))))))))))....(((((..(....)..)))))... (-26.40 = -26.18 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	15,889,944 – 15,890,040
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-23.92
Consensus MFE	-16.22
Energy contribution	-16.00
Covariance contribution	-0.22
Combinations/Pair	1.16
Mean z-score	-1.96
Structure conservation index	0.68
SVM decision value	0.62
SVM RNA-class probability	0.803136
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15889944 96 + 27905053
CAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUUUU-----UUUUCAC----------CCAGC-------GAC-
.....-.((((...((..(((((((((..(........)..)))))))))))((((.(((((..(....)..))))).))))-----.......----------)))).-------...- ( -20.30)
>DroVir_CAF1 10440 103 + 1
CAUUAAACUGGCAAGUUAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUUCU-GCGCUGCUCAC----------CCGCCA------AGCA
........((((......(((((((((..(........)..)))))))))(((.((.(((((..(....)..))))).)).)-)).........----------..))))------.... ( -26.10)
>DroGri_CAF1 12327 97 + 1
UAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUUCU-CGACUGCUCAA----------C-----------UGCG
.....-..(((((.(((.(((((((((..(........)..))))))))).......(((((..(....)..))))).....-.)))))).)).----------.-----------.... ( -23.20)
>DroEre_CAF1 9322 93 + 1
CAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUU--------UUUCAC-----------CAGCA------GAC-
.....-.((((.......(((((((((..(........)..)))))))))(.((((.(((((..(....)..))))).))--------)).).)-----------)))..------...- ( -21.10)
>DroMoj_CAF1 9819 119 + 1
CAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUGCCACUCGCACUCCUCUCGGCUGUGUGGACGCUAUUCCAUUGCC
.....-..(((((.(((((((((((((..(........)..)))))))))((((.......)))).....)))).)))))..............(((...(((((......))))).))) ( -31.40)
>DroAna_CAF1 7201 96 + 1
CAUUA-ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUUUU-----UUUUCAC-----------CAGGA------GAC-
.....-.((((...((..(((((((((..(........)..)))))))))))((((.(((((..(....)..))))).))))-----......)-----------)))..------...- ( -21.40)
>consensus
CAUUA_ACUGGCAAGUCAAGCUUAUUAGCUGCAAUAAAAAAUAAUAAGCUGCAAAGUUAUGUUGCAAUUGUGGCAUAUUUCU_____UUCUCAC__________CCAGCA______GAC_
..............(((.(((((((((..(........)..))))))))).......(((((..(....)..))))).......................................))). (-16.22 = -16.00 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:44 2006