Locus 136

Sequence ID	2L_DroMel_CAF1
Location	421,958 – 422,060
Length	102
Max. P	0.785840

overview

Window 1

Location	421,958 – 422,060
Length	102
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-28.67
Consensus MFE	-18.82
Energy contribution	-19.02
Covariance contribution	0.20
Combinations/Pair	1.24
Mean z-score	-2.08
Structure conservation index	0.66
SVM decision value	0.57
SVM RNA-class probability	0.785840
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 421958 102 + 22407834
GAUAAAAAUAAGCCUCCUCCC---------UCAGAAGCUCCAGCUAACAUUCCUCAUGGCGGUAAAAAUCUGCCCAAGUCCAUACAGAUCCUGGAAAUUGGAGGGAGUAUG
................(((((---------((..((..(((((..............(((((.......)))))...(((......))).)))))..)).))))))).... ( -26.30)
>DroSec_CAF1 1883 102 + 1
GAUAAAAAUAAGCCCCCUCCC---------GCAGAAGCCCCAGCUAACAUUCCUCAUGGCGGUAAAAAUCUGCCCAAAUCCAUACAGAUCCUGGAAAUUGGAGGGAGUAUG
...........((.((((((.---------(((((.((((((..............))).))).....)))))(((.(((......)))..))).....)))))).))... ( -26.64)
>DroSim_CAF1 1876 102 + 1
GAUAAAAAUAAGCCCCCUCCC---------GCUGAAACUCCAGCUAACAUUCCUCACGGCGGUAAAAAUCUGCCCAAAUCCAUACAGAUCCUGGAAAUUGGAGGGAGUAUG
...........((.((((((.---------((((......)))).....((((....(((((.......)))))...(((......)))...))))...)))))).))... ( -28.20)
>DroEre_CAF1 1825 102 + 1
GAUAAACACAAGCCGCCUCCG---------GCAGAAACUCAAGCUAACAUUCCGCAUGGCGGGAAGAAUCUGCCCAAAUCCAUACAGAUCCUGGAAAUUGGAGGGAGCAUG
...........((..((((((---------(((((..((..........((((((...))))))))..))))))....((((.........))))....)))))..))... ( -29.60)
>DroYak_CAF1 1862 102 + 1
GAUAAAAACAAGCCCCCUCCG---------AAAGAAGCUCCAGCUAACAUUCCGCACGGCGGUAAAAAUCUGCCCAAAUCCAUACAGAUCAUGGAAAUUGGAGGGAGUAUG
........((.((.(((((((---------(....(((....)))............(((((.......)))))....(((((.......)))))..)))))))).)).)) ( -28.70)
>DroMoj_CAF1 1751 108 + 1
GACAGGCACAAACCACCACCGCCGCCAACAACAGAUG---CCGUAGCCACACCGCAUGGCGGCAAACACCUGCCUAAGUUUAUACAGGUGCUGGAAAUUGGAGGCAGCAUG
....((......))......(((.((((...(((.((---((((.((......))...))))))..((((((............)))))))))....)))).)))...... ( -32.60)
>consensus
GAUAAAAACAAGCCCCCUCCC_________GCAGAAGCUCCAGCUAACAUUCCGCAUGGCGGUAAAAAUCUGCCCAAAUCCAUACAGAUCCUGGAAAUUGGAGGGAGUAUG
...........((.((((((.....................................(((((.......)))))....((((.........))))....)))))).))... (-18.82 = -19.02 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	421,958 – 422,060
Length	102
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.40
Mean single sequence MFE	-34.43
Consensus MFE	-22.21
Energy contribution	-22.05
Covariance contribution	-0.16
Combinations/Pair	1.21
Mean z-score	-1.82
Structure conservation index	0.65
SVM decision value	0.30
SVM RNA-class probability	0.677971
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 421958 102 - 22407834
CAUACUCCCUCCAAUUUCCAGGAUCUGUAUGGACUUGGGCAGAUUUUUACCGCCAUGAGGAAUGUUAGCUGGAGCUUCUGA---------GGGAGGAGGCUUAUUUUUAUC
....(((((((....(((((((((((((..........)))))))....((.......))........)))))).....))---------)))))................ ( -28.00)
>DroSec_CAF1 1883 102 - 1
CAUACUCCCUCCAAUUUCCAGGAUCUGUAUGGAUUUGGGCAGAUUUUUACCGCCAUGAGGAAUGUUAGCUGGGGCUUCUGC---------GGGAGGGGGCUUAUUUUUAUC
....((((((((.....((((.((((....))))))))(((((......(((((((.....)))...)).))....)))))---------.))))))))............ ( -32.00)
>DroSim_CAF1 1876 102 - 1
CAUACUCCCUCCAAUUUCCAGGAUCUGUAUGGAUUUGGGCAGAUUUUUACCGCCGUGAGGAAUGUUAGCUGGAGUUUCAGC---------GGGAGGGGGCUUAUUUUUAUC
....(((((((((((((((..(((((....)))))..)).))))).......((....)).......(((((....)))))---------.))))))))............ ( -33.20)
>DroEre_CAF1 1825 102 - 1
CAUGCUCCCUCCAAUUUCCAGGAUCUGUAUGGAUUUGGGCAGAUUCUUCCCGCCAUGCGGAAUGUUAGCUUGAGUUUCUGC---------CGGAGGCGGCUUGUGUUUAUC
((.(((.(((((........((((((....)))))).((((((..(((.((((...))))...(....)..)))..)))))---------)))))).))).))........ ( -33.70)
>DroYak_CAF1 1862 102 - 1
CAUACUCCCUCCAAUUUCCAUGAUCUGUAUGGAUUUGGGCAGAUUUUUACCGCCGUGCGGAAUGUUAGCUGGAGCUUCUUU---------CGGAGGGGGCUUGUUUUUAUC
((..((((((((....((((((.....))))))(((.(((.(((..((.((((...)))))).))).))).))).......---------.))))))))..))........ ( -32.10)
>DroMoj_CAF1 1751 108 - 1
CAUGCUGCCUCCAAUUUCCAGCACCUGUAUAAACUUAGGCAGGUGUUUGCCGCCAUGCGGUGUGGCUACGG---CAUCUGUUGUUGGCGGCGGUGGUGGUUUGUGCCUGUC
((.((..((.((.......(((((((((.((....)).))))))))).(((((((.((((....((....)---)..))))...))))))))).))..)).))........ ( -47.60)
>consensus
CAUACUCCCUCCAAUUUCCAGGAUCUGUAUGGAUUUGGGCAGAUUUUUACCGCCAUGAGGAAUGUUAGCUGGAGCUUCUGC_________CGGAGGGGGCUUAUUUUUAUC
....((((((((.......(((((((((..........))))))))).....((....))...............................))))))))............ (-22.21 = -22.05 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:07 2006