Locus 6457

Sequence ID	2L_DroMel_CAF1
Location	18,140,124 – 18,140,259
Length	135
Max. P	0.613410

overview

Window 2

Location	18,140,124 – 18,140,219
Length	95
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	67.46
Mean single sequence MFE	-20.67
Consensus MFE	-5.12
Energy contribution	-5.23
Covariance contribution	0.11
Combinations/Pair	1.33
Mean z-score	-2.09
Structure conservation index	0.25
SVM decision value	0.16
SVM RNA-class probability	0.613410
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18140124 95 + 22407834
GAUUAAGA-UUGCGA------UGUUUAUGU---------GAACUUAGUCAAGAUUGUUUAUGGCGGCGAUGAAUUGAAAAUUACCAAAAACAAGGCCGCAAAAUGUAAUCA
(((((((.-(..((.------......)).---------.).)))))))..(((((......(((((..((..(((........)))...))..)))))......))))). ( -22.20)
>DroSec_CAF1 4314 95 + 1
GAUUAAGA-UCGCGG------UGUUUAUGU---------GAACUUAGUCAAGAUUGUUUAUCGCGGCGAUGAAUUGAAAAUUACCAAAAACAAGGCCGCAAAAUGUAAUCA
(((((((.-(((((.------......)))---------)).)))))))..(((((......(((((..((..(((........)))...))..)))))......))))). ( -24.60)
>DroSim_CAF1 4325 95 + 1
GAUUAAGA-UCGCGG------UGUUUAUGU---------GAACUUAGUCAAGAUUGUUUAUCGCGGCGAUGAAUUGAAAAUUACCAAAAACAAGGCCGCAAAAUGUAAUCA
(((((((.-(((((.------......)))---------)).)))))))..(((((......(((((..((..(((........)))...))..)))))......))))). ( -24.60)
>DroEre_CAF1 4300 72 + 1
GAUUAAGA-UCGCGG------UGUUUAUGU---------GAACUUAAUCAAGAUUGUUUAUCGCAUCGAUGGACUGAAAA-UACGAAAA----------------------
(((((((.-(((((.------......)))---------)).)))))))......((((((((...))))))))......-........---------------------- ( -18.40)
>DroYak_CAF1 4344 73 + 1
GAUUAAGA-UCGCGG------UGUUUAUGU---------GAACUUAAUCAAGAUUGUUUAUCGCAGCGAUGAACUAAACAUUACCAAAA----------------------
(((((((.-(((((.------......)))---------)).)))))))......((((((((...))))))))...............---------------------- ( -18.80)
>DroAna_CAF1 3890 107 + 1
CAUCAAGAAUUUCAACUUUUUGGCUUAUGAAAAAUUAGGGAGUUUCAUAAAUAUUGUUUAUCGCUUCAGCUAAUUAGGGAAUACUUCGAA----UCGGAGAAUUUUAAUCA
......((.......((..((((((..(....).....(((((...((((((...)))))).)))))))))))..))(((((.(((((..----.))))).)))))..)). ( -15.40)
>consensus
GAUUAAGA_UCGCGG______UGUUUAUGU_________GAACUUAAUCAAGAUUGUUUAUCGCGGCGAUGAAUUGAAAAUUACCAAAAA____GCCGCAAAAUGUAAUCA
(((((((...................................)))))))......((((((((...))))))))..................................... ( -5.12 =  -5.23 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	18,140,148 – 18,140,259
Length	111
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	86.67
Mean single sequence MFE	-23.92
Consensus MFE	-17.70
Energy contribution	-19.20
Covariance contribution	1.50
Combinations/Pair	0.96
Mean z-score	-1.89
Structure conservation index	0.74
SVM decision value	-0.03
SVM RNA-class probability	0.517141
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18140148 111 - 22407834
CCUGGCCGUAGUGUACGUACAUACGUACACACAUACUCGUUGAUUACAUUUUGCGGCCUUGUUUUUGGUAAUUUUCAAUUCAUCGCCGCCAUAAACAAUCUUGACUAAGUU
...(((((((((((((((....))))))))........((.....))....)))))))((((((.((((..................)))).))))))............. ( -30.57)
>DroSec_CAF1 4338 93 - 1
CCUGGCCGUAGUGUA------------------UACACGUUGAUUACAUUUUGCGGCCUUGUUUUUGGUAAUUUUCAAUUCAUCGCCGCGAUAAACAAUCUUGACUAAGUU
..........(((..------------------..)))(((((((.....(((((((..((...((((......))))..))..))))))).....))))..)))...... ( -20.20)
>DroSim_CAF1 4349 93 - 1
CCUGGACGUAGUGUA------------------UACACGUUGAUUACAUUUUGCGGCCUUGUUUUUGGUAAUUUUCAAUUCAUCGCCGCGAUAAACAAUCUUGACUAAGUU
....(((((.((...------------------.)))))))((((.....(((((((..((...((((......))))..))..))))))).....))))........... ( -21.00)
>consensus
CCUGGCCGUAGUGUA__________________UACACGUUGAUUACAUUUUGCGGCCUUGUUUUUGGUAAUUUUCAAUUCAUCGCCGCGAUAAACAAUCUUGACUAAGUU
..........((((((((............))))))))(((((((.....(((((((..((...((((......))))..))..))))))).....))))..)))...... (-17.70 = -19.20 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:42 2006