Locus 2718

Sequence ID	2R_DroMel_CAF1
Location	9,530,599 – 9,530,750
Length	151
Max. P	0.769300

overview

Window 7

Location	9,530,599 – 9,530,691
Length	92
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	81.93
Mean single sequence MFE	-25.82
Consensus MFE	-15.07
Energy contribution	-15.63
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.13
Structure conservation index	0.58
SVM decision value	0.34
SVM RNA-class probability	0.696603
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9530599 92 + 20766785
------AUAGCAAAUGAUGUGCGGGAUAUAUAGA--------CGCCGGCAUAAAUUAUUGCCGAGCUUAACGGGAAUAAUAUUGUUGCAAAAGGCAAUUC-----GUACGA
------...........(((((((..........--------.(((((((........))))).)).................(((((.....)))))))-----))))). ( -22.00)
>DroSec_CAF1 7600 100 + 1
------AUAGCAAAUGAUGUGCGGGAUAUAUAGAUAUAUAGCUGCCGGCAUAAAUUAUUGCCGGGCUUAACGGGAAUAAUAUUGUUGCAAAAGGCAAUUC-----GUACGA
------...........((((((((.(((((....)))))..((((.((((((((((((.(((.......))).)))))).))).)))....)))).)))-----))))). ( -27.10)
>DroSim_CAF1 6254 100 + 1
------AUAGCAAAUGAUGUGCGGGAUAUAUAGAUAUAUAGCCGACGGCAUAAAUUAUUGCCGGGCUUAACGGGAAUAAUAUUGUUGCAAAAGGCAAUUC-----GUACGA
------...........((((((((.(((((....)))))(((....((((((((((((.(((.......))).)))))).))).)))....)))..)))-----))))). ( -27.50)
>DroEre_CAF1 9151 102 + 1
CGGUAUAUAACAAAUGAUGUGCGGGAUA--------UAUAGCAGCCGGCAUAAAUUAUUGCCGCGCUUU-CUGGCAUAAUAUUGUUGCAAAAGGCAAUGCAAUUUCUUCGA
(((.........((((.(((((.(((..--------...(((.((.((((........))))))))).)-)).))))).))))((((((........))))))....))). ( -26.70)
>consensus
______AUAGCAAAUGAUGUGCGGGAUAUAUAGA__UAUAGCCGCCGGCAUAAAUUAUUGCCGGGCUUAACGGGAAUAAUAUUGUUGCAAAAGGCAAUUC_____GUACGA
.......((((((....(((((.((...................)).))))).((((((.(((.......))).)))))).))))))........................ (-15.07 = -15.63 +   0.56)

alignment

secondary structure

dotplot

Window 8

Location	9,530,656 – 9,530,750
Length	94
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	82.63
Mean single sequence MFE	-23.30
Consensus MFE	-15.24
Energy contribution	-16.24
Covariance contribution	1.00
Combinations/Pair	1.15
Mean z-score	-2.00
Structure conservation index	0.65
SVM decision value	0.51
SVM RNA-class probability	0.764558
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9530656 94 + 20766785
GGGAAUAAUAUUGUUGCAAAAGGCAAUUC-----GUACGAUUAUUUCUUAUCAUUUAUUGCAUCAUCUUGGCCAAUAAGCUGAAGCUGGGCCAAGAAUU
(((((((((...(((((.....)))))..-----.....))))))))).................((((((((....(((....))).))))))))... ( -27.20)
>DroSec_CAF1 7665 91 + 1
GGGAAUAAUAUUGUUGCAAAAGGCAAUUC-----GUACGAUUA---CUUAUCAUUUAUUGCAUCAUCUUGGCCAAUGAGUUGAAGCUCGGCCAAGAUUU
.(.(((((....(((((.....)))))..-----....(((..---...)))..))))).)...(((((((((...((((....))))))))))))).. ( -24.00)
>DroSim_CAF1 6319 94 + 1
GGGAAUAAUAUUGUUGCAAAAGGCAAUUC-----GUACGAUUAUUUCUUAUCGUUUAUUGCAUCAUCUUGGCCAAUGAGUUGAAGUUUGGCCAAGAUUU
.(.((((....)))).).....(((((..-----..(((((........)))))..)))))...(((((((((((...........))))))))))).. ( -26.20)
>DroEre_CAF1 9213 98 + 1
UGGCAUAAUAUUGUUGCAAAAGGCAAUGCAAUUUCUUCGAUUAUUUCUUAUCAUUUAUUGCAUCAUCUUGGU-AAUGAAUCGGGGCUCAGCCAAGACUU
((((........((((((........))))))..((((((((.....((((((...............))))-))..))))))))....))))...... ( -19.56)
>DroYak_CAF1 8336 94 + 1
UGGCAUAAUAU-GUUGCAAAAGGCAAUGCAAAUUCUUCAAU---UCCUUAUCAUUUAUUGCAUCGUCUUGGU-AAUGAAUUGCAGCUCAGCCAAGAGUU
((((.......-(((((.....))))).......((.((((---((.((((((...............))))-)).)))))).))....))))...... ( -19.56)
>consensus
GGGAAUAAUAUUGUUGCAAAAGGCAAUUC_____GUACGAUUAUUUCUUAUCAUUUAUUGCAUCAUCUUGGCCAAUGAGUUGAAGCUCGGCCAAGAUUU
.(.(((((....(((((.....)))))...........(((........)))..))))).)....((((((((...((((....))))))))))))... (-15.24 = -16.24 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	9,530,656 – 9,530,750
Length	94
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	82.63
Mean single sequence MFE	-20.20
Consensus MFE	-12.77
Energy contribution	-14.05
Covariance contribution	1.28
Combinations/Pair	1.19
Mean z-score	-2.08
Structure conservation index	0.63
SVM decision value	0.52
SVM RNA-class probability	0.769300
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9530656 94 - 20766785
AAUUCUUGGCCCAGCUUCAGCUUAUUGGCCAAGAUGAUGCAAUAAAUGAUAAGAAAUAAUCGUAC-----GAAUUGCCUUUUGCAACAAUAUUAUUCCC
...((((((((.(((....)))....))))))))....(((((..(((((.(....).)))))..-----..)))))...................... ( -21.40)
>DroSec_CAF1 7665 91 - 1
AAAUCUUGGCCGAGCUUCAACUCAUUGGCCAAGAUGAUGCAAUAAAUGAUAAG---UAAUCGUAC-----GAAUUGCCUUUUGCAACAAUAUUAUUCCC
..(((((((((((...........)))))))))))..(((((.....(((..(---((....)))-----..))).....))))).............. ( -21.80)
>DroSim_CAF1 6319 94 - 1
AAAUCUUGGCCAAACUUCAACUCAUUGGCCAAGAUGAUGCAAUAAACGAUAAGAAAUAAUCGUAC-----GAAUUGCCUUUUGCAACAAUAUUAUUCCC
..(((((((((((...........)))))))))))...(((((..(((((.(....).)))))..-----..)))))...................... ( -23.60)
>DroEre_CAF1 9213 98 - 1
AAGUCUUGGCUGAGCCCCGAUUCAUU-ACCAAGAUGAUGCAAUAAAUGAUAAGAAAUAAUCGAAGAAAUUGCAUUGCCUUUUGCAACAAUAUUAUGCCA
..(((((((.((((......))))..-.)))))))((((((((...((((.(....).)))).....))))))))((.....))............... ( -17.80)
>DroYak_CAF1 8336 94 - 1
AACUCUUGGCUGAGCUGCAAUUCAUU-ACCAAGACGAUGCAAUAAAUGAUAAGGA---AUUGAAGAAUUUGCAUUGCCUUUUGCAAC-AUAUUAUGCCA
......(((((((..(((((......-...(((.((((((((.............---..........)))))))).))))))))..-...))).)))) ( -16.40)
>consensus
AAAUCUUGGCCGAGCUUCAACUCAUUGGCCAAGAUGAUGCAAUAAAUGAUAAGAAAUAAUCGUAC_____GAAUUGCCUUUUGCAACAAUAUUAUUCCC
..(((((((((((...........)))))))))))..(((((...(((((........))))).................))))).............. (-12.77 = -14.05 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:46 2006