Locus 1504

Sequence ID	3L_DroMel_CAF1
Location	4,336,374 – 4,336,574
Length	200
Max. P	0.707322

overview

Window 0

Location	4,336,374 – 4,336,479
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.15
Mean single sequence MFE	-32.73
Consensus MFE	-21.42
Energy contribution	-22.90
Covariance contribution	1.48
Combinations/Pair	1.04
Mean z-score	-1.75
Structure conservation index	0.65
SVM decision value	0.02
SVM RNA-class probability	0.541676
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4336374 105 - 23771897
CCUCCACAU-----GGAGGAGCUAUGGCGGAAAUCGUUAAAUA-----CUCGG-----GCGAUAAGACUGAAAGUGUUGCCGCAACAUGUUGCAGGGGCGAAGUCAUUGAACCGCAGGAA
(((((....-----))))).......((((..((((((.....-----....)-----)))))..((((.....((((.(.((((....)))).).)))).))))......))))..... ( -32.50)
>DroSec_CAF1 22716 104 - 1
CCUCCACAU-----GGAGGAGCUAUGGCGGAAAUCGUUAAAUA-----CUUUG-----GCGAUAAGACUGAAAGUGUUGCCGCAACAUGUUGCUG-AGCGAAGUCAUUGAACCGCAGGAA
(((((....-----))))).......((((..((((((((...-----..)))-----)))))..((((.....((((.(.((((....)))).)-)))).))))......))))..... ( -32.60)
>DroSim_CAF1 22731 104 - 1
CCUCCACAU-----GGAGGAGCUAUGGCGGAAAUCGUUAAAUA-----CUCUG-----GCGAUAAGACUGAAAGUGUUGCCGCAACAUGUUGCUG-GGCGAAGUCAUUGAACCGCAGGAA
(((((....-----))))).......((((..(((((((....-----...))-----)))))..((((.......(((((((((....))))..-)))))))))......))))..... ( -33.11)
>DroYak_CAF1 22164 104 - 1
CCUCCACAU-----GGAGGAGCUAUGGCGGAAAUCGUUAAAUA-----CUCUG-----GCGAUAAGACUGGAAAUGUUGCCGCAACAUGUUGCUG-GGCGAAGUCAUUGAACCGCAGGAA
(((((....-----))))).......((((..(((((((....-----...))-----)))))..((((.......(((((((((....))))..-)))))))))......))))..... ( -33.11)
>DroAna_CAF1 25345 113 - 1
CCUCCACAUGAAGUGGAGGAACUAUGGCGGAAAUCAUUAAAAAAAGCAAGCUGGAAAUGCGAUAAGAGUCAAGAUGUUGCUGCAACAUGUUGCAG-------GUCAUUGAACCGGCACUG
(((((((.....))))))).......((.................))..(((((......(((....)))..((((...((((((....))))))-------..))))...))))).... ( -32.33)
>consensus
CCUCCACAU_____GGAGGAGCUAUGGCGGAAAUCGUUAAAUA_____CUCUG_____GCGAUAAGACUGAAAGUGUUGCCGCAACAUGUUGCUG_GGCGAAGUCAUUGAACCGCAGGAA
(((((.........))))).......((((..(((((.....................)))))..((((.....((((.(.((((....)))).).)))).))))......))))..... (-21.42 = -22.90 +   1.48)

alignment

secondary structure

dotplot

Window 1

Location	4,336,444 – 4,336,541
Length	97
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	80.34
Mean single sequence MFE	-17.82
Consensus MFE	-12.71
Energy contribution	-12.52
Covariance contribution	-0.19
Combinations/Pair	1.09
Mean z-score	-1.49
Structure conservation index	0.71
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4336444 97 + 23771897
UUAACGAUUUCCGCCAUAGCUCCUCCAUGUGGAGGAG-UUUUUAACUUGCCCACACA-------AUG---------CAAAAAAGUAAAAAAAAAAAAUACAAUAAAGUUUGUUC
..(((((..........(((((((((....)))))))-))......((((.......-------..)---------))).............................))))). ( -17.20)
>DroSec_CAF1 22785 103 + 1
UUAACGAUUUCCGCCAUAGCUCCUCCAUGUGGAGGAG-UU-CCAACUUGCCCACACA-------AAAAAAAAAAUCUGAAAAAGUUAA--GAAAAAAGGCAACAAAGUUUGUUC
............(((..(((((((((....)))))))-))-..(((((.........-------.................)))))..--.......))).............. ( -21.17)
>DroSim_CAF1 22800 110 + 1
UUAACGAUUUCCGCCAUAGCUCCUCCAUGUGGAGGAG-UU-CCAACUUGCCCACACACCAAAAAAAAAAAAAAAUCCAAAAAAGUAGA--GAAAAAAUACAACAAAGUUUGUUC
..(((((..........(((((((((....)))))))-))-..........................................(((..--.......)))........))))). ( -16.10)
>DroYak_CAF1 22233 103 + 1
UUAACGAUUUCCGCCAUAGCUCCUCCAUGUGGAGGAGGUU-CCAGCUUGCCCACACA-------CAAAUAAAAGUAUGAAAAAA-AAA--CAACAAAGACAACAUAGUUUGUUU
............((...(.(((((((....))))))).).-...)).......((.(-------(........)).))......-...--......((((((......)))))) ( -16.80)
>consensus
UUAACGAUUUCCGCCAUAGCUCCUCCAUGUGGAGGAG_UU_CCAACUUGCCCACACA_______AAAAAAAAAAUCCAAAAAAGUAAA__GAAAAAAGACAACAAAGUUUGUUC
...................(((((((....))))))).............................................................((((......)))).. (-12.71 = -12.52 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	4,336,479 – 4,336,574
Length	95
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	75.55
Mean single sequence MFE	-14.95
Consensus MFE	-8.06
Energy contribution	-8.75
Covariance contribution	0.69
Combinations/Pair	1.14
Mean z-score	-1.98
Structure conservation index	0.54
SVM decision value	0.37
SVM RNA-class probability	0.707322
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4336479 95 + 23771897
AG-UUUUUAACUUGCCCACACA-------AUG---------CAAAAAAGUAAAAAAAAAAAAUACAAUAAAGUUUGUUCGAAUU-UUUGCAACAAACAAGAUGGCCAAGCAAA
..-.......((((.((((...-------.((---------(......)))....................((((((((((...-.))).)))))))..).))).)))).... ( -14.00)
>DroSec_CAF1 22820 101 + 1
AG-UU-CCAACUUGCCCACACA-------AAAAAAAAAAUCUGAAAAAGUUAA--GAAAAAAGGCAACAAAGUUUGUUCGAAUU-UUUGCAACAAACAGCAUGGCCAAGCAAG
..-..-....(((((.......-------..........(((..........)--)).....(((......((((((((((...-.))).)))))))......)))..))))) ( -17.60)
>DroSim_CAF1 22835 108 + 1
AG-UU-CCAACUUGCCCACACACCAAAAAAAAAAAAAAAUCCAAAAAAGUAGA--GAAAAAAUACAACAAAGUUUGUUCGAAUU-UUUGCAACAAACAGCAUGGCCAAGCAAG
..-..-....((((.(((..(...........................(((..--.......)))......((((((((((...-.))).))))))).)..))).)))).... ( -13.90)
>DroYak_CAF1 22268 97 + 1
AGGUU-CCAGCUUGCCCACACA-------CAAAUAAAAGUAUGAAAAAA-AAA--CAACAAAGACAACAUAGUUUGUUUGAAUUUUUUGCAACAAACAAGAUGG-----CAAG
.....-....((((((......-------((((((((..((((......-...--............)))).))))))))....(((((.......))))).))-----)))) ( -14.30)
>consensus
AG_UU_CCAACUUGCCCACACA_______AAAAAAAAAAUCCAAAAAAGUAAA__GAAAAAAGACAACAAAGUUUGUUCGAAUU_UUUGCAACAAACAACAUGGCCAAGCAAG
..........((((((((..............................(((...........)))......((((((((((.....))).)))))))....)))....))))) ( -8.06 =  -8.75 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:22 2006