Locus 3936

Sequence ID	3R_DroMel_CAF1
Location	10,671,254 – 10,671,454
Length	200
Max. P	0.893813

overview

Window 3

Location	10,671,254 – 10,671,374
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-44.72
Consensus MFE	-38.90
Energy contribution	-39.82
Covariance contribution	0.92
Combinations/Pair	1.11
Mean z-score	-1.17
Structure conservation index	0.87
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10671254 120 + 27905053
GGCUCGCCAGCAGGUGGAGGCCAGUAGAUGCCUUCAACUUCAUCGCAAUGUGGAAAAUUUGAGGGAUCUCGAGAUGGAAGUGGCCCGUGCCCACACAGCGUUGGCUGUCAAGAACAAGAU
(((..((((((((((((((((........)))))).))))....((..(((((....((((((....))))))((((.......))))..)))))..)))))))).)))........... ( -39.60)
>DroSec_CAF1 12688 120 + 1
GGCUCGCCAGCAGGUGGAGGCCAGCAGAUGCCUGCAACUCCAUCGCAAUGUGGAAAAUUUGAGGGAUCUCGAGAUGGAGGUGGCCCGGGCCCACACAGCCUUGGCUGUCAAGAACAAGAU
(((((((((.....))).(((((((((....))))..(((((((......(....)..(((((....)))))))))))).)))))))))))...(((((....)))))............ ( -45.90)
>DroSim_CAF1 14234 120 + 1
GGCUCGCCAGCAGGUGGAGGCCAGCAGAUGCCUGCAACUCCAUCGCAAUGUGGAAAAUUUGAGGGAUCUGGAGAUGGAGGUGGCCCGGGCCCACACAGCCUUGGCUGUCAAGAACAAGAU
((((((((....))))..))))..(((((.(((.(((.(((((......)))))....)))))).)))))........((..(((.((((.......)))).)))..))........... ( -42.60)
>DroEre_CAF1 9955 120 + 1
GGCCCGCCAGCAGGUGGAGGCCAGCAGAUGCCUGCAACUCCAUCGCAAUGUGGAGAAUCUGAGGGAUCUCGAGAUGGAGGUGGCCCGGGCUCACACUGCCUUGGCAGUUAAGUACAAGAU
(((((((((.....))).(((((((((....))))..(((((((.(.....)((((.((....)).))))..))))))).)))))))))))...(((((....)))))............ ( -47.70)
>DroYak_CAF1 4614 120 + 1
GGCCCGCCAGCAGGUGGAGGCCAGCAGGUGCCUGCAACUCCAUCGCAAUGUGGAGAAUCUGAGGGAUCUCGAGAUGGAGGUGGCCCGGGCACACACUGCCUUGGCUGUUAAGAACAAGAU
((((((((....))))..)))).((((....))))..(((((((.(.....)((((.((....)).))))..)))))))(..(((.(((((.....))))).)))..)............ ( -47.80)
>consensus
GGCUCGCCAGCAGGUGGAGGCCAGCAGAUGCCUGCAACUCCAUCGCAAUGUGGAAAAUUUGAGGGAUCUCGAGAUGGAGGUGGCCCGGGCCCACACAGCCUUGGCUGUCAAGAACAAGAU
(((((((((.....))).(((((((((....))))..(((((((.(.....)......(((((....)))))))))))).)))))))))))...(((((....)))))............ (-38.90 = -39.82 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	10,671,334 – 10,671,454
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.33
Mean single sequence MFE	-39.93
Consensus MFE	-32.98
Energy contribution	-33.54
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-1.70
Structure conservation index	0.83
SVM decision value	0.98
SVM RNA-class probability	0.893813
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10671334 120 - 27905053
UUUCCACGGCUCGCUGUUCCGCCAAAGCUUCGGCCCGCUCCCGCUGCUUAUCUUCCACCGUUUGUUUGAUAUUGUUGGUGAUCUUGUUCUUGACAGCCAACGCUGUGUGGGCACGGGCCA
.......(((..........)))........((((((..(((((.((.((((...((.....))...))))..((((((..((........))..))))))))...)))))..)))))). ( -40.30)
>DroSec_CAF1 12768 120 - 1
UUUCCACGGCUCGCUGCUCCGCCAAAGCCUCGGCCCGCUCCCGCUGCUUAUCUUCCACCGUCUGUUUGAUAUUAUUGGUGAUCUUGUUCUUGACAGCCAAGGCUGUGUGGGCCCGGGCCA
.......((((.((......))...))))..((((((..(((((...........(((((...((.....))...)))))............(((((....))))))))))..)))))). ( -42.80)
>DroSim_CAF1 14314 120 - 1
UUUCCACGGCUCGCUGCUCCGCCAAAGCUUCGGCCCGCUCCCGCUGCUUAUCUUCCACCGUCUGUUUGAUAUUGUUGAUGAUCUUGUUCUUGACAGCCAAGGCUGUGUGGGCCCGGGCCA
.......(((..........)))........((((((..(((((...(((((...((..(((.....)))..))..)))))...........(((((....))))))))))..)))))). ( -39.30)
>DroEre_CAF1 10035 120 - 1
UUUCCACGGCUCUCUGCUUCGCCAAAGCCUCGGCCCGCUCCCGCUGCUUAUCUUCCACCGUCUGCUUGAUAUUUUGGCUGAUCUUGUACUUAACUGCCAAGGCAGUGUGAGCCCGGGCCA
.......((((....((...))...))))..(((((((((.((((((((..........(((.....)))....((((.................)))))))))))).))))..))))). ( -39.53)
>DroYak_CAF1 4694 120 - 1
UUUCCACGGCUCGCUGCUCCGCCAAAGCCUCGGCCCGCUCCCGCUGCUUAUCCUCCACCGUCUGCUUGAUAUUAAGGGUGAUCUUGUUCUUAACAGCCAAGGCAGUGUGUGCCCGGGCCA
.......((((.((......))...))))..((((((..(((((((((((((((.....(((.....)))....))))))).((((...........)))))))))).).)..)))))). ( -37.70)
>consensus
UUUCCACGGCUCGCUGCUCCGCCAAAGCCUCGGCCCGCUCCCGCUGCUUAUCUUCCACCGUCUGUUUGAUAUUAUUGGUGAUCUUGUUCUUGACAGCCAAGGCUGUGUGGGCCCGGGCCA
.......((((.((......))...))))..((((((..(((((...........(((((((.....)))......))))............(((((....))))))))))..)))))). (-32.98 = -33.54 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:49 2006