Locus 6009

Sequence ID	2R_DroMel_CAF1
Location	18,874,971 – 18,875,131
Length	160
Max. P	0.874845

overview

Window 9

Location	18,874,971 – 18,875,091
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-39.03
Consensus MFE	-33.84
Energy contribution	-35.15
Covariance contribution	1.31
Combinations/Pair	1.12
Mean z-score	-1.76
Structure conservation index	0.87
SVM decision value	0.72
SVM RNA-class probability	0.832798
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18874971 120 + 20766785
AGCAACAGAGGAUCGAGCUGGAGAAGCGCACCAAGCAGAUCGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGUACAGGUUGGGAACUGCGAGAAUCUGCAGGAGCAGCUGCAAG
......(((...(((.(((.....))).).....((((.((..(((.(..((((..(((((........)))))..))))..).))).)).))))))...)))((((......))))... ( -37.10)
>DroSim_CAF1 7383 120 + 1
AGCAACAGAGGAUCGAGCUGGAGAAGCGAGGCAAGCAGAUCGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGCACAGGUUGGGAACUGCGAGAAUCUGCAGGAGCAGCUGCAGG
.((..(.(.....)..(((.....))))..))..((((.((..(((.(..((((..(((((........)))))..))))..).))).)).))))......((((((......)))))). ( -40.30)
>DroEre_CAF1 7280 120 + 1
AGCAGCAGAGGAUCGAGCUGGAGAAGAGCGCCAAGAAGAUCGGCGAGCGAUGCGCACAGCUGGAAAAUGAGUUGGACGCACAGGUUGGGAACUGCGAAAAUCUGCAGGUGCAGUUGCAGG
.(((((((....((((.(((.....(..((((.........))))..)..((((..(((((........)))))..))))))).))))...))))......((((....)))).)))... ( -40.40)
>DroYak_CAF1 7405 120 + 1
AACAGCAGAGGAUCGAGCUGGAGAAGCGCGCCAAGCAGAUCGGCGAGCGUUGCGGACAGCUGGAAAAGGAGUUGGACGCACAGGUUGGGAAUUGCGAAAAUCUGCAGGAGCAGCUACAGA
....((((....((((.(((.....((.((((.........)))).))..((((..(((((........)))))..))))))).))))...))))......((((....))))....... ( -38.30)
>consensus
AGCAACAGAGGAUCGAGCUGGAGAAGCGCGCCAAGCAGAUCGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGCACAGGUUGGGAACUGCGAAAAUCUGCAGGAGCAGCUGCAGG
.(((((......((((.(((.....((.((((.........)))).))..((((..(((((........)))))..))))))).))))...(((((......))))).....)))))... (-33.84 = -35.15 +   1.31)

alignment

secondary structure

dotplot

Window 0

Location	18,874,971 – 18,875,091
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.67
Mean single sequence MFE	-32.17
Consensus MFE	-26.97
Energy contribution	-28.16
Covariance contribution	1.19
Combinations/Pair	1.13
Mean z-score	-1.97
Structure conservation index	0.84
SVM decision value	0.89
SVM RNA-class probability	0.874845
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18874971 120 - 20766785
CUUGCAGCUGCUCCUGCAGAUUCUCGCAGUUCCCAACCUGUACGUCCAGCUCCUUUUCCAGCUGUCCGCAUCGCUCGCCGAUCUGCUUGGUGCGCUUCUCCAGCUCGAUCCUCUGUUGCU
...(((((.((.((.(((((((..(((((........)))).((..(((((........)))))..))........)..)))))))..)).))(((.....)))..........))))). ( -34.40)
>DroSim_CAF1 7383 120 - 1
CCUGCAGCUGCUCCUGCAGAUUCUCGCAGUUCCCAACCUGUGCGUCCAGCUCCUUUUCCAGCUGUCCGCAUCGCUCGCCGAUCUGCUUGCCUCGCUUCUCCAGCUCGAUCCUCUGUUGCU
...(((((.((....(((((((..((.(((.........(((((..(((((........)))))..))))).)))))..)))))))..))...(((.....)))..........))))). ( -34.20)
>DroEre_CAF1 7280 120 - 1
CCUGCAACUGCACCUGCAGAUUUUCGCAGUUCCCAACCUGUGCGUCCAACUCAUUUUCCAGCUGUGCGCAUCGCUCGCCGAUCUUCUUGGCGCUCUUCUCCAGCUCGAUCCUCUGCUGCU
...(((.((((....))))......((((.((.......(((((..((.((........)).))..))))).(((((((((.....)))))).........)))..))....))))))). ( -30.10)
>DroYak_CAF1 7405 120 - 1
UCUGUAGCUGCUCCUGCAGAUUUUCGCAAUUCCCAACCUGUGCGUCCAACUCCUUUUCCAGCUGUCCGCAACGCUCGCCGAUCUGCUUGGCGCGCUUCUCCAGCUCGAUCCUCUGCUGUU
(((((((......)))))))....................((((..((.((........)).))..))))..((.((((((.....)))))).)).....((((..........)))).. ( -30.00)
>consensus
CCUGCAGCUGCUCCUGCAGAUUCUCGCAGUUCCCAACCUGUGCGUCCAACUCCUUUUCCAGCUGUCCGCAUCGCUCGCCGAUCUGCUUGGCGCGCUUCUCCAGCUCGAUCCUCUGCUGCU
.((((((......))))))......((((........(((((((..(((((........)))))..))))..((.((((((.....)))))).)).....))).........)))).... (-26.97 = -28.16 +   1.19)

alignment

secondary structure

dotplot

Window 1

Location	18,875,011 – 18,875,131
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.17
Mean single sequence MFE	-44.74
Consensus MFE	-37.24
Energy contribution	-37.76
Covariance contribution	0.52
Combinations/Pair	1.15
Mean z-score	-1.37
Structure conservation index	0.83
SVM decision value	0.24
SVM RNA-class probability	0.650043
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18875011 120 + 20766785
CGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGUACAGGUUGGGAACUGCGAGAAUCUGCAGGAGCAGCUGCAAGUGCGGGGACUACCCGUGGAAGCCAAGGAUGUGCUGUCCAU
.(((..(((.((((..(((((........)))))..))))).(((((....(((((......)))))...)))))))....(((((.....)))))....)))..((((.....)))).. ( -45.20)
>DroSec_CAF1 7473 120 + 1
CGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGCACAGGUUGGAAACUGCGAGAAUCUGCAGGAGCAGCUGCAGGUGCGGGGACUGCCCGUGGAUGCCAAGGAUGUGCUGUCCAU
.((((.(((.((((..(((((........)))))..))))......(....))))....((((((((......))))))))(((((.....)))))...))))..((((.....)))).. ( -47.80)
>DroSim_CAF1 7423 120 + 1
CGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGCACAGGUUGGGAACUGCGAGAAUCUGCAGGAGCAGCUGCAGGUGCGGGGACUGCCCGUGGAUGCAAAGGAUGUGCUGUCCAU
.(((((.(..((((..(((((........)))))..))))..).)).....((.((...((((((((......)))))))).)).))...))).(((((((((.......))).)))))) ( -46.70)
>DroEre_CAF1 7320 120 + 1
CGGCGAGCGAUGCGCACAGCUGGAAAAUGAGUUGGACGCACAGGUUGGGAACUGCGAAAAUCUGCAGGUGCAGUUGCAGGAUCGCGGACUGCCCGUGGAUGCCAAGGAUGUGCUGUCCAU
((((..(((...)))...))))..........((((((((((..((((.(.((((((....((((....))))))))))..((((((.....)))))).).))))...))))).))))). ( -45.90)
>DroYak_CAF1 7445 120 + 1
CGGCGAGCGUUGCGGACAGCUGGAAAAGGAGUUGGACGCACAGGUUGGGAAUUGCGAAAAUCUGCAGGAGCAGCUACAGAUGCGAGGUCUGCCAGUGGAUGCGAAGGAUGUGCUGUCCAU
.(((.(((.(((((..(((((........)))))..)))).).)))(((..((((....(((((.((......)).)))))))))..)))))).(((((((((.......))).)))))) ( -38.10)
>consensus
CGGCGAGCGAUGCGGACAGCUGGAAAAGGAGCUGGACGCACAGGUUGGGAACUGCGAGAAUCUGCAGGAGCAGCUGCAGGUGCGGGGACUGCCCGUGGAUGCCAAGGAUGUGCUGUCCAU
.(((((.(..((((..(((((........)))))..))))..).))(((..((.((...((((((((......)))))))).)).))....)))......)))..((((.....)))).. (-37.24 = -37.76 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:22 2006