Locus 8541

Sequence ID	3L_DroMel_CAF1
Location	22,320,837 – 22,320,997
Length	160
Max. P	0.933251

overview

Window 4

Location	22,320,837 – 22,320,957
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-40.83
Consensus MFE	-38.83
Energy contribution	-39.50
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.95
SVM decision value	0.89
SVM RNA-class probability	0.875684
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320837 120 + 23771897
CUAAUGAUGCUCUCUGGCCUGCAUCGAGAAGCCAAGGCACCAAGGCAUCAGCGGCAUCGCUGGCCGAAGCCACUCGAUGUCCAUCAUUCAUUUGGCAUCGAUGUACGAGCCAUGUUUAUG
..............(((((((((((((...((((((((.....(((..(((((....))))))))...)))....(((....)))......))))).)))))))).).))))........ ( -41.00)
>DroSec_CAF1 1 114 + 1
------AUGCUCUCUGGCCUGCAUCGAGAAGCCAAGGCACCAAGGCAUCAGCGGCAUCGCUGGCCAAAGCCACUCGAUGUCCAUCAUUCAUUUGGCUCCGAUGUACGAGCCAUGUUUAUG
------........((((((((((((.((.((((((((......))....(.(((((((.((((....))))..))))))))........))))))))))))))).).))))........ ( -40.50)
>DroSim_CAF1 115 120 + 1
CUAAUGAUGCUCUCUGGCCUGCAUCGAGAAGCCAAGGCACCAAGGCAUCAGCGGCAUCGCUGGCCAAAGCCACUCGAUGUCCAUCAUUCAUUUGGCUUCGAUGUACGAGCCAUGUUUAUG
..............(((((((((((((..(((((((((......))....(.(((((((.((((....))))..))))))))........))))))))))))))).).))))........ ( -41.00)
>consensus
CUAAUGAUGCUCUCUGGCCUGCAUCGAGAAGCCAAGGCACCAAGGCAUCAGCGGCAUCGCUGGCCAAAGCCACUCGAUGUCCAUCAUUCAUUUGGCUUCGAUGUACGAGCCAUGUUUAUG
..............(((((((((((((..(((((((((......))....(.(((((((.((((....))))..))))))))........))))))))))))))).).))))........ (-38.83 = -39.50 +   0.67)

alignment

secondary structure

dotplot

Window 5

Location	22,320,837 – 22,320,957
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-45.00
Consensus MFE	-42.39
Energy contribution	-42.17
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.94
SVM decision value	1.21
SVM RNA-class probability	0.930920
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320837 120 - 23771897
CAUAAACAUGGCUCGUACAUCGAUGCCAAAUGAAUGAUGGACAUCGAGUGGCUUCGGCCAGCGAUGCCGCUGAUGCCUUGGUGCCUUGGCUUCUCGAUGCAGGCCAGAGAGCAUCAUUAG
.........(((((((...(((((((((.........))).)))))).((((....)))))))).)))..(((((((((.(.((((..((........))))))).))).)))))).... ( -46.20)
>DroSec_CAF1 1 114 - 1
CAUAAACAUGGCUCGUACAUCGGAGCCAAAUGAAUGAUGGACAUCGAGUGGCUUUGGCCAGCGAUGCCGCUGAUGCCUUGGUGCCUUGGCUUCUCGAUGCAGGCCAGAGAGCAU------
........((((((........)))))).(((.....(((.(((((((.((((..((((((((....)))))..((....)))))..)))).)))))))....))).....)))------ ( -44.20)
>DroSim_CAF1 115 120 - 1
CAUAAACAUGGCUCGUACAUCGAAGCCAAAUGAAUGAUGGACAUCGAGUGGCUUUGGCCAGCGAUGCCGCUGAUGCCUUGGUGCCUUGGCUUCUCGAUGCAGGCCAGAGAGCAUCAUUAG
........(((((((.....)).)))))(((((.((.(((.(((((((.((((..((((((((....)))))..((....)))))..)))).)))))))....))).....))))))).. ( -44.60)
>consensus
CAUAAACAUGGCUCGUACAUCGAAGCCAAAUGAAUGAUGGACAUCGAGUGGCUUUGGCCAGCGAUGCCGCUGAUGCCUUGGUGCCUUGGCUUCUCGAUGCAGGCCAGAGAGCAUCAUUAG
........(((((((.....))).)))).(((.....(((.(((((((.((((..((((((((....)))))..((....)))))..)))).)))))))....))).....)))...... (-42.39 = -42.17 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	22,320,877 – 22,320,997
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-38.30
Consensus MFE	-37.72
Energy contribution	-37.50
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	0.98
SVM decision value	1.23
SVM RNA-class probability	0.933251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22320877 120 - 23771897
CGUCGUCUAACUGUGACUCAUGUCCAUAACAGUCAAUAAACAUAAACAUGGCUCGUACAUCGAUGCCAAAUGAAUGAUGGACAUCGAGUGGCUUCGGCCAGCGAUGCCGCUGAUGCCUUG
............((.((((((((((((....((......)).......(((((((.....))).))))........)))))))).)))).))...((((((((....)))))..)))... ( -38.00)
>DroSec_CAF1 35 120 - 1
CGUCGUCUAACUGUGACUCAUGUCCAUAACAGUCAAUAAACAUAAACAUGGCUCGUACAUCGGAGCCAAAUGAAUGAUGGACAUCGAGUGGCUUUGGCCAGCGAUGCCGCUGAUGCCUUG
............((.((((((((((((....((......)).......((((((........))))))........)))))))).)))).))...((((((((....)))))..)))... ( -39.20)
>DroSim_CAF1 155 120 - 1
CGUCGUCUAACUGUGACUCAUGUCCAUAACAGUCAAUAAACAUAAACAUGGCUCGUACAUCGAAGCCAAAUGAAUGAUGGACAUCGAGUGGCUUUGGCCAGCGAUGCCGCUGAUGCCUUG
............((.((((((((((((....((......)).......(((((((.....)).)))))........)))))))).)))).))...((((((((....)))))..)))... ( -37.70)
>consensus
CGUCGUCUAACUGUGACUCAUGUCCAUAACAGUCAAUAAACAUAAACAUGGCUCGUACAUCGAAGCCAAAUGAAUGAUGGACAUCGAGUGGCUUUGGCCAGCGAUGCCGCUGAUGCCUUG
............((.((((((((((((....((......)).......(((((((.....))).))))........)))))))).)))).))...((((((((....)))))..)))... (-37.72 = -37.50 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:32 2006