Locus 7811

Sequence ID	2L_DroMel_CAF1
Location	22,097,119 – 22,097,439
Length	320
Max. P	0.968571

overview

Window 6

Location	22,097,119 – 22,097,239
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-39.48
Consensus MFE	-36.81
Energy contribution	-36.62
Covariance contribution	-0.19
Combinations/Pair	1.08
Mean z-score	-1.57
Structure conservation index	0.93
SVM decision value	0.34
SVM RNA-class probability	0.695077
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22097119 120 + 22407834
CAUGCACUUCUAUCUCUUUAAGAGGGAGUUCCCUGAGUGUGGCAGAGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGACUGAUGAU
..........((((........((((....))))..(((((((((((((((.((((....))))((((.((((((....)))).))))))....))))))))).))))))....)))).. ( -38.70)
>DroSec_CAF1 4622 120 + 1
CAUGCACUUCUAUCUCUUUAAGAGGGAGUUCCCUGAGUGUGGCAGGGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAU
........(((((((((((...((((....))))..(.....))))))))))))..(((((((((.(.(((...((((((((((......)))))))))).)))...).))))))).)). ( -38.60)
>DroSim_CAF1 4792 120 + 1
CAUGCACUUCUAUCUCUUUAAGAGGGAGUUCCCUGAGUGUGGCAGGGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAU
........(((((((((((...((((....))))..(.....))))))))))))..(((((((((.(.(((...((((((((((......)))))))))).)))...).))))))).)). ( -38.60)
>DroYak_CAF1 8456 120 + 1
CAUGCACUUCUACCUCUUUAAGAGGGAGUUCCCAGAGUGUGGCAGGGAGGUGAAUUUCUCAAUCGAGCGAAAGUGGAAGCACUGUGGCUUUAAUGCUUCUCUGCCCACAAGGUUGAUGAU
......(.((.((((........(((....)))...(((.(((((((((((((.....))....((((.(.((((....)))).).))))....)))))))))))))).)))).)).).. ( -42.00)
>consensus
CAUGCACUUCUAUCUCUUUAAGAGGGAGUUCCCUGAGUGUGGCAGGGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAU
......(.((.(((........((((....))))..(((.(((((((((((.((((....))))((((...((((....))))...))))....))))))))))))))..))).)).).. (-36.81 = -36.62 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	22,097,159 – 22,097,279
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-45.62
Consensus MFE	-43.35
Energy contribution	-43.10
Covariance contribution	-0.25
Combinations/Pair	1.08
Mean z-score	-2.23
Structure conservation index	0.95
SVM decision value	1.63
SVM RNA-class probability	0.968571
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22097159 120 + 22407834
GGCAGAGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGACUGAUGAUACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGG
(((((((((((.((((....))))((((.((((((....)))).))))))....)))))))))))..................((((((((.((((((......)))))).)))))))). ( -45.40)
>DroSec_CAF1 4662 120 + 1
GGCAGGGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAUACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGG
(((((((((((.((((....))))((((.((((((....)))).))))))....)))))))))))..................((((((((.((((((......)))))).)))))))). ( -44.50)
>DroSim_CAF1 4832 120 + 1
GGCAGGGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAUACACGGCUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGG
(((((((((((.((((....))))((((.((((((....)))).))))))....)))))))))))....(((((((.(((((.(((((((.....))))))).)))..))..))))))). ( -47.50)
>DroYak_CAF1 8496 120 + 1
GGCAGGGAGGUGAAUUUCUCAAUCGAGCGAAAGUGGAAGCACUGUGGCUUUAAUGCUUCUCUGCCCACAAGGUUGAUGAUACAUGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGG
(((((((((((((.....))....((((.(.((((....)))).).))))....)))))))))))..................((((((((.((((((......)))))).)))))))). ( -45.10)
>consensus
GGCAGGGAGGUGGAUUUCUCAAUCGAGCGCAAAUGGAGGCAUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAUACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGG
(((((((((((.((((....))))((((...((((....))))...))))....)))))))))))..................((((((((.((((((......)))))).)))))))). (-43.35 = -43.10 +  -0.25)

alignment

secondary structure

dotplot

Window 8

Location	22,097,199 – 22,097,319
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-37.00
Consensus MFE	-33.86
Energy contribution	-34.17
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-1.60
Structure conservation index	0.92
SVM decision value	0.09
SVM RNA-class probability	0.579242
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22097199 120 + 22407834
AUUGUGGCUUUAAUGCUUCUCUGCCCACACGACUGAUGAUACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUG
((((((.((((.((((((((..((((.((....))........((((((((.((((((......)))))).))))))))))..))..)))).)))).(((......))))))))))))). ( -36.70)
>DroSec_CAF1 4702 120 + 1
AUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAUACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUG
((((((.((((.((((((((..((...(.(((((((.((..(((((((((.....)))).).))))..))..))))))))...))..)))).)))).(((......))))))))))))). ( -37.00)
>DroSim_CAF1 4872 120 + 1
AUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAUACACGGCUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUG
((((((.((((.((((((((..((...(.(((((((.(((((.(((((((.....))))))).)))..))..))))))))...))..)))).)))).(((......))))))))))))). ( -40.60)
>DroYak_CAF1 8536 120 + 1
ACUGUGGCUUUAAUGCUUCUCUGCCCACAAGGUUGAUGAUACAUGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAAAAUGCAUACCUGAAAAAAGGGGAGUACAAUG
..((((.((((.((((.((((.(((.....))).)).))((((((((((((.((((((......)))))).)))))))...)))))......)))).(((......)))))))))))... ( -33.70)
>consensus
AUUGUGGCUUUAAUGCUUCUCUGCCCACACGAUUGAUGAUACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUG
((((((((......))....((.(((.................((((((((.((((((......)))))).))))))))((((((.......)))).))........))).)))))))). (-33.86 = -34.17 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	22,097,239 – 22,097,359
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.17
Mean single sequence MFE	-39.15
Consensus MFE	-33.95
Energy contribution	-33.45
Covariance contribution	-0.50
Combinations/Pair	1.13
Mean z-score	-2.53
Structure conservation index	0.87
SVM decision value	1.48
SVM RNA-class probability	0.957641
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22097239 120 + 22407834
ACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUGUGAUCGUUGUCGAUUGGAGCGCAAGCUCAGCCAACAUAAA
.....(((((..((((((......))))))...((((((((((((.......)))).)))............(.((((((....))))))))))))((((....))))..)))))..... ( -39.70)
>DroSec_CAF1 4742 120 + 1
ACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUGUGAUCGUAGUCGAUUGGAGCGCGAGCUCAGCCAACUUAAA
...((((((((.((((((......)))))).))))))))((((((.......)))).))......(((..(.((.......(((((....))))).((((....)))).)))..)))... ( -38.70)
>DroSim_CAF1 4912 120 + 1
ACACGGCUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUGUGAUCGUAGUCGAUUGGAGCGCGAGCUCAGCCAACUUAAA
((.(((((((.....))))))).))((((....((((((((((((.......)))).)))..........((.(((.........))).)))))))((((....))))))))........ ( -40.30)
>DroYak_CAF1 8576 120 + 1
ACAUGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAAAAUGCAUACCUGAAAAAAGGGGAGUACAAUGUGAUCGUUGCCGAUUGGAGUUCAAGUUCAGCUAAUAUAAA
...(((((((((((((((......))))))((((((((((...........(((...(((......)))...)))(((((....))))))))))))))).....)))))))))....... ( -37.90)
>consensus
ACACGGUUGGAUGAGCCAGUCGCGUGGCUCUUUCAAUCGGGAUGUGAAGAAUGCAUACCUAAAAAAAGGGGAGUACAAUGUGAUCGUAGUCGAUUGGAGCGCAAGCUCAGCCAACAUAAA
...((((((((.((((((......)))))).))))))))((((((.......)))).))........((............(((((....))))).((((....))))..))........ (-33.95 = -33.45 +  -0.50)

alignment

secondary structure

dotplot

Window 0

Location	22,097,319 – 22,097,439
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-36.80
Consensus MFE	-32.89
Energy contribution	-32.20
Covariance contribution	-0.69
Combinations/Pair	1.20
Mean z-score	-1.77
Structure conservation index	0.89
SVM decision value	0.83
SVM RNA-class probability	0.862298
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22097319 120 + 22407834
UGAUCGUUGUCGAUUGGAGCGCAAGCUCAGCCAACAUAAACUACUUUUCGGUGGUAAAGCUUAUAGAGACCUUUGGAGCUGAGUUGGCCCAAUUUAUAAGGAACCUCAAUCGUCAGUUUG
......(((.((((((((((....)))).((((((....((((((....))))))..(((((..((....))...)))))..))))))..................)))))).))).... ( -38.90)
>DroSec_CAF1 4822 120 + 1
UGAUCGUAGUCGAUUGGAGCGCGAGCUCAGCCAACUUAAACUACUUUUCGGUGGUGAAGCUCAUAGAGACCUUUGGAGCUGAGUUGGCCCAAUUUAUAAGGAACCUCAAUCGUCAGUUUG
........(.((((((((((....)))).((((((((..((((((....))))))..(((((.((((....)))))))))))))))))..................)))))).)...... ( -41.00)
>DroSim_CAF1 4992 120 + 1
UGAUCGUAGUCGAUUGGAGCGCGAGCUCAGCCAACUUAAACUACUUUUCGGUGGUGAAGCUCAUUGAGACCUUUGGAGCUGAGUUGGCCCAAUUUAUAAGGAACCUCAAUCGUCAGUUUG
........(.((((((((((....)))).((((((((..((((((....))))))..(((((...((....))..)))))))))))))..................)))))).)...... ( -39.90)
>DroYak_CAF1 8656 120 + 1
UGAUCGUUGCCGAUUGGAGUUCAAGUUCAGCUAAUAUAAACUACUUUUCGGUGGUAAAGCUUAUAGAGACCCUUGGAGCUCAGUUGGCCCAAUUUAUAAGGGACCUUAAUCGUCAGUUUG
......(((.((((((..((((.................((((((....))))))....((((((((.....((((.(((.....)))))))))))))))))))..)))))).))).... ( -27.40)
>consensus
UGAUCGUAGUCGAUUGGAGCGCAAGCUCAGCCAACAUAAACUACUUUUCGGUGGUAAAGCUCAUAGAGACCUUUGGAGCUGAGUUGGCCCAAUUUAUAAGGAACCUCAAUCGUCAGUUUG
........(.((((((((((....)))).((((((....((((((....))))))..(((((..((....))...)))))..))))))..................)))))).)...... (-32.89 = -32.20 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:25 2006