Locus 8542

Sequence ID	3L_DroMel_CAF1
Location	22,321,185 – 22,321,371
Length	186
Max. P	0.986898

overview

Window 7

Location	22,321,185 – 22,321,305
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-35.45
Consensus MFE	-35.45
Energy contribution	-35.45
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	1.00
SVM decision value	0.07
SVM RNA-class probability	0.568372
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22321185 120 + 23771897
CCUGUCAGUGUCAGUUGCCCUGAGUGGAGCUCAAGUGUGCCCCGCUCCUCCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGU
.((((((..((.((((((((.(((.(((((.............)))))..))).)).(((((((......)))))))...))))))....))....)))))).....(((....)))... ( -35.12)
>DroSec_CAF1 355 120 + 1
CCUGUCAGUGUCAGUUGCCCUGAGUGGAGCUCGAGUGUGCCCCGCUCCCUCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGU
.((((((..((.((((((((.(((.(((((.............)))))..))).)).(((((((......)))))))...))))))....))....)))))).....(((....)))... ( -35.62)
>DroSim_CAF1 475 120 + 1
CCUGUCAGUGUCAGUUGCCCUGAGUGGAGCUCGAGUGUGCACCGCUCCCUCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGU
.((((((..((.((((((((.(((.(((((.............)))))..))).)).(((((((......)))))))...))))))....))....)))))).....(((....)))... ( -35.62)
>consensus
CCUGUCAGUGUCAGUUGCCCUGAGUGGAGCUCGAGUGUGCCCCGCUCCCUCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGU
.((((((..((.((((((((.(((.(((((.............)))))..))).)).(((((((......)))))))...))))))....))....)))))).....(((....)))... (-35.45 = -35.45 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	22,321,185 – 22,321,305
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-41.15
Consensus MFE	-40.11
Energy contribution	-40.22
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-4.15
Structure conservation index	0.97
SVM decision value	2.06
SVM RNA-class probability	0.986898
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22321185 120 - 23771897
ACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGGAGGAGCGGGGCACACUUGAGCUCCACUCAGGGCAACUGACACUGACAGG
...(((....))).....((((((.........(((((((((.(((((((......)))))))....(((..(((((.((.....))...))))).))).)))))))))....)))))). ( -40.52)
>DroSec_CAF1 355 120 - 1
ACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGAGGGAGCGGGGCACACUCGAGCUCCACUCAGGGCAACUGACACUGACAGG
...(((....))).....((((((.........(((((((((.(((((((......)))))))......((((((((.(((....)))..))))).))).)))))))))....)))))). ( -42.52)
>DroSim_CAF1 475 120 - 1
ACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGAGGGAGCGGUGCACACUCGAGCUCCACUCAGGGCAACUGACACUGACAGG
...(((....))).....((((((.........(((((((((.(((((((......)))))))......(((((((((((....)))...))))).))).)))))))))....)))))). ( -40.42)
>consensus
ACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGAGGGAGCGGGGCACACUCGAGCUCCACUCAGGGCAACUGACACUGACAGG
...(((....))).....((((((.........(((((((((.(((((((......)))))))....(((..(((((.(((....)))..))))).))).)))))))))....)))))). (-40.11 = -40.22 +   0.11)

alignment

secondary structure

dotplot

Window 9

Location	22,321,225 – 22,321,345
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-31.83
Consensus MFE	-31.75
Energy contribution	-31.53
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.28
Structure conservation index	1.00
SVM decision value	1.49
SVM RNA-class probability	0.958679
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22321225 120 + 23771897
CCCGCUCCUCCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCG
...((((..((...)).(((((((......))))))).))))......((((.......((((....))))....(((((((((...)))))))))..(((......)))))))...... ( -30.30)
>DroSec_CAF1 395 120 + 1
CCCGCUCCCUCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCG
...((((((.....)).(((((((......))))))).))))......((((.......((((....))))....(((((((((...)))))))))..(((......)))))))...... ( -32.60)
>DroSim_CAF1 515 120 + 1
ACCGCUCCCUCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCG
...((((((.....)).(((((((......))))))).))))......((((.......((((....))))....(((((((((...)))))))))..(((......)))))))...... ( -32.60)
>consensus
CCCGCUCCCUCUCUGGUUAUUUGCUUAAGUGCAAAUAUGAGCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCG
...((((((.....)).(((((((......))))))).))))......((((.......((((....))))....(((((((((...)))))))))..(((......)))))))...... (-31.75 = -31.53 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	22,321,225 – 22,321,345
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-30.83
Consensus MFE	-29.47
Energy contribution	-29.80
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.96
SVM decision value	1.14
SVM RNA-class probability	0.921608
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22321225 120 - 23771897
CGAAAAUUGCGAAUCAUUCUUCAUGCUGUCAAAAUGUCUGACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGGAGGAGCGGG
......((((......((((((..(((((((.......))))))).....((((((...(((......)))....))))))..(((((((......)))))))....))))))..)))). ( -29.70)
>DroSec_CAF1 395 120 - 1
CGAAAAUUGCGAAUCAUUCUUCAUGCUGUCAAAAUGUCUGACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGAGGGAGCGGG
.....((((((((......)))..(((((((.......)))))))......)))))((((((..........))))))((((.(((((((......))))))).((.....))))))... ( -31.40)
>DroSim_CAF1 515 120 - 1
CGAAAAUUGCGAAUCAUUCUUCAUGCUGUCAAAAUGUCUGACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGAGGGAGCGGU
.....((((((((......)))..(((((((.......)))))))......)))))((((((..........))))))((((.(((((((......))))))).((.....))))))... ( -31.40)
>consensus
CGAAAAUUGCGAAUCAUUCUUCAUGCUGUCAAAAUGUCUGACAGCUAAUCAGCAAUAACUGUCAUUUAGCAAAUAGUUGCUCAUAUUUGCACUUAAGCAAAUAACCAGAGAGGGAGCGGG
.....((((((((......)))..(((((((.......)))))))......)))))((((((..........))))))((((.(((((((......))))))).((.....))))))... (-29.47 = -29.80 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	22,321,265 – 22,321,371
Length	106
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-35.00
Consensus MFE	-31.78
Energy contribution	-32.03
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.91
SVM decision value	0.18
SVM RNA-class probability	0.621681
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22321265 106 + 23771897
GCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCGUUCGGCUUGGAC--------------UGGCAGCCCGGUUA
((((....))))....((.(((((...(((((...(((((((((...)))))))))(((((((.((.....)).))))))))))))...)))--------------)).))......... ( -32.20)
>DroSec_CAF1 435 120 + 1
GCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCGUUCGGCUUGGACUCGGCUUGGAGCCCUGGCAGCCCGGUUA
..((((..((((((......((((...(((((...(((((((((...)))))))))(((((((.((.....)).))))))))))))...)))).(((.....))).))))))...)))). ( -36.40)
>DroSim_CAF1 555 120 + 1
GCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCGUUCGGCUUGGACUCGGCUUGGAGCCCUGGCAGCCCGGUUA
..((((..((((((......((((...(((((...(((((((((...)))))))))(((((((.((.....)).))))))))))))...)))).(((.....))).))))))...)))). ( -36.40)
>consensus
GCAACUAUUUGCUAAAUGACAGUUAUUGCUGAUUAGCUGUCAGACAUUUUGACAGCAUGAAGAAUGAUUCGCAAUUUUCGUUCGGCUUGGACUCGGCUUGGAGCCCUGGCAGCCCGGUUA
..((((..((((((.......(((...(((((...(((((((((...)))))))))(((((((.((.....)).))))))))))))...)))..(((.....))).))))))...)))). (-31.78 = -32.03 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:37 2006