Locus 3880

Sequence ID	2L_DroMel_CAF1
Location	11,359,051 – 11,359,143
Length	92
Max. P	0.811297

overview

Window 1

Location	11,359,051 – 11,359,143
Length	92
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	84.76
Mean single sequence MFE	-27.60
Consensus MFE	-17.68
Energy contribution	-18.24
Covariance contribution	0.56
Combinations/Pair	1.20
Mean z-score	-2.38
Structure conservation index	0.64
SVM decision value	0.65
SVM RNA-class probability	0.811297
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11359051 92 + 22407834
CCACUCGGCUUUCGAGUUUGUCGCUUCUCGGUUUCGGACUCG---UUUCGCUUCCAGCCCCGAGAUUCCGAUUCGAUUCCCGAUUCCGAUUUCGA
....((((...((((....((((..((((((..(.(((..((---...))..))).)..))))))...))))))))...))))...((....)). ( -24.80)
>DroSec_CAF1 76261 92 + 1
CCACUCGGCUUUCGAGUUUGUCGCCUCUCGGUUUCGGACUCG---UUUCGCUUCCAGCCCCGAGAUUCCGAUUCGAUUCCCGAUUCCGAUUUCGA
......((((..((((((((..(((....)))..))))))))---..........)))).((((((.(.((.(((.....))).)).))))))). ( -26.30)
>DroSim_CAF1 81016 92 + 1
CCACUCGGCUUUCGAGUUUGUCGCCUCUCGGUUUCGGACUCG---UUUCGCUUCCAGCCCCGAGAUUCCGAUUCGAUUCCCGAUUCCGAUUUCGA
......((((..((((((((..(((....)))..))))))))---..........)))).((((((.(.((.(((.....))).)).))))))). ( -26.30)
>DroEre_CAF1 79813 92 + 1
CCACUCGGCUGUCGAGUUUGUCGCCUCUCGGUUUCGGACUCG---UUUCGCUUCCAGCCCCGAGAUUCCGAUUCGAUUCCCGAUUCCGAUUUCGA
......(((((.((((((((..(((....)))..))))))))---.........))))).((((((.(.((.(((.....))).)).))))))). ( -29.30)
>DroAna_CAF1 68118 87 + 1
CUGCUUCGUAUUCGCAUUCG--GAUACUCGCUUUCGGAUUGGGAUAUUCGGAUUCAGU-CUGAGAUUCCGA-----CUCCCGAUUCCGAUUCCGA
.......(((((((....))--)))))(((...(((((((((((...(((((.((...-....)).)))))-----.)))))).)))))...))) ( -31.30)
>consensus
CCACUCGGCUUUCGAGUUUGUCGCCUCUCGGUUUCGGACUCG___UUUCGCUUCCAGCCCCGAGAUUCCGAUUCGAUUCCCGAUUCCGAUUUCGA
...(((((....((((((((..(((....)))..)))))))).......((.....)).)))))..((.((.(((.....))).)).))...... (-17.68 = -18.24 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	11,359,051 – 11,359,143
Length	92
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	84.76
Mean single sequence MFE	-28.92
Consensus MFE	-19.32
Energy contribution	-21.16
Covariance contribution	1.84
Combinations/Pair	1.04
Mean z-score	-2.15
Structure conservation index	0.67
SVM decision value	0.55
SVM RNA-class probability	0.776925
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11359051 92 - 22407834
UCGAAAUCGGAAUCGGGAAUCGAAUCGGAAUCUCGGGGCUGGAAGCGAAA---CGAGUCCGAAACCGAGAAGCGACAAACUCGAAAGCCGAGUGG
(((...((((...(((((.((......)).)))))(((((.(........---).)))))....))))....)))...(((((.....))))).. ( -28.50)
>DroSec_CAF1 76261 92 - 1
UCGAAAUCGGAAUCGGGAAUCGAAUCGGAAUCUCGGGGCUGGAAGCGAAA---CGAGUCCGAAACCGAGAGGCGACAAACUCGAAAGCCGAGUGG
.((...((((..(((((.......(((...((((((...((((..((...---))..))))...))))))..)))....)))))...)))).)). ( -28.90)
>DroSim_CAF1 81016 92 - 1
UCGAAAUCGGAAUCGGGAAUCGAAUCGGAAUCUCGGGGCUGGAAGCGAAA---CGAGUCCGAAACCGAGAGGCGACAAACUCGAAAGCCGAGUGG
.((...((((..(((((.......(((...((((((...((((..((...---))..))))...))))))..)))....)))))...)))).)). ( -28.90)
>DroEre_CAF1 79813 92 - 1
UCGAAAUCGGAAUCGGGAAUCGAAUCGGAAUCUCGGGGCUGGAAGCGAAA---CGAGUCCGAAACCGAGAGGCGACAAACUCGACAGCCGAGUGG
.((...((((..(((((.......(((...((((((...((((..((...---))..))))...))))))..)))....)))))...)))).)). ( -28.90)
>DroAna_CAF1 68118 87 - 1
UCGGAAUCGGAAUCGGGAG-----UCGGAAUCUCAG-ACUGAAUCCGAAUAUCCCAAUCCGAAAGCGAGUAUC--CGAAUGCGAAUACGAAGCAG
(((.(.(((((...((((.-----(((((.((....-...)).)))))...))))..(((....).))...))--))).).)))........... ( -29.40)
>consensus
UCGAAAUCGGAAUCGGGAAUCGAAUCGGAAUCUCGGGGCUGGAAGCGAAA___CGAGUCCGAAACCGAGAGGCGACAAACUCGAAAGCCGAGUGG
......((((..(((((.......(((...((((((...((((..((......))..))))...))))))..)))....)))))...)))).... (-19.32 = -21.16 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:33 2006