Locus 2318

Sequence ID	3R_DroMel_CAF1
Location	6,594,582 – 6,594,742
Length	160
Max. P	0.995112

overview

Window 0

Location	6,594,582 – 6,594,702
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.84
Mean single sequence MFE	-47.37
Consensus MFE	-41.71
Energy contribution	-41.93
Covariance contribution	0.23
Combinations/Pair	1.06
Mean z-score	-2.22
Structure conservation index	0.88
SVM decision value	0.61
SVM RNA-class probability	0.800326
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6594582 120 + 27905053
CAUCUUCAGCGGCUUUUAGGGCUUUAGCUUCUUCGGCUGCUUUUUGGGCGGCAGCUUCAGCCAGGAGAGCCUCUUCGGCAGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUAG
..........((((...((((((..((((......((((((.....))))))))))...((((((((.(((.(((((....)))....)).)))))))).)))))))))...)))).... ( -46.10)
>DroSec_CAF1 7038 117 + 1
CAUCUUCAGCGGCUUUUAAGGC---AGCUUCUUCGGCAGCUUUUUGGGCUGCAGCUUCGGCCAGGAGAGCCUCUUCGGCUGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGG
......(((.((((...(((((---....(((((.((((((.....)))))).((....))..)))))(((.....((((((.......)))))).....))).)))))...))))))). ( -50.10)
>DroSim_CAF1 7858 117 + 1
CAUCUUCAGCUGCUUUUAAGGC---AGCUUCUUCUGCAGCUUUUUGGGCGGCAGCUUCGGCCAGGAGAGCCUCUUCGGCAGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGG
........(((((((..(((((---.((.......)).)))))..)))))))......(((((((((.(((.....))).........(((.(((.....))).)))))))))))).... ( -45.90)
>consensus
CAUCUUCAGCGGCUUUUAAGGC___AGCUUCUUCGGCAGCUUUUUGGGCGGCAGCUUCGGCCAGGAGAGCCUCUUCGGCAGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGG
..........((((...(((((...((((......((((((.....))))))))))...((((((((.(((.(((((....)))....)).)))))))).))).)))))...)))).... (-41.71 = -41.93 +   0.23)

alignment

secondary structure

dotplot

Window 1

Location	6,594,622 – 6,594,742
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.00
Mean single sequence MFE	-52.08
Consensus MFE	-43.68
Energy contribution	-44.36
Covariance contribution	0.68
Combinations/Pair	1.11
Mean z-score	-2.38
Structure conservation index	0.84
SVM decision value	2.54
SVM RNA-class probability	0.995112
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6594622 120 + 27905053
UUUUUGGGCGGCAGCUUCAGCCAGGAGAGCCUCUUCGGCAGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUAGCAGCAGCCUGCUUUUCGGCCUCAGCCGUCAGGCGAUCCCU
.....(((.(((.(((.(.((((((((.(((.(((((....)))....)).)))))))).))).(((.....)))....).))).)))(((((..((((....))))..)))))..))). ( -49.00)
>DroSec_CAF1 7075 120 + 1
UUUUUGGGCUGCAGCUUCGGCCAGGAGAGCCUCUUCGGCUGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGGCAGCAGCCAGCUUUUCGGCCUCAGCCGUCAGGCGAUCCCU
......((((((.(((..(((((((((((((.....))))........(((.(((.....))).))))))))))))..))).)))))).((((..((((....))))..))))....... ( -56.70)
>DroSim_CAF1 7895 120 + 1
UUUUUGGGCGGCAGCUUCGGCCAGGAGAGCCUCUUCGGCAGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGGCAGCAGCCUGCUUUUCGGCCUCAGCCGUCAGGCGAUCCCU
.....((((.((.(((..(((((((((.(((.....))).........(((.(((.....))).))))))))))))..))).)).))))((((..((((....))))..))))....... ( -51.90)
>DroEre_CAF1 7450 120 + 1
UUUUUGGGCGGCAGCUUCGGCCAGGAGAGCCUCUUCGGCAGCGAUCUUGGCGGCUUCCUCGGCCGCCUUUUUGGCCUUGGCAGCAGCCUGCUUCUCGGCCUCAGCUGUCAGACGUUCCCU
....(((.(((.....))).)))((.((((.(((..((((((......(((((((.....))))))).....((((..(((((....)))))....))))...))))))))).)))))). ( -51.80)
>DroYak_CAF1 7475 120 + 1
UUUUUGUGCGGCAGCUUCGGCCUGGACAGCUGCCUCGGCAGCAAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGGCAGCAGCCUGCUUCUCGGCCUCAGCUGUCAGACGUUCCCU
.....((..(((((((..((((.(((..((((((..(((..(((....(((.(((.....))).)))...))))))..))))))((....))))).))))..)))))))..))....... ( -51.00)
>consensus
UUUUUGGGCGGCAGCUUCGGCCAGGAGAGCCUCUUCGGCAGCGAUUUUGGCGGCCUCCUCGGCAGCCUUUUUGGCCUUGGCAGCAGCCUGCUUUUCGGCCUCAGCCGUCAGGCGAUCCCU
.....((((.((.(((..(((((((((.(((.....))).........(((.(((.....))).))))))))))))..))).)).))))((((..((((....))))..))))....... (-43.68 = -44.36 +   0.68)

alignment

secondary structure

dotplot

Window 2

Location	6,594,622 – 6,594,742
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.00
Mean single sequence MFE	-50.66
Consensus MFE	-40.94
Energy contribution	-41.34
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-2.55
Structure conservation index	0.81
SVM decision value	2.20
SVM RNA-class probability	0.990187
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6594622 120 - 27905053
AGGGAUCGCCUGACGGCUGAGGCCGAAAAGCAGGCUGCUGCUAAGGCCAAAAAGGCUGCCGAGGAGGCCGCCAAAAUCGCUGCCGAAGAGGCUCUCCUGGCUGAAGCUGCCGCCCAAAAA
.(((...(((((.((((....)))).....))))).((.(((..(((((....(((.(((.....))).))).........(((.....))).....)))))..))).))..)))..... ( -50.30)
>DroSec_CAF1 7075 120 - 1
AGGGAUCGCCUGACGGCUGAGGCCGAAAAGCUGGCUGCUGCCAAGGCCAAAAAGGCUGCCGAGGAGGCCGCCAAAAUCGCAGCCGAAGAGGCUCUCCUGGCCGAAGCUGCAGCCCAAAAA
.(((.....(((.(((((..(((((...((((((((((.((....))......(((.(((.....))).)))......)))))).....))))....)))))..)))))))))))..... ( -51.90)
>DroSim_CAF1 7895 120 - 1
AGGGAUCGCCUGACGGCUGAGGCCGAAAAGCAGGCUGCUGCCAAGGCCAAAAAGGCUGCCGAGGAGGCCGCCAAAAUCGCUGCCGAAGAGGCUCUCCUGGCCGAAGCUGCCGCCCAAAAA
.(((...(((((.((((....)))).....))))).((.((...(((((....(((.(((.....))).))).........(((.....))).....)))))...)).))..)))..... ( -50.20)
>DroEre_CAF1 7450 120 - 1
AGGGAACGUCUGACAGCUGAGGCCGAGAAGCAGGCUGCUGCCAAGGCCAAAAAGGCGGCCGAGGAAGCCGCCAAGAUCGCUGCCGAAGAGGCUCUCCUGGCCGAAGCUGCCGCCCAAAAA
.(((......((.(((((..(((((((((((.((((........)))).....((((((.......))))))......)))(((.....)))))))..))))..))))).)))))..... ( -50.80)
>DroYak_CAF1 7475 120 - 1
AGGGAACGUCUGACAGCUGAGGCCGAGAAGCAGGCUGCUGCCAAGGCCAAAAAGGCUGCCGAGGAGGCCGCCAAAAUUGCUGCCGAGGCAGCUGUCCAGGCCGAAGCUGCCGCACAAAAA
.(....)((.((.(((((..(((((.....).(((.((((((..((((((...(((.(((.....))).)))....)))..)))..)))))).)))..))))..))))).)).))..... ( -50.10)
>consensus
AGGGAUCGCCUGACGGCUGAGGCCGAAAAGCAGGCUGCUGCCAAGGCCAAAAAGGCUGCCGAGGAGGCCGCCAAAAUCGCUGCCGAAGAGGCUCUCCUGGCCGAAGCUGCCGCCCAAAAA
.(((.......(.(((((..((((....(((.((((........)))).....(((.(((.....))).)))......)))(((.....)))......))))..))))))..)))..... (-40.94 = -41.34 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:30 2006