Locus 8178

Sequence ID	3L_DroMel_CAF1
Location	21,525,378 – 21,525,565
Length	187
Max. P	0.925846

overview

Window 1

Location	21,525,378 – 21,525,487
Length	109
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	86.01
Mean single sequence MFE	-36.38
Consensus MFE	-26.75
Energy contribution	-26.38
Covariance contribution	-0.38
Combinations/Pair	1.08
Mean z-score	-1.70
Structure conservation index	0.74
SVM decision value	0.35
SVM RNA-class probability	0.700650
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21525378 109 - 23771897
CCAGGUCUGUCCCAGUCGGGGCACACUC-ACAUCUGGAUCCUUGCAACCAUGCAUCCCAUGCAUCCAUGCAUCCAUGUGCAUUUCUGGGUC--------UCUGGAUCUGCGGAUUUGC
.((((((((((((....)))))......-......((((((.((((....)))).((((((((..((((....))))))))....))))..--------...))))))..))))))). ( -34.30)
>DroSec_CAF1 30781 100 - 1
CCAGGUCUGUCCCAGUCGGGGCACACUC-GCAUCUGGAUCCUUGCAUCCAUGCAUCGCA---------GCAUCCAUGUGCAUUUCUGGGUC--------UCUGGAUCUGCGGAUUUGC
.((((((((((((....))))))....(-((((((((((((.(((((..((((......---------))))....))))).....)))))--------)..)))..)))))))))). ( -33.90)
>DroSim_CAF1 30853 100 - 1
CCAGGUCUGUCCCAGUCGGGGCACACUC-GCAUCUGGAUCCUUGCAUCCAUGCAUCCCA---------GCAUCCAUGUGCAUUUCUGGGUC--------UCUGGAUCUGCGGAUUUGC
.((((((((((((....))))))....(-((((((((((((.(((((..((((......---------))))....))))).....)))))--------)..)))..)))))))))). ( -33.90)
>DroYak_CAF1 5850 117 - 1
CCAGGUCUGUCCCAGUCGGGGUAUACUAGGCAUCUGGAUCCUUGCAACCAUGCAUCC-AGGCAUUCAGGCAUCCAUGUGCAUUUCUGGAUCUCUGGAUCUCUGGAUCUGCGGAGUUGC
(((((((((((((....)))).....)))))..))))......(((((..(((((((-(((.(((((((.(((((.(......).))))).))))))).))))))..))))..))))) ( -43.40)
>consensus
CCAGGUCUGUCCCAGUCGGGGCACACUC_GCAUCUGGAUCCUUGCAACCAUGCAUCCCA_________GCAUCCAUGUGCAUUUCUGGGUC________UCUGGAUCUGCGGAUUUGC
(((((((((((((....)))))..............(((((.((((....))))..............((((....))))......)))))...........))))))).)....... (-26.75 = -26.38 +  -0.38)

alignment

secondary structure

dotplot

Window 2

Location	21,525,408 – 21,525,526
Length	118
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	90.46
Mean single sequence MFE	-36.45
Consensus MFE	-29.62
Energy contribution	-29.93
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.81
SVM decision value	0.25
SVM RNA-class probability	0.651183
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21525408 118 - 23771897
UUCUUUGUUUUAUGGCGAAAGCCCAGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC-ACAUCUGGAUCCUUGCAACCAUGCAUCCCAUGCAUCCAUGCAUCCAUGUGC
.............(((....)))..((.(.....(((((...(((.((((((....)))))).))).-.)))))(((....((((...((((((...))))))...)))))))..).)) ( -33.90)
>DroSec_CAF1 30811 109 - 1
UUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC-GCAUCUGGAUCCUUGCAUCCAUGCAUCGCA---------GCAUCCAUGUGC
.............(((....))).(((.((.....)).))).(((.((((((....)))))).))).-((((.(((((.((((((....))))....)---------).))))).)))) ( -37.00)
>DroSim_CAF1 30883 109 - 1
UUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC-GCAUCUGGAUCCUUGCAUCCAUGCAUCCCA---------GCAUCCAUGUGC
.............(((....))).(((.((.....)).))).(((.((((((....)))))).))).-((((.(((((.((((((....))))....)---------).))))).)))) ( -37.00)
>DroYak_CAF1 5888 118 - 1
UUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGUAUACUAGGCAUCUGGAUCCUUGCAACCAUGCAUCC-AGGCAUUCAGGCAUCCAUGUGC
.............(((....)))..((.(.....(((((((.(((.(..(((....)))..).))).)))))))((((.((((.....((((....-..)))).)))).))))..).)) ( -37.90)
>consensus
UUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC_GCAUCUGGAUCCUUGCAACCAUGCAUCCCA_________GCAUCCAUGUGC
.............(((....))).(((.((.....)).))).(((.((((((....)))))).)))..((((.(((((.(.((((....))))..............).))))).)))) (-29.62 = -29.93 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	21,525,448 – 21,525,565
Length	117
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	97.45
Mean single sequence MFE	-34.05
Consensus MFE	-32.58
Energy contribution	-32.45
Covariance contribution	-0.13
Combinations/Pair	1.06
Mean z-score	-2.22
Structure conservation index	0.96
SVM decision value	1.17
SVM RNA-class probability	0.925846
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21525448 117 - 23771897
CCAUCUCCAUCAUAAACAACUGGCUCUUCUCGCCCAUAUUUCUUUGUUUUAUGGCGAAAGCCCAGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC-ACAUCUGGAUC
.....(((...........((((..(((.(((((.(((...........))))))))))).))))........(((((...(((.((((((....)))))).))).-.)))))))).. ( -31.70)
>DroSec_CAF1 30842 117 - 1
CCAUCUCCAUCAUAAACAACUGGCUCUUCUCGCCCAUAUUUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC-GCAUCUGGAUC
.....(((...........((((..(((.(((((.(((...........))))))))))).))))........((((((..(((.((((((....)))))).))).-))))))))).. ( -34.40)
>DroSim_CAF1 30914 117 - 1
CCAUCUCCAUCAUAAACAACUGGCUCUUCUCGCCCAUAUUUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC-GCAUCUGGAUC
.....(((...........((((..(((.(((((.(((...........))))))))))).))))........((((((..(((.((((((....)))))).))).-))))))))).. ( -34.40)
>DroYak_CAF1 5927 118 - 1
CCAUCUCCAUCAUAAACAACUGGCUCUUCUCGCCCAUAUUUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGUAUACUAGGCAUCUGGAUC
.....(((...........((((..(((.(((((.(((...........))))))))))).))))........(((((((.(((.(..(((....)))..).))).)))))))))).. ( -35.70)
>consensus
CCAUCUCCAUCAUAAACAACUGGCUCUUCUCGCCCAUAUUUCUUUGUUUUAUGGCGAAAGCCCGGCUCUCAAUAGGUGCCAGGUCUGUCCCAGUCGGGGCACACUC_GCAUCUGGAUC
.....(((...........((((..(((.(((((.(((...........))))))))))).))))........((((((..(((.((((((....)))))).)))..))))))))).. (-32.58 = -32.45 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:43 2006