Locus 6529

Sequence ID	2L_DroMel_CAF1
Location	18,382,211 – 18,382,385
Length	174
Max. P	0.999350

overview

Window 2

Location	18,382,211 – 18,382,327
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.44
Mean single sequence MFE	-48.55
Consensus MFE	-28.88
Energy contribution	-28.99
Covariance contribution	0.11
Combinations/Pair	1.28
Mean z-score	-3.29
Structure conservation index	0.59
SVM decision value	0.56
SVM RNA-class probability	0.781092
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18382211 116 - 22407834
GUGCUGGCUGC----CAUUUCCAGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGAUCCGCCUUCUUUUGCGCCUCCAAUUUAUCGGUUACGGGGGGCGUGGCCUCCU
((((.(((.((----((....((((((((........)))))))))))).)))))))..............(((.......((((((((.......((....)))))))))))))..... ( -48.02)
>DroVir_CAF1 341039 113 - 1
---UUGUUGGC----CAUUUCCGGCCGCAAUUACGGCUGCAGCUGUGGCUGCGGCACUUUUCUUAAGAUCUGCCUUCUUUUGCGCCUCCAAUUUAUCUGUGACCGGGGGCGUGGCCUCUU
---.....(((----(.......((((((.(((((((....))))))).))))))..........................((((((((...............)))))))))))).... ( -43.06)
>DroGri_CAF1 274533 113 - 1
---CUGUUGGC----CAUUUCCGGCCGCAAUAACCGCUGCAGCAGUCGCUGCGGCGCUCUUCUUUAGAUCGGCCUUCUUUUGGGCCUCCAAUUUAUCCGUGACGGGGGGCGUGACCUCCU
---..((((((----(......))))((......(((((((((....)))))))))..............(((((......)))))............)))))(((((......))))). ( -43.80)
>DroWil_CAF1 300264 119 - 1
CUGUU-GCUGCUGUGCAUUGCCGGCAGCAAUUACAGCUGCUGCUGUGGCAGCAGCACUUUUCUUCAGAUCGGCCUUCUUUUGUGCCUCCAAUUUAUCAGUUACUGGAGGCGUAGCCUCCU
(((((-(((((((.((...))))))))))).....((((((((....)))))))).........)))...(((.......((((((((((.............))))))))))))).... ( -47.63)
>DroYak_CAF1 236329 116 - 1
GUGCUGGCUGC----CAUUUCCAGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGGUCCGCCUUCUUUUGCGCCUCCAAUUUAUCGGUUACGGGGGGCGUGGCCUCCU
((((.(((.((----((....((((((((........)))))))))))).)))))))........(((((((((((((.....(((...........)))...)))))))).)))))... ( -52.20)
>DroAna_CAF1 205708 116 - 1
GUGCUGGCUGC----CAUUUCCGGCGGCUAUGACCGCCGCCGCCGUGGCCGCCGCACUCUUCUUCAGAUCGGCCUUCUUUUGCGCCUCCAACUUGUCAGUGACGGGGGGCGUGGCCUCCU
((((.(((.((----(((...(((((((.......)))))))..))))).))))))).............((((.......((((((((.(((....)))....)))))))))))).... ( -56.61)
>consensus
GUGCUGGCUGC____CAUUUCCGGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGAUCGGCCUUCUUUUGCGCCUCCAAUUUAUCAGUGACGGGGGGCGUGGCCUCCU
.....................((((((((........)))))))).((((((.((..(((.....)))...))..........((((((...............)))))))))))).... (-28.88 = -28.99 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	18,382,251 – 18,382,352
Length	101
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.64
Mean single sequence MFE	-39.20
Consensus MFE	-21.60
Energy contribution	-21.85
Covariance contribution	0.25
Combinations/Pair	1.32
Mean z-score	-3.14
Structure conservation index	0.55
SVM decision value	2.30
SVM RNA-class probability	0.991963
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18382251 101 + 22407834
AAAGAAGGCGGAUCUGAAGAAGAGUGCGGCAGCCACAGCGGCAGCGGUUAUUGCCGCUGGAAAUG----GCAGCCAGCACAAUUUAAAUGG---------CAUCGAGGCUCCCA
...(..(((...(((.....)))(((((((.(((((((((((((......)))))))))....))----)).))).))))...........---------.......)))..). ( -36.60)
>DroGri_CAF1 274573 92 + 1
AAAGAAGGCCGAUCUAAAGAAGAGCGCCGCAGCGACUGCUGCAGCGGUUAUUGCGGCCGGAAAUG----GCCAACAG---------AAUAA---------UGCCGAUGCACCCA
......(((((.(((.....)))(.(((((((..(((((....)))))..)))))))).....))----))).....---------.....---------(((....))).... ( -32.40)
>DroEre_CAF1 226533 101 + 1
AAAGAAGGCGGAUCUGAAGAAGAGUGCGGCAGCCACAGCGGCAGCGGUUAUUGCCGCUGGAAAUG----GCAGCCAGCACAACUUAAAUGG---------GAUCGAGGCUCCCA
.....((.(.(((((.(..(((.(((((((.(((((((((((((......)))))))))....))----)).))).))))..)))...).)---------))))..).)).... ( -40.30)
>DroWil_CAF1 300304 110 + 1
AAAGAAGGCCGAUCUGAAGAAAAGUGCUGCUGCCACAGCAGCAGCUGUAAUUGCUGCCGGCAAUGCACAGCAGC-AACAGAAUGGCAAUAG---CAGCGCAACUGAGGCACCAA
.......(((..((....))...((((((((((((((((....)))))..(((((((.(((...)).).)))))-))......)))...))---))))))......)))..... ( -41.10)
>DroYak_CAF1 236369 101 + 1
AAAGAAGGCGGACCUGAAGAAGAGUGCGGCAGCCACAGCGGCAGCGGUUAUUGCCGCUGGAAAUG----GCAGCCAGCACAAUUUAAACGG---------GAUCGAGGCUCCCA
..((....(((.((((..(((..(((((((.(((((((((((((......)))))))))....))----)).))).))))..)))...)))---------).)))...)).... ( -40.20)
>DroAna_CAF1 205748 107 + 1
AAAGAAGGCCGAUCUGAAGAAGAGUGCGGCGGCCACGGCGGCGGCGGUCAUAGCCGCCGGAAAUG----GCAGCCAGCACAAUUUAAACGGCAGUAG---CAUCGAAGCUCCCA
.......((((.(((.....)))(((((((.((((...(((((((.......)))))))....))----)).))).))))........)))).(.((---(......))).).. ( -44.60)
>consensus
AAAGAAGGCCGAUCUGAAGAAGAGUGCGGCAGCCACAGCGGCAGCGGUUAUUGCCGCCGGAAAUG____GCAGCCAGCACAAUUUAAAUGG_________CAUCGAGGCUCCCA
.......((...(((.....)))..))((.((((.(((((((((......)))))))))..........((.....))............................)))).)). (-21.60 = -21.85 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	18,382,251 – 18,382,352
Length	101
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.64
Mean single sequence MFE	-39.52
Consensus MFE	-19.19
Energy contribution	-19.12
Covariance contribution	-0.08
Combinations/Pair	1.43
Mean z-score	-3.32
Structure conservation index	0.49
SVM decision value	2.35
SVM RNA-class probability	0.992764
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18382251 101 - 22407834
UGGGAGCCUCGAUG---------CCAUUUAAAUUGUGCUGGCUGC----CAUUUCCAGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGAUCCGCCUUCUUU
..(((((......)---------)..........((((.(((.((----((....((((((((........)))))))))))).)))))))...........)))......... ( -35.40)
>DroGri_CAF1 274573 92 - 1
UGGGUGCAUCGGCA---------UUAUU---------CUGUUGGC----CAUUUCCGGCCGCAAUAACCGCUGCAGCAGUCGCUGCGGCGCUCUUCUUUAGAUCGGCCUUCUUU
.((.(((...((((---------.....---------.))))(((----(......)))))))....))((((((((....))))))))(((..((....))..)))....... ( -33.60)
>DroEre_CAF1 226533 101 - 1
UGGGAGCCUCGAUC---------CCAUUUAAGUUGUGCUGGCUGC----CAUUUCCAGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGAUCCGCCUUCUUU
.(((((.(..((((---------......(((..((((.(((.((----((....((((((((........)))))))))))).))))))).))).....)))).).))))).. ( -39.40)
>DroWil_CAF1 300304 110 - 1
UUGGUGCCUCAGUUGCGCUG---CUAUUGCCAUUCUGUU-GCUGCUGUGCAUUGCCGGCAGCAAUUACAGCUGCUGCUGUGGCAGCAGCACUUUUCUUCAGAUCGGCCUUCUUU
..(((((.......))))).---.....(((..((((((-(((((((.((...))))))))))).....((((((((....)))))))).........))))..)))....... ( -45.30)
>DroYak_CAF1 236369 101 - 1
UGGGAGCCUCGAUC---------CCGUUUAAAUUGUGCUGGCUGC----CAUUUCCAGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGGUCCGCCUUCUUU
.((((.......))---------)).........((((.(((.((----((....((((((((........)))))))))))).)))))))........(((....)))..... ( -40.00)
>DroAna_CAF1 205748 107 - 1
UGGGAGCUUCGAUG---CUACUGCCGUUUAAAUUGUGCUGGCUGC----CAUUUCCGGCGGCUAUGACCGCCGCCGCCGUGGCCGCCGCACUCUUCUUCAGAUCGGCCUUCUUU
.((.(((......)---)).))((((........((((.(((.((----(((...(((((((.......)))))))..))))).)))))))(((.....))).))))....... ( -43.40)
>consensus
UGGGAGCCUCGAUC_________CCAUUUAAAUUGUGCUGGCUGC____CAUUUCCAGCGGCAAUAACCGCUGCCGCUGUGGCUGCCGCACUCUUCUUCAGAUCCGCCUUCUUU
.((.((((............................((.....))..........((((((((........)))))))).)))).))((..(((.....)))...))....... (-19.19 = -19.12 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	18,382,291 – 18,382,385
Length	94
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	91.68
Mean single sequence MFE	-32.89
Consensus MFE	-31.62
Energy contribution	-30.93
Covariance contribution	-0.69
Combinations/Pair	1.15
Mean z-score	-2.21
Structure conservation index	0.96
SVM decision value	3.53
SVM RNA-class probability	0.999350
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18382291 94 + 22407834
GCAGCGGUUAUUGCCGCUGGAAAUGGCAGCCAGCACAAUUUAAAUGG------CAUCGAGGCUCCCAAGCCGCCAAAUACUUCCGUUUAAGCCGUUU--AGG
.(((((((....))))))).(((((((.((((............)))------).....((((....))))...................)))))))--... ( -32.10)
>DroSec_CAF1 226040 92 + 1
GCAGCGGUUAUUGCCGCUGGAAAUGGCAGCCAGCACAAUUUAAAUGG------CAUCGAGGCUCCCAAGCCGCCAAAUACUUCCGUUUGAGCCGUUU--A--
.(((((((....))))))).(((((((.((((............)))------).....((((....))))..(((((......))))).)))))))--.-- ( -33.30)
>DroSim_CAF1 234620 92 + 1
GCAGCGGUUAUUGCCGCUGGAAAUGGCAGCCAGCACAAUUUAAAUGG------CAUCGAGGCUCCCAAGCCGCCAAAUACUUCCGUUUGAGCCGUUU--A--
.(((((((....))))))).(((((((.((((............)))------).....((((....))))..(((((......))))).)))))))--.-- ( -33.30)
>DroEre_CAF1 226573 92 + 1
GCAGCGGUUAUUGCCGCUGGAAAUGGCAGCCAGCACAACUUAAAUGG------GAUCGAGGCUCCCAAGCCGCCAAAUACUUCCGUUUGAGCCGUUU--A--
.(((((((....))))))).(((((((.(....).....((((((((------((....((((....)))).........)))))))))))))))))--.-- ( -32.32)
>DroYak_CAF1 236409 92 + 1
GCAGCGGUUAUUGCCGCUGGAAAUGGCAGCCAGCACAAUUUAAACGG------GAUCGAGGCUCCCAAGCCGCCAAAUACUUCCGUUUGAGCCGUUU--A--
.(((((((....))))))).(((((((.(....).....((((((((------((....((((....)))).........)))))))))))))))))--.-- ( -34.22)
>DroAna_CAF1 205788 100 + 1
GCGGCGGUCAUAGCCGCCGGAAAUGGCAGCCAGCACAAUUUAAACGGCAGUAGCAUCGAAGCUCCCAAGCCGCCAAACACGUCCGUUUAGGCCGUUUUGA--
.(((((((....)))))))((((((((.................((((.(.(((......))).)...))))..((((......))))..))))))))..-- ( -32.10)
>consensus
GCAGCGGUUAUUGCCGCUGGAAAUGGCAGCCAGCACAAUUUAAAUGG______CAUCGAGGCUCCCAAGCCGCCAAAUACUUCCGUUUGAGCCGUUU__A__
.(((((((....))))))).(((((((.(....).....((((((((............((((....))))...........)))))))))))))))..... (-31.62 = -30.93 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:30 2006