Locus 6870

Sequence ID	3R_DroMel_CAF1
Location	18,172,521 – 18,172,667
Length	146
Max. P	0.952162

overview

Window 1

Location	18,172,521 – 18,172,612
Length	91
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.63
Mean single sequence MFE	-26.13
Consensus MFE	-15.95
Energy contribution	-17.05
Covariance contribution	1.10
Combinations/Pair	1.12
Mean z-score	-2.86
Structure conservation index	0.61
SVM decision value	1.26
SVM RNA-class probability	0.937089
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18172521 91 + 27905053
CCAAAAAGCAAAAGUUU------GC------ACCGCCAGUGC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAA
.......((((....))------))------...((((.(((-----------------(((((...))))..((((((....))))))))))..)))).(((((((.....))))))). ( -25.70)
>DroGri_CAF1 217034 114 + 1
CCAAAAAGCAAAAGUUU------GCCUUCAGGCUGCAAGUGGACGUCGAGACGCAUUUGUAUACACAAUGUUUGUGCUGAUUGCAGCGCAGCAAAUAGCUUCUGAUUUCACAAAUCAAAA
.............((..------(((....))).))..(((((.(((.(((.((((((((..((.....)).(((((((....))))))))))))).)).)))))))))))......... ( -29.60)
>DroEre_CAF1 216676 91 + 1
CCAAAAAGCAAAAGUUU------GC------ACCGCCAGUGC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAA
.......((((....))------))------...((((.(((-----------------(((((...))))..((((((....))))))))))..)))).(((((((.....))))))). ( -25.70)
>DroYak_CAF1 211228 91 + 1
CCAAAAAGCAAAAGUUU------GC------ACCGCCAGUGC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAA
.......((((....))------))------...((((.(((-----------------(((((...))))..((((((....))))))))))..)))).(((((((.....))))))). ( -25.70)
>DroMoj_CAF1 257710 100 + 1
CCAAAAAGCAAAAGUUUUUUGCUGCCUGCUGCCUGC----UGACUGC----------------UACAAUGUUUGUGCUGAUUGCAGCGCUGCAAAUAGCUUUUGAUUUCACAAAUCAAAA
..(((((((....)))))))((((..(((.((((((----.....((----------------.(((.....))))).....)))).)).)))..)))).(((((((.....))))))). ( -27.10)
>DroAna_CAF1 195853 91 + 1
CCAAAAAGCAAAAGUUU------CC------ACUGCCAGUGC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAA
........((((((((.------..------..(((..((((-----------------((((((((.....)))).....)))))))).)))...))))))))................ ( -23.00)
>consensus
CCAAAAAGCAAAAGUUU______GC______ACCGCCAGUGC_________________UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAA
..................................((((((((..................))))....((((.((((((....))))))))))..)))).(((((((.....))))))). (-15.95 = -17.05 +   1.10)

alignment

secondary structure

dotplot

Window 2

Location	18,172,549 – 18,172,649
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.16
Mean single sequence MFE	-34.93
Consensus MFE	-28.04
Energy contribution	-28.27
Covariance contribution	0.22
Combinations/Pair	1.07
Mean z-score	-3.08
Structure conservation index	0.80
SVM decision value	1.13
SVM RNA-class probability	0.919770
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18172549 100 + 27905053
GC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCAG
((-----------------.(((((...((((.((((((....))))))))))...(((((((((((.....)))))))))))((.((((((---...)))))).))..)))))..)).. ( -34.80)
>DroGri_CAF1 217068 115 + 1
GGACGUCGAGACGCAUUUGUAUACACAAUGUUUGUGCUGAUUGCAGCGCAGCAAAUAGCUUCUGAUUUCACAAAUCAAAAGUUUCUUGUGC-----GCCGCACGUGAUUUAUGCCUGCAG
((.((((((((.((..((((....))))....(((((((....)))))))))....(((((.(((((.....))))).)))))))))).))-----)))(((.((.......)).))).. ( -31.80)
>DroEre_CAF1 216704 100 + 1
GC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCGG
((-----------------.(((((...((((.((((((....))))))))))...(((((((((((.....)))))))))))...))))))---).(((((.((.......)).))))) ( -35.30)
>DroYak_CAF1 211256 100 + 1
GC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCGG
((-----------------.(((((...((((.((((((....))))))))))...(((((((((((.....)))))))))))...))))))---).(((((.((.......)).))))) ( -35.30)
>DroMoj_CAF1 257746 99 + 1
UGACUGC----------------UACAAUGUUUGUGCUGAUUGCAGCGCUGCAAAUAGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGC-----AGCGCACGUGAUUUAUGCCUGCAG
...((((----------------.(((.....)))((.(((..(.((((((((...(((((((((((.....))))))))))).....)))-----)))))..)..)))...))..)))) ( -35.50)
>DroAna_CAF1 195881 103 + 1
GC-----------------UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCGCCGCGCCGCACGUGAUUUAUGCCUGCGG
((-----------------.((.(((((((((.((((((....))))))))))...(((((((((((.....)))))))))))..))))).)).)).(((((.((.......)).))))) ( -36.90)
>consensus
GC_________________UGCAUACAAUGUUUGUGCUGAUUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG___CGCCGCACGUGAUUUAUGCCUGCAG
................................(((((((....)))))))(((...(((((((((((.....)))))))))))((.((((((......)))))).))........))).. (-28.04 = -28.27 +   0.22)

alignment

secondary structure

dotplot

Window 3

Location	18,172,549 – 18,172,649
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.16
Mean single sequence MFE	-31.52
Consensus MFE	-24.36
Energy contribution	-24.83
Covariance contribution	0.47
Combinations/Pair	1.08
Mean z-score	-2.75
Structure conservation index	0.77
SVM decision value	0.55
SVM RNA-class probability	0.777668
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18172549 100 - 27905053
CUGCAGGCAUAAAUCACGUGCGGCG---CGCACAAGAAACUUUUGAUUUGUGAAAUCAAAAGCCAUUUGCUGUGCUGCAAUCAGCACAAACAUUGUAUGCA-----------------GC
((((((((.........(((((...---))))).......((((((((.....)))))))))))......(((((((....))))))).........))))-----------------). ( -32.00)
>DroGri_CAF1 217068 115 - 1
CUGCAGGCAUAAAUCACGUGCGGC-----GCACAAGAAACUUUUGAUUUGUGAAAUCAGAAGCUAUUUGCUGCGCUGCAAUCAGCACAAACAUUGUGUAUACAAAUGCGUCUCGACGUCC
......((((........((((((-----(((((((...(((((((((.....)))))))))...)))).)))))))))....(((((.....)))))......))))............ ( -34.50)
>DroEre_CAF1 216704 100 - 1
CCGCAGGCAUAAAUCACGUGCGGCG---CGCACAAGAAACUUUUGAUUUGUGAAAUCAAAAGCCAUUUGCUGUGCUGCAAUCAGCACAAACAUUGUAUGCA-----------------GC
(((((.(.........).))))).(---((.((((....(((((((((.....)))))))))........(((((((....)))))))....)))).))).-----------------.. ( -29.80)
>DroYak_CAF1 211256 100 - 1
CCGCAGGCAUAAAUCACGUGCGGCG---CGCACAAGAAACUUUUGAUUUGUGAAAUCAAAAGCCAUUUGCUGUGCUGCAAUCAGCACAAACAUUGUAUGCA-----------------GC
(((((.(.........).))))).(---((.((((....(((((((((.....)))))))))........(((((((....)))))))....)))).))).-----------------.. ( -29.80)
>DroMoj_CAF1 257746 99 - 1
CUGCAGGCAUAAAUCACGUGCGCU-----GCACAAGAAACUUUUGAUUUGUGAAAUCAAAAGCUAUUUGCAGCGCUGCAAUCAGCACAAACAUUGUA----------------GCAGUCA
.(((((((((.......))))(((-----(((.((....(((((((((.....)))))))))...)))))))).)))))....(((((.....))).----------------))..... ( -29.40)
>DroAna_CAF1 195881 103 - 1
CCGCAGGCAUAAAUCACGUGCGGCGCGGCGCACAAGAAACUUUUGAUUUGUGAAAUCAAAAGCCAUUUGCUGUGCUGCAAUCAGCACAAACAUUGUAUGCA-----------------GC
..(((.(((........((((...((((((((((((...(((((((((.....)))))))))...)))).)))))))).....))))......))).))).-----------------.. ( -33.64)
>consensus
CCGCAGGCAUAAAUCACGUGCGGCG___CGCACAAGAAACUUUUGAUUUGUGAAAUCAAAAGCCAUUUGCUGUGCUGCAAUCAGCACAAACAUUGUAUGCA_________________GC
..((((((.........(((((......))))).......((((((((.....)))))))))))...)))(((((((....)))))))................................ (-24.36 = -24.83 +   0.47)

alignment

secondary structure

dotplot

Window 4

Location	18,172,572 – 18,172,667
Length	95
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	91.37
Mean single sequence MFE	-32.37
Consensus MFE	-26.65
Energy contribution	-26.77
Covariance contribution	0.11
Combinations/Pair	1.10
Mean z-score	-2.94
Structure conservation index	0.82
SVM decision value	1.42
SVM RNA-class probability	0.952162
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18172572 95 + 27905053
UUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCAGCAGGAGC-AAGUCCAGAU---U
((((.((((((.....(((((((((((.....)))))))))))..)))))).---.((.(((.((.......)).))).))....))-))........---. ( -27.60)
>DroSim_CAF1 208673 95 + 1
UUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCGGCAGGAGC-AAGUCCAGAU---U
((((.((((((.....(((((((((((.....)))))))))))..)))))).---.((((((.((.......)).))))))....))-))........---. ( -33.70)
>DroEre_CAF1 216727 95 + 1
UUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCGGCAGGGGC-AAGUCCAGAU---U
..((.((((((.....(((((((((((.....)))))))))))..)))))))---)((((((.((.......)).))))))..(((.-...)))....---. ( -33.90)
>DroYak_CAF1 211279 95 + 1
UUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG---CGCCGCACGUGAUUUAUGCCUGCGGCAGGAGC-AAGUCCAGAU---U
((((.((((((.....(((((((((((.....)))))))))))..)))))).---.((((((.((.......)).))))))....))-))........---. ( -33.70)
>DroMoj_CAF1 257770 89 + 1
UUGCAGCGCUGCAAAUAGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGC-----AGCGCACGUGAUUUAUGCCUGCAGCAG--------UCCAAAUGUCU
.....((((((((...(((((((((((.....))))))))))).....)))-----)))))((((......(((.....))).--------.....)))).. ( -30.90)
>DroAna_CAF1 195904 99 + 1
UUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCGCCGCGCCGCACGUGAUUUAUGCCUGCGGCAGGAGCCGAGUCCAGAU---U
..((.((.((.(((..(((((((((((.....)))))))))))..))))).)).))((((((.((.......)).)))))).(((......)))....---. ( -34.40)
>consensus
UUGCAGCACAGCAAAUGGCUUUUGAUUUCACAAAUCAAAAGUUUCUUGUGCG___CGCCGCACGUGAUUUAUGCCUGCGGCAGGAGC_AAGUCCAGAU___U
.(((.(((..(((...(((((((((((.....)))))))))))((.((((((......)))))).))....))).))).)))(((......)))........ (-26.65 = -26.77 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:03 2006