Locus 4487

Sequence ID	2L_DroMel_CAF1
Location	12,856,552 – 12,856,676
Length	124
Max. P	0.990438

overview

Window 5

Location	12,856,552 – 12,856,652
Length	100
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	89.51
Mean single sequence MFE	-34.75
Consensus MFE	-28.27
Energy contribution	-28.60
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.08
Structure conservation index	0.81
SVM decision value	1.29
SVM RNA-class probability	0.938280
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12856552 100 + 22407834
--------------GAGUGUAUGUGUG-UCUAAACGGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAG
--------------...(((.((((((-((...((....))(....)...)))).)))).))).............((((.((((((((((((......)))))))))))))))) ( -33.50)
>DroVir_CAF1 40329 100 + 1
--------------GAGUGUGUGUGUGCUCUAAACGGAAGUGGCAACAUUGGCGCCACA-GCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAG
--------------.((((((((.(((((....((....))(....)...)))))))))-(((((....)))))))))((.((((((((((((......)))))))))))))).. ( -35.00)
>DroPse_CAF1 46549 96 + 1
--G----------------UGUGUGUG-UCUAAACGGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAG
--.----------------((((.(((-((...((....))(....)...))))))))).(((((....)))))..((((.((((((((((((......)))))))))))))))) ( -34.90)
>DroSec_CAF1 37086 100 + 1
--------------GAGUGUAUGUGUG-UCUAAGCGGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAG
--------------...(((.((((((-((...((....))(....)...)))).)))).))).............((((.((((((((((((......)))))))))))))))) ( -33.80)
>DroMoj_CAF1 71820 100 + 1
--------------GUGUGUGUAUGUUCUCUAAACGGAAGUGGCAACAUUGGCGCCACA-GCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAC
--------------(((.(((((((((((....((....)))).)))))..))))))).-(((((....)))))...(((.((((((((((((......))))))))))))))). ( -30.80)
>DroAna_CAF1 61174 114 + 1
UUGUGUGUGCUUAGAUGUGUGUUGGUG-UCUAAACGGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCGG
.......(((((.(.((.((((..(((-(....((....))....))))..)))))))))))).............((((.((((((((((((......)))))))))))))))) ( -40.50)
>consensus
______________GAGUGUGUGUGUG_UCUAAACGGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAG
......................................((((....))))((((.((.((((....)))).)).))))((.((((((((((((......)))))))))))))).. (-28.27 = -28.60 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	12,856,552 – 12,856,652
Length	100
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	89.51
Mean single sequence MFE	-25.93
Consensus MFE	-22.69
Energy contribution	-22.55
Covariance contribution	-0.14
Combinations/Pair	1.04
Mean z-score	-2.75
Structure conservation index	0.87
SVM decision value	2.16
SVM RNA-class probability	0.989330
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12856552 100 - 22407834
CUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCCGUUUAGA-CACACAUACACUC--------------
....(((((.((((((......)))))).)))))((((((((.........))))).((((((.......)))))).........))-)............-------------- ( -25.20)
>DroVir_CAF1 40329 100 - 1
CUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGC-UGUGGCGCCAAUGUUGCCACUUCCGUUUAGAGCACACACACACUC--------------
(((((((((.((((((......)))))).))))).)))).............(((-(((((((.......))))))...(.....)))))...........-------------- ( -25.10)
>DroPse_CAF1 46549 96 - 1
CUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCCGUUUAGA-CACACACA----------------C--
....(((((.((((((......)))))).)))))((((((((.........))))).((((((.......)))))).........))-).......----------------.-- ( -25.20)
>DroSec_CAF1 37086 100 - 1
CUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCCGCUUAGA-CACACAUACACUC--------------
....(((((.((((((......)))))).)))))(((((((.((((....))))...((((((.......))))))...))))..))-)............-------------- ( -26.90)
>DroMoj_CAF1 71820 100 - 1
GUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGC-UGUGGCGCCAAUGUUGCCACUUCCGUUUAGAGAACAUACACACAC--------------
(((.(((((.((((((......)))))).))))).(((((((.........))))-)((((((.......)))))).........)).......)))....-------------- ( -25.40)
>DroAna_CAF1 61174 114 - 1
CCGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCCGUUUAGA-CACCAACACACAUCUAAGCACACACAA
..(((((((.((((((......)))))).))))).))(((((.........))))).((((((.......))))))....(((((((-............)))))))........ ( -27.80)
>consensus
CUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCCGUUUAGA_CACACACACACUC______________
..(((((((.((((((......)))))).))))).))((((.((((....))))...((((((.......))))))...))))................................ (-22.69 = -22.55 +  -0.14)

alignment

secondary structure

dotplot

Window 7

Location	12,856,572 – 12,856,676
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.22
Mean single sequence MFE	-38.65
Consensus MFE	-33.01
Energy contribution	-32.78
Covariance contribution	-0.22
Combinations/Pair	1.08
Mean z-score	-3.82
Structure conservation index	0.85
SVM decision value	2.21
SVM RNA-class probability	0.990438
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12856572 104 + 22407834
GGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAGCG-CACAUUU-CGGUG------CUCAAAGGGU--------
...((((....))))((((((..((((....)))).(((((((((.((((((((((((......))))))))))))))))))-.)))...-.))))------))........-------- ( -42.10)
>DroVir_CAF1 40350 99 + 1
GGAAGUGGCAACAUUGGCGCCACA-GCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAGUG-CACAUUU-----G------CCAAAAGUGU--------
....(((((.........))))).-(((((......(((((((((.((((((((((((......))))))))))))))))))-.))))))-----)------).........-------- ( -37.20)
>DroGri_CAF1 58967 107 + 1
GGAAGUGGCAACGUUGGCGCCACA-GCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAGUG-CACAUUU-----G------CCAAAACUGGGUAGGGGG
((...((((((.((((......))-)).........(((((((((.((((((((((((......))))))))))))))))))-.))).))-----)------)))...)).......... ( -38.90)
>DroWil_CAF1 54016 112 + 1
GGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAGCGACACAUUUUCGGUGAGGAGUUUCAAAGGGA--------
....(((((.........))))).............(((((((((.((((((((((((......)))))))))))))))))))))...(..(..((((....))))..)..)-------- ( -43.10)
>DroMoj_CAF1 71841 99 + 1
GGAAGUGGCAACAUUGGCGCCACA-GCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCACUG-CACAUUU-----G------CCAAAAGUUG--------
((((((((((.....((((.((.(-((....)))..)).))))((.((((((((((((......))))))))))))))..))-).)))))-----.------))........-------- ( -31.70)
>DroAna_CAF1 61208 103 + 1
GGAAGUGGCAACAUUGGCGCCACAAGCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCGGCG-CACAUUU-UGGAG------ACCAAG-AAG--------
....(((((.........))))).............(((((((((.((((((((((((......))))))))))))))))))-.)))(((-(((..------.)))))-)..-------- ( -38.90)
>consensus
GGAAGUGGCAACAUUGGCGCCACA_GCAAAAGUUUUUGUCGCUGACAGGAAGUUGCAAUUUUGUUUGCAAUUUCCUUCAGCG_CACAUUU_____G______CCAAAAGUGG________
....(((((.........))))).............((.((((((.((((((((((((......)))))))))))))))))).))................................... (-33.01 = -32.78 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	12,856,572 – 12,856,676
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.22
Mean single sequence MFE	-32.48
Consensus MFE	-22.88
Energy contribution	-23.22
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.63
Structure conservation index	0.70
SVM decision value	0.58
SVM RNA-class probability	0.790273
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12856572 104 - 22407834
--------ACCCUUUGAG------CACCG-AAAUGUG-CGCUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCC
--------.......(((------((...-.....((-(((((((((((.((((((......)))))).))))).)))))).))........)))))((((((.......)))))).... ( -36.39)
>DroVir_CAF1 40350 99 - 1
--------ACACUUUUGG------C-----AAAUGUG-CACUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGC-UGUGGCGCCAAUGUUGCCACUUCC
--------........((------(-----(((.((.-(.(((((((((.((((((......)))))).))))).)))).)......)).)))))-)((((((.......)))))).... ( -31.00)
>DroGri_CAF1 58967 107 - 1
CCCCCUACCCAGUUUUGG------C-----AAAUGUG-CACUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGC-UGUGGCGCCAACGUUGCCACUUCC
................((------(-----(((.((.-(.(((((((((.((((((......)))))).))))).)))).)......)).)))))-)((((((.......)))))).... ( -31.00)
>DroWil_CAF1 54016 112 - 1
--------UCCCUUUGAAACUCCUCACCGAAAAUGUGUCGCUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCC
--------...................(((((.(.((((((((((((((.((((((......)))))).))))).)))))))))...).)))))...((((((.......)))))).... ( -37.00)
>DroMoj_CAF1 71841 99 - 1
--------CAACUUUUGG------C-----AAAUGUG-CAGUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGC-UGUGGCGCCAAUGUUGCCACUUCC
--------.......(((------(-----((..(((-(.....(((((.((((((......)))))).)))))..((((((.........))))-))..)))).....))))))..... ( -29.70)
>DroAna_CAF1 61208 103 - 1
--------CUU-CUUGGU------CUCCA-AAAUGUG-CGCCGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGCUUGUGGCGCCAAUGUUGCCACUUCC
--------...-..((((------...((-...((.(-(((((((((((.((((((......)))))).))))).)).((((((((....)))).))))))))))).))..))))..... ( -29.80)
>consensus
________CCACUUUGGG______C_____AAAUGUG_CACUGAAGGAAAUUGCAAACAAAAUUGCAACUUCCUGUCAGCGACAAAAACUUUUGC_UGUGGCGCCAAUGUUGCCACUUCC
...................................((.(.(((((((((.((((((......)))))).))))).)))).).)).............((((((.......)))))).... (-22.88 = -23.22 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:59 2006