Locus 8030

Sequence ID	3R_DroMel_CAF1
Location	21,568,773 – 21,568,905
Length	132
Max. P	0.990244

overview

Window 3

Location	21,568,773 – 21,568,884
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.64
Mean single sequence MFE	-26.81
Consensus MFE	-17.92
Energy contribution	-18.09
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.67
SVM decision value	0.09
SVM RNA-class probability	0.579045
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21568773 111 + 27905053
CUCC---AUUCUCCACAGCAGCGAAGGAAUUUUCAAUCAAAUCGCUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGCG--CUAACUUUUAU----
....---..........(.(((((..((........))...))))))(((((((((.((((((.(........).)))))).))))..(((((......))))--)..)))))...---- ( -29.50)
>DroVir_CAF1 45535 106 + 1
-------UUCCCCGGCCACUGCAAAAGAAUUUUCAAUCAAAUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGG---UAAACUUUUAU----
-------...((((((....)).......................((((((.((((.....(((((................))))).))))))))))))))---...........---- ( -23.69)
>DroWil_CAF1 38344 113 + 1
UGCC---AUUCGUCGUCGUUCGCAAAGAAUUUCCAAUCAAAUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGUUGAAAAACUUUUAU----
(((.---...((....))...)))............((((.((((.(((((.((((.....(((((................))))).)))))))))))))))))...........---- ( -24.39)
>DroMoj_CAF1 43785 109 + 1
-UCG---UUCCCCUGCCAAUGCAAAAGAAUUUUCAAUCAAAUCGUUCAAAGAGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGC---UAAACUUUUAU----
-..(---(((...(((....)))...))))....................((((((.((((((.(........).)))))).))))))..(((......)))---...........---- ( -23.60)
>DroAna_CAF1 39236 118 + 1
CGCCACCCACCGGCGGAGAUGCGAAGGAAUUUUCAAUCAAAUCGCUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGCG--CAAACUUUUAUACGA
((((.......))))..((.((((..((........))...))))))(((((((((.((((((.(........).)))))).))))..(((((......))))--)..)))))....... ( -36.00)
>DroPer_CAF1 52728 106 + 1
C--------CUCUCAGAGAUCCAAAAGAAUUUUCAAUCAAAUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCUCUCGCGCCUUUGAUGGCG--CAAACUUUUAU----
.--------......((((.......((....)).........(((.....(((((......)))))....)))..........))))(((((......))))--)..........---- ( -23.70)
>consensus
C_CC___AUCCCCCGCAGAUGCAAAAGAAUUUUCAAUCAAAUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGCG__CAAACUUUUAU____
.........................................(((.((((((.((((.....(((((................))))).)))))))))))))................... (-17.92 = -18.09 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	21,568,773 – 21,568,884
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.64
Mean single sequence MFE	-35.77
Consensus MFE	-23.02
Energy contribution	-24.05
Covariance contribution	1.03
Combinations/Pair	1.30
Mean z-score	-2.62
Structure conservation index	0.64
SVM decision value	0.55
SVM RNA-class probability	0.778379
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21568773 111 - 27905053
----AUAAAAGUUAG--CGCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAGCGAUUUGAUUGAAAAUUCCUUCGCUGCUGUGGAGAAU---GGAG
----...(((((..(--((((......)))))..(((((((((.((((......)))).)))))))))))))).(((((...((.(....).))..))))).((((.....))---)).. ( -37.50)
>DroVir_CAF1 45535 106 - 1
----AUAAAAGUUUA---CCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAUUUGAUUGAAAAUUCUUUUGCAGUGGCCGGGGAA-------
----...........---(((.....((((((((((((......))))....))))))))....((.((((..(((.(((((......))))).)))...)))))).)))...------- ( -30.00)
>DroWil_CAF1 38344 113 - 1
----AUAAAAGUUUUUCAACCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAUUUGAUUGGAAAUUCUUUGCGAACGACGACGAAU---GGCA
----......((..(((.....((((((((....))(((((((.((((......)))).)))))))...)))))).((.((((...((.....))...)))))).....))).---.)). ( -30.50)
>DroMoj_CAF1 43785 109 - 1
----AUAAAAGUUUA---GCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCUCUUUGAACGAUUUGAUUGAAAAUUCUUUUGCAUUGGCAGGGGAA---CGA-
----......(((((---(((......)))..(((((((((((.((((......)))).)))))))))))..)))))..............(((((((((....)))))))))---...- ( -38.30)
>DroAna_CAF1 39236 118 - 1
UCGUAUAAAAGUUUG--CGCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAGCGAUUUGAUUGAAAAUUCCUUCGCAUCUCCGCCGGUGGGUGGCG
..(((........))--)((((((...((((.(((((((((((.((((......)))).))))))))).......((((...((.(....).))..))))...))))))....)))))). ( -45.00)
>DroPer_CAF1 52728 106 - 1
----AUAAAAGUUUG--CGCCAUCAAAGGCGCGAGAGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAUUUGAUUGAAAAUUCUUUUGGAUCUCUGAGAG--------G
----.......((((--((((......)))))))).(((((((.((((......)))).)))))))...((((.(..((((..(..((....))..)..))))..).))))--------. ( -33.30)
>consensus
____AUAAAAGUUUG__CGCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAUUUGAUUGAAAAUUCUUUUGCAUCGGCGGGGGAA___GG_G
......................((((((((....))(((((((.((((......)))).)))))))...)))))).................((((((((....))))))))........ (-23.02 = -24.05 +   1.03)

alignment

secondary structure

dotplot

Window 5

Location	21,568,810 – 21,568,905
Length	95
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	76.01
Mean single sequence MFE	-31.37
Consensus MFE	-16.74
Energy contribution	-17.07
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.53
SVM decision value	0.99
SVM RNA-class probability	0.895271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21568810 95 + 27905053
AUCGCUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGCG--CUAACUUUUAUGCGAAAGAAG--CGGCC----------UG-----C--CGC
.((((..(((((((((.((((((.(........).)))))).))))..(((((......))))--)..)))))...)))).....(--(((..----------..-----)--))) ( -36.20)
>DroPse_CAF1 52468 99 + 1
AUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCUCUCGCGCCUUUGAUGGCG--CAAACUUUUAUGGGGCGGGAU--GAGGC----------UAAAAA-A--GAC
.((((((....(((((......)))))..............(((((..(((((......))))--)...(......))))))))))--))...----------......-.--... ( -30.80)
>DroGri_CAF1 43467 113 + 1
AUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGC---UAAACUUUUAUGCCAAACAGGAACGAGCAACGGAGAUCUGAAUGGAAUCAC
.(((((((...(((((......))))).................(((((..(((....((((---...........))))...)))..)))))..........)))))))...... ( -31.80)
>DroWil_CAF1 38381 103 + 1
AUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGUUGAAAAACUUUUAUGCGGAGCAGGGAUGAGC----------UGAGUC-U--CUG
...(((.....(((((......)))))....)))..........((((.(((...(((.((((....)))).))).)))))))((((((....----------...)))-)--)). ( -29.70)
>DroMoj_CAF1 43821 101 + 1
AUCGUUCAAAGAGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGC---UAAACUUUUAUGCCCCGGCC------------AAGAUCUGAACGGCAGCAC
.(((((((..((((((.((((((.(........).)))))).))))))(.(((......(((---...........)))..))))------------......)))))))...... ( -29.80)
>DroPer_CAF1 52760 95 + 1
AUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCUCUCGCGCCUUUGAUGGCG--CAAACUUUUAUGGGGCGGGAU--GGGGC----------UG-----A--GAC
.((((((....(((((......)))))..............(((((..(((((......))))--)...(......))))))))))--))...----------..-----.--... ( -29.90)
>consensus
AUCGUUCAAAGUGCGCAUUUAGGCGCAAAUAAACACUUAAACGCGCUCGCGCCUUUGAUGGCG__CAAACUUUUAUGCGGAGGAAG__CGGGC__________UGAA___A__CAC
.(((.((((((.((((.....(((((................))))).)))))))))))))....................................................... (-16.74 = -17.07 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	21,568,810 – 21,568,905
Length	95
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	76.01
Mean single sequence MFE	-33.47
Consensus MFE	-20.50
Energy contribution	-21.03
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-2.59
Structure conservation index	0.61
SVM decision value	2.20
SVM RNA-class probability	0.990244
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21568810 95 - 27905053
GCG--G-----CA----------GGCCG--CUUCUUUCGCAUAAAAGUUAG--CGCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAGCGAU
(((--(-----..----------..)))--).....((((...(((((..(--((((......)))))..(((((((((.((((......)))).))))))))))))))..)))). ( -43.30)
>DroPse_CAF1 52468 99 - 1
GUC--U-UUUUUA----------GCCUC--AUCCCGCCCCAUAAAAGUUUG--CGCCAUCAAAGGCGCGAGAGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAU
...--.-......----------...((--(....((..........((((--((((......)))))))).(((((((.((((......)))).)))))))))....)))..... ( -26.80)
>DroGri_CAF1 43467 113 - 1
GUGAUUCCAUUCAGAUCUCCGUUGCUCGUUCCUGUUUGGCAUAAAAGUUUA---GCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAU
.(((......)))......((((((((((.(((...((((.(((....)))---))))....))).))))))(((((((.((((......)))).)))))))........)))).. ( -36.10)
>DroWil_CAF1 38381 103 - 1
CAG--A-GACUCA----------GCUCAUCCCUGCUCCGCAUAAAAGUUUUUCAACCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAU
(((--(-(....(----------((........))).(((((....(((....)))......((((((((((((......))))....))))))))..)))))..)))))...... ( -26.60)
>DroMoj_CAF1 43821 101 - 1
GUGCUGCCGUUCAGAUCUU------------GGCCGGGGCAUAAAAGUUUA---GCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCUCUUUGAACGAU
(((((.(((..(((...))------------)..))))))))....(((((---(((......)))..(((((((((((.((((......)))).)))))))))))..)))))... ( -40.30)
>DroPer_CAF1 52760 95 - 1
GUC--U-----CA----------GCCCC--AUCCCGCCCCAUAAAAGUUUG--CGCCAUCAAAGGCGCGAGAGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAU
.((--(-----(.----------((...--.....)).............(--((((......))))))))).(((((((((((.((((((....)))))).)))).))))))).. ( -27.70)
>consensus
GUG__U___UUCA__________GCCCC__CUUCCGCCGCAUAAAAGUUUG__CGCCAUCAAAGGCGCGAGCGCGUUUAAGUGUUUAUUUGCGCCUAAAUGCGCACUUUGAACGAU
..............................................((((....(((......)))....(((((((((.((((......)))).))))))))).....))))... (-20.50 = -21.03 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:49 2006