Locus 9625

Sequence ID	3R_DroMel_CAF1
Location	25,430,358 – 25,430,497
Length	139
Max. P	0.980843

overview

Window 5

Location	25,430,358 – 25,430,466
Length	108
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	80.58
Mean single sequence MFE	-26.42
Consensus MFE	-13.88
Energy contribution	-13.68
Covariance contribution	-0.20
Combinations/Pair	1.17
Mean z-score	-2.48
Structure conservation index	0.53
SVM decision value	1.15
SVM RNA-class probability	0.922881
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25430358 108 + 27905053
AAUGUUAUCGUUGUAAAUUAUAAAAUGGAAUCCAUUAAUGCAGCCAGC-ACACAUACUAGAGUGUACAUACAUAGUGUAUAGU---GUGUGUGGGUGCAGCCGCACAGCGGA
.......(((((((.........(((((...)))))..((((.(((.(-((((((.......(((((((.....)))))))))---)))))))).)))).....))))))). ( -33.81)
>DroSec_CAF1 113184 93 + 1
AAUGUUAUCGUUGUAAAUUAUAAAAUGGAAUCCAUUAAUGCAGCCAGAUAUGCA----------CACAUACAUAGUG---------GUGUGUUGGUGCAGCCGCACAGUGGA
.......(((((...........)))))..((((((..(((.((......((((----------(((((((......---------))))))..))))))).))).)))))) ( -21.40)
>DroSim_CAF1 115211 86 + 1
AAUGUUAUCGUUGUAAAUUAUAAAAUGGAAUCCAUUAAUGCAAC-------ACA----------UACACACAUAGUG---------GUGUGUGGGUGCAGCCGCACAGCGGA
.......(((((((.........(((((...)))))..((((.(-------(((----------(((.(((...)))---------)))))))..)))).....))))))). ( -26.10)
>DroEre_CAF1 120419 99 + 1
AAUGUUAUCGUUGUAAAUUAUAAAAUGGAAUCCAUUAAUGCAGCCAGAUAUGCA----------CACAUGCAUAGUAUAUUGC---GUGCAUAGAUGCACCCACACAGCGGA
.......(((((((.........(((((...)))))...((((.....((((((----------....)))))).....))))---(((((....)))))....))))))). ( -24.70)
>DroYak_CAF1 123342 102 + 1
AAUGUUAUCGUUGUAAAUUAUAAAAUGGAAUCCAUUAAUGCAGCCAGAUGUGCA----------CACAUACAUAGUAUAUACUGUAGUGUGUAGAUGCACCCACACAGCGGA
.......(((((((.........(((((...))))).............(((((----------((((((((((((....))))).)))))).).)))))....))))))). ( -26.10)
>consensus
AAUGUUAUCGUUGUAAAUUAUAAAAUGGAAUCCAUUAAUGCAGCCAGAUAUGCA__________CACAUACAUAGUGUAU______GUGUGUAGGUGCAGCCGCACAGCGGA
.......(((((((.........(((((...)))))..((((((.......))..............((((((.............))))))...)))).....))))))). (-13.88 = -13.68 +  -0.20)

alignment

secondary structure

dotplot

Window 6

Location	25,430,393 – 25,430,497
Length	104
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	78.19
Mean single sequence MFE	-28.72
Consensus MFE	-15.96
Energy contribution	-15.64
Covariance contribution	-0.32
Combinations/Pair	1.38
Mean z-score	-2.05
Structure conservation index	0.56
SVM decision value	0.81
SVM RNA-class probability	0.855351
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25430393 104 + 27905053
UAAUGCAGCCAGC-ACACAUACUAGAGUGUACAUACAUAGUGUAUAGU---GUGUGUGGGUGCAGCCGCACAGCGGAAUGGUGGGCCAUCUAUGCAAAAUUCAUUUGC
...((((.(((.(-((((((.......(((((((.....)))))))))---)))))))).)))).((((...)))).((((....))))....(((((.....))))) ( -33.51)
>DroSec_CAF1 113219 89 + 1
UAAUGCAGCCAGAUAUGCA----------CACAUACAUAGUG---------GUGUGUUGGUGCAGCCGCACAGUGGAAUGGCGGGCCAUCUAUGCAAAAUUCAUUUGC
...((((...((((.((((----------(((((((......---------))))))..))))).((((.((......))))))...)))).))))............ ( -26.60)
>DroSim_CAF1 115246 82 + 1
UAAUGCAAC-------ACA----------UACACACAUAGUG---------GUGUGUGGGUGCAGCCGCACAGCGGAAUGGCGGGCCAUCUAUGCAAAAUUCAUUUGC
...((((.(-------(((----------(((.(((...)))---------)))))))..)))).((((.((......)))))).........(((((.....))))) ( -26.00)
>DroEre_CAF1 120454 95 + 1
UAAUGCAGCCAGAUAUGCA----------CACAUGCAUAGUAUAUUGC---GUGCAUAGAUGCACCCACACAGCGGAAUGGCGGGCCAUCUAUGCAAAAUGCAAUUGC
....(((......((((((----------....))))))....(((((---(((((((((((..(((.(.((......))).))).))))))))))...))))))))) ( -30.80)
>DroYak_CAF1 123377 98 + 1
UAAUGCAGCCAGAUGUGCA----------CACAUACAUAGUAUAUACUGUAGUGUGUAGAUGCACCCACACAGCGGAAUGGCGAGCCAUCUAUGCAAAAUUCAUUUGC
...((((((((...(((((----------((((((((((((....))))).)))))).).)))))((.......))..))))((....))..))))............ ( -26.70)
>consensus
UAAUGCAGCCAGAUAUGCA__________CACAUACAUAGUGUAU______GUGUGUAGGUGCAGCCGCACAGCGGAAUGGCGGGCCAUCUAUGCAAAAUUCAUUUGC
....((((........................((((...)))).........((((((((((...((((.((......))))))..))))))))))........)))) (-15.96 = -15.64 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	25,430,393 – 25,430,497
Length	104
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	78.19
Mean single sequence MFE	-29.24
Consensus MFE	-15.92
Energy contribution	-14.92
Covariance contribution	-1.00
Combinations/Pair	1.32
Mean z-score	-2.50
Structure conservation index	0.54
SVM decision value	1.87
SVM RNA-class probability	0.980843
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25430393 104 - 27905053
GCAAAUGAAUUUUGCAUAGAUGGCCCACCAUUCCGCUGUGCGGCUGCACCCACACAC---ACUAUACACUAUGUAUGUACACUCUAGUAUGUGU-GCUGGCUGCAUUA
(((((.....)))))...(((((....)))))((((...)))).((((.((((((((---(.(((((.....)))))(((......))))))))-).))).))))... ( -30.40)
>DroSec_CAF1 113219 89 - 1
GCAAAUGAAUUUUGCAUAGAUGGCCCGCCAUUCCACUGUGCGGCUGCACCAACACAC---------CACUAUGUAUGUG----------UGCAUAUCUGGCUGCAUUA
(((((.....)))))...(((((....))))).....(((((((((((((((((...---------.....))).)).)----------)))......)))))))).. ( -25.00)
>DroSim_CAF1 115246 82 - 1
GCAAAUGAAUUUUGCAUAGAUGGCCCGCCAUUCCGCUGUGCGGCUGCACCCACACAC---------CACUAUGUGUGUA----------UGU-------GUUGCAUUA
(((((.....)))))...(((((....))))).....(((((((.(((..((((((.---------.....))))))..----------)))-------))))))).. ( -27.10)
>DroEre_CAF1 120454 95 - 1
GCAAUUGCAUUUUGCAUAGAUGGCCCGCCAUUCCGCUGUGUGGGUGCAUCUAUGCAC---GCAAUAUACUAUGCAUGUG----------UGCAUAUCUGGCUGCAUUA
((((((((....((((((((((((((((((......)).)))))).)))))))))).---)))))....((((((....----------))))))......))).... ( -37.10)
>DroYak_CAF1 123377 98 - 1
GCAAAUGAAUUUUGCAUAGAUGGCUCGCCAUUCCGCUGUGUGGGUGCAUCUACACACUACAGUAUAUACUAUGUAUGUG----------UGCACAUCUGGCUGCAUUA
(((((.....))))).......((..((((..((((...))))((((....(((((.((((..........))))))))----------)))))...)))).)).... ( -26.60)
>consensus
GCAAAUGAAUUUUGCAUAGAUGGCCCGCCAUUCCGCUGUGCGGCUGCACCCACACAC______AUACACUAUGUAUGUG__________UGCAUAUCUGGCUGCAUUA
(((.........(((((((((((....)))).....((((.((......)).))))............)))))))...............((.......))))).... (-15.92 = -14.92 +  -1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:34 2006