Locus 594

Sequence ID	X_DroMel_CAF1
Location	1,665,484 – 1,665,675
Length	191
Max. P	0.999960

overview

Window 0

Location	1,665,484 – 1,665,601
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	79.10
Mean single sequence MFE	-33.37
Consensus MFE	-20.55
Energy contribution	-23.00
Covariance contribution	2.45
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.62
SVM decision value	0.13
SVM RNA-class probability	0.598199
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665484 117 + 22224390
CCUAAUUAGAUUACAUGCAAAUUAAAUGCAGCACGUAGAUACAUAUGUAUGGGUGCGUGCCACUAUAUAGUGGAGUACAUGCUCGAUUGGUGGUGGUGUCGAGCGU---UUGGGCUCAUG
.............((((....((((((((.((((.(..((((....))))).))))(..(((((((.((((.((((....)))).)))))))))))..)...))))---))))...)))) ( -36.00)
>DroSim_CAF1 683 114 + 1
CCUAAUUAGAUUACAUGCAAAUUAAAUGCAGCACGUACAUGCAUAUGUAUGUGUGCGUGCCACUAUAUAGUGGAGUACAUGCUCGAUUGGUG---GCGUUGAGCGU---UUGGGCUCAUU
.........................(((((.(((((((((....))))))))))))))(((((((....((.((((....)))).)))))))---))..(((((..---....))))).. ( -37.60)
>DroYak_CAF1 729 98 + 1
CCUAAUUAGAUUACAUGCAAAUUAAAUGCAGCACGU------------AUGUGUGCGUGCCACUAC-------UGUACAUGCUCGAUUGGUG---CUGACGAGCGAGCGUUGAGCUUAUG
...........((((((((.......))))((((((------------(....)))))))......-------))))...(((((((...((---((....))))...)))))))..... ( -26.50)
>consensus
CCUAAUUAGAUUACAUGCAAAUUAAAUGCAGCACGUA_AU_CAUAUGUAUGUGUGCGUGCCACUAUAUAGUGGAGUACAUGCUCGAUUGGUG___GUGUCGAGCGU___UUGGGCUCAUG
.((((((........((((.......))))((((((((((....))))))))))((((((((((....)))))....)))))..))))))..........((((.........))))... (-20.55 = -23.00 +   2.45)

alignment

secondary structure

dotplot

Window 1

Location	1,665,484 – 1,665,601
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.10
Mean single sequence MFE	-25.43
Consensus MFE	-18.08
Energy contribution	-17.98
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-1.56
Structure conservation index	0.71
SVM decision value	0.30
SVM RNA-class probability	0.679678
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665484 117 - 22224390
CAUGAGCCCAA---ACGCUCGACACCACCACCAAUCGAGCAUGUACUCCACUAUAUAGUGGCACGCACCCAUACAUAUGUAUCUACGUGCUGCAUUUAAUUUGCAUGUAAUCUAAUUAGG
..(((((....---..))))).................(((((((...((((....))))(((.((((..((((....))))....)))))))........)))))))............ ( -26.00)
>DroSim_CAF1 683 114 - 1
AAUGAGCCCAA---ACGCUCAACGC---CACCAAUCGAGCAUGUACUCCACUAUAUAGUGGCACGCACACAUACAUAUGCAUGUACGUGCUGCAUUUAAUUUGCAUGUAAUCUAAUUAGG
..(((((....---..)))))....---..........(((((((..(((((....)))))...((((((.(((((....))))).))).)))........)))))))............ ( -29.10)
>DroYak_CAF1 729 98 - 1
CAUAAGCUCAACGCUCGCUCGUCAG---CACCAAUCGAGCAUGUACA-------GUAGUGGCACGCACACAU------------ACGUGCUGCAUUUAAUUUGCAUGUAAUCUAAUUAGG
.....((.....((..(((((....---.......)))))..))...-------...(..(((((.......------------.)))))..).........))................ ( -21.20)
>consensus
CAUGAGCCCAA___ACGCUCGACAC___CACCAAUCGAGCAUGUACUCCACUAUAUAGUGGCACGCACACAUACAUAUG_AU_UACGUGCUGCAUUUAAUUUGCAUGUAAUCUAAUUAGG
..(((((.........))))).................(((((((.........((.(..(((((....................)))))..)))......)))))))............ (-18.08 = -17.98 +  -0.11)

alignment

secondary structure

dotplot

Window 2

Location	1,665,524 – 1,665,635
Length	111
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	72.13
Mean single sequence MFE	-38.67
Consensus MFE	-23.71
Energy contribution	-26.10
Covariance contribution	2.39
Combinations/Pair	1.06
Mean z-score	-2.94
Structure conservation index	0.61
SVM decision value	4.90
SVM RNA-class probability	0.999960
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665524 111 + 22224390
ACAUAUGUAUGGGUGCGUGCCACUAUAUAGUGGAGUACAUGCUCGAUUGGUGGUGGUGUCGAGCGU---UUGGGCUCAUGUACAAACA------UGAUGGUAAUGGCCGAUUUUUGGCCC
.(((((((....((((((((((((((.((((.((((....)))).))))))))))))...((((..---....))))))))))..)))------).))).....((((((...)))))). ( -40.70)
>DroSim_CAF1 723 114 + 1
GCAUAUGUAUGUGUGCGUGCCACUAUAUAGUGGAGUACAUGCUCGAUUGGUG---GCGUUGAGCGU---UUGGGCUCAUUUACAUACAUGUACAUGGUAGUAAUGGCCGAUUUUUGGCCC
((.((((((((((((.(((((((((....((.((((....)))).)))))))---))..(((((..---....)))))...)).))))))))))))))......((((((...)))))). ( -42.70)
>DroYak_CAF1 765 89 + 1
--------AUGUGUGCGUGCCACUAC-------UGUACAUGCUCGAUUGGUG---CUGACGAGCGAGCGUUGAGCUUAUGUACA-------------UGGUAAUGGCCGAUUUUUGGCCA
--------.........(((((....-------((((((((((((((...((---((....))))...)))))))..)))))))-------------))))).(((((((...))))))) ( -32.60)
>consensus
_CAUAUGUAUGUGUGCGUGCCACUAUAUAGUGGAGUACAUGCUCGAUUGGUG___GUGUCGAGCGU___UUGGGCUCAUGUACA_ACA______UG_UGGUAAUGGCCGAUUUUUGGCCC
...((((((((((.((((((..(........)..)))).((((((((..........))))))))........)).))))))))))..................((((((...)))))). (-23.71 = -26.10 +   2.39)

alignment

secondary structure

dotplot

Window 3

Location	1,665,524 – 1,665,635
Length	111
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	72.13
Mean single sequence MFE	-29.98
Consensus MFE	-15.55
Energy contribution	-16.44
Covariance contribution	0.89
Combinations/Pair	1.11
Mean z-score	-3.53
Structure conservation index	0.52
SVM decision value	3.92
SVM RNA-class probability	0.999708
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665524 111 - 22224390
GGGCCAAAAAUCGGCCAUUACCAUCA------UGUUUGUACAUGAGCCCAA---ACGCUCGACACCACCACCAAUCGAGCAUGUACUCCACUAUAUAGUGGCACGCACCCAUACAUAUGU
((((........((......)).(((------(((....))))))))))..---..((((((............)))))).(((...(((((....)))))...)))............. ( -29.70)
>DroSim_CAF1 723 114 - 1
GGGCCAAAAAUCGGCCAUUACUACCAUGUACAUGUAUGUAAAUGAGCCCAA---ACGCUCAACGC---CACCAAUCGAGCAUGUACUCCACUAUAUAGUGGCACGCACACAUACAUAUGC
.((((.......))))...........(((.((((((((...(((((....---..)))))..((---(((.....(((......))).........)))))......)))))))).))) ( -31.54)
>DroYak_CAF1 765 89 - 1
UGGCCAAAAAUCGGCCAUUACCA-------------UGUACAUAAGCUCAACGCUCGCUCGUCAG---CACCAAUCGAGCAUGUACA-------GUAGUGGCACGCACACAU--------
...........((((((((((..-------------(((((((.(((.....))).(((((....---.......))))))))))))-------)))))))).)).......-------- ( -28.70)
>consensus
GGGCCAAAAAUCGGCCAUUACCA_CA______UGU_UGUACAUGAGCCCAA___ACGCUCGACAC___CACCAAUCGAGCAUGUACUCCACUAUAUAGUGGCACGCACACAUACAUAUG_
.((((.......)))).............................((((.......(((((..............)))))(((((......))))).).))).................. (-15.55 = -16.44 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	1,665,564 – 1,665,675
Length	111
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	81.61
Mean single sequence MFE	-29.67
Consensus MFE	-22.96
Energy contribution	-23.41
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-2.71
Structure conservation index	0.77
SVM decision value	1.99
SVM RNA-class probability	0.984995
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1665564 111 - 22224390
CCAAGUUCCAUCGGAUGGGCAGGUAAAUAAACACUUACCAGGGCCAAAAAUCGGCCAUUACCAUCA------UGUUUGUACAUGAGCCCAA---ACGCUCGACACCACCACCAAUCGAGC
............(..(((((.(((((........)))))..((((.......)))).......(((------(((....))))))))))).---.)((((((............)))))) ( -34.80)
>DroSim_CAF1 763 114 - 1
CCAAGUUCCAUCGGAUGGGCAGGUAAAUAAACACUUACCAGGGCCAAAAAUCGGCCAUUACUACCAUGUACAUGUAUGUAAAUGAGCCCAA---ACGCUCAACGC---CACCAAUCGAGC
....((((.((.((...(((.(((((........)))))..((((.......)))).((((...(((....)))...)))).(((((....---..)))))..))---).)).)).)))) ( -30.00)
>DroYak_CAF1 790 104 - 1
CAAAGUUCCAUCGGAUGGGCAGGUAAAUAAACACUUAACAUGGCCAAAAAUCGGCCAUUACCA-------------UGUACAUAAGCUCAACGCUCGCUCGUCAG---CACCAAUCGAGC
..........((((.(((((((((((.(((....)))...(((((.......)))))))))).-------------)))......(((..(((......))).))---).))).)))).. ( -24.20)
>consensus
CCAAGUUCCAUCGGAUGGGCAGGUAAAUAAACACUUACCAGGGCCAAAAAUCGGCCAUUACCA_CA______UGU_UGUACAUGAGCCCAA___ACGCUCGACAC___CACCAAUCGAGC
......(((...)))(((((.(((((........)))))..((((.......)))).............................)))))......(((((..............))))) (-22.96 = -23.41 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:52 2006