Locus 4573

Sequence ID	2R_DroMel_CAF1
Location	14,939,425 – 14,939,576
Length	151
Max. P	0.993441

overview

Window 7

Location	14,939,425 – 14,939,517
Length	92
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	68.12
Mean single sequence MFE	-25.36
Consensus MFE	-9.58
Energy contribution	-8.88
Covariance contribution	-0.70
Combinations/Pair	1.58
Mean z-score	-2.20
Structure conservation index	0.38
SVM decision value	1.53
SVM RNA-class probability	0.961722
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14939425 92 - 20766785
ACACACAC---------GCACGGACACGAAUGUGUGUAUAUGGCGCGGCGCUUGUGUGUG--AAAGUGUAUUCGUA-UAAAUAAUAUGACAUAAUCGACGUGUG----------------
.(((((((---------(((((........))))))).((((((((..(((......)))--...))))..(((((-(.....))))))))))......)))))---------------- ( -26.50)
>DroSim_CAF1 25450 92 - 1
ACACACAC---------GCACGGACACGAAUGUGUGUAUAUGGCGCGGCGCUUGUGUGUG--AAAGUGUAUUCGUA-UAAAUAAUAUGACAUAAUCGACGUGUG----------------
.(((((((---------(((((........))))))).((((((((..(((......)))--...))))..(((((-(.....))))))))))......)))))---------------- ( -26.50)
>DroWil_CAF1 36269 119 - 1
ACAUAUAUAAAAUAGAUGUACAUACAUACGUGUAUGUGUGUGUUGUG-UGUAUGUGUAUUAAAAAGUGUGUAUAAAUUAAAUAAUAUGACAUAAUCGACGUGUGUGCAUCUGUGUGAGUG
...........((((((((((((((...((..(((((.((((((((.-..((((..((((....))))..))))......)))))))))))))..))..))))))))))))))....... ( -32.70)
>DroYak_CAF1 25637 92 - 1
ACACACAC---------GCACGGACACGAAUGUGUGUAUAUGGCGCGACGCUUGUGUGCG--AAAGUGUAUUCGUA-UAAAUAAUAUGACAUAAUCGACGUGUG----------------
..((((((---------(..((....))..))))))).....(((((.((.((((((((.--...)).....((((-(.....))))))))))).)).))))).---------------- ( -27.30)
>DroAna_CAF1 24061 70 - 1
ACAUACAC-----------------ACGAA-AUGUGUACAUGUUGCGACCC---------------UGUAUUUGUA-UAAAUAAUAUGACAUAAUCGACGUGUG----------------
.....(((-----------------(((..-.(((((.((((((((((...---------------.....)))))-......)))))))))).....))))))---------------- ( -13.80)
>consensus
ACACACAC_________GCACGGACACGAAUGUGUGUAUAUGGCGCGACGCUUGUGUGUG__AAAGUGUAUUCGUA_UAAAUAAUAUGACAUAAUCGACGUGUG________________
.(((((.................(((((....))))).....(((..((((((..........))))))...)))........................)))))................ ( -9.58 =  -8.88 +  -0.70)

alignment

secondary structure

dotplot

Window 8

Location	14,939,449 – 14,939,557
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.17
Mean single sequence MFE	-32.59
Consensus MFE	-22.01
Energy contribution	-23.82
Covariance contribution	1.81
Combinations/Pair	1.17
Mean z-score	-2.34
Structure conservation index	0.68
SVM decision value	2.40
SVM RNA-class probability	0.993441
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14939449 108 + 20766785
UUA-UACGAAUACACUUU--CACACACAAGCGCCGCGCCAUAUACACACAUUCGUGUCCGUGC---------GUGUGUGUGUAUGAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUG
...-...(((......))--)...(((..((((((...((((((((((((..(((......))---------)))))))))))))..)))))).(((((.(((....))).))))).))) ( -37.70)
>DroSim_CAF1 25474 108 + 1
UUA-UACGAAUACACUUU--CACACACAAGCGCCGCGCCAUAUACACACAUUCGUGUCCGUGC---------GUGUGUGUGUAUGAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUG
...-...(((......))--)...(((..((((((...((((((((((((..(((......))---------)))))))))))))..)))))).(((((.(((....))).))))).))) ( -37.70)
>DroWil_CAF1 36309 114 + 1
UUAAUUUAUACACACUUUUUAAUACACAUACA-CACAACACACACAUACACGUAUGUAUGUACAUCUAUUUUAUAUAUGUAAAUUAACGGCGUCUCGUU-----AACCGGCAACGGCGUG
..........(((.........((((.(((..-..........(((((((....)))))))............))).))))..(((((((....)))))-----))(((....))).))) ( -19.35)
>DroYak_CAF1 25661 108 + 1
UUA-UACGAAUACACUUU--CGCACACAAGCGUCGCGCCAUAUACACACAUUCGUGUCCGUGC---------GUGUGUGUGUAUCAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUG
...-..((((......))--))..(((..(((..(((((..((((((((((.(((......))---------).))))))))))....))))))))............(((...)))))) ( -35.60)
>consensus
UUA_UACGAAUACACUUU__CACACACAAGCGCCGCGCCAUAUACACACAUUCGUGUCCGUGC_________GUGUGUGUGUAUGAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUG
........................(((..((((((...(((((((((((((.....................)))))))))))))..)))))).(((((.(((....))).))))).))) (-22.01 = -23.82 +   1.81)

alignment

secondary structure

dotplot

Window 9

Location	14,939,449 – 14,939,557
Length	108
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	76.17
Mean single sequence MFE	-37.80
Consensus MFE	-21.85
Energy contribution	-22.60
Covariance contribution	0.75
Combinations/Pair	1.21
Mean z-score	-2.43
Structure conservation index	0.58
SVM decision value	1.91
SVM RNA-class probability	0.982110
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14939449 108 - 20766785
CACGGCAUUGCCGGUGACGAGAAUGCGACGCCGUUCAUACACACACAC---------GCACGGACACGAAUGUGUGUAUAUGGCGCGGCGCUUGUGUGUG--AAAGUGUAUUCGUA-UAA
.((((((((..((....))..))))).((((..(((((((((((((((---------(..((....))..)))))))....((((...)))).)))))))--)).))))...))).-... ( -39.80)
>DroSim_CAF1 25474 108 - 1
CACGGCAUUGCCGGUGACGAGAAUGCGACGCCGUUCAUACACACACAC---------GCACGGACACGAAUGUGUGUAUAUGGCGCGGCGCUUGUGUGUG--AAAGUGUAUUCGUA-UAA
.((((((((..((....))..))))).((((..(((((((((((((((---------(..((....))..)))))))....((((...)))).)))))))--)).))))...))).-... ( -39.80)
>DroWil_CAF1 36309 114 - 1
CACGCCGUUGCCGGUU-----AACGAGACGCCGUUAAUUUACAUAUAUAAAAUAGAUGUACAUACAUACGUGUAUGUGUGUGUUGUG-UGUAUGUGUAUUAAAAAGUGUGUAUAAAUUAA
(((((((((..((...-----..)).))))...(((((.((((((((((....(.(..((((((((....))))))))..).)..))-)))))))).)))))...))))).......... ( -32.00)
>DroYak_CAF1 25661 108 - 1
CACGGCAUUGCCGGUGACGAGAAUGCGACGCCGUUGAUACACACACAC---------GCACGGACACGAAUGUGUGUAUAUGGCGCGACGCUUGUGUGCG--AAAGUGUAUUCGUA-UAA
..((((...))))...(((((....((.((((((..(((((((((..(---------(........))..)))))))))))))))))...)))))(((((--((......))))))-).. ( -39.60)
>consensus
CACGGCAUUGCCGGUGACGAGAAUGCGACGCCGUUCAUACACACACAC_________GCACGGACACGAAUGUGUGUAUAUGGCGCGGCGCUUGUGUGUG__AAAGUGUAUUCGUA_UAA
(((.(((((..((....))..)))))..(((((((((((.(((((((.......................))))))).))))).))))))...............)))............ (-21.85 = -22.60 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	14,939,486 – 14,939,576
Length	90
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	67.23
Mean single sequence MFE	-27.56
Consensus MFE	-13.92
Energy contribution	-15.52
Covariance contribution	1.60
Combinations/Pair	1.25
Mean z-score	-1.78
Structure conservation index	0.51
SVM decision value	0.81
SVM RNA-class probability	0.855456
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14939486 90 + 20766785
UAUACACACAUUCGUGUCCGUGC---------GUGUGUGUGUAUGAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUGAAAAAAUCGAUGGU---CAAUU---------
(((((((((((.(((......))---------).)))))))))))...(((((((.(((....((((.(((...)))))))...))))))).))---)....--------- ( -30.80)
>DroSim_CAF1 25511 90 + 1
UAUACACACAUUCGUGUCCGUGC---------GUGUGUGUGUAUGAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUGAAAAAAUCGAUGGU---CAAUU---------
(((((((((((.(((......))---------).)))))))))))...(((((((.(((....((((.(((...)))))))...))))))).))---)....--------- ( -30.80)
>DroWil_CAF1 36348 105 + 1
CACACAUACACGUAUGUAUGUACAUCUAUUUUAUAUAUGUAAAUUAACGGCGUCUCGUU-----AACCGGCAACGGCGUGAAA-AAUCGAUAUGGCUGCGCUUUUACAGUU
...(((((((....)))))))..(((.(((((.(((.......(((((((....)))))-----))(((....))).))).))-))).)))..(((((........))))) ( -21.70)
>DroYak_CAF1 25698 90 + 1
UAUACACACAUUCGUGUCCGUGC---------GUGUGUGUGUAUCAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUGAAAAAAUCGAUGGG---CAAUA---------
.((((((((((.(((......))---------).))))))))))......(((((.(((....((((.(((...)))))))...))))))))..---.....--------- ( -28.60)
>DroAna_CAF1 24109 84 + 1
UGUACACAU-UUCGU-----------------GUGUAUGUGUAUAGACGGCGUC------CCGUCACCGGCAAUGCCGUGAAAAAAUCGAUGCG--UCCUCUUUCACAGA-
.((((((((-...))-----------------))))))(((...(((.(((((.------.((((((.(((...)))))))......))..)))--)).)))..)))...- ( -25.90)
>consensus
UAUACACACAUUCGUGUCCGUGC_________GUGUGUGUGUAUGAACGGCGUCGCAUUCUCGUCACCGGCAAUGCCGUGAAAAAAUCGAUGGG___CAAUU_________
(((((((((((.......................))))))))))).(((((((.((.............)).)))))))................................ (-13.92 = -15.52 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:25 2006