Locus 1398

Sequence ID	3R_DroMel_CAF1
Location	4,079,404 – 4,079,604
Length	200
Max. P	0.951551

overview

Window 4

Location	4,079,404 – 4,079,524
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-29.33
Consensus MFE	-26.54
Energy contribution	-26.43
Covariance contribution	-0.11
Combinations/Pair	1.05
Mean z-score	-1.70
Structure conservation index	0.90
SVM decision value	-0.01
SVM RNA-class probability	0.526649
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4079404 120 - 27905053
AACUGCAACGGCUAAUUGCCGUUGAAAGUGUGUACAUUUUGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACCUGUCCCACGGGGCGUAUACUCACUAACGUAUUGGCUAUUAGCUGUCA
.......(((((((((.((((......(.((((((...........((((((..(......)..))))))....((((....)))))))))).)((....))..)))).))))))))).. ( -33.90)
>DroEre_CAF1 7932 120 - 1
AACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUUGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACUUGUCACACGGGGCGUAUACUCACUAACGAAUUGGCUAUUAGCUGUCA
.(((((((.((((((((..(((((..((((((..(...........((((((..(......)..)))))).((((.....)))))..))))))...))))))))))))).)).))))).. ( -27.20)
>DroYak_CAF1 4988 120 - 1
AACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUAGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACUUGUCACACGGGGCGUAUACUCACUAACGUAUUGGCUAUUAGCUGUCA
.(((((((.(((((((...(((((..((((((..(...........((((((..(......)..)))))).((((.....)))))..))))))...))))).))))))).)).))))).. ( -26.90)
>consensus
AACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUUGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACUUGUCACACGGGGCGUAUACUCACUAACGUAUUGGCUAUUAGCUGUCA
.(((((((.(((((((...(((((..((((((..(...........((((((..(......)..)))))).((((.....)))))..))))))...))))).))))))).)).))))).. (-26.54 = -26.43 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	4,079,444 – 4,079,564
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-30.90
Consensus MFE	-22.14
Energy contribution	-23.70
Covariance contribution	1.56
Combinations/Pair	1.05
Mean z-score	-2.83
Structure conservation index	0.72
SVM decision value	0.09
SVM RNA-class probability	0.578759
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4079444 120 + 27905053
UGGGACAGGUAAACAUAAAAUAUUAUAAAUGUUUUCUGGCAAAAUGUACACACUUUCAACGGCAAUUAGCCGUUGCAGUUAAAUGUUUUUCUUAGCCAAACCUUUGGGAAUGGCUAAAAU
.....((((.((((((............))))))))))(.(((((((....(((..(((((((.....))))))).)))...))))))).)(((((((..((....))..)))))))... ( -29.60)
>DroEre_CAF1 7972 120 + 1
UGUGACAAGUAAACAUAAAAUAUUAUAAAUGUUUUCUGGCAAAAUGUACAUACUUUCAACGGCAAUUAGCCUUUGCCGUUGAAUGUUUUUCUUAGCCAAACCUUUGGGCCUCGGAAAGAU
(((((((......((.(((((((.....))))))).))......))).))))..(((((((((((.......))))))))))).((((((((..(((.........)))...)))))))) ( -30.50)
>DroYak_CAF1 5028 120 + 1
UGUGACAAGUAAACAUAAAAUAUUAUAAAUGUUUUCUGGCUAAAUGUACAUACUUUCAACGGCAAUUAGCCUUUGCCGUUGAAUGUUUUUCUUAGCCAAACCAUUGGGCCUCGGAAAGAU
(((((((..((..((.(((((((.....))))))).))..))..))).))))..(((((((((((.......))))))))))).((((((((..(((.........)))...)))))))) ( -32.60)
>consensus
UGUGACAAGUAAACAUAAAAUAUUAUAAAUGUUUUCUGGCAAAAUGUACAUACUUUCAACGGCAAUUAGCCUUUGCCGUUGAAUGUUUUUCUUAGCCAAACCUUUGGGCCUCGGAAAGAU
(((((((......((.(((((((.....))))))).))......))).))))..(((((((((((.......))))))))))).((((((((.((((((....))))..)).)))))))) (-22.14 = -23.70 +   1.56)

alignment

secondary structure

dotplot

Window 6

Location	4,079,444 – 4,079,564
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-31.50
Consensus MFE	-22.27
Energy contribution	-22.50
Covariance contribution	0.23
Combinations/Pair	1.06
Mean z-score	-3.28
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.661315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4079444 120 - 27905053
AUUUUAGCCAUUCCCAAAGGUUUGGCUAAGAAAAACAUUUAACUGCAACGGCUAAUUGCCGUUGAAAGUGUGUACAUUUUGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACCUGUCCCA
.(((((((((..((....))..)))))))))...........((((((((((.....)))))))((((((....))))))..))).((((((..(......)..)))))).......... ( -33.30)
>DroEre_CAF1 7972 120 - 1
AUCUUUCCGAGGCCCAAAGGUUUGGCUAAGAAAAACAUUCAACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUUGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACUUGUCACA
.......((((.........((((((.((((...((((((((((((((.......))))))))))....))))...))))))))))((((((..(......)..)))))).))))..... ( -29.00)
>DroYak_CAF1 5028 120 - 1
AUCUUUCCGAGGCCCAAUGGUUUGGCUAAGAAAAACAUUCAACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUAGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACUUGUCACA
.......((((....((((.((((((((((....((((((((((((((.......))))))))))....))))...))))))))))...))))(((((....)))))....))))..... ( -32.20)
>consensus
AUCUUUCCGAGGCCCAAAGGUUUGGCUAAGAAAAACAUUCAACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUUGCCAGAAAACAUUUAUAAUAUUUUAUGUUUACUUGUCACA
....................((((((.((((...((((((((((((((.......))))))))))....))))...))))))))))((((((..(......)..)))))).......... (-22.27 = -22.50 +   0.23)

alignment

secondary structure

dotplot

Window 7

Location	4,079,484 – 4,079,604
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-36.03
Consensus MFE	-29.40
Energy contribution	-30.07
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-3.84
Structure conservation index	0.82
SVM decision value	1.28
SVM RNA-class probability	0.939519
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4079484 120 + 27905053
AAAAUGUACACACUUUCAACGGCAAUUAGCCGUUGCAGUUAAAUGUUUUUCUUAGCCAAACCUUUGGGAAUGGCUAAAAUGCAUUGUUGCAAAUGCCACAGGGGCUAAAAGUACUAAAAA
.....((((..(((..(((((((.....))))))).)))............((((((...((....))..((((.....((((....))))...))))....))))))..))))...... ( -34.10)
>DroEre_CAF1 8012 120 + 1
AAAAUGUACAUACUUUCAACGGCAAUUAGCCUUUGCCGUUGAAUGUUUUUCUUAGCCAAACCUUUGGGCCUCGGAAAGAUGCAUUGUUGCAACUGCAAAAGUGGCUAAAAGUACUAAAAA
.....((((..((.(((((((((((.......))))))))))).)).....(((((((.........((.((.....)).))....((((....))))...)))))))..))))...... ( -36.40)
>DroYak_CAF1 5068 120 + 1
UAAAUGUACAUACUUUCAACGGCAAUUAGCCUUUGCCGUUGAAUGUUUUUCUUAGCCAAACCAUUGGGCCUCGGAAAGAUGCAUUGUUGCAACUGCAAAAGGGGCUAAAAGUACUAAAAA
.....((((..((.(((((((((((.......))))))))))).)).....((((((...((....))(((.....((.((((....)))).)).....)))))))))..))))...... ( -37.60)
>consensus
AAAAUGUACAUACUUUCAACGGCAAUUAGCCUUUGCCGUUGAAUGUUUUUCUUAGCCAAACCUUUGGGCCUCGGAAAGAUGCAUUGUUGCAACUGCAAAAGGGGCUAAAAGUACUAAAAA
.....((((..((.(((((((((((.......))))))))))).)).....((((((...((....))...........((((....))))...........))))))..))))...... (-29.40 = -30.07 +   0.67)

alignment

secondary structure

dotplot

Window 8

Location	4,079,484 – 4,079,604
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	91.11
Mean single sequence MFE	-37.83
Consensus MFE	-32.01
Energy contribution	-31.57
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-4.21
Structure conservation index	0.85
SVM decision value	1.41
SVM RNA-class probability	0.951551
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4079484 120 - 27905053
UUUUUAGUACUUUUAGCCCCUGUGGCAUUUGCAACAAUGCAUUUUAGCCAUUCCCAAAGGUUUGGCUAAGAAAAACAUUUAACUGCAACGGCUAAUUGCCGUUGAAAGUGUGUACAUUUU
......((((.....(((.....)))...((((....))))(((((((((..((....))..)))))))))...((((((.....(((((((.....))))))).))))))))))..... ( -38.90)
>DroEre_CAF1 8012 120 - 1
UUUUUAGUACUUUUAGCCACUUUUGCAGUUGCAACAAUGCAUCUUUCCGAGGCCCAAAGGUUUGGCUAAGAAAAACAUUCAACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUU
......((((((((((((((((....((.((((....)))).))....)))(((....))).)))))))))...((.(((((((((((.......))))))))))).))..))))..... ( -37.90)
>DroYak_CAF1 5068 120 - 1
UUUUUAGUACUUUUAGCCCCUUUUGCAGUUGCAACAAUGCAUCUUUCCGAGGCCCAAUGGUUUGGCUAAGAAAAACAUUCAACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUA
......((((((((((((((((....((.((((....)))).))....))))((....))...))))))))...((.(((((((((((.......))))))))))).))..))))..... ( -36.70)
>consensus
UUUUUAGUACUUUUAGCCCCUUUUGCAGUUGCAACAAUGCAUCUUUCCGAGGCCCAAAGGUUUGGCUAAGAAAAACAUUCAACGGCAAAGGCUAAUUGCCGUUGAAAGUAUGUACAUUUU
......((((((((((((...((((....((((....))))......))))(((....)))..))))))))...((.(((((((((((.......))))))))))).))..))))..... (-32.01 = -31.57 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:09 2006