Locus 4511

Sequence ID	2R_DroMel_CAF1
Location	14,809,883 – 14,810,042
Length	159
Max. P	0.999547

overview

Window 6

Location	14,809,883 – 14,810,002
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.49
Mean single sequence MFE	-32.90
Consensus MFE	-30.84
Energy contribution	-30.84
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.94
SVM decision value	2.88
SVM RNA-class probability	0.997540
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14809883 119 + 20766785
GCCCCUCCGAGUUUGAU-UCCCAUGCCCAUAUUCAAUUCUAGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGA
(((.(.((((((((((.-.....((((...((((.......))))..))))..(((((((.....)))))))(((.((....)).)))..........))))))..)))).).))).... ( -32.80)
>DroSec_CAF1 11719 119 + 1
GCCCCUCCGAGUUUGAU-UCCCAUGCCCAUAUUCAAUUCUAGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGA
(((.(.((((((((((.-.....((((...((((.......))))..))))..(((((((.....)))))))(((.((....)).)))..........))))))..)))).).))).... ( -32.80)
>DroSim_CAF1 6004 119 + 1
GCCCCUCCGAGUUUGAU-UCCCAUGCCCAUAUUCAAUUCUAGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGA
(((.(.((((((((((.-.....((((...((((.......))))..))))..(((((((.....)))))))(((.((....)).)))..........))))))..)))).).))).... ( -32.80)
>DroEre_CAF1 4550 120 + 1
CCCCCACCGAUUUUGAUUUCCCAUGCCCAUAUUCUAUUCUAGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGA
.......................((((...((((((...))))))..))))..(((((((.....)))))))(((.((....)).)))....(((((.((((....)))).))))).... ( -32.40)
>DroYak_CAF1 5774 120 + 1
UCCCCGCCGAUUUUGAUUUCCCAUGCCCAUAUUCAAUUCUAGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGA
..((((((((((((((.......((((...((((.......))))..))))..(((((((.....)))))))(((.((....)).)))..........)))))..))))))).))..... ( -33.70)
>consensus
GCCCCUCCGAGUUUGAU_UCCCAUGCCCAUAUUCAAUUCUAGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGA
.......................((((...((((.......))))..))))..(((((((.....)))))))(((.((....)).)))....(((((.((((....)))).))))).... (-30.84 = -30.84 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	14,809,883 – 14,810,002
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.49
Mean single sequence MFE	-39.98
Consensus MFE	-36.08
Energy contribution	-36.48
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.90
SVM decision value	2.31
SVM RNA-class probability	0.992196
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14809883 119 - 20766785
UCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCUAGAAUUGAAUAUGGGCAUGGGA-AUCAAACUCGGAGGGGC
....(((((.((.............(((((((.(((((....)))))))))))).((..((((..((..((((.(((((.......)))).).))))..)).-.))))..)))).))))) ( -38.10)
>DroSec_CAF1 11719 119 - 1
UCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCUAGAAUUGAAUAUGGGCAUGGGA-AUCAAACUCGGAGGGGC
....(((((.((.............(((((((.(((((....)))))))))))).((..((((..((..((((.(((((.......)))).).))))..)).-.))))..)))).))))) ( -38.10)
>DroSim_CAF1 6004 119 - 1
UCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCUAGAAUUGAAUAUGGGCAUGGGA-AUCAAACUCGGAGGGGC
....(((((.((.............(((((((.(((((....)))))))))))).((..((((..((..((((.(((((.......)))).).))))..)).-.))))..)))).))))) ( -38.10)
>DroEre_CAF1 4550 120 - 1
UCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCUAGAAUAGAAUAUGGGCAUGGGAAAUCAAAAUCGGUGGGGG
.....(((((((.............(((((((.(((((....)))))))))))).((..((((..((..((((.(((((((...)))))).).))))...))..))))..))))))))). ( -42.50)
>DroYak_CAF1 5774 120 - 1
UCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCUAGAAUUGAAUAUGGGCAUGGGAAAUCAAAAUCGGCGGGGA
.....(((((((.............(((((((.(((((....)))))))))))).((..((((..((..((((.(((((.......)))).).))))...))..))))..))))))))). ( -43.10)
>consensus
UCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCUAGAAUUGAAUAUGGGCAUGGGA_AUCAAACUCGGAGGGGC
....(((((.((.............(((((((.(((((....)))))))))))).((..((((..((..((((.(((((.......)))).).))))...))..))))..)))).))))) (-36.08 = -36.48 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	14,809,922 – 14,810,042
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-31.94
Consensus MFE	-30.78
Energy contribution	-30.78
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.49
Structure conservation index	0.96
SVM decision value	3.71
SVM RNA-class probability	0.999547
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14809922 120 + 20766785
AGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGAAAAGCAAAAGAAAAUCGGCGAGCGAGCAGCGAAAUACAAA
.(((((..(((..(((((((.....))))))))))....)))))(((.....(((((.((((....)))).))))).....................((......)).)))......... ( -32.20)
>DroSec_CAF1 11758 120 + 1
AGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGAAAAGCAAAAGAAAAUCGGCGAGCGAGCAGCGAAAUACAAA
.(((((..(((..(((((((.....))))))))))....)))))(((.....(((((.((((....)))).))))).....................((......)).)))......... ( -32.20)
>DroSim_CAF1 6043 120 + 1
AGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGAAAAGCAAAAGAAAAUCGGCGAGCGAGCAGCGAAAUACAAA
.(((((..(((..(((((((.....))))))))))....)))))(((.....(((((.((((....)))).))))).....................((......)).)))......... ( -32.20)
>DroEre_CAF1 4590 120 + 1
AGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGAAAAGCUAAAGAAAAUCGGCGAGCGAGCACCAGAAUACAAA
.(.((((.(((..(((((((.....)))))))))).........(((.....(((((.((((....)))).))))).......((..(......)..))..))).......)))).)... ( -32.10)
>DroYak_CAF1 5814 120 + 1
AGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGAAAAGCAAAAGAAAAUCGGCGAGCGAGCACCAAAAUACAAA
.(((((..(((..(((((((.....))))))))))....)))))(((.....(((((.((((....)))).))))).......((....(.....).))..)))................ ( -31.00)
>consensus
AGAAUUCGGCAAUGACGUCAAGGCCUGACGUCUGCAGAAAAUUCCGCAAAACGCCUCUUCAAAUUAUUGGCGAGGCAAGAAAAGCAAAAGAAAAUCGGCGAGCGAGCAGCGAAAUACAAA
.(((((..(((..(((((((.....))))))))))....)))))(((.....(((((.((((....)))).))))).......((....(.....).))..)))................ (-30.78 = -30.78 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	14,809,922 – 14,810,042
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-33.18
Consensus MFE	-30.82
Energy contribution	-30.82
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-1.96
Structure conservation index	0.93
SVM decision value	2.20
SVM RNA-class probability	0.990094
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14809922 120 - 20766785
UUUGUAUUUCGCUGCUCGCUCGCCGAUUUUCUUUUGCUUUUCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCU
.....(((((((.((......((.((......)).)).......(((((..(((....)))..)))))))...))))))).(((.(((((((((((...))))))))..))).))).... ( -32.80)
>DroSec_CAF1 11758 120 - 1
UUUGUAUUUCGCUGCUCGCUCGCCGAUUUUCUUUUGCUUUUCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCU
.....(((((((.((......((.((......)).)).......(((((..(((....)))..)))))))...))))))).(((.(((((((((((...))))))))..))).))).... ( -32.80)
>DroSim_CAF1 6043 120 - 1
UUUGUAUUUCGCUGCUCGCUCGCCGAUUUUCUUUUGCUUUUCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCU
.....(((((((.((......((.((......)).)).......(((((..(((....)))..)))))))...))))))).(((.(((((((((((...))))))))..))).))).... ( -32.80)
>DroEre_CAF1 4590 120 - 1
UUUGUAUUCUGGUGCUCGCUCGCCGAUUUUCUUUAGCUUUUCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCU
...(.(((((((((......)))))..........((.......(((((..(((....)))..)))))....((((((....))))))((((((((...))))))))...)).)))).). ( -33.40)
>DroYak_CAF1 5814 120 - 1
UUUGUAUUUUGGUGCUCGCUCGCCGAUUUUCUUUUGCUUUUCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCU
........((((((......)))))).....((((((......((((((..(((....)))..))))))....))))))..(((.(((((((((((...))))))))..))).))).... ( -34.10)
>consensus
UUUGUAUUUCGCUGCUCGCUCGCCGAUUUUCUUUUGCUUUUCUUGCCUCGCCAAUAAUUUGAAGAGGCGUUUUGCGGAAUUUUCUGCAGACGUCAGGCCUUGACGUCAUUGCCGAAUUCU
.....(((((((.((......((.((......)).)).......(((((..(((....)))..)))))))...))))))).(((.(((((((((((...))))))))..))).))).... (-30.82 = -30.82 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:47 2006