Locus 4704

Sequence ID	2R_DroMel_CAF1
Location	15,405,937 – 15,406,056
Length	119
Max. P	0.993429

overview

Window 1

Location	15,405,937 – 15,406,056
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.36
Mean single sequence MFE	-24.85
Consensus MFE	-17.43
Energy contribution	-17.79
Covariance contribution	0.36
Combinations/Pair	1.11
Mean z-score	-3.36
Structure conservation index	0.70
SVM decision value	2.40
SVM RNA-class probability	0.993429
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15405937 119 + 20766785
AAUCGAAUUACAAGCCAUCCGAAGUGAGUGAAAUGAAAAUUAAUUGAAGACAAUGGAAUGCAAAAUGCAAUUUCAAUUAAUUUUCAUUCUUUGCACACUGCGACCGCCGCACGUACAUA-
........(((...........((((.(..(((((((((((((((((((.(....)..(((.....))).)))))))))))))))))..))..).))))(((.....)))..)))....- ( -28.20)
>DroPse_CAF1 240757 95 + 1
AAUCGAAUUACAGCCAAUUCAGAGUGAUUGAAAUGAAAAUUAAUUGAAGACAAUGGAAUGCAGCAUGCAUUUUCAAUUAAUUUUCAUUCUCUGCA-------------------------
....(((((......)))))((((.......((((((((((((((((........((((((.....))))))))))))))))))))))))))...------------------------- ( -23.41)
>DroWil_CAF1 419367 97 + 1
AAACGUAUUACAAGCCAUUCGCAGUGAUUGAAAUGAAAAUUAAUUGAAGACAAUGGCAUGCAAAAUGGAUUUUCAAUUAAUUUUCAUUCUUUU---------------------AC-UU-
.............((.....))(((((..(((.(((((((((((((((((..((.(....)...))...))))))))))))))))))))..))---------------------))-).- ( -22.40)
>DroMoj_CAF1 307090 110 + 1
ACUCAAUUUGCUUGCUAUUGGAAAUGAUUGAAAUGAAAAUUAAUUGAAGACAAUGGCAUGCAAAAUGCAUUUUCAAUUAAUUUUCAUUCUUUAU-------GACA---ACAUAUUCAUAU
..((((((...((.(....).))..))))))(((((((((((((((((((.....((((.....)))).)))))))))))))))))))...(((-------((..---......))))). ( -26.70)
>DroAna_CAF1 189092 107 + 1
AAUCGAAUUACAAGCUAUAUGAAGCGAACGAAAUGAAAAUUAAUUGAAGACAAUGGAAUGCAAAAUGCAUUUUCAAUUAAUUUUCAUUCUUUGCAGAAGA---------AACGUGG----
.......................(((((.(((.((((((((((((((........((((((.....))))))))))))))))))))))))))))......---------.......---- ( -25.00)
>DroPer_CAF1 200777 95 + 1
AAUCGAAUUACAGCCAAUUCAGAGUGAUUGAAAUGAAAAUUAAUUGAAGACAAUGGAAUGCAGCAUGCAUUUUCAAUUAAUUUUCAUUCUCUGCA-------------------------
....(((((......)))))((((.......((((((((((((((((........((((((.....))))))))))))))))))))))))))...------------------------- ( -23.41)
>consensus
AAUCGAAUUACAAGCAAUUCGAAGUGAUUGAAAUGAAAAUUAAUUGAAGACAAUGGAAUGCAAAAUGCAUUUUCAAUUAAUUUUCAUUCUUUGCA____________________C____
...................(((((.......(((((((((((((((((((........(((.....)))))))))))))))))))))))))))........................... (-17.43 = -17.79 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	15,405,937 – 15,406,056
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.36
Mean single sequence MFE	-24.65
Consensus MFE	-17.78
Energy contribution	-18.45
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-3.11
Structure conservation index	0.72
SVM decision value	2.33
SVM RNA-class probability	0.992470
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15405937 119 - 20766785
-UAUGUACGUGCGGCGGUCGCAGUGUGCAAAGAAUGAAAAUUAAUUGAAAUUGCAUUUUGCAUUCCAUUGUCUUCAAUUAAUUUUCAUUUCACUCACUUCGGAUGGCUUGUAAUUCGAUU
-..((((((((((.....)))).))))))..((((((((((((((((((..(((.....)))..........))))))))))))))))))........((((((........)))))).. ( -33.00)
>DroPse_CAF1 240757 95 - 1
-------------------------UGCAGAGAAUGAAAAUUAAUUGAAAAUGCAUGCUGCAUUCCAUUGUCUUCAAUUAAUUUUCAUUUCAAUCACUCUGAAUUGGCUGUAAUUCGAUU
-------------------------(((((.(((((((((((((((((((((((.....)))))........))))))))))))))))))(((((.....).)))).)))))........ ( -25.00)
>DroWil_CAF1 419367 97 - 1
-AA-GU---------------------AAAAGAAUGAAAAUUAAUUGAAAAUCCAUUUUGCAUGCCAUUGUCUUCAAUUAAUUUUCAUUUCAAUCACUGCGAAUGGCUUGUAAUACGUUU
-..-((---------------------(...((((((((((((((((((..........(((......))).)))))))))))))))))).......(((((.....))))).))).... ( -18.20)
>DroMoj_CAF1 307090 110 - 1
AUAUGAAUAUGU---UGUC-------AUAAAGAAUGAAAAUUAAUUGAAAAUGCAUUUUGCAUGCCAUUGUCUUCAAUUAAUUUUCAUUUCAAUCAUUUCCAAUAGCAAGCAAAUUGAGU
..((((.((((.---...)-------)))..(((((((((((((((((((((((((.....))).))))...))))))))))))))))))...))))....................... ( -21.60)
>DroAna_CAF1 189092 107 - 1
----CCACGUU---------UCUUCUGCAAAGAAUGAAAAUUAAUUGAAAAUGCAUUUUGCAUUCCAUUGUCUUCAAUUAAUUUUCAUUUCGUUCGCUUCAUAUAGCUUGUAAUUCGAUU
----.......---------.....(((((.(((((((((((((((((((((((.....)))))........)))))))))))))))))).....(((......))))))))........ ( -25.10)
>DroPer_CAF1 200777 95 - 1
-------------------------UGCAGAGAAUGAAAAUUAAUUGAAAAUGCAUGCUGCAUUCCAUUGUCUUCAAUUAAUUUUCAUUUCAAUCACUCUGAAUUGGCUGUAAUUCGAUU
-------------------------(((((.(((((((((((((((((((((((.....)))))........))))))))))))))))))(((((.....).)))).)))))........ ( -25.00)
>consensus
____G____________________UGCAAAGAAUGAAAAUUAAUUGAAAAUGCAUUUUGCAUUCCAUUGUCUUCAAUUAAUUUUCAUUUCAAUCACUUCGAAUAGCUUGUAAUUCGAUU
...............................(((((((((((((((((((((((.....)))))........)))))))))))))))))).............................. (-17.78 = -18.45 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:15 2006