Locus 8390

Sequence ID	3R_DroMel_CAF1
Location	22,359,156 – 22,359,254
Length	98
Max. P	0.995051

overview

Window 4

Location	22,359,156 – 22,359,254
Length	98
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.47
Mean single sequence MFE	-25.72
Consensus MFE	-17.34
Energy contribution	-17.58
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-2.93
Structure conservation index	0.67
SVM decision value	2.54
SVM RNA-class probability	0.995051
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22359156 98 + 27905053
AAAAGGCGCGUGUAUCUGCAAGAUACAUUUCUAUCUCAAGAGCGCA-----AAAUUGCGCGGCAAACCAAAG--------CUCGCAAAAAGCA---------AAAAAUCGCAUAUAUGAA
.....(((((((((((.....))))))).(((......))))))).-----...(((((.(((........)--------)))))))...((.---------.......))......... ( -24.50)
>DroSim_CAF1 70858 98 + 1
AAAAGGCGCGUGUAUCUGCAAGAUACAUUUCUAUCUCGAGAGCGCA-----AAUUUGCGCGGCAAACCAAAG--------CUCGCAAAAAGCG---------AAAAAUCGCAUAUAUGAA
.....(((((((((((.....))))))).(((......))))))).-----..((((((.(((........)--------))))))))..(((---------(....))))......... ( -29.10)
>DroEre_CAF1 69350 95 + 1
AAAAGGCGCGUGUAUCUUCAAGAUACAUUUCUAUCUCGAGAGCGCA-----AAUUUGCGCGGCAAACCGAAG--------CUCGCC---AGCA---------AAAAAUCGCAUAUAUGAA
....(((..(((((((.....))))))).........(((.(((((-----....)))))((....))....--------))))))---.((.---------.......))......... ( -25.60)
>DroWil_CAF1 75030 118 + 1
-AAAGGCGCGUGUAUCUAGAAGAUACAUUUCUAGCUU-AGAGUGCACGACGAAUUUGCGCGGCAAGAAAAAAAAAAUAAAGACGAAAAAAGAACUAAAUAAAUAAAGUCGCAUAAAUGAA
-....((((.((((((.....))))))(((((.(((.-...(((((.........)))))))).))))).....................................).)))......... ( -20.30)
>DroYak_CAF1 68858 95 + 1
AAAAGGCGCGUGUAUCUCGAAGAUACAUUUCUAUCUCGAGAGCGCA-----AAUUUGCGCGGCAAACCGAAG--------CUCGCC---AGCA---------AAAAAUCGCAUAUAUGAA
....((((.((...((((((.((((......))))))))))(((((-----....)))))((....))...)--------).))))---.((.---------.......))......... ( -29.10)
>consensus
AAAAGGCGCGUGUAUCUGCAAGAUACAUUUCUAUCUCGAGAGCGCA_____AAUUUGCGCGGCAAACCAAAG________CUCGCAAAAAGCA_________AAAAAUCGCAUAUAUGAA
.....(((((((((((.....))))))).............(((((.........))))).))....................((.....)).................))......... (-17.34 = -17.58 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	22,359,156 – 22,359,254
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.47
Mean single sequence MFE	-27.40
Consensus MFE	-16.56
Energy contribution	-17.16
Covariance contribution	0.60
Combinations/Pair	1.09
Mean z-score	-2.60
Structure conservation index	0.60
SVM decision value	1.73
SVM RNA-class probability	0.974669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22359156 98 - 27905053
UUCAUAUAUGCGAUUUUU---------UGCUUUUUGCGAG--------CUUUGGUUUGCCGCGCAAUUU-----UGCGCUCUUGAGAUAGAAAUGUAUCUUGCAGAUACACGCGCCUUUU
.........(((..((((---------(((((...(((((--------(....)))))).(((((....-----)))))....))).))))))((((((.....)))))))))....... ( -26.00)
>DroSim_CAF1 70858 98 - 1
UUCAUAUAUGCGAUUUUU---------CGCUUUUUGCGAG--------CUUUGGUUUGCCGCGCAAAUU-----UGCGCUCUCGAGAUAGAAAUGUAUCUUGCAGAUACACGCGCCUUUU
.........(((...(((---------(...(((((.(((--------(...(((((((...)))))))-----...)))).)))))..))))((((((.....)))))))))....... ( -27.30)
>DroEre_CAF1 69350 95 - 1
UUCAUAUAUGCGAUUUUU---------UGCU---GGCGAG--------CUUCGGUUUGCCGCGCAAAUU-----UGCGCUCUCGAGAUAGAAAUGUAUCUUGAAGAUACACGCGCCUUUU
.........(((......---------....---((((((--------(....)))))))(((((....-----)))))((((((((((......))))))).)))....)))....... ( -32.70)
>DroWil_CAF1 75030 118 - 1
UUCAUUUAUGCGACUUUAUUUAUUUAGUUCUUUUUUCGUCUUUAUUUUUUUUUUCUUGCCGCGCAAAUUCGUCGUGCACUCU-AAGCUAGAAAUGUAUCUUCUAGAUACACGCGCCUUU-
.........(((.......................................(((((.(((((((......).))))......-..)).)))))((((((.....)))))))))......- ( -16.20)
>DroYak_CAF1 68858 95 - 1
UUCAUAUAUGCGAUUUUU---------UGCU---GGCGAG--------CUUCGGUUUGCCGCGCAAAUU-----UGCGCUCUCGAGAUAGAAAUGUAUCUUCGAGAUACACGCGCCUUUU
.........(((......---------....---((((((--------(....)))))))(((((....-----)))))((((((((((......)))).))))))....)))....... ( -34.80)
>consensus
UUCAUAUAUGCGAUUUUU_________UGCUUUUUGCGAG________CUUUGGUUUGCCGCGCAAAUU_____UGCGCUCUCGAGAUAGAAAUGUAUCUUGCAGAUACACGCGCCUUUU
........((((...............(((.....))).............(((....)))))))..........(((((((......)))..((((((.....)))))).))))..... (-16.56 = -17.16 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:22 2006