Locus 5598

Sequence ID	3L_DroMel_CAF1
Location	15,363,082 – 15,363,207
Length	125
Max. P	0.866529

overview

Window 8

Location	15,363,082 – 15,363,184
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.01
Mean single sequence MFE	-26.87
Consensus MFE	-23.22
Energy contribution	-22.50
Covariance contribution	-0.72
Combinations/Pair	1.11
Mean z-score	-1.44
Structure conservation index	0.86
SVM decision value	0.00
SVM RNA-class probability	0.536004
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15363082 102 + 23771897
------------------CCUGCACAGCAUGCGAGUUUAUAGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAACGCGCUUUUUGCGGAUACGCUU
------------------.(((((.(((..(((.((((...((.(((....)))))....((((((.......))))))))))((((.....))))..))))))...)))))........ ( -24.70)
>DroVir_CAF1 93113 102 + 1
------------------UUUGCACAGCAUGCGGCUUUAUAGUCGAUUUUUAUCACAGCAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACGAUA
------------------((((((.(((..((((((((...((.(((....))))).....(((((.......))))))))))((((.....))))..))))))...))))))....... ( -25.80)
>DroPse_CAF1 96482 102 + 1
------------------UCCGCACAGCAUGCGAGUUUAUAGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACGCUU
------------------((((((.(((..((((((((...((.(((....)))))....((((((.......))))))))))((((.....)))).)))))))...))))))....... ( -29.40)
>DroGri_CAF1 94118 102 + 1
------------------UUUGCACAGCAUGCGGCUUUAUAGUCGAUUUUUAUCACAGCAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACAAUA
------------------((((((.(((..((((((((...((.(((....))))).....(((((.......))))))))))((((.....))))..))))))...))))))....... ( -25.80)
>DroMoj_CAF1 91594 102 + 1
------------------UUUGCACAGCAUGCGGCUUUAUAGUCGAUUUUUAUCACAGCGUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACGAUA
------------------((((((.(((...(((((....)))))............(((((((((.......))))))....((((.....))))..))))))...))))))....... ( -26.20)
>DroAna_CAF1 230240 120 + 1
CUUUCAUCGAAAAAAAAACCCGCACAGCAUGCGAGUUUAUAGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAACGCGCUUUUUGCGGAUACGCUU
.....(((((.....((((.((((.....)))).))))....)))))..........(((((((...........(((((((((((............)))))))))))))))))).... ( -29.30)
>consensus
__________________UCUGCACAGCAUGCGACUUUAUAGUCGAUUUUUAUCACAGCAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACGAUA
...................(((((.(((..(((........((.(((....))))).((.((((((.......))))))..))((((.....))))..))))))...)))))........ (-23.22 = -22.50 +  -0.72)

alignment

secondary structure

dotplot

Window 9

Location	15,363,104 – 15,363,207
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.17
Mean single sequence MFE	-21.32
Consensus MFE	-17.89
Energy contribution	-17.95
Covariance contribution	0.06
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.84
SVM decision value	0.85
SVM RNA-class probability	0.866529
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15363104 103 + 23771897
AGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAACGCGCUUUUUGCGGAUACGCUUUAUU-------CUUUUU--UCCCCC---ACUUAUU-----
.((.(((....)))))(((..(((((.......)))))(((((((((.....))))....(((.....))).....)))))...-------......--......---)))....----- ( -19.90)
>DroPse_CAF1 96504 102 + 1
AGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACGCUUUAUU-------CUCCUU--CU-------ACUUAUUUCU--
.((.(((....)))))((((.(((((.......)))))(((((((((.....))))(((.(((.....))))))..)))))...-------......--.)-------))).......-- ( -22.90)
>DroGri_CAF1 94140 108 + 1
AGUCGAUUUUUAUCACAGCAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACAAUAUUUU-------CAUUUUUUUUUUUCUAUUUUUGUC-----
.((.(((....))))).((.((((((.......))))))..))((((.....))))(((.(((.....))))))..........-------........................----- ( -18.20)
>DroEre_CAF1 95025 89 + 1
AGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAACGCGCUUUUUGCGAAUACGCUUCAUU-------CUUGU------------------------
.((.(((....))))).....(((((.......)))))(((((((((.....))))....(((.....))).....)))))...-------.....------------------------ ( -21.80)
>DroMoj_CAF1 91616 115 + 1
AGUCGAUUUUUAUCACAGCGUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAUCGCGCUUUUUGCGGAUACGAUAUUUCUCGUCGUCUCUUUUUUUCUUUUCUUUUUGUU-----
.(.(((....((((...((..(((((.......)))))...))((((.....))))(((.(((.....))))))..))))....))).)..........................----- ( -24.10)
>DroAna_CAF1 230280 103 + 1
AGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAACGCGCUUUUUGCGGAUACGCUUUAUU-------CUCUUU--U--------ACUUAUUUGGAA
.((.(((....)))))((((.(((((.......)))))(((((((((.....))))....(((.....))).....)))))...-------......--)--------)))......... ( -21.00)
>consensus
AGUCGAUUUUUAUCACAGUAUUUGAAUUAUUAUUUCAGGAAGCGCGCUAUUUGCGCAACGCGCUUUUUGCGGAUACGCUUUAUU_______CUCUUU__UU_______ACUUAUU_____
.((.(((....))))).(((((((...........(((((((((((............))))))))))))))))))............................................ (-17.89 = -17.95 +   0.06)

alignment

secondary structure

dotplot

Window 0

Location	15,363,104 – 15,363,207
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-19.67
Consensus MFE	-13.05
Energy contribution	-13.05
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.66
SVM decision value	0.65
SVM RNA-class probability	0.812990
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15363104 103 - 23771897
-----AAUAAGU---GGGGGA--AAAAAG-------AAUAAAGCGUAUCCGCAAAAAGCGCGUUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAAUACUGUGAUAAAAAUCGACU
-----....(((---(.((((--(.....-------......(((....))).....((((((((......)))))))))))))(((.......)))...)))).((((....))))... ( -21.50)
>DroPse_CAF1 96504 102 - 1
--AGAAAUAAGU-------AG--AAGGAG-------AAUAAAGCGUAUCCGCAAAAAGCGCGAUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAAUACUGUGAUAAAAAUCGACU
--.......(((-------((--((((.(-------......((((((((((.....))).)))))))......).).)))).((((.......))))..)))).((((....))))... ( -21.00)
>DroGri_CAF1 94140 108 - 1
-----GACAAAAAUAGAAAAAAAAAAAUG-------AAAAUAUUGUAUCCGCAAAAAGCGCGAUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAAUGCUGUGAUAAAAAUCGACU
-----......................((-------((..((((((((((((.....))).)))((((.....))))..........)))))).)))).......((((....))))... ( -15.90)
>DroEre_CAF1 95025 89 - 1
------------------------ACAAG-------AAUGAAGCGUAUUCGCAAAAAGCGCGUUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAAUACUGUGAUAAAAAUCGACU
------------------------....(-------(((...(((....)))...((((((((((......))))))))))............))))........((((....))))... ( -19.40)
>DroMoj_CAF1 91616 115 - 1
-----AACAAAAAGAAAAGAAAAAAAGAGACGACGAGAAAUAUCGUAUCCGCAAAAAGCGCGAUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAACGCUGUGAUAAAAAUCGACU
-----............................(((....((((((((((((.....))).)))))....((((((.......((((.......))))..))))))))))....)))... ( -20.90)
>DroAna_CAF1 230280 103 - 1
UUCCAAAUAAGU--------A--AAAGAG-------AAUAAAGCGUAUCCGCAAAAAGCGCGUUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAAUACUGUGAUAAAAAUCGACU
...((....(((--------(--...(((-------......(((....)))...((((((((((......)))))))))).............)))...)))).))............. ( -19.30)
>consensus
_____AAUAAGU_______AA__AAAAAG_______AAUAAAGCGUAUCCGCAAAAAGCGCGAUGCGCAAAUAGCGCGCUUCCUGAAAUAAUAAUUCAAAUACUGUGAUAAAAAUCGACU
.............................................(((.((((..(((((((............)))))))..((((.......)))).....))))))).......... (-13.05 = -13.05 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:19 2006