Locus 6895

Sequence ID	3R_DroMel_CAF1
Location	18,222,244 – 18,222,351
Length	107
Max. P	0.825718

overview

Window 5

Location	18,222,244 – 18,222,351
Length	107
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	86.38
Mean single sequence MFE	-36.30
Consensus MFE	-33.78
Energy contribution	-33.78
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.93
SVM decision value	0.70
SVM RNA-class probability	0.825718
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18222244 107 + 27905053
UCGAAGACGAGGUGGCCGAGAGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGGAAAAUAUCCUUUUUAAAUA
.....((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))(((.....))).......... ( -37.30)
>DroVir_CAF1 34500 102 + 1
--CAUGACGAGGUGGCCGAGUGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGCAA--UGGCUUUUUUUG-UC
--...(((((((((((.((((.......((((((((.......)))))))))))).)).)))(((((.......))))).))))))((..--..))........-.. ( -34.21)
>DroEre_CAF1 24328 107 + 1
UCGAAGACGAGGUGGCCGAGAGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGGAGGAUACCCUUUUUGAAAA
(((((((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......)))))))))))).((((....)))))))))... ( -40.20)
>DroWil_CAF1 22991 101 + 1
---AUGACGAGGUGGCCGAGUGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGAGAACUUUCUCUG---AUAU
---..(((((((((((.((((.......((((((((.......)))))))))))).)).)))(((((.......))))).))))))((((....))))..---.... ( -36.61)
>DroYak_CAF1 19855 102 + 1
UCGAAGACGAGGUGGCCGAGAGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGUUAAAUAUCCUUUUU-----
.....((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))................----- ( -35.40)
>DroMoj_CAF1 34147 101 + 1
--GAAGACGAGGUGGCCGAGUGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGCAC--UUGGUU-UUUGG-UC
--((((((.((((((.((((((((..((((((((((.......)))))))).))..)).)))(((((.......)))))..))).).)))--)).)))-)))..-.. ( -34.10)
>consensus
__GAAGACGAGGUGGCCGAGAGGUUAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGCAAAAUAUCCUUUUU_A_UA
.....((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))..................... (-33.78 = -33.78 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	18,222,244 – 18,222,351
Length	107
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	86.38
Mean single sequence MFE	-30.38
Consensus MFE	-28.97
Energy contribution	-28.97
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.27
Structure conservation index	0.95
SVM decision value	0.35
SVM RNA-class probability	0.701636
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18222244 107 - 27905053
UAUUUAAAAAGGAUAUUUUCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCUCUCGGCCACCUCGUCUUCGA
..........(((.....)))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))..... ( -31.90)
>DroVir_CAF1 34500 102 - 1
GA-CAAAAAAAGCCA--UUGCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCACUCGGCCACCUCGUCAUG--
..-........((..--..))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))...-- ( -29.80)
>DroEre_CAF1 24328 107 - 1
UUUUCAAAAAGGGUAUCCUCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCUCUCGGCCACCUCGUCUUCGA
..........(((.....)))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))..... ( -30.20)
>DroWil_CAF1 22991 101 - 1
AUAU---CAGAGAAAGUUCUCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCACUCGGCCACCUCGUCAU---
....---..((((....))))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))..--- ( -32.80)
>DroYak_CAF1 19855 102 - 1
-----AAAAAGGAUAUUUAACGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCUCUCGGCCACCUCGUCUUCGA
-----................(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))..... ( -28.80)
>DroMoj_CAF1 34147 101 - 1
GA-CCAAA-AACCAA--GUGCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCACUCGGCCACCUCGUCUUC--
..-.....-......--....(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))...-- ( -28.80)
>consensus
GA_U_AAAAAAGAUAUUUUCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUAACCACUCGGCCACCUCGUCUUC__
.....................(((((((.((((.......)))).((((((...)))).((((((.....)))))).))................)))))))..... (-28.97 = -28.97 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:45 2006