Locus 6016

Sequence ID	2L_DroMel_CAF1
Location	16,941,892 – 16,941,986
Length	94
Max. P	0.958853

overview

Window 2

Location	16,941,892 – 16,941,986
Length	94
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	77.21
Mean single sequence MFE	-21.05
Consensus MFE	-15.03
Energy contribution	-15.03
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	0.71
SVM decision value	0.34
SVM RNA-class probability	0.693912
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16941892 94 + 22407834
CG-----CCU--GUUUUA----------GCCUGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUAUGGAACCUAUUUUUCCCUCCGCUU
..-----...--.....(----------((..(((((((((((.....((.....))..)))))).)))))(((((....)))))...((((.......))))....))). ( -17.20)
>DroVir_CAF1 69649 94 + 1
CAUUCGUCCU-----GUU----------GCCUGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUGUGGAAA--AUUUUUUCCCAUGACG
....((((.(-----(..----------....(((((((((((.....((.....))..)))))).)))))(((((....)))))...(((((--....))))))).)))) ( -21.10)
>DroPse_CAF1 56412 98 + 1
CA-----CCC--AUUGGAUGGAUCCU--GGCUGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUAUGGAAGCCAUUUUUUCAC----UU
..-----.((--((...))))....(--(((((((((((((((.....((.....))..)))))).)))))(((((....)))))......))))).........----.. ( -22.80)
>DroGri_CAF1 58357 99 + 1
CACCCCUCCUCACUCCUU----------GCCGGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUGUGGGAA--AUUUUUUCCCAUGACG
..................----------....(((((((((((.....((.....))..)))))).)))))(((((....))))).(((((((--.....))))))).... ( -22.60)
>DroAna_CAF1 50652 99 + 1
UG-----CCU--GUUUUA----UCCUCGGCCUGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUAUGGAUCCUAUUUUU-CCCCUGCCA
..-----...--......----.....(((..(((((((((((.....((.....))..)))))).)))))(((((....)))))...(((.........)-))...))). ( -19.80)
>DroPer_CAF1 57046 98 + 1
CA-----CCC--AUUGGAUGGAUCCU--GGCUGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUAUGGAAGCCAUUUUUUCAC----UU
..-----.((--((...))))....(--(((((((((((((((.....((.....))..)))))).)))))(((((....)))))......))))).........----.. ( -22.80)
>consensus
CA_____CCU__AUUGUA__________GCCUGCAAUGAAAACAAAAAGCGAUUUGCAAGUUUUCUAUUGCGCAUAAAAGUAUGCUAUGGAAAC_AUUUUUUCCC_UG_CU
.......((.......................(((((((((((.....((.....))..)))))).)))))(((((....)))))...))..................... (-15.03 = -15.03 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	16,941,892 – 16,941,986
Length	94
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	77.21
Mean single sequence MFE	-25.47
Consensus MFE	-17.38
Energy contribution	-17.38
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.68
SVM decision value	1.49
SVM RNA-class probability	0.958853
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16941892 94 - 22407834
AAGCGGAGGGAAAAAUAGGUUCCAUAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCAGGC----------UAAAAC--AGG-----CG
.(((....((((.......))))...(((((....)))))(((((.((((((..((.....)).....)))))))))))..))----------).....--...-----.. ( -21.90)
>DroVir_CAF1 69649 94 - 1
CGUCAUGGGAAAAAAU--UUUCCACAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCAGGC----------AAC-----AGGACGAAUG
((((.(((((((....--))))).))(((((....)))))(((((.((((((..((.....)).....))))))))))).(..----------..)-----..)))).... ( -26.50)
>DroPse_CAF1 56412 98 - 1
AA----GUGAAAAAAUGGCUUCCAUAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCAGCC--AGGAUCCAUCCAAU--GGG-----UG
..----.........(((((......(((((....)))))(((((.((((((..((.....)).....)))))))))))))))--)..((((((...))--)))-----). ( -27.10)
>DroGri_CAF1 58357 99 - 1
CGUCAUGGGAAAAAAU--UUCCCACAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCCGGC----------AAGGAGUGAGGAGGGGUG
.((..((((((.....--))))))..)).(((((((.((((((((.((((((..((.....)).....)))))))))))..))----------)))))))).......... ( -27.30)
>DroAna_CAF1 50652 99 - 1
UGGCAGGGG-AAAAAUAGGAUCCAUAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCAGGCCGAGGA----UAAAAC--AGG-----CA
.(((...((-(.........)))...(((((....)))))(((((.((((((..((.....)).....)))))))))))..))).....----......--...-----.. ( -22.90)
>DroPer_CAF1 57046 98 - 1
AA----GUGAAAAAAUGGCUUCCAUAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCAGCC--AGGAUCCAUCCAAU--GGG-----UG
..----.........(((((......(((((....)))))(((((.((((((..((.....)).....)))))))))))))))--)..((((((...))--)))-----). ( -27.10)
>consensus
AA_CA_GGGAAAAAAU_GCUUCCAUAGCAUACUUUUAUGCGCAAUAGAAAACUUGCAAAUCGCUUUUUGUUUUCAUUGCAGGC__________UACAAC__AGG_____UG
.....................((...(((((....)))))(((((.((((((..((.....)).....))))))))))).......................))....... (-17.38 = -17.38 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:54 2006