Locus 960

Sequence ID	3L_DroMel_CAF1
Location	2,857,792 – 2,857,900
Length	108
Max. P	0.727996

overview

Window 5

Location	2,857,792 – 2,857,885
Length	93
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	77.81
Mean single sequence MFE	-22.67
Consensus MFE	-14.55
Energy contribution	-14.55
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.64
SVM decision value	0.31
SVM RNA-class probability	0.684500
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2857792 93 + 23771897
--------GAAGAGAACCUGCAGCGAGGAAAA-AAAAACACAAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU
--------...(.(((..(((((((((.....-...((((.....))))((....)).....)))))))))..)))).....((((((.......)))))). ( -21.50)
>DroPse_CAF1 122210 75 + 1
--------GGAGAGAACCUGCAG-------------------AAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU
--------((((((.....(((.-------------------...)))((((((...........)))))))))))).....((((((.......)))))). ( -25.00)
>DroSec_CAF1 102532 94 + 1
--------GAAGAGAACCUGCAGCGAGGAAAAAAAAAACACAAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU
--------...(.(((..(((((((((.........((((.....))))((....)).....)))))))))..)))).....((((((.......)))))). ( -21.50)
>DroMoj_CAF1 122066 86 + 1
--------AAA--GA--GCA-GAAGAGAGAACAAAAAA---UUGAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGACUGCGUUUCGCGUU
--------...--..--(((-(..(((((..(((....---)))....((((((...........)))))))))))(((.....))).)))).......... ( -20.40)
>DroAna_CAF1 91842 94 + 1
CUAAAACUGUAGAGAACCUGCAGCA--GA------AGAGAAAAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU
.((((((.(.((((....(((((((--((------..........(((.((....)).))).)))))))))))))).))))))(((((.......))))).. ( -22.60)
>DroPer_CAF1 123161 75 + 1
--------GGAGAGAACCUGCAG-------------------AAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU
--------((((((.....(((.-------------------...)))((((((...........)))))))))))).....((((((.......)))))). ( -25.00)
>consensus
________GAAGAGAACCUGCAGCG__GA______AAA___AAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU
................................................((((((...........))))))...........((((((.......)))))). (-14.55 = -14.55 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	2,857,809 – 2,857,900
Length	91
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.79
Mean single sequence MFE	-21.23
Consensus MFE	-14.40
Energy contribution	-14.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.68
SVM decision value	0.42
SVM RNA-class probability	0.727996
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2857809 91 + 23771897
AGGA---AAA-AAAAACACAAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU-------UCCACUUCUG-----GCCUU
.(((---((.-........((((((.((((((...........)))))).....)))))).(((((.......)))))))-------))).......-----..... ( -20.30)
>DroGri_CAF1 122343 89 + 1
AGAA---GGAAAAAAA---UUGAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGACUUCGUUUCGCGUU-------UCCACUUUGGC-----CAGC
....---(((((((((---(.((...((((((...........))))))...)).))))).(((((.......)))))))-------)))........-----.... ( -21.30)
>DroWil_CAF1 94221 82 + 1
AGGA---AGA-------AAAAACUUUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU-------UCCACUUUUU--------AU
.(((---(..-------.(((((...((((((...........))))))......)))))((((((.......)))))))-------))).......--------.. ( -19.70)
>DroYak_CAF1 107845 94 + 1
AGGAAGAAAA-AAAAACACAAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU-------UCCACUUCUG-----GCCUU
(((.((((..-..((((..((((((.((((((...........)))))).....))))))..((((.......)))))))-------)....)))).-----.))). ( -21.80)
>DroMoj_CAF1 122078 101 + 1
AGAG---AACAAAAAA---UUGAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGACUGCGUUUCGCGUUUCGCGAUUCCACUUUGGCAUCGGCAGA
....---..((.((((---(.((...((((((...........))))))...)).))))).))...((((.....(((...)))(((.((.....)).))).)))). ( -24.80)
>DroAna_CAF1 91867 84 + 1
--GA---------AGAGAAAAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU-------UCCACUUCUG-----GCCUU
--((---------((.(((((((((.((((((...........)))))).....))))))((((((.......)))))))-------))..))))..-----..... ( -19.50)
>consensus
AGGA___AAA_AAAAA_A_AAAAUGUUGCAGCUGCCACAAUUUGCUGCACUUUCCGUUUUAUGCGAUUCCGUUUCGCGUU_______UCCACUUCUG_____GCCUU
..........................((((((...........))))))...........((((((.......))))))............................ (-14.40 = -14.40 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:25 2006