Locus 8727

Sequence ID	3R_DroMel_CAF1
Location	23,310,507 – 23,310,640
Length	133
Max. P	0.896075

overview

Window 3

Location	23,310,507 – 23,310,610
Length	103
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	80.50
Mean single sequence MFE	-27.87
Consensus MFE	-18.05
Energy contribution	-19.08
Covariance contribution	1.03
Combinations/Pair	1.18
Mean z-score	-1.55
Structure conservation index	0.65
SVM decision value	0.19
SVM RNA-class probability	0.627891
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23310507 103 - 27905053
AGGACACA-UCCUUUGCCCUCUCUUUGGGGCAAACAAUCGAAGAUUUAUUGCCCCUCGGCGCAUUCU-UUGGCACUG--CGAA-UGUGCAAAUUCGCGCUGAAAUAUA
((((....-)))).............(((((((..((((...))))..)))))))(((((((.....-...((((..--....-.))))......)))))))...... ( -31.24)
>DroPse_CAF1 111070 97 - 1
-----GCGCUCUGUUGC-----CUUUCUGGCAAACAAUCGAAGAUUUAUUGUCCCCAGGCGGAUUCC-UUGGCAAUGUGCGAGUUUUGCAAAUUUACGCUCAAAUAUA
-----((((...(((((-----(..(((((...(((((.........)))))..))))).((...))-..))))))))))((((.............))))....... ( -20.52)
>DroEre_CAF1 114249 102 - 1
AGGACACA-UCCUUUGCCC-CUCUUUGGGGCAAACAAUCGAAGAUUUAUUGCCCCUCGGCGCAUUCU-UUGGCACUG--CGAA-UGUGCAAAUUCGCGCUGAAAUAUA
.(((....-)))(((((((-(.....))))))))...(((((((.....((((....))))...)))-))))((.((--((((-(......))))))).))....... ( -33.90)
>DroYak_CAF1 118908 103 - 1
AGGACACA-UCCUUUGCCCUCUCUUUGGGGCAAACAAUCGAAGAUUUAUUGCCCCUCGGCGCAUUCU-UUGGCACUG--CGAA-UGUGCAAAUUCGCGCUGAAAUAUA
((((....-)))).............(((((((..((((...))))..)))))))(((((((.....-...((((..--....-.))))......)))))))...... ( -31.24)
>DroAna_CAF1 102617 103 - 1
AGGACAUA-UCCUUUGGUCUGU-UUGGGGGAAAACAAUUGAAGAUUUAUCGUCCCUCGGCGCAUUCUUUUGGCACUG--CCAA-UGUGCAAAUUUGCGUUGAAAUAUA
.(((((((-..(((..((.(((-((......)))))))..)))...))).)))).((((((((....((((.(((..--....-.)))))))..))))))))...... ( -29.80)
>DroPer_CAF1 111570 97 - 1
-----GCGCUCUGUUGC-----CUUUCUGGCAAACAAUCGAAGAUUUAUUGUCCCCAGGCGGAUUCC-UUGGCAAUGUGCGAGUUUUGCAAAUUUACGCUCAAAUAUA
-----((((...(((((-----(..(((((...(((((.........)))))..))))).((...))-..))))))))))((((.............))))....... ( -20.52)
>consensus
AGGACACA_UCCUUUGCCC_CUCUUUGGGGCAAACAAUCGAAGAUUUAUUGCCCCUCGGCGCAUUCU_UUGGCACUG__CGAA_UGUGCAAAUUCGCGCUGAAAUAUA
..........................(((((((..((((...))))..)))))))(((((((.........((((..........))))......)))))))...... (-18.05 = -19.08 +   1.03)

alignment

secondary structure

dotplot

Window 4

Location	23,310,544 – 23,310,640
Length	96
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	86.83
Mean single sequence MFE	-43.38
Consensus MFE	-28.94
Energy contribution	-29.20
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-2.77
Structure conservation index	0.67
SVM decision value	0.99
SVM RNA-class probability	0.896075
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23310544 96 + 27905053
AGAAUGCGCCGAGGGGCAAUAAAUCUUCGAUUGUUUGCCCCAAAGAGAGGGCAAAGGAUGUGUCCUGG--U--------GUCCUUGCGUCCGCGCGUCCUCUCGUC
............(((((((..((((...))))..)))))))...((((((((.(((((..(......)--.--------.)))))(((....)))))))))))... ( -40.40)
>DroSec_CAF1 107987 104 + 1
AGAAUGCGCCGAGGGGCAAUAAAUCUUCGAUUGUUUGCCCCAAAGAGAGGGCAAAGGAUGUGUCCUGG--UGUCCUGGUGUCCUCGCGUCCGCGAGUCCUGUCGUC
.((..(((((..(((((((..((((...))))..)))))))......((((((.((((....))))..--))))))))))).(((((....))))).....))... ( -41.90)
>DroSim_CAF1 112172 104 + 1
AGAAUGCGCCGAGGGGCAAUAAAUCUUCGAUUGUUUGCCCCAAAGAGAGGGCAAAGGAUGUGUCCUGG--UGUCCCGGUGUCCUCGCGUCCGCGAGUCCUGCCGUC
.....((((((.(((((((..((((...))))..))))))).......(((((.((((....))))..--))))))))))).(((((....))))).......... ( -42.10)
>DroYak_CAF1 118945 98 + 1
AGAAUGCGCCGAGGGGCAAUAAAUCUUCGAUUGUUUGCCCCAAAGAGAGGGCAAAGGAUGUGUCCUGGCGUGUCCUGGUGCCCUGGCA--------UUCCGGCGUC
.....((((((.(((((((..((((...))))..)))))))...(..((((((.((((..(((....)))..))))..))))))..).--------...)))))). ( -49.10)
>consensus
AGAAUGCGCCGAGGGGCAAUAAAUCUUCGAUUGUUUGCCCCAAAGAGAGGGCAAAGGAUGUGUCCUGG__UGUCCUGGUGUCCUCGCGUCCGCGAGUCCUGUCGUC
...((((.....(((((((..((((...))))..))))))).....(((((((.((((....))))............)))))))))))................. (-28.94 = -29.20 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:13 2006