Locus 1958

Sequence ID	3R_DroMel_CAF1
Location	5,529,928 – 5,530,025
Length	97
Max. P	0.858321

overview

Window 4

Location	5,529,928 – 5,530,025
Length	97
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	86.54
Mean single sequence MFE	-29.56
Consensus MFE	-19.92
Energy contribution	-19.96
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-2.00
Structure conservation index	0.67
SVM decision value	0.20
SVM RNA-class probability	0.630430
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5529928 97 + 27905053
CUUUGCAGCGG--CAACUCGAGAAUGGAAGGCGGAAAAUGUAGGAAUCCGACGCCAAAAGGCAGGC--CCAUUCCCAUUCCCAUUCCCAUUCUCAUUCCCA---------
..((((....)--)))...((((((((((.(.(((..(((..(((((((...(((....))).)).--..)))))))))))).)).)))))))).......--------- ( -27.20)
>DroSec_CAF1 10823 93 + 1
CUUUGCAGCGGGACAACUCGAGAAUGGAAGGCGGAAAAUGUAGGAAUCCGACGCCAAAAGGCAGGC--CCAUUCCCA------UUCCCAUUCUCAUUCCCA---------
.........((((......((((((((...(((.....))).(((((((...(((....))).)).--..)))))..------...))))))))..)))).--------- ( -26.20)
>DroSim_CAF1 8867 99 + 1
CUUUGCAGCGGGACAACUCGAGAAUGGAAGGCGGAAAAUGUAGGAAUCCGACGCCAAAAGGCAGGC--CCAUUCCCAUUCCCAUUCCCAUUCUCAUUCCCA---------
.........((((......((((((((((.(.(((..(((..(((((((...(((....))).)).--..)))))))))))).)).))))))))..)))).--------- ( -28.80)
>DroEre_CAF1 9216 106 + 1
CUUUGCAGCGG--CAACUCGAGAAUGGAAGGCGGAAAAUGUAGGAAUCCGAUGCCAAAAGGCAGGC--ACAUUCUCAUUCCCCUUUCCAUUCCCAUUCACAUGCACACUC
...(((((.(.--...).)(.((((((((((.(((..(((.((((......((((....))))...--...)))))))))).)))))))))).).......))))..... ( -32.30)
>DroYak_CAF1 9063 108 + 1
CUUUGCAGCGG--CAACUCGAGAAUGGAAGGCGGAAAAUGUAGGAAUCCGAUGCCAAAAGGCAGGCCCAUAUUCCCCUUCCCAUUUCCAUUCUCAUUCACAUGCACAUUC
...(((((.(.--...).)(((((((((((..(((((((((.((...((..((((....)))))))).)))))....))))..))))))))))).......))))..... ( -33.30)
>consensus
CUUUGCAGCGG__CAACUCGAGAAUGGAAGGCGGAAAAUGUAGGAAUCCGACGCCAAAAGGCAGGC__CCAUUCCCAUUCCCAUUCCCAUUCUCAUUCCCA_________
...................((((((((...(((.....))).(((((((...(((....))).)).....)))))...........))))))))................ (-19.92 = -19.96 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	5,529,928 – 5,530,025
Length	97
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	86.54
Mean single sequence MFE	-37.16
Consensus MFE	-26.38
Energy contribution	-27.14
Covariance contribution	0.76
Combinations/Pair	1.10
Mean z-score	-2.28
Structure conservation index	0.71
SVM decision value	0.82
SVM RNA-class probability	0.858321
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5529928 97 - 27905053
---------UGGGAAUGAGAAUGGGAAUGGGAAUGGGAAUGG--GCCUGCCUUUUGGCGUCGGAUUCCUACAUUUUCCGCCUUCCAUUCUCGAGUUG--CCGCUGCAAAG
---------.((.(((((((((((((.(((((((((((((.(--((..(((....)))))).).))))))...))))))..))))))))))..))).--))......... ( -35.70)
>DroSec_CAF1 10823 93 - 1
---------UGGGAAUGAGAAUGGGAA------UGGGAAUGG--GCCUGCCUUUUGGCGUCGGAUUCCUACAUUUUCCGCCUUCCAUUCUCGAGUUGUCCCGCUGCAAAG
---------.((((.(((((((((((.------(((((((((--(((((((....))))..))...))))...))))))..))))))))))).....))))......... ( -33.60)
>DroSim_CAF1 8867 99 - 1
---------UGGGAAUGAGAAUGGGAAUGGGAAUGGGAAUGG--GCCUGCCUUUUGGCGUCGGAUUCCUACAUUUUCCGCCUUCCAUUCUCGAGUUGUCCCGCUGCAAAG
---------.((((.(((((((((((.(((((((((((((.(--((..(((....)))))).).))))))...))))))..))))))))))).....))))......... ( -38.50)
>DroEre_CAF1 9216 106 - 1
GAGUGUGCAUGUGAAUGGGAAUGGAAAGGGGAAUGAGAAUGU--GCCUGCCUUUUGGCAUCGGAUUCCUACAUUUUCCGCCUUCCAUUCUCGAGUUG--CCGCUGCAAAG
.((((.(((......(((((((((((.((..((((.((((.(--(..((((....)))).)).))))...))))..))...)))))))))))...))--)))))...... ( -39.40)
>DroYak_CAF1 9063 108 - 1
GAAUGUGCAUGUGAAUGAGAAUGGAAAUGGGAAGGGGAAUAUGGGCCUGCCUUUUGGCAUCGGAUUCCUACAUUUUCCGCCUUCCAUUCUCGAGUUG--CCGCUGCAAAG
.....((((.(..(.((((((((((...(((..((..(((.((((((((((....))))..))...)))).)))..)).)))))))))))))..)..--)...))))... ( -38.60)
>consensus
_________UGGGAAUGAGAAUGGGAAUGGGAAUGGGAAUGG__GCCUGCCUUUUGGCGUCGGAUUCCUACAUUUUCCGCCUUCCAUUCUCGAGUUG__CCGCUGCAAAG
...............(((((((((((..((((((((((((.....((((((....))))..)))))))))...)))))...))))))))))).................. (-26.38 = -27.14 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:51 2006