Locus 4801

Sequence ID	2L_DroMel_CAF1
Location	13,706,371 – 13,706,479
Length	108
Max. P	0.975589

overview

Window 6

Location	13,706,371 – 13,706,479
Length	108
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	77.95
Mean single sequence MFE	-24.09
Consensus MFE	-18.80
Energy contribution	-18.83
Covariance contribution	0.03
Combinations/Pair	1.17
Mean z-score	-2.03
Structure conservation index	0.78
SVM decision value	1.52
SVM RNA-class probability	0.960996
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13706371 108 + 22407834
GUU-UUGCCGCCGCCGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUGGCAAUAAGGCGACAAA-AAGAGAGCUUGAAUUAAAAAAAAAAAAAAA--------A
.((-(((.((((((((.((((......)))).))))...(((((...............))))).....)))).))))-).............................--------. ( -28.26)
>DroVir_CAF1 89714 107 + 1
GUU-UUGCCGCCAACGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUAGCAAUAAGGCGACAAA-AAAUGGUA-GAAA---ACA-----ACAACAACGGUGCAA
.((-((((((((..((.((((......)))).))....))).....................((......))......-....))))-))).---...-----............... ( -18.40)
>DroPse_CAF1 74961 98 + 1
GUU-UCGCCGCCGCCGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUAGCAAUAAGGCGACAAA-AA-AGAGC------A-AAAAAA--AAAAGA--------G
...-((((((((((((.((((......)))).))))..)))...................((....)).)))))....-..-.....------.-......--......--------. ( -23.60)
>DroEre_CAF1 62904 113 + 1
GUU-UUGCCGCCGCCGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUGGCAAUAAGGCGACAAA-AAGAGAGCUUGAAUACAAAAAACAAGGAAAAACA---AA
.((-(((.((((((((.((((......)))).))))...(((((...............))))).....)))).))))-)......((((...........))))........---.. ( -29.36)
>DroWil_CAF1 217451 92 + 1
GUUUUUGCCGCCAUCGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUAGCAAUAAGGCGACGAAAAAAAGAGCAAGAA--------------------------
.((((((.((((...(.((((......)))).)(((...)))...........................)))).))))))............-------------------------- ( -18.50)
>DroAna_CAF1 68817 102 + 1
GUU-UUGCCGCCGCCGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUAGCAAUAAGGCGACAAG-GAGCGGGCUGGGAAAAAA------AUGCGA--------C
.((-((.(((..(((.(((((.(((((......(((...)))....................((......))))))).-))))))))))).))))..------......--------. ( -26.40)
>consensus
GUU_UUGCCGCCGCCGUGCUUAUUGUCAAGCUCGGCCAGGCCAUAAAAAACAAACUUCAAUAGCAAUAAGGCGACAAA_AAGAGAGCUGGAA_A_AAA_____AAAAAA________A
....((((((((((((.((((......)))).))))..))).............((.....))......)))))............................................ (-18.80 = -18.83 +   0.03)

alignment

secondary structure

dotplot

Window 7

Location	13,706,371 – 13,706,479
Length	108
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	77.95
Mean single sequence MFE	-29.77
Consensus MFE	-27.39
Energy contribution	-27.33
Covariance contribution	-0.05
Combinations/Pair	1.12
Mean z-score	-2.67
Structure conservation index	0.92
SVM decision value	1.75
SVM RNA-class probability	0.975589
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13706371 108 - 22407834
U--------UUUUUUUUUUUUUUUAAUUCAAGCUCUCUU-UUUGUCGCCUUAUUGCCAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGGCGGCGGCAA-AAC
.--------.............................(-(((((((((.....(((((.((((.....)))).)))))...((((.(((((....))))).))))))))))))-)). ( -34.30)
>DroVir_CAF1 89714 107 - 1
UUGCACCGUUGUUGU-----UGU---UUUC-UACCAUUU-UUUGUCGCCUUAUUGCUAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGUUGGCGGCAA-AAC
..(((.((....)).-----)))---....-.......(-(((((((((....((((((((((((((.........(((...)))))))))..)))).))))....))))))))-)). ( -25.00)
>DroPse_CAF1 74961 98 - 1
C--------UCUUUU--UUUUUU-U------GCUCU-UU-UUUGUCGCCUUAUUGCUAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGGCGGCGGCGA-AAC
.--------......--......-.------.....-.(-(((((((((.....(((((.((((.....)))).)))))...((((.(((((....))))).))))))))))))-)). ( -31.70)
>DroEre_CAF1 62904 113 - 1
UU---UGUUUUUCCUUGUUUUUUGUAUUCAAGCUCUCUU-UUUGUCGCCUUAUUGCCAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGGCGGCGGCAA-AAC
..---........((((..(.....)..))))......(-(((((((((.....(((((.((((.....)))).)))))...((((.(((((....))))).))))))))))))-)). ( -35.30)
>DroWil_CAF1 217451 92 - 1
--------------------------UUCUUGCUCUUUUUUUCGUCGCCUUAUUGCUAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGAUGGCGGCAAAAAC
--------------------------...........(((((.((((((....((((((((((((((.........(((...)))))))))..)))).))))....))))))))))). ( -21.90)
>DroAna_CAF1 68817 102 - 1
G--------UCGCAU------UUUUUUCCCAGCCCGCUC-CUUGUCGCCUUAUUGCUAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGGCGGCGGCAA-AAC
.--------......------..................-.((((((((.....(((((.((((.....)))).)))))...((((.(((((....))))).))))))))))))-... ( -30.40)
>consensus
U________UCUUUU_____UUU_U_UUCAAGCUCUCUU_UUUGUCGCCUUAUUGCUAUUGAAGUUUGUUUUUUAUGGCCUGGCCGAGCUUGACAAUAAGCACGGCGGCGGCAA_AAC
.........................................((((((((.....(((((.((((.....)))).)))))...((((.(((((....))))).)))))))))))).... (-27.39 = -27.33 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:40 2006