Locus 1299

Sequence ID	X_DroMel_CAF1
Location	3,882,259 – 3,882,375
Length	116
Max. P	0.953923

overview

Window 8

Location	3,882,259 – 3,882,375
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.28
Mean single sequence MFE	-21.95
Consensus MFE	-11.32
Energy contribution	-11.57
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.52
SVM decision value	0.46
SVM RNA-class probability	0.744804
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3882259 116 + 22224390
-CUCGAUGAUUACAUCAUCUUGUGUGCUGUGUCUUUGGUAAUACAAAUUUCUUAUCGAAUAUAUUUU---GUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUUCGACUGGCAAAAAAAA
-...((((((...)))))).....(((((.(((...(((((...((((((...(((((.((.....)---))))))(((((....)))))))))))..)))))..))))))))....... ( -24.30)
>DroVir_CAF1 62865 91 + 1
AAUCGAUGAUUACAUCAUCUUG----------------UAUUACAAAUUUCUUAUCGAAUAUAUUUC---GUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUGUCAUUG----------
...(((((((((((......))----------------))...(((((.......((((.....)))---)....((((((....)))))).....)))))..)))))))---------- ( -16.40)
>DroGri_CAF1 52441 91 + 1
AAUCGAUGAUUACAUCAUCUUG----------------UAUUACAAAUUUCUUAUCGAAUAUAUUUC---GUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUGUCAUUG----------
...(((((((((((......))----------------))...(((((.......((((.....)))---)....((((((....)))))).....)))))..)))))))---------- ( -16.40)
>DroSec_CAF1 4 93 + 1
----------------------UGUGCU--GUCUUUGGUAAUACAAAUUUCUUAUCGAAUAUAUUUU---GUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUUCGACUGGCAAAAAAAA
----------------------..((((--(((...(((((...((((((...(((((.((.....)---))))))(((((....)))))))))))..)))))..))).))))....... ( -19.50)
>DroEre_CAF1 422 118 + 1
--UCGAUGAUUACAUCAUCUUGUGUGUGUUGUCUUCGGUAAUACAAAUUUCUUAUCGAAUAUAUUUUGUUGUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUUCGACUGGCACACAAAA
--..((((((...))))))((((((((..(((.((((((((..........)))))))).))).......(((((((((((....))))))............)))))..)))))))).. ( -31.20)
>DroYak_CAF1 2531 116 + 1
-CUCGAUGAUUACAUCAUCUUGUGUGUUGUGUCUUUGGUAAUACAAAUUUCUUAUCGAAUAUAUUUU---GUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUUCGACUGGCAAAAAAAA
-.((((..(.(((((......)))))..((((.((((((((..........)))))))).)))).).---.))))((((((....))))))..(((.((((((......)))))).))). ( -23.90)
>consensus
__UCGAUGAUUACAUCAUCUUGUGUG_U__GUCUUUGGUAAUACAAAUUUCUUAUCGAAUAUAUUUU___GUCGAUUACCCCCUUGGGUAAAAUUUAUUUGCUUCGACUGGCAAAAAAAA
....((((((...))))))........................(((((......((((.............))))((((((....)))))).....)))))................... (-11.32 = -11.57 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	3,882,259 – 3,882,375
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.28
Mean single sequence MFE	-20.20
Consensus MFE	-15.15
Energy contribution	-15.40
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.75
SVM decision value	1.44
SVM RNA-class probability	0.953923
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3882259 116 - 22224390
UUUUUUUUGCCAGUCGAAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGAC---AAAAUAUAUUCGAUAAGAAAUUUGUAUUACCAAAGACACAGCACACAAGAUGAUGUAAUCAUCGAG-
.......(((..(((.......(((((((((((((....)))).(((((.---.........)))))..))))))))).........)))...))).....((((((...))))))...- ( -20.99)
>DroVir_CAF1 62865 91 - 1
----------CAAUGACAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGAC---GAAAUAUAUUCGAUAAGAAAUUUGUAAUA----------------CAAGAUGAUGUAAUCAUCGAUU
----------........((((((.....((((((....))))))....(---(((.....)))).......))))))....----------------...((((((...)))))).... ( -17.80)
>DroGri_CAF1 52441 91 - 1
----------CAAUGACAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGAC---GAAAUAUAUUCGAUAAGAAAUUUGUAAUA----------------CAAGAUGAUGUAAUCAUCGAUU
----------........((((((.....((((((....))))))....(---(((.....)))).......))))))....----------------...((((((...)))))).... ( -17.80)
>DroSec_CAF1 4 93 - 1
UUUUUUUUGCCAGUCGAAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGAC---AAAAUAUAUUCGAUAAGAAAUUUGUAUUACCAAAGAC--AGCACA----------------------
.......(((..(((.......(((((((((((((....)))).(((((.---.........)))))..))))))))).........)))--.)))..---------------------- ( -16.39)
>DroEre_CAF1 422 118 - 1
UUUUGUGUGCCAGUCGAAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGACAACAAAAUAUAUUCGAUAAGAAAUUUGUAUUACCGAAGACAACACACACAAGAUGAUGUAAUCAUCGA--
(((((((((...(((((............((((((....)))))))))))...........((((.(((..........))).)))).......)))))))))(((((....))))).-- ( -27.40)
>DroYak_CAF1 2531 116 - 1
UUUUUUUUGCCAGUCGAAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGAC---AAAAUAUAUUCGAUAAGAAAUUUGUAUUACCAAAGACACAACACACAAGAUGAUGUAAUCAUCGAG-
...((((((...(((((............((((((....)))))))))))---..(((((((((.....)))...))))))..))))))............((((((...))))))...- ( -20.80)
>consensus
UUUUUUUUGCCAGUCGAAGCAAAUAAAUUUUACCCAAGGGGGUAAUCGAC___AAAAUAUAUUCGAUAAGAAAUUUGUAUUACCAAAGAC__A_CACACAAGAUGAUGUAAUCAUCGA__
..................((((((......(((((....)))))(((((.............))))).....)))))).......................((((((...)))))).... (-15.15 = -15.40 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:03 2006