Locus 991

Sequence ID	X_DroMel_CAF1
Location	2,880,306 – 2,880,396
Length	90
Max. P	0.999393

overview

Window 3

Location	2,880,306 – 2,880,396
Length	90
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	70.49
Mean single sequence MFE	-19.62
Consensus MFE	-12.17
Energy contribution	-12.17
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.76
Structure conservation index	0.62
SVM decision value	3.57
SVM RNA-class probability	0.999393
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2880306 90 + 22224390
AGAAGUGUGGGCAGUUGGCUGCCGUUUU-UCGCGCAAGCGAAUAUAAAAAAAAAAAAAGAAGCGAAA--AAAUCAGGA----------A-AAAAUCACAGGUAA
.....(((((((((....)))))....(-((((....))))).........................--.........----------.-.....))))..... ( -21.90)
>DroPse_CAF1 368573 93 + 1
CGACGUGUGGGCAGUCGUCUGCCGUUUUCUCGCGCUCCAAAAUAUCAAA--A---GGAAAAGCAAAA---AACAUGGUACCAUAAUAACAAAAACCA---GAAA
...(((((.(((((....)))))........((..(((...........--.---)))...))....---.))))).....................---.... ( -17.30)
>DroSim_CAF1 237169 93 + 1
AGAAGUGUGGGCAGUUGGCUGCCGUUUU-UCGCGCAAGCGAAUAUAAAAAAAAAAAAAUGAGCGAAAAAAAAUCAAGA----------AAAAAAUUACAGGUAA
.....(((((((((....)))))....(-((((....)))))....................................----------.......))))..... ( -19.90)
>DroYak_CAF1 275621 88 + 1
AGAAGUGUGGGCAGUUGGCUGCCGUUUU-UCGCGCAAGCGAGUAUAAAA------AAA-AAACGAAA--AAAUCUGGAAAAAA------AAAAAUCACAGGUAA
.....(((((((((....)))))(((((-((((....))))........------..)-))))....--..............------......))))..... ( -21.70)
>DroPer_CAF1 388511 93 + 1
CGACGUGUGGGCAGUCGUCUGCCGUUUUCUCGCGCUCCAAAAUAUCAAA--A---GGAAAAGCAAAA---AACAUGGUACCAUAAUAACAAAAACCA---GUAA
...(((((.(((((....)))))........((..(((...........--.---)))...))....---.))))).....................---.... ( -17.30)
>consensus
AGAAGUGUGGGCAGUUGGCUGCCGUUUU_UCGCGCAAGCGAAUAUAAAA__A___AAAAAAGCGAAA__AAAUCUGGAA__A______AAAAAAUCACAGGUAA
....((((((((((....))))).......)))))..................................................................... (-12.17 = -12.17 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	2,880,306 – 2,880,396
Length	90
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	70.49
Mean single sequence MFE	-17.29
Consensus MFE	-8.63
Energy contribution	-8.23
Covariance contribution	-0.40
Combinations/Pair	1.22
Mean z-score	-1.78
Structure conservation index	0.50
SVM decision value	0.61
SVM RNA-class probability	0.797909
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2880306 90 - 22224390
UUACCUGUGAUUUU-U----------UCCUGAUUU--UUUCGCUUCUUUUUUUUUUUUUAUAUUCGCUUGCGCGA-AAAACGGCAGCCAACUGCCCACACUUCU
.....((((.....-.----------.......((--((((((............................))))-)))).(((((....)))))))))..... ( -16.59)
>DroPse_CAF1 368573 93 - 1
UUUC---UGGUUUUUGUUAUUAUGGUACCAUGUU---UUUUGCUUUUCC---U--UUUGAUAUUUUGGAGCGCGAGAAAACGGCAGACGACUGCCCACACGUCG
....---((((..(..(....)..).))))..((---((((((..((((---.--...........)))).))))))))..(((((....)))))......... ( -19.20)
>DroSim_CAF1 237169 93 - 1
UUACCUGUAAUUUUUU----------UCUUGAUUUUUUUUCGCUCAUUUUUUUUUUUUUAUAUUCGCUUGCGCGA-AAAACGGCAGCCAACUGCCCACACUUCU
.....(((........----------.........((((((((.((......................)).))))-)))).(((((....))))).)))..... ( -15.65)
>DroYak_CAF1 275621 88 - 1
UUACCUGUGAUUUUU------UUUUUUCCAGAUUU--UUUCGUUU-UUU------UUUUAUACUCGCUUGCGCGA-AAAACGGCAGCCAACUGCCCACACUUCU
.....((((......------..............--....((((-(..------........((((....))))-)))))(((((....)))))))))..... ( -15.80)
>DroPer_CAF1 388511 93 - 1
UUAC---UGGUUUUUGUUAUUAUGGUACCAUGUU---UUUUGCUUUUCC---U--UUUGAUAUUUUGGAGCGCGAGAAAACGGCAGACGACUGCCCACACGUCG
....---((((..(..(....)..).))))..((---((((((..((((---.--...........)))).))))))))..(((((....)))))......... ( -19.20)
>consensus
UUACCUGUGAUUUUUG______U__UUCCAGAUUU__UUUCGCUUUUUU___U__UUUUAUAUUCGCUUGCGCGA_AAAACGGCAGCCAACUGCCCACACUUCU
.......................................((((............................))))......(((((....)))))......... ( -8.63 =  -8.23 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:50 2006