Locus 8008

Sequence ID	X_DroMel_CAF1
Location	19,911,280 – 19,911,417
Length	137
Max. P	0.908358

overview

Window 5

Location	19,911,280 – 19,911,395
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.86
Mean single sequence MFE	-40.90
Consensus MFE	-21.89
Energy contribution	-22.12
Covariance contribution	0.22
Combinations/Pair	1.16
Mean z-score	-3.22
Structure conservation index	0.54
SVM decision value	0.10
SVM RNA-class probability	0.582278
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19911280 115 + 22224390
GUGCUCUCGAUUGCAAAUCCCG-GCCAUAAUUUAUGCCUAUGGC-CG-GAGUCUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGUUGAACUGAGCUGACAGACAGCUGGCACAGGA--CU
((((((((((((((.....(((-((((((.........))))))-))-)....(((((..(....)..)))))..)))))))))........(((((.....))))))))))....--.. ( -47.50)
>DroPse_CAF1 26955 116 + 1
CCUCUCUCGAUGCCAAAUCCCGGGCCGUAAUUUAUGCCUAUGGCCCG-AAGUACGCAUUGAUAUUUUGAUGCAAAGCAGUUGAGUUAA---CAACUGACAAACAGCUGGCACGAGCAGCU
...((((((.((((......(((((((((.........)))))))))-.(((..((((..(....)..))))...(((((((......---)))))).).....))))))))))).)).. ( -42.30)
>DroEre_CAF1 23064 116 + 1
GUGCUCUCGAUUGCAAAUCCCG-GCCAUAAUUUAUGCCUAUGGCCCG-GAGUGUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGUUCAACUGAGCUGACAGACAGCUGGCAUGGGA--CU
((((((((((((((...(((.(-((((((.........))))))).)-))...(((((..(....)..)))))..)))))))))........(((((.....))))))))))....--.. ( -44.10)
>DroYak_CAF1 24915 116 + 1
GUGCUCUCGAUUGCAAAUCCCG-GCUAUAAUUUAUGCCUAUGGCCCG-GAGUGUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGCCGAACUGAGCUGACAGACAGCUGGCACAGGA--CU
((((((((((((((...(((.(-((((((.........))))))).)-))...(((((..(....)..)))))..)))))))))........(((((.....))))))))))....--.. ( -43.90)
>DroAna_CAF1 47546 111 + 1
---CACUCGAUUGCAAAUCCUGGGCUGUAAUUUAUGCCUAUGACCCAAAAGUAUGCAUUGAUAUUUUGAUGCAAAGCAGUUGAGUUAA---CAACUGACAGGCAGCUGGCACC-GA--CU
---.((((((((((...((.(((((..........))))).))..........(((((..(....)..)))))..))))))))))...---((.(((.....))).)).....-..--.. ( -31.40)
>DroPer_CAF1 30227 116 + 1
CCUCUCUCGAUGCCACAUCCCAGGCCGUAAUUUAUGCCUAUGGCCCA-AAGUACGCAUUGAUAUUUUGAUGCAAAGCAGUUGAGUUAA---CAACUGACAAACAGCUGGCACGAGCAGCU
...((((((.((((........(((((((.........)))))))..-.(((..((((..(....)..))))...(((((((......---)))))).).....))))))))))).)).. ( -36.20)
>consensus
GUGCUCUCGAUUGCAAAUCCCG_GCCAUAAUUUAUGCCUAUGGCCCG_AAGUAUGCAUUGAUAUUUUGAUGCAAAGCAGUUGAGUUAA___CAACUGACAGACAGCUGGCACGGGA__CU
.....(((((((((......((.((((((.........)))))).)).......((((..(....)..))))...)))))))))..........(((.....)))............... (-21.89 = -22.12 +   0.22)

alignment

secondary structure

dotplot

Window 6

Location	19,911,319 – 19,911,417
Length	98
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	71.31
Mean single sequence MFE	-33.00
Consensus MFE	-18.52
Energy contribution	-18.48
Covariance contribution	-0.04
Combinations/Pair	1.21
Mean z-score	-1.83
Structure conservation index	0.56
SVM decision value	1.06
SVM RNA-class probability	0.908358
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19911319 98 + 22224390
UGGC-CG-GAGUCUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGUUGAACUGAGCUGACAGACAGCUGGCACAGGACUCAGAGGACUUGGAAGAC------------------UCGGA
...(-((-.(((((((((..(....)..)))).((((..(((((((...((((((((.....)))))....))))))))))..).)))...))))------------------)))). ( -31.70)
>DroSec_CAF1 25454 90 + 1
UGGCCCG-GAGUCUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGUUGAACUGAGCUGACAGACAGCUGGCACAGGACUC---------GGAAGAC------------------UCGGA
(((((.(-..((((((((..(....)..))))...((((((.((.....)).))))).)))))..).))).)).((.((---------....)).------------------))... ( -28.50)
>DroEre_CAF1 23103 108 + 1
UGGCCCG-GAGUGUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGUUCAACUGAGCUGACAGACAGCUGGCAUGGGACUCAGAGGACUGG---------GAGGACUGGGCGGACUGGGA
..(((((-(.((((((((..(....)..))))....((((((....))))))(((((.....))))).))))....(((((....))))---------)....))))))......... ( -38.00)
>DroYak_CAF1 24954 117 + 1
UGGCCCG-GAGUGUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGCCGAACUGAGCUGACAGACAGCUGGCACAGGACUCGGAGGACUCGAAGGACUCGGAGGACUCAGAGGACUGGAA
.((((((-(....(((((..(....)..)))))......)))))))......(((((.....)))))....(((..(((.(((..(((((.....)).)))..))).)))..)))... ( -47.30)
>DroAna_CAF1 47583 85 + 1
UGACCCAAAAGUAUGCAUUGAUAUUUUGAUGCAAAGCAGUUGAGUUAA---CAACUGACAGGCAGCUGGCACC-GACUCCAAGUCCUUU-----------------------------
.(((......((.(((((..(....)..)))))...((((((......---)))))))).((.((.((....)-).))))..)))....----------------------------- ( -19.50)
>consensus
UGGCCCG_GAGUCUGCAUUGAUAUUUUGAUGCAAAGCAGUUGGGUUGAACUGAGCUGACAGACAGCUGGCACAGGACUCAGAGGACUUG_A_GAC__________________UCGGA
.((((((...((.(((((..(....)..)))))..))...))))))......(((((.....)))))................................................... (-18.52 = -18.48 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:09 2006