Locus 5563

Sequence ID	X_DroMel_CAF1
Location	14,380,603 – 14,380,750
Length	147
Max. P	0.990312

overview

Window 6

Location	14,380,603 – 14,380,711
Length	108
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	86.92
Mean single sequence MFE	-25.50
Consensus MFE	-19.12
Energy contribution	-20.12
Covariance contribution	1.00
Combinations/Pair	1.12
Mean z-score	-1.84
Structure conservation index	0.75
SVM decision value	0.55
SVM RNA-class probability	0.778936
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14380603 108 + 22224390
--CACAUGCACGCAUAUUCUCGUCCUGCGACGAUGCAUAUAUGUAUGUGAAUGGAUCUGUGUGAGUGAGUUGGCUCACGUCAGCUAGACAUAAACCAAACAAUAAACAAA
--((((((((...((((.((((((....))))).).)))).))))))))..(((......((((((......))))))(((.....))).....)))............. ( -28.90)
>DroSec_CAF1 96632 104 + 1
--CACACACACGCACAUUUUAGUCCUGCGACGAUGCAUAUA----UGUGAAUGGGUCUGUGUGAGUGAGUUGGCUCACGUCAGCUAGACAUAAACCAAACAAUAAACAAA
--....(((.((((((.....(((....)))(((.(((...----.....))).))))))))).)))(((((((....)))))))......................... ( -25.30)
>DroSim_CAF1 90461 104 + 1
--CACACACACGCACAUUCUAGUCCUGCGACGAUGCAUAUA----UGUGAAUGGGUCUGUGUGAGUGAGUUGGCUCACGUCAGCUAGACAUAAACCAAACAAUAAACAAA
--..((((((.((.(((((..(((....)))...(((....----)))))))).)).)))))).(((((....)))))(((.....)))..................... ( -27.10)
>DroYak_CAF1 98580 94 + 1
CACACACGCACACACAUUCUAGUCCUGCGACCAUGUAUACA----U------------GUGUGAGUGAGUUGGCUCACGUCAGCUAGACAUAAACCAAACAAUAAACAAA
(((((.((((...((......))..))))...(((....))----)------------))))).(((((....)))))(((.....)))..................... ( -20.70)
>consensus
__CACACACACGCACAUUCUAGUCCUGCGACGAUGCAUAUA____UGUGAAUGGGUCUGUGUGAGUGAGUUGGCUCACGUCAGCUAGACAUAAACCAAACAAUAAACAAA
....(((.(((((........(((....)))(((.(((............))).))).))))).)))(((((((....)))))))......................... (-19.12 = -20.12 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	14,380,603 – 14,380,711
Length	108
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	86.92
Mean single sequence MFE	-34.62
Consensus MFE	-26.79
Energy contribution	-26.97
Covariance contribution	0.19
Combinations/Pair	1.13
Mean z-score	-3.45
Structure conservation index	0.77
SVM decision value	2.21
SVM RNA-class probability	0.990312
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14380603 108 - 22224390
UUUGUUUAUUGUUUGGUUUAUGUCUAGCUGACGUGAGCCAACUCACUCACACAGAUCCAUUCACAUACAUAUAUGCAUCGUCGCAGGACGAGAAUAUGCGUGCAUGUG--
(((((....((.((((((((((((.....))))))))))))..)).....)))))......(((((.((..((((..(((((....)))))...))))..)).)))))-- ( -31.90)
>DroSec_CAF1 96632 104 - 1
UUUGUUUAUUGUUUGGUUUAUGUCUAGCUGACGUGAGCCAACUCACUCACACAGACCCAUUCACA----UAUAUGCAUCGUCGCAGGACUAAAAUGUGCGUGUGUGUG--
(((((....((.((((((((((((.....))))))))))))..)).....)))))......((((----(((((((((.(((....)))......)))))))))))))-- ( -33.60)
>DroSim_CAF1 90461 104 - 1
UUUGUUUAUUGUUUGGUUUAUGUCUAGCUGACGUGAGCCAACUCACUCACACAGACCCAUUCACA----UAUAUGCAUCGUCGCAGGACUAGAAUGUGCGUGUGUGUG--
(((((....((.((((((((((((.....))))))))))))..)).....)))))......((((----(((((((((..((.........))..)))))))))))))-- ( -34.40)
>DroYak_CAF1 98580 94 - 1
UUUGUUUAUUGUUUGGUUUAUGUCUAGCUGACGUGAGCCAACUCACUCACAC------------A----UGUAUACAUGGUCGCAGGACUAGAAUGUGUGUGCGUGUGUG
............((((((((((((.....))))))))))))......(((((------------(----(((((((((((((....)))).....))))))))))))))) ( -38.60)
>consensus
UUUGUUUAUUGUUUGGUUUAUGUCUAGCUGACGUGAGCCAACUCACUCACACAGACCCAUUCACA____UAUAUGCAUCGUCGCAGGACUAGAAUGUGCGUGCGUGUG__
............((((((((((((.....))))))))))))......(((((.((.....))........((((((((((((....)))).....))))))))))))).. (-26.79 = -26.97 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	14,380,640 – 14,380,750
Length	110
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	87.75
Mean single sequence MFE	-22.52
Consensus MFE	-19.01
Energy contribution	-19.20
Covariance contribution	0.20
Combinations/Pair	1.04
Mean z-score	-2.09
Structure conservation index	0.84
SVM decision value	0.69
SVM RNA-class probability	0.825075
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14380640 110 - 22224390
UACUUGCCAGCAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUCUAGCU-GACGUGAGCCAACU-CACUCACACAGAUCCAUUCACAUACAUA
.......((((....(((..(((((((((((.((((((....))))))))))))))))))))...)))-)..(((((......-..)))))..................... ( -21.70)
>DroSec_CAF1 96669 106 - 1
UACUUGCCAGCAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUCUAGCU-GACGUGAGCCAACU-CACUCACACAGACCCAUUCACA----UA
.......((((....(((..(((((((((((.((((((....))))))))))))))))))))...)))-)..(((((......-..)))))...............----.. ( -21.70)
>DroSim_CAF1 90498 106 - 1
UACUUGCCAGCAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUCUAGCU-GACGUGAGCCAACU-CACUCACACAGACCCAUUCACA----UA
.......((((....(((..(((((((((((.((((((....))))))))))))))))))))...)))-)..(((((......-..)))))...............----.. ( -21.70)
>DroEre_CAF1 86386 106 - 1
UACUUGCCGGCAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUAUAGCU-GACGUGAGCCAACU-CACGCACACAGACGCACUCGCA----UG
....(((((((....(((..(((((((((((.((((((....))))))))))))))))))))...)))-).((((((....))-))))...............)))----.. ( -24.60)
>DroYak_CAF1 98619 94 - 1
UACUUGCCAGCAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUCUAGCU-GACGUGAGCCAACU-CACUCACAC------------A----UG
.......((((....(((..(((((((((((.((((((....))))))))))))))))))))...)))-)..(((((......-..)))))..------------.----.. ( -21.70)
>DroAna_CAF1 163507 96 - 1
UACUUGCCAACAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUCUAGCUAGACGUGGGCCAAGUACACUCAUCC------------G----AG
((((((((.((.........(((((((((((.((((((....))))))))))))))))).((((....)))))).)).))))))..(((....------------)----)) ( -23.70)
>consensus
UACUUGCCAGCAUUCACAACUAAAUUAGAUGCAUAAACUUUUGUUUAUUGUUUGGUUUAUGUCUAGCU_GACGUGAGCCAACU_CACUCACACAGACCCAUUCACA____UA
.........(((((.............)))))((((((....))))))...((((((((((((......))))))))))))............................... (-19.01 = -19.20 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:59 2006