Locus 2058

Sequence ID	X_DroMel_CAF1
Location	5,651,256 – 5,651,413
Length	157
Max. P	0.992304

overview

Window 5

Location	5,651,256 – 5,651,354
Length	98
Sequences	3
Columns	100
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-35.10
Consensus MFE	-33.29
Energy contribution	-33.40
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.95
SVM decision value	1.13
SVM RNA-class probability	0.919856
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5651256 98 + 22224390
UUAUUGUUCCUUCCCGUUAUGCAUUU--ACCGAGUGUAUAUUUGAGUUCCCUGCUCGAAGGACUGCCACUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAA
..........(((((..(((((((((--...)))))))))(((((((.....)))))))((((((((((((((....))))).)))).))))).))))). ( -37.10)
>DroSec_CAF1 40585 100 + 1
UUAUUGUUCCUUCCCGUUAUGCAUUUGCACCGAGUUUAUAUUUGAGUUACCUGCUCGAAGGACUGCCAGUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAA
......(((((.((((...(((....)))((((.((....(((((((.....)))))))((.(..((.....))..))))).))))))))...))))).. ( -32.10)
>DroSim_CAF1 39665 100 + 1
UUAUUGUUCCUUCCCGUUAUGCAUUUGCACCGAGUGUAUAUUUGAGUUACCUGCUCGAAGGACUACCAGCUGGGUGGCCAAGUUGGCGGGUCUGGGGAAA
......(((((.(((((((((((((((...))))))))))(((((((.....)))))))((.(((((.....)))))))......)))))...))))).. ( -36.10)
>consensus
UUAUUGUUCCUUCCCGUUAUGCAUUUGCACCGAGUGUAUAUUUGAGUUACCUGCUCGAAGGACUGCCAGUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAA
......(((((.((((((((((((((.....)))))))))(((((((.....)))))))((.(((((.....)))))))......)))))...))))).. (-33.29 = -33.40 +   0.11)

alignment

secondary structure

dotplot

Window 6

Location	5,651,282 – 5,651,385
Length	103
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	77.38
Mean single sequence MFE	-40.47
Consensus MFE	-24.96
Energy contribution	-26.40
Covariance contribution	1.44
Combinations/Pair	1.18
Mean z-score	-2.56
Structure conservation index	0.62
SVM decision value	2.32
SVM RNA-class probability	0.992304
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5651282 103 + 22224390
----ACCGAGUGUAUAUUUGAGUUCCCUGCUCGAAGGACUGCCACUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCCGAAUGGGUUAACAAC-UCACA-----
----..............((((((.(((.(((..((..(((((((((((....))))).))))))..)).)))...)))((((((((....)))))))))))-)))..----- ( -42.80)
>DroSec_CAF1 40613 104 + 1
----ACCGAGUUUAUAUUUGAGUUACCUGCUCGAAGGACUGCCAGUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCUGAAUGGGUUAACAGCCCCACA-----
----............(((((((.....)))))))((((((((((((((....)))).))))).)))))((((......((((((((....))))))))..))))...----- ( -39.90)
>DroSim_CAF1 39693 103 + 1
----ACCGAGUGUAUAUUUGAGUUACCUGCUCGAAGGACUACCAGCUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCUGAGUGGGUUAACAAC-CCACA-----
----.((.........(((((((.....)))))))(((((.((((((((....)).))))))..))))))).....(((.....)))..((((((.....))-)))).----- ( -35.90)
>DroEre_CAF1 40696 101 + 1
AUUUGCCGAGUGUGCACUGGAGCUGCCUGCUCGA-GGACUGCCUGCUGGGUAACCAGGUUG----------GGAACAGGGUUAACCUGCUUGG-UUGACUCCCUCGCAGCAGG
....(((.(((....))).).))..(((((((((-((....(((.((((....))))...)----------))....(((((((((.....))-)))))))))))).)))))) ( -43.30)
>consensus
____ACCGAGUGUAUAUUUGAGUUACCUGCUCGAAGGACUGCCAGCUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCUGAAUGGGUUAACAAC_CCACA_____
....(((((((....))))).))..(((.(((..((..(((((((((((....)).)))))))))..)).)))...)))((((((((....)))))))).............. (-24.96 = -26.40 +   1.44)

alignment

secondary structure

dotplot

Window 7

Location	5,651,314 – 5,651,413
Length	99
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	73.54
Mean single sequence MFE	-34.33
Consensus MFE	-17.79
Energy contribution	-19.22
Covariance contribution	1.44
Combinations/Pair	1.17
Mean z-score	-2.10
Structure conservation index	0.52
SVM decision value	0.82
SVM RNA-class probability	0.858925
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5651314 99 + 22224390
GACUGCCACUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCCGAAUGGGUUAACAAC-UCACA-------UAGCGAUUA---GUAAGCAAAGCCAUAUU-CC
(((((((((((((....))))).)))).))))...((((..((((((((((....))))))))...-.....-------..((.....---....))....))...))-)) ( -33.10)
>DroSec_CAF1 40645 101 + 1
GACUGCCAGUUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCUGAAUGGGUUAACAGCCCCACA-------UAGCGAAUAU--AUAAGCAAAGCCAUAUU-CC
(((((((((((((....)))).))))).))))(((((......((((((((....))))))))..)))))..-------....((((((--....((...)).)))))-). ( -34.20)
>DroSim_CAF1 39725 100 + 1
GACUACCAGCUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCUGAGUGGGUUAACAAC-CCACA-------AAGCGAAUAU--AUAAGCAAAGCCAUAUU-CC
((((.((((((((....)).))))))..))))...((((...((((.......((((((.....))-)))).-------..((......--....))..))))...))-)) ( -31.50)
>DroEre_CAF1 40731 100 + 1
GACUGCCUGCUGGGUAACCAGGUUG----------GGAACAGGGUUAACCUGCUUGG-UUGACUCCCUCGCAGCAGGCAAUUCGAAUCGAGCCCGGCAAAGCCGUAUCUAA
...(((((((((.((..((.....)----------)..)).(((((((((.....))-))))))).....))))))))).........((...((((...))))..))... ( -38.50)
>consensus
GACUGCCAGCUGGGUGGCCAAGUUGGCGGGUCUGGGGAAAAGGGUUAACCUGAAUGGGUUAACAAC_CCACA_______AAGCGAAUAU__AUAAGCAAAGCCAUAUU_CC
..(((((((((((....)).)))))))))............((((((((((....))))))))..................((............))....))........ (-17.79 = -19.22 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:14 2006