Locus 6579

Sequence ID	X_DroMel_CAF1
Location	16,429,572 – 16,429,805
Length	233
Max. P	0.951519

overview

Window 0

Location	16,429,572 – 16,429,685
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.74
Mean single sequence MFE	-33.90
Consensus MFE	-23.41
Energy contribution	-23.98
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.39
Structure conservation index	0.69
SVM decision value	1.41
SVM RNA-class probability	0.951519
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16429572 113 + 22224390
UAGAUGGGCUCGAAAAUGUUUACACCAUUCGAUCGUUCGAGUACGGUGGGCAC-------CACAGACUUUUACGGCCCACUGUACGUUCCACCAGUUAGUCAGUCAGUCAUCAAAACAUU
..(((((.((.((...((...((.....((((....))))(((((((((((..-------..............))))))))))).........))....)).)))))))))........ ( -31.19)
>DroSec_CAF1 1530 106 + 1
CAGAUGGGCUCGAAAAUGUUUACACCAUUCGAUCGUUCGAGUACAGUGGGCAC-------CAAAGACUUUUAGGGCCCACUGUACGUUUCACCAGUCAGUCG-------AUUAAAACAUU
..(((.((((.((...((...((.....((((....))))(((((((((((.(-------(...........)))))))))))))))..))....)))))).-------)))........ ( -34.80)
>DroSim_CAF1 2174 106 + 1
CAGAUGGGCUCGAAAAUGUUUACACCAUUCGAUCGUUCGAGUACAGUGGGCAC-------CAAAGACUUUUACGGCCCACUGUACGUUUCACCAGUCAGUCG-------AUCAAAACAUU
..(((.((((.((...((...((.....((((....))))(((((((((((..-------.(((....)))...)))))))))))))..))....)))))).-------)))........ ( -34.00)
>DroYak_CAF1 2005 109 + 1
UAGAUGGGGUCGAAAAUGUUCACACCAUUCGAUCGUUCGAGUACAGUGGGCACCGGGCACCAAUGGCUUUAAUGGCCCCCUGUUGGUUGCACCAGC----GC-------AUCAAAAUAUU
..((((.(........(((((((...((((((....))))))...)))))))..((((((((((((((.....))))....))))).))).))..)----.)-------)))........ ( -35.60)
>consensus
CAGAUGGGCUCGAAAAUGUUUACACCAUUCGAUCGUUCGAGUACAGUGGGCAC_______CAAAGACUUUUACGGCCCACUGUACGUUUCACCAGUCAGUCG_______AUCAAAACAUU
....((((.(((((..((....))...))))).)......(((((((((((.......................)))))))))))......))).......................... (-23.41 = -23.98 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	16,429,685 – 16,429,805
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.54
Mean single sequence MFE	-37.48
Consensus MFE	-24.22
Energy contribution	-24.82
Covariance contribution	0.60
Combinations/Pair	1.17
Mean z-score	-1.96
Structure conservation index	0.65
SVM decision value	0.65
SVM RNA-class probability	0.813040
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16429685 120 + 22224390
GCCAAUUAGUGGGAGUGGGCAAGGGCUGCGCCAGUUCGGAUUUCCAUUGACCCACUGUACGGUGGGUGGGGGAAGUCAAUGCAGAUUGCUUGAAUUUUCUGCUUGGUGGUCUACUUGGGU
(((....((((((....(((....))).((((((....(((((((.((.(((((((....))))))).)))))))))...(((((............))))))))))).))))))..))) ( -45.40)
>DroSec_CAF1 1636 106 + 1
GCCAAUUAGUGGGAGUGGG-----------CCAGCUCGGAUUUCCAAUGACCCACUGUACGGUGGGUG---GAAGUCAACGCAGAUUGCUUGAAUUUUCUGCUUGGUGGUCUAUUUGGGU
.(((.....)))(((((((-----------(((.(...(((((((....(((((((....))))))))---))))))...(((((............)))))..).)))))))))).... ( -40.90)
>DroSim_CAF1 2280 106 + 1
GCCAAUUAGUGGGAGUGGG-----------CCAGCUCGGAUUUCCAAUGACCCACUGUACGGUGGGUG---GAAGUCAACGCAGAUUGCUUGAAUUUUCUGCUUGGUGGUCUUUUUGGGU
.(((.....)))(((.(((-----------(((.(...(((((((....(((((((....))))))))---))))))...(((((............)))))..).)))))).))).... ( -36.80)
>DroEre_CAF1 1860 102 + 1
GCCAAUUUCAAGGC----A-----------AGAGCUCGGAUUUUAAAUAACCCACUGUAAGGUGGGUG---AAACUCUGCGCAGGUUGCUUGAAUUGUCUGCUUGGUGGUCUAUUUUGAU
(((((.((((((.(----(-----------(..((.((((.(((.....(((((((....))))))).---))).)))).))...)))))))))........))))).(((......))) ( -27.80)
>DroYak_CAF1 2114 103 + 1
GCCAAUUUCAGGGC-UCCG-----------CCAGCUCGAAUUUCAAAUGACCCACUGUACGGUGGGUG---AAAGUCAGCGCAGAUUGCUUCAAUUGUCUGCCUGGUGGUCUAUUUUG--
(((........)))-.(((-----------((((((.((.((((.....(((((((....))))))))---))).)))))((((((..........)))))).)))))).........-- ( -36.50)
>consensus
GCCAAUUAGUGGGAGUGGG___________CCAGCUCGGAUUUCCAAUGACCCACUGUACGGUGGGUG___GAAGUCAACGCAGAUUGCUUGAAUUUUCUGCUUGGUGGUCUAUUUGGGU
((((...(((((((...................((...((((((.....(((((((....)))))))....))))))...)).((((.....)))))))))))...)))).......... (-24.22 = -24.82 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	16,429,685 – 16,429,805
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.54
Mean single sequence MFE	-27.37
Consensus MFE	-17.80
Energy contribution	-17.28
Covariance contribution	-0.52
Combinations/Pair	1.26
Mean z-score	-1.88
Structure conservation index	0.65
SVM decision value	0.53
SVM RNA-class probability	0.769520
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16429685 120 - 22224390
ACCCAAGUAGACCACCAAGCAGAAAAUUCAAGCAAUCUGCAUUGACUUCCCCCACCCACCGUACAGUGGGUCAAUGGAAAUCCGAACUGGCGCAGCCCUUGCCCACUCCCACUAAUUGGC
..((((.(((........(((((............)))))...((.((((...((((((......))))))....)))).)).....(((.((((...)))))))......))).)))). ( -29.10)
>DroSec_CAF1 1636 106 - 1
ACCCAAAUAGACCACCAAGCAGAAAAUUCAAGCAAUCUGCGUUGACUUC---CACCCACCGUACAGUGGGUCAUUGGAAAUCCGAGCUGG-----------CCCACUCCCACUAAUUGGC
..((((.(((.....((((((((............))))).))).....---............(((((((((((((....))))..)))-----------))))))....))).)))). ( -29.70)
>DroSim_CAF1 2280 106 - 1
ACCCAAAAAGACCACCAAGCAGAAAAUUCAAGCAAUCUGCGUUGACUUC---CACCCACCGUACAGUGGGUCAUUGGAAAUCCGAGCUGG-----------CCCACUCCCACUAAUUGGC
..((((..((.....((((((((............))))).))).....---............(((((((((((((....))))..)))-----------))))))....))..)))). ( -27.30)
>DroEre_CAF1 1860 102 - 1
AUCAAAAUAGACCACCAAGCAGACAAUUCAAGCAACCUGCGCAGAGUUU---CACCCACCUUACAGUGGGUUAUUUAAAAUCCGAGCUCU-----------U----GCCUUGAAAUUGGC
..............((((((((..............))))(((((((((---.((((((......))))))............)))))).-----------)----)).......)))). ( -22.66)
>DroYak_CAF1 2114 103 - 1
--CAAAAUAGACCACCAGGCAGACAAUUGAAGCAAUCUGCGCUGACUUU---CACCCACCGUACAGUGGGUCAUUUGAAAUUCGAGCUGG-----------CGGA-GCCCUGAAAUUGGC
--.........((.(((.(((((............)))))(((((.(((---(((((((......)))))).....)))).)).))))))-----------.)).-(((........))) ( -28.10)
>consensus
ACCCAAAUAGACCACCAAGCAGAAAAUUCAAGCAAUCUGCGUUGACUUC___CACCCACCGUACAGUGGGUCAUUGGAAAUCCGAGCUGG___________CCCACUCCCACUAAUUGGC
..............(((((((((............)))))(((((.(((....((((((......)))))).....))).))..)))............................)))). (-17.80 = -17.28 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:28 2006