Locus 18

Sequence ID	sy_ha.0
Location	765,300 – 1,588,702
Length	823402
Max. P	0.999678

overview

Window 9

Location	1,588,593 – 1,588,702
Length	109
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	75.30
Mean single sequence MFE	-41.37
Consensus MFE	-36.20
Energy contribution	-36.77
Covariance contribution	0.57
Combinations/Pair	1.24
Mean z-score	-6.24
Structure conservation index	0.88
SVM decision value	1.97
SVM RNA-class probability	0.984433
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1588593 109 - 2685015
GGCAAGGUUGACUAGAAUU-AAAAAAGAUUGUUACAAGUGCAUUUUUA-GCCAGUCAACUACUGCCAAUAUAUAUUUG--AAGCCUGAGGCAUUGAAUUAUGCCACAGGCUCA
((((.((((((((.(...(-(((((.((((......))).).))))))-.).))))))))..))))..........((--(.(((((.(((((......))))).)))))))) ( -36.10)
>sy_au.0 808671 112 + 2809422
GGCAAGGUUGACUAGAAUUGAAAAAAGCUUGUUACAAGCGCAUUUUCG-UUCAGUCAACUACUGCCAAUAUAACUUUGUAGAGCAUUGAACAUUGAUUUAUGUCUCAAGCUCA
((((.((((((((.((((.(((((..(((((...)))))...))))))-)))))))))))..))))..............((((.((((((((......)))).)))))))). ( -38.80)
>sy_sa.0 622241 110 + 2516575
GGCAAGGAUGACUAGGAUUGAAAAUAGCUUGAUAUAAGCGCAUUUUCACUUCAGUCAUCUACUGCCUAAAUGAAAAAG---GGUCUGAGACAUCUAUUUUUGUCUCAGACUCU
((((.((((((((.(((.(((((((.(((((...)))))..))))))).)))))))))))..))))..........((---(((((((((((........))))))))))))) ( -49.20)
>consensus
GGCAAGGUUGACUAGAAUUGAAAAAAGCUUGUUACAAGCGCAUUUUCA_UUCAGUCAACUACUGCCAAUAUAAAUUUG___AGCCUGAGACAUUGAUUUAUGUCUCAGGCUCA
((((.((((((((.(((.((((((..(((((...)))))...)))))).)))))))))))..))))...............((((((((((((......)))))))))))).. (-36.20 = -36.77 +   0.57)

alignment

secondary structure

dotplot

Window 0

Location	1,588,593 – 1,588,702
Length	109
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	75.30
Mean single sequence MFE	-36.67
Consensus MFE	-29.10
Energy contribution	-31.00
Covariance contribution	1.90
Combinations/Pair	1.16
Mean z-score	-5.18
Structure conservation index	0.79
SVM decision value	3.88
SVM RNA-class probability	0.999678
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1588593 109 - 2685015
UGAGCCUGUGGCAUAAUUCAAUGCCUCAGGCUU--CAAAUAUAUAUUGGCAGUAGUUGACUGGC-UAAAAAUGCACUUGUAACAAUCUUUUUU-AAUUCUAGUCAACCUUGCC
.(((((((.(((((......))))).)))))))--............(((((..(((((((((.-(((((((((....))).......)))))-)...))))))))).))))) ( -36.11)
>sy_au.0 808671 112 + 2809422
UGAGCUUGAGACAUAAAUCAAUGUUCAAUGCUCUACAAAGUUAUAUUGGCAGUAGUUGACUGAA-CGAAAAUGCGCUUGUAACAAGCUUUUUUCAAUUCUAGUCAACCUUGCC
.(((((((((.(((......)))))))).))))..............(((((..((((((((((-.(((((...(((((...)))))..)))))..))).))))))).))))) ( -32.50)
>sy_sa.0 622241 110 + 2516575
AGAGUCUGAGACAAAAAUAGAUGUCUCAGACC---CUUUUUCAUUUAGGCAGUAGAUGACUGAAGUGAAAAUGCGCUUAUAUCAAGCUAUUUUCAAUCCUAGUCAUCCUUGCC
((.((((((((((........)))))))))).---))..........(((((..((((((((...((((((((.((((.....))))))))))))....)))))))).))))) ( -41.40)
>consensus
UGAGCCUGAGACAUAAAUCAAUGUCUCAGGCU___CAAAUUUAUAUUGGCAGUAGUUGACUGAA_UGAAAAUGCGCUUGUAACAAGCUUUUUUCAAUUCUAGUCAACCUUGCC
.(((((((.(((((......))))).)))))))..............(((((..((((((((((.((((((...((((.....))))..)))))).))).))))))).))))) (-29.10 = -31.00 +   1.90) 
# Strand winner: forward (1.00)

alignment

secondary structure

dotplot

Window 1

Location	1,588,593 – 1,588,702
Length	109
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	75.30
Mean single sequence MFE	-41.37
Consensus MFE	-36.20
Energy contribution	-36.77
Covariance contribution	0.57
Combinations/Pair	1.24
Mean z-score	-6.24
Structure conservation index	0.88
SVM decision value	1.97
SVM RNA-class probability	0.984433
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1588593 109 - 2685015/0-113
GGCAAGGUUGACUAGAAUU-AAAAAAGAUUGUUACAAGUGCAUUUUUA-GCCAGUCAACUACUGCCAAUAUAUAUUUG--AAGCCUGAGGCAUUGAAUUAUGCCACAGGCUCA
((((.((((((((.(...(-(((((.((((......))).).))))))-.).))))))))..))))..........((--(.(((((.(((((......))))).)))))))) ( -36.10)
>sy_au.0 808671 112 + 2809422/0-113
GGCAAGGUUGACUAGAAUUGAAAAAAGCUUGUUACAAGCGCAUUUUCG-UUCAGUCAACUACUGCCAAUAUAACUUUGUAGAGCAUUGAACAUUGAUUUAUGUCUCAAGCUCA
((((.((((((((.((((.(((((..(((((...)))))...))))))-)))))))))))..))))..............((((.((((((((......)))).)))))))). ( -38.80)
>sy_sa.0 622241 110 + 2516575/0-113
GGCAAGGAUGACUAGGAUUGAAAAUAGCUUGAUAUAAGCGCAUUUUCACUUCAGUCAUCUACUGCCUAAAUGAAAAAG---GGUCUGAGACAUCUAUUUUUGUCUCAGACUCU
((((.((((((((.(((.(((((((.(((((...)))))..))))))).)))))))))))..))))..........((---(((((((((((........))))))))))))) ( -49.20)
>consensus
GGCAAGGUUGACUAGAAUUGAAAAAAGCUUGUUACAAGCGCAUUUUCA_UUCAGUCAACUACUGCCAAUAUAAAUUUG___AGCCUGAGACAUUGAUUUAUGUCUCAGGCUCA
((((.((((((((.(((.((((((..(((((...)))))...)))))).)))))))))))..))))...............((((((((((((......)))))))))))).. (-36.20 = -36.77 +   0.57)

alignment

secondary structure

dotplot

Window 2

Location	1,588,593 – 1,588,702
Length	109
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	75.30
Mean single sequence MFE	-36.67
Consensus MFE	-29.10
Energy contribution	-31.00
Covariance contribution	1.90
Combinations/Pair	1.16
Mean z-score	-5.18
Structure conservation index	0.79
SVM decision value	3.88
SVM RNA-class probability	0.999678
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1588593 109 - 2685015/0-113
UGAGCCUGUGGCAUAAUUCAAUGCCUCAGGCUU--CAAAUAUAUAUUGGCAGUAGUUGACUGGC-UAAAAAUGCACUUGUAACAAUCUUUUUU-AAUUCUAGUCAACCUUGCC
.(((((((.(((((......))))).)))))))--............(((((..(((((((((.-(((((((((....))).......)))))-)...))))))))).))))) ( -36.11)
>sy_au.0 808671 112 + 2809422/0-113
UGAGCUUGAGACAUAAAUCAAUGUUCAAUGCUCUACAAAGUUAUAUUGGCAGUAGUUGACUGAA-CGAAAAUGCGCUUGUAACAAGCUUUUUUCAAUUCUAGUCAACCUUGCC
.(((((((((.(((......)))))))).))))..............(((((..((((((((((-.(((((...(((((...)))))..)))))..))).))))))).))))) ( -32.50)
>sy_sa.0 622241 110 + 2516575/0-113
AGAGUCUGAGACAAAAAUAGAUGUCUCAGACC---CUUUUUCAUUUAGGCAGUAGAUGACUGAAGUGAAAAUGCGCUUAUAUCAAGCUAUUUUCAAUCCUAGUCAUCCUUGCC
((.((((((((((........)))))))))).---))..........(((((..((((((((...((((((((.((((.....))))))))))))....)))))))).))))) ( -41.40)
>consensus
UGAGCCUGAGACAUAAAUCAAUGUCUCAGGCU___CAAAUUUAUAUUGGCAGUAGUUGACUGAA_UGAAAAUGCGCUUGUAACAAGCUUUUUUCAAUUCUAGUCAACCUUGCC
.(((((((.(((((......))))).)))))))..............(((((..((((((((((.((((((...((((.....))))..)))))).))).))))))).))))) (-29.10 = -31.00 +   1.90) 
# Strand winner: forward (1.00)

alignment

secondary structure

dotplot

Window 3

Location	765,300 – 765,418
Length	118
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	76.26
Mean single sequence MFE	-19.42
Consensus MFE	-13.13
Energy contribution	-12.47
Covariance contribution	-0.66
Combinations/Pair	1.25
Mean z-score	-1.49
Structure conservation index	0.68
SVM decision value	0.38
SVM RNA-class probability	0.711119
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 765300 118 + 2685015/196-316
UAUAUAACAGAUAGCUUGUUGUGAAUCGUUCAAGUUAC-AUCGAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUUG-UCGGCUAGCAGAUGACUAGCCGAUUUUUUUGUGUC
......((((((((((((.((.....))..))))))).-............................................(-(((((((((....).)))))))))...)))))... ( -21.50)
>sy_au.0 442485 114 - 2809422/196-316
UAUAUAACAGAUAGCUUUU----AAUCGUUCAAGUUAC-AUCACAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUUG-UCGGCUAGCACGUGACUAGCCGAUUUUUUUAUGCA
..((((((((((((.....----....((..((((...-........................))))))........)))))))-(((((((((....).)))))))).....))))).. ( -16.16)
>sy_sa.0 635941 118 + 2516575/196-316
UACAUAUAGUUUUGUUAACAUCUAUUUGUUCGAGUUACUAAUCAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUUAACCGGCUAGCGAC--GCUAGUCGGUUUUAUUUUGUA
((((..((((..(...((((......))))...)..))))...........................................(((((((((((...--)))))))))))......)))) ( -20.60)
>consensus
UAUAUAACAGAUAGCUUAU____AAUCGUUCAAGUUAC_AUCAAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUUG_UCGGCUAGCAAAUGACUAGCCGAUUUUUUUAUGUA
.....................................................................................((((((((.......))))))))............ (-13.13 = -12.47 +  -0.66)

alignment

secondary structure

dotplot

Window 4

Location	765,300 – 765,418
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	76.26
Mean single sequence MFE	-21.83
Consensus MFE	-13.88
Energy contribution	-13.78
Covariance contribution	-0.10
Combinations/Pair	1.26
Mean z-score	-1.70
Structure conservation index	0.64
SVM decision value	0.61
SVM RNA-class probability	0.798392
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_ha.0 765300 118 + 2685015/196-316
GACACAAAAAAAUCGGCUAGUCAUCUGCUAGCCGA-CAAAUAGAAAGGAAAGUAAGUAAUAAAUAUUGAAGAUGUUUCGAU-GUAACUUGAACGAUUCACAACAAGCUAUCUGUUAUAUA
............(((((((((.....)))))))))-..((((((.((...............(((((((((...)))))))-))..((((............)))))).))))))..... ( -24.60)
>sy_au.0 442485 114 - 2809422/196-316
UGCAUAAAAAAAUCGGCUAGUCACGUGCUAGCCGA-CAAAUAGAAAGGAAAGUAAGUAAUAAAUAUUGAAGAUGUUGUGAU-GUAACUUGAACGAUU----AAAAGCUAUCUGUUAUAUA
............(((((((((.....)))))))))-..((((((.((.....(((((.((.((((((...))))))...))-...)))))..(....----....))).))))))..... ( -19.70)
>sy_sa.0 635941 118 + 2516575/196-316
UACAAAAUAAAACCGACUAGC--GUCGCUAGCCGGUUAAAUAGAAAGGAAAGUAAGUAAUAAAUAUUGAAGAUGUUUGAUUAGUAACUCGAACAAAUAGAUGUUAACAAAACUAUAUGUA
((((......(((((.(((((--...))))).)))))........................((((((.....(((((((........)))))))....))))))............)))) ( -21.20)
>consensus
UACAAAAAAAAAUCGGCUAGUCACCUGCUAGCCGA_CAAAUAGAAAGGAAAGUAAGUAAUAAAUAUUGAAGAUGUUUCGAU_GUAACUUGAACGAUU____AAAAGCUAUCUGUUAUAUA
............(((((((((.....)))))))))....(((....(((.(((...........((((..((.(((........)))))...)))).........))).)))....))). (-13.88 = -13.78 +  -0.10) 
# Strand winner: reverse (0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:51:55 2006