Locus 27

Sequence ID sy_sa.0
Location 846,508 – 846,623
Length 115
Max. P 0.999994
window145 window146 window147 window148 window149

overview

Window 5

Location 846,508 – 846,623
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.59
Mean single sequence MFE -40.90
Consensus MFE -32.41
Energy contribution -31.97
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.26
Structure conservation index 0.79
SVM decision value 0.83
SVM RNA-class probability 0.862114
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 846508 115 + 2516575/80-200
GAACACAGAAGUUAAGCUCCUUAGCGCCGAUGGUAGUCGGACUUACGUUCCGCAAGAGUAGGACGUUGCCAGGCAG--CA--UUAAUAGGAUGCGAUGA-GCCGAGACCGAGAGGUCUCU
...............((((......(((..((((((.((..(((((....(....).))))).))))))))))).(--((--((.....)))))...))-)).((((((....)))))). ( -41.00)
>sy_au.0 534023 117 + 2809422/80-200
GAACACAGAAGUUAAGCUCCUUAGCGUCGAUGGUAGUCGAACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGCAA--AAAAUGGAUGCGAUGAGCCGC-AUUGAGACCGCAAGGUCUCU
...............((((....(((((.((....(((......((((((..(....)..)))))).....)))..--...)).)))))...))))...-...((((((....)))))). ( -38.80)
>sy_ha.0 145838 120 - 2685015/80-200
GAACACAGAAGUUAAGCUCCUUAGCGCCGAUGGUAGUUGGAUUUACGUUCCGCUAGAGUAGGACGUUGCCAGGCAAAUCGUAUGAAUGCGAUGAGCCGAUAUCGAGACCGAAAGGUCUCU
..........((((((...))))))...((((.....(((....((((((..(....)..))))))..)))(((..((((((....))))))..)))..))))((((((....)))))). ( -42.90)
>consensus
GAACACAGAAGUUAAGCUCCUUAGCGCCGAUGGUAGUCGGACUUACGUUCCGCUAGAGUAGGACGUUGCCAGGCAA__CA_AUGAAUGCGAUGAGCCGA_AUCGAGACCGAAAGGUCUCU
..........((((((...))))))(((..(((((.........((((((..(....)..)))))))))))))).............................((((((....)))))). (-32.41 = -31.97 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 846,508 – 846,618
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.60
Mean single sequence MFE -34.87
Consensus MFE -21.45
Energy contribution -21.23
Covariance contribution -0.21
Combinations/Pair 1.20
Mean z-score -2.97
Structure conservation index 0.62
SVM decision value 5.83
SVM RNA-class probability 0.999994
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 846508 110 + 2516575/120-240
ACUUACGUUCCGCAAGAGUAGGACGUUGCCAGGCAG--CA--UUAAUAGGAUGCGAUGA-GCCGAGACCGAGAGGUCUCUUUUUUU-AUGUCAAAAAA----GGCUUAACUUCUCCAGUU
.(((((....(....).)))))..(((((...))))--).--......(((...(.(((-(((((((((....)))))).((((((-.....))))))----)))))).)...))).... ( -34.50)
>sy_au.0 534023 107 + 2809422/120-240
ACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGCAA--AAAAUGGAUGCGAUGAGCCGC-AUUGAGACCGCAAGGUCUCUUUUUUUUAUGUCUAAAAC----GUCAAAAU------AAAA
....((((((..(....)..))))))....(((((.--((((..((((((......)))-)))((((((....))))))....)))).))))).....----........------.... ( -33.50)
>sy_ha.0 145838 119 - 2685015/120-240
AUUUACGUUCCGCUAGAGUAGGACGUUGCCAGGCAAAUCGUAUGAAUGCGAUGAGCCGAUAUCGAGACCGAAAGGUCUCUUUUUUU-AUGCACAAAAACAAAACCGAAGGUUUAAUGAAA
....((((((..(....)..))))))(((..(((..((((((....))))))..)))......((((((....)))))).......-..)))........(((((...)))))....... ( -36.60)
>consensus
ACUUACGUUCCGCUAGAGUAGGACGUUGCCAGGCAA__CA_AUGAAUGCGAUGAGCCGA_AUCGAGACCGAAAGGUCUCUUUUUUU_AUGUCAAAAAA____GCCAAAACUU____AAAA
....((((((..(....)..)))))).....((((..............(((........)))((((((....)))))).........))))............................ (-21.45 = -21.23 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 846,508 – 846,619
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 57.26
Mean single sequence MFE -26.95
Consensus MFE -13.07
Energy contribution -13.07
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.48
SVM decision value 3.76
SVM RNA-class probability 0.999591
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 846508 111 + 2516575/160-280
--UUAAUAGGAUGCGAUGA-GCCGAGACCGAGAGGUCUCUUUUUUU-AUGUCAAAAAA----GGCUUAACUUCUCCAGUUCGAAGAACUGAAAAGCCUAAAAUAAGCUAUU-AUGAGAAA
--..............(((-(((((((((....)))))).((((((-.....))))))----))))))..(((((((((((...))))))...(((.........)))...-..))))). ( -31.60)
>sy_au.0 534023 105 + 2809422/160-280
AAUGGAUGCGAUGAGCCGC-AUUGAGACCGCAAGGUCUCUUUUUUUUAUGUCUAAAAC----GUCAAAAU------AAAAAGCAAACACAAAGA----AAAAUGGCUUGGCGAAGUGAAA
........((..((((((.-...((((((....))))))((((((((.(((.......----........------.........))).)))))----))).))))))..))........ ( -25.26)
>sy_ha.0 145838 116 - 2685015/160-280
UAUGAAUGCGAUGAGCCGAUAUCGAGACCGAAAGGUCUCUUUUUUU-AUGCACAAAAACAAAACCGAAGGUUUAAUGAAAUCAAUAAAUCAAAA---UGUAGUAGCUUUACGAAGAGUAA
......(((((((......))))((((((....)))))).......-..)))................((((((.((....)).))))))....---.......(((((....))))).. ( -24.00)
>consensus
_AUGAAUGCGAUGAGCCGA_AUCGAGACCGAAAGGUCUCUUUUUUU_AUGUCAAAAAA____GCCAAAACUU____AAAAAGAAAAAAUAAAAA___UAAAAUAGCUUAACGAAGAGAAA
.......................((((((....))))))................................................................................. (-13.07 = -13.07 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 846,508 – 846,619
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 57.26
Mean single sequence MFE -24.19
Consensus MFE -10.10
Energy contribution -10.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.42
SVM decision value 1.32
SVM RNA-class probability 0.941723
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 846508 111 + 2516575/160-280
UUUCUCAU-AAUAGCUUAUUUUAGGCUUUUCAGUUCUUCGAACUGGAGAAGUUAAGCC----UUUUUUGACAU-AAAAAAAGAGACCUCUCGGUCUCGGC-UCAUCGCAUCCUAUUAA--
.......(-(((((.........(((((((((((((...))))).)))))))).((((----((((((.....-.))))))((((((....)))))))))-).........)))))).-- ( -31.00)
>sy_au.0 534023 105 + 2809422/160-280
UUUCACUUCGCCAAGCCAUUUU----UCUUUGUGUUUGCUUUUU------AUUUUGAC----GUUUUAGACAUAAAAAAAAGAGACCUUGCGGUCUCAAU-GCGGCUCAUCGCAUCCAUU
.........((..((((..(((----(.((((((((((......------........----....)))))))))).))))((((((....))))))...-..))))....))....... ( -23.97)
>sy_ha.0 145838 116 - 2685015/160-280
UUACUCUUCGUAAAGCUACUACA---UUUUGAUUUAUUGAUUUCAUUAAACCUUCGGUUUUGUUUUUGUGCAU-AAAAAAAGAGACCUUUCGGUCUCGAUAUCGGCUCAUCGCAUUCAUA
...........(((((....((.---....(.((((.((....)).)))).)....))...))))).((((..-.......((((((....))))))(((........)))))))..... ( -17.60)
>consensus
UUUCUCUUCGAAAAGCUAUUUUA___UUUUCAUUUAUUCAUUUU____AAAUUUAGAC____UUUUUAGACAU_AAAAAAAGAGACCUUUCGGUCUCGAU_UCGGCUCAUCGCAUUCAU_
.................................................................................((((((....))))))....................... (-10.10 = -10.10 +  -0.00) 
# Strand winner: forward (0.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 846,508 – 846,622
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 59.94
Mean single sequence MFE -26.91
Consensus MFE -13.17
Energy contribution -13.07
Covariance contribution -0.11
Combinations/Pair 1.20
Mean z-score -2.66
Structure conservation index 0.49
SVM decision value 3.95
SVM RNA-class probability 0.999724
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 846508 114 + 2516575/183-303
GAGACCGAGAGGUCUCUUUUUUU-AUGUCAAAAAA----GGCUUAACUUCUCCAGUUCGAAGAACUGAAAAGCCUAAAAUAAGCUAUU-AUGAGAAAGCGUUUGAAGCUGACGAACUGAG
((((((....)))))).......-.(((((..(((----.((((....((((((((((...))))))...(((.........)))...-..)))))))).))).....)))))....... ( -30.60)
>sy_au.0 534023 106 + 2809422/183-303
GAGACCGCAAGGUCUCUUUUUUUUAUGUCUAAAAC----GUCAAAAU------AAAAAGCAAACACAAAGA----AAAAUGGCUUGGCGAAGUGAAAACGUUUGAAUCUGACGAAACGAG
((((((....))))))..................(----((((....------...((((...........----......))))..((((((....)).))))....)))))....... ( -23.63)
>sy_ha.0 145838 116 - 2685015/183-303
GAGACCGAAAGGUCUCUUUUUUU-AUGCACAAAAACAAAACCGAAGGUUUAAUGAAAUCAAUAAAUCAAAA---UGUAGUAGCUUUACGAAGAGUAAGUGUUUAAAACUAAAGUAUUGAG
((((((....))))))...((((-(.((((...............((((((.((....)).))))))....---.......(((((....)))))..)))).)))))............. ( -26.50)
>consensus
GAGACCGAAAGGUCUCUUUUUUU_AUGUCAAAAAA____GCCAAAACUU____AAAAAGAAAAAAUAAAAA___UAAAAUAGCUUAACGAAGAGAAAGCGUUUGAAACUGACGAAAUGAG
((((((....))))))..................................................................................((((.......))))....... (-13.17 = -13.07 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:52:38 2006