Locus 118

Sequence ID sy_sa.0
Location 841,490 – 841,564
Length 74
Max. P 0.999994
window752 window753 window754 window755

overview

Window 2

Location 841,490 – 841,564
Length 74
Sequences 6
Columns 74
Reading direction forward
Mean pairwise identity 90.45
Mean single sequence MFE -26.37
Consensus MFE -26.80
Energy contribution -25.30
Covariance contribution -1.50
Combinations/Pair 1.16
Mean z-score -2.93
Structure conservation index 1.02
SVM decision value 5.31
SVM RNA-class probability 0.999983
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 841490 74 + 2516575
UAUGCGGGUGUAGUUUAAUGGCAAAACCUCAGCCUUCCAAGCUGAUGUUGUGGGUUCGAUUCCCAUCACCCGCU
...(((((((..............(((.(((((.......))))).)))(((((.......)))))))))))). ( -27.10)
>sy_ha.0 970994 74 + 2685015
UAUGCGGGUGUAGUUUAAUGGCAAAACCUCAGCCUUCCAAGCUGAUGUUGUGGGUUCGAUUCCCAUCACCCGCU
...(((((((..............(((.(((((.......))))).)))(((((.......)))))))))))). ( -27.10)
>sy_au.0 692011 74 - 2809422
UAAGCGGGUGUAGUUUAAUGGCAAAACCUCAGCCUUCCAAGCUGAUGUUGUGGGUUCGAUUCCCAUCACCCGCU
..((((((((..............(((.(((((.......))))).)))(((((.......))))))))))))) ( -27.80)
>sp_mu.0 23302 74 + 2030921
UUAGCGGGUGUAGUUUAGUGGUAAAACCACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCU
..((((((((.......((((.....))))(((.......)))......(((((.......))))))))))))) ( -26.00)
>sp_ag.0 28383 74 + 2160267
UUAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCU
..((((((((...............((.(((((.......))))).)).(((((.......))))))))))))) ( -25.40)
>sp_pn.0 347556 74 - 2038615
UAUGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCU
...(((((((...............((.(((((.......))))).)).(((((.......)))))))))))). ( -24.80)
>consensus
UAAGCGGGUGUAGUUUAAUGGCAAAACCACAGCCUUCCAAGCUGAUGUCGCGAGUUCGAUUCCCAUCACCCGCU
...(((((((...............((.(((((.......))))).)).(((((.......)))))))))))). (-26.80 = -25.30 +  -1.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 841,490 – 841,564
Length 74
Sequences 6
Columns 74
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -28.45
Consensus MFE -29.80
Energy contribution -28.05
Covariance contribution -1.75
Combinations/Pair 1.20
Mean z-score -3.93
Structure conservation index 1.05
SVM decision value 5.83
SVM RNA-class probability 0.999994
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 841490 74 + 2516575
AGCGGGUGAUGGGAAUCGAACCCACAACAUCAGCUUGGAAGGCUGAGGUUUUGCCAUUAAACUACACCCGCAUA
.(((((((.((((.......)))).....((((((.....))))))((.....)).........)))))))... ( -28.90)
>sy_ha.0 970994 74 + 2685015
AGCGGGUGAUGGGAAUCGAACCCACAACAUCAGCUUGGAAGGCUGAGGUUUUGCCAUUAAACUACACCCGCAUA
.(((((((.((((.......)))).....((((((.....))))))((.....)).........)))))))... ( -28.90)
>sy_au.0 692011 74 - 2809422
AGCGGGUGAUGGGAAUCGAACCCACAACAUCAGCUUGGAAGGCUGAGGUUUUGCCAUUAAACUACACCCGCUUA
((((((((.((((.......)))).....((((((.....))))))((.....)).........)))))))).. ( -28.70)
>sp_mu.0 23302 74 + 2030921
AGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUGGUUUUACCACUAAACUACACCCGCUAA
((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))).. ( -28.20)
>sp_ag.0 28383 74 + 2160267
AGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUAA
((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))).. ( -28.20)
>sp_pn.0 347556 74 - 2038615
AGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCAUA
.(((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))... ( -27.80)
>consensus
AGCGGGUGACGAGAAUCGAACCCACAACAACAGCUUGGAAGGCUGAGGUUUUACCACUAAACUACACCCGCAUA
.(((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))... (-29.80 = -28.05 +  -1.75) 
# Strand winner: reverse (0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 841,490 – 841,564
Length 74
Sequences 6
Columns 74
Reading direction forward
Mean pairwise identity 90.45
Mean single sequence MFE -26.37
Consensus MFE -26.80
Energy contribution -25.30
Covariance contribution -1.50
Combinations/Pair 1.16
Mean z-score -2.93
Structure conservation index 1.02
SVM decision value 5.31
SVM RNA-class probability 0.999983
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 841490 74 + 2516575/0-74
UAUGCGGGUGUAGUUUAAUGGCAAAACCUCAGCCUUCCAAGCUGAUGUUGUGGGUUCGAUUCCCAUCACCCGCU
...(((((((..............(((.(((((.......))))).)))(((((.......)))))))))))). ( -27.10)
>sy_ha.0 970994 74 + 2685015/0-74
UAUGCGGGUGUAGUUUAAUGGCAAAACCUCAGCCUUCCAAGCUGAUGUUGUGGGUUCGAUUCCCAUCACCCGCU
...(((((((..............(((.(((((.......))))).)))(((((.......)))))))))))). ( -27.10)
>sy_au.0 692011 74 - 2809422/0-74
UAAGCGGGUGUAGUUUAAUGGCAAAACCUCAGCCUUCCAAGCUGAUGUUGUGGGUUCGAUUCCCAUCACCCGCU
..((((((((..............(((.(((((.......))))).)))(((((.......))))))))))))) ( -27.80)
>sp_mu.0 23302 74 + 2030921/0-74
UUAGCGGGUGUAGUUUAGUGGUAAAACCACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCU
..((((((((.......((((.....))))(((.......)))......(((((.......))))))))))))) ( -26.00)
>sp_ag.0 28383 74 + 2160267/0-74
UUAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCU
..((((((((...............((.(((((.......))))).)).(((((.......))))))))))))) ( -25.40)
>sp_pn.0 347556 74 - 2038615/0-74
UAUGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCU
...(((((((...............((.(((((.......))))).)).(((((.......)))))))))))). ( -24.80)
>consensus
UAAGCGGGUGUAGUUUAAUGGCAAAACCACAGCCUUCCAAGCUGAUGUCGCGAGUUCGAUUCCCAUCACCCGCU
...(((((((...............((.(((((.......))))).)).(((((.......)))))))))))). (-26.80 = -25.30 +  -1.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 841,490 – 841,564
Length 74
Sequences 6
Columns 74
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -28.45
Consensus MFE -29.80
Energy contribution -28.05
Covariance contribution -1.75
Combinations/Pair 1.20
Mean z-score -3.93
Structure conservation index 1.05
SVM decision value 5.83
SVM RNA-class probability 0.999994
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 841490 74 + 2516575/0-74
AGCGGGUGAUGGGAAUCGAACCCACAACAUCAGCUUGGAAGGCUGAGGUUUUGCCAUUAAACUACACCCGCAUA
.(((((((.((((.......)))).....((((((.....))))))((.....)).........)))))))... ( -28.90)
>sy_ha.0 970994 74 + 2685015/0-74
AGCGGGUGAUGGGAAUCGAACCCACAACAUCAGCUUGGAAGGCUGAGGUUUUGCCAUUAAACUACACCCGCAUA
.(((((((.((((.......)))).....((((((.....))))))((.....)).........)))))))... ( -28.90)
>sy_au.0 692011 74 - 2809422/0-74
AGCGGGUGAUGGGAAUCGAACCCACAACAUCAGCUUGGAAGGCUGAGGUUUUGCCAUUAAACUACACCCGCUUA
((((((((.((((.......)))).....((((((.....))))))((.....)).........)))))))).. ( -28.70)
>sp_mu.0 23302 74 + 2030921/0-74
AGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUGGUUUUACCACUAAACUACACCCGCUAA
((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))).. ( -28.20)
>sp_ag.0 28383 74 + 2160267/0-74
AGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUAA
((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))).. ( -28.20)
>sp_pn.0 347556 74 - 2038615/0-74
AGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCAUA
.(((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))... ( -27.80)
>consensus
AGCGGGUGACGAGAAUCGAACCCACAACAACAGCUUGGAAGGCUGAGGUUUUACCACUAAACUACACCCGCAUA
.(((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))... (-29.80 = -28.05 +  -1.75) 
# Strand winner: reverse (0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:01:10 2006