Locus 2

Sequence ID sp_pn.0
Location 1,789,618 – 1,789,724
Length 106
Max. P 0.999597
window3 window4 window5

overview

Window 3

Location 1,789,618 – 1,789,722
Length 104
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.26
Mean single sequence MFE -33.53
Consensus MFE -30.80
Energy contribution -30.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.92
SVM decision value 3.00
SVM RNA-class probability 0.998078
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1789618 104 + 2038615/40-160
CGAGUCUAAAAUAACUUGCGUUAUCUUAAA---CGGUCCCGACGGGAAUCGAACCCGCGAUCUUCGCCGUGACAGGGCGACGUGAUAACCGCUACACUACGGGACCU-------------
...((.(((.(((((....))))).))).)---)(((((((..(((.......)))((((((.(((((.......)))))...)))...))).......))))))).------------- ( -35.00)
>sp_ag.0 2138742 82 - 2160267/40-160
CGAGUCUA-------------------------CGGUCCCGACGGGAAUCGAACCCGCGAUCUUCGCCGUGACAGGGCGACGUGAUAACCGCUACACUACGGGACCU-------------
........-------------------------.(((((((..(((.......)))((((((.(((((.......)))))...)))...))).......))))))).------------- ( -30.80)
>sp_mu.0 1683671 120 + 2030921/40-160
CGAGUCGAUGAUCCCUCUCUUUUCAGAAAAAGACGGUCCCGACGGGAAUCGAACCCGCGAUCUUCGCCGUGACAGGGCGACGUGAUAACCGCUACACCACGGGACCUCUAACUAAUCACU
.(((..(......)..)))...........(((.(((((((..(((.......)))((((((.(((((.......)))))...)))...))).......))))))))))........... ( -34.80)
>consensus
CGAGUCUA__AU__CU__C_UU_____AAA___CGGUCCCGACGGGAAUCGAACCCGCGAUCUUCGCCGUGACAGGGCGACGUGAUAACCGCUACACUACGGGACCU_____________
..................................(((((((..(((.......)))((((((.(((((.......)))))...)))...))).......))))))).............. (-30.80 = -30.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,789,618 – 1,789,722
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.26
Mean single sequence MFE -41.53
Consensus MFE -32.50
Energy contribution -32.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.78
SVM decision value 3.77
SVM RNA-class probability 0.999597
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1789618 104 + 2038615/40-160
-------------AGGUCCCGUAGUGUAGCGGUUAUCACGUCGCCCUGUCACGGCGAAGAUCGCGGGUUCGAUUCCCGUCGGGACCG---UUUAAGAUAACGCAAGUUAUUUUAGACUCG
-------------.(((((((.......((((((......(((((.......))))).))))))(((.......)))..)))))))(---(((((((((((....))))))))))))... ( -47.30)
>sp_ag.0 2138742 82 - 2160267/40-160
-------------AGGUCCCGUAGUGUAGCGGUUAUCACGUCGCCCUGUCACGGCGAAGAUCGCGGGUUCGAUUCCCGUCGGGACCG-------------------------UAGACUCG
-------------.(((((((.......((((((......(((((.......))))).))))))(((.......)))..))))))).-------------------------........ ( -32.50)
>sp_mu.0 1683671 120 + 2030921/40-160
AGUGAUUAGUUAGAGGUCCCGUGGUGUAGCGGUUAUCACGUCGCCCUGUCACGGCGAAGAUCGCGGGUUCGAUUCCCGUCGGGACCGUCUUUUUCUGAAAAGAGAGGGAUCAUCGACUCG
.......((((.((((((((((((((.......)))))).(((((.......))))).....(((((.......))))).))))))((((((((((....))))))))))..)))))).. ( -44.80)
>consensus
_____________AGGUCCCGUAGUGUAGCGGUUAUCACGUCGCCCUGUCACGGCGAAGAUCGCGGGUUCGAUUCCCGUCGGGACCG___UUU_____AA_G__AG__AU__UAGACUCG
..............(((((((.......((((((......(((((.......))))).))))))(((.......)))..))))))).................................. (-32.50 = -32.50 +   0.00) 
# Strand winner: reverse (0.92)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,789,618 – 1,789,724
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.13
Mean single sequence MFE -36.97
Consensus MFE -33.19
Energy contribution -32.97
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.76
Structure conservation index 0.90
SVM decision value 0.72
SVM RNA-class probability 0.831224
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1789618 106 + 2038615/160-280
--------------UUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCUAGAGCUAAGCGACUUCCCUAUCUCACAGGGG
--------------.((((((.....(((.(((......))))))((((((.....))))))....))))))(((.((((...........)))).))).....((((.......)))). ( -34.30)
>sp_ag.0 2138742 105 - 2160267/160-280
--------------AUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCUUU-GCUAAGCGACUACCUUAUCUCACAGGGG
--------------..(((((((...(((.(((......))))))((((((.....)))))).((((........))))..))))))).((-((...))))...((((.......)))). ( -31.90)
>sp_mu.0 1683671 120 + 2030921/160-280
UUAGUUACUUAGUUAUGGGAGUUAACGGGCUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAACUGAGCUAAACUCCCUCUUGCUAAGCGACGACCCUAUCUCACAGGGG
...((..((((((...(((((((...(((.(((......))))))((((((.....)))))).((((........))))..)))))))....))))))..))..((((.......)))). ( -44.70)
>consensus
______________AUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCUAU_GCUAAGCGACUACCCUAUCUCACAGGGG
................(((((((...(((.(((......))))))((((((.....)))))).((((........))))..)))))))................((((.......)))). (-33.19 = -32.97 +  -0.22)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:50:17 2006