Locus 124

Sequence ID sp_pn.0
Location 247,381 – 247,500
Length 119
Max. P 0.989135
window801 window802 window803 window804

overview

Window 1

Location 247,381 – 247,500
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.94
Mean single sequence MFE -27.67
Consensus MFE -25.85
Energy contribution -23.97
Covariance contribution -1.88
Combinations/Pair 1.27
Mean z-score -2.00
Structure conservation index 0.93
SVM decision value 1.34
SVM RNA-class probability 0.943988
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 247381 119 + 2038615/40-160
AAUAAUAGACGGUACUUUUUACUUUUGGUCUCUCAAGAGUGUACAGGGACGUGCUGACAAAUGUUGCAAAAGUACACACAGAUGAUAUCUGUCACCAAGUGUAUCAUCACC-AAAAAUAA
...........(((((((((((((((((....)))))))))....(.(((((........))))).))))))))).....((((((((((.......)).))))))))...-........ ( -28.20)
>sp_mu.0 333916 119 + 2030921/40-160
UAUGAUAAAUGGUACUUUUUACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAAAUGUUGCAAA-GUACACACAGAUUAGGACUGUCACCAAGUGCCUAAUCACCCAAAAAUAA
.........(((((((((.(((((((((....)))))))))....(..((((........))))..))))-)))).))..((((((((((.......))).)))))))............ ( -27.80)
>sp_ag.0 393162 119 - 2160267/40-160
UAUGAUAAACGGUACUUUU-ACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAAUUGUUGCAAAAGUACACGCAGAUAUAGGCUGUCACCAAGUGCUAUAUCAACCAAAAAUAA
.........((((((((((-.......((((((...........))))))..((.(((....))))))))))))).))..((((((((((.......))).)))))))............ ( -27.00)
>consensus
UAUGAUAAACGGUACUUUUUACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAAAUGUUGCAAAAGUACACACAGAUAAAGACUGUCACCAAGUGCAUAAUCACCCAAAAAUAA
...........((((((((.((((((((....))))))))((((......)))).............)))))))).....((((((((((.......))).)))))))............ (-25.85 = -23.97 +  -1.88)

alignment

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secondary structure

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dotplot

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Window 2

Location 247,381 – 247,500
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.94
Mean single sequence MFE -30.03
Consensus MFE -26.49
Energy contribution -24.93
Covariance contribution -1.55
Combinations/Pair 1.19
Mean z-score -2.08
Structure conservation index 0.88
SVM decision value 0.89
SVM RNA-class probability 0.876131
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 247381 119 + 2038615/40-160
UUAUUUUU-GGUGAUGAUACACUUGGUGACAGAUAUCAUCUGUGUGUACUUUUGCAACAUUUGUCAGCACGUCCCUGUACACUCUUGAGAGACCAAAAGUAAAAAGUACCGUCUAUUAUU
((((((((-((((((((((...(((....))).))))))).(.((((((...(((.((....))..))).......)))))).).......))))))))))).................. ( -28.80)
>sp_mu.0 333916 119 + 2030921/40-160
UUAUUUUUGGGUGAUUAGGCACUUGGUGACAGUCCUAAUCUGUGUGUAC-UUUGCAACAUUUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGUAAAAAGUACCAUUUAUCAUA
((((((((((..(((((((.(((.(....)))))))))))...((((((-..(((.((....))..))).......))))))..........)))))))))).................. ( -30.40)
>sp_ag.0 393162 119 - 2160267/40-160
UUAUUUUUGGUUGAUAUAGCACUUGGUGACAGCCUAUAUCUGCGUGUACUUUUGCAACAAUUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGU-AAAAGUACCGUUUAUCAUA
.......((((.(((((((...(((....))).))))))).(((.((((((((((......((....)).((((((...........)))))).....))-)))))))))))..)))).. ( -30.90)
>consensus
UUAUUUUUGGGUGAUAAAGCACUUGGUGACAGACAUAAUCUGUGUGUACUUUUGCAACAUUUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGUAAAAAGUACCGUUUAUCAUA
((((((((((..(((((((...(((....))).)))))))...((((((...(((.((....))..))).......))))))..........)))))))))).................. (-26.49 = -24.93 +  -1.55) 
# Strand winner: reverse (0.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 247,381 – 247,499
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.47
Mean single sequence MFE -28.43
Consensus MFE -26.83
Energy contribution -24.83
Covariance contribution -2.00
Combinations/Pair 1.25
Mean z-score -2.70
Structure conservation index 0.94
SVM decision value 2.15
SVM RNA-class probability 0.989135
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 247381 118 + 2038615/56-176
UUUUACUUUUGGUCUCUCAAGAGUGUACAGGGACGUGCUGACAAAUGUUGCAAAAGUACACACAGAUGAUAUCUGUCACCAAGUGUAUCAUCACC-AAAAAUAAAAAAAC-ACAGGAGAA
(((((.(((((((.........((((((.(.(((((........))))).)....))))))...((((((((((.......)).)))))))))))-)))).)))))....-......... ( -28.90)
>sp_mu.0 333916 118 + 2030921/56-176
UUUUACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAAAUGUUGCAAA-GUACACACAGAUUAGGACUGUCACCAAGUGCCUAAUCACCCAAAAAUAAAAAAAU-ACAGGAGAA
(((((.((((((..........((((((...(((((........))))).....-))))))...((((((((((.......))).)))))))..)))))).)))))....-......... ( -29.50)
>sp_ag.0 393162 119 - 2160267/56-176
UUU-ACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAAUUGUUGCAAAAGUACACGCAGAUAUAGGCUGUCACCAAGUGCUAUAUCAACCAAAAAUAAAAAACUUACAGGAGAA
(((-(.(((((((.........((((((.......(((.(((....))))))...))))))...((((((((((.......))).))))))).))))))).))))............... ( -26.90)
>consensus
UUUUACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAAAUGUUGCAAAAGUACACACAGAUAAAGACUGUCACCAAGUGCAUAAUCACCCAAAAAUAAAAAAAU_ACAGGAGAA
.....((((((...........((((((.......(((.(((....))))))...))))))...((((((((((.......))).)))))))....................)))))).. (-26.83 = -24.83 +  -2.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 247,381 – 247,499
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.47
Mean single sequence MFE -30.50
Consensus MFE -27.69
Energy contribution -26.13
Covariance contribution -1.55
Combinations/Pair 1.18
Mean z-score -2.36
Structure conservation index 0.91
SVM decision value 1.43
SVM RNA-class probability 0.953107
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 247381 118 + 2038615/56-176
UUCUCCUGU-GUUUUUUUAUUUUU-GGUGAUGAUACACUUGGUGACAGAUAUCAUCUGUGUGUACUUUUGCAACAUUUGUCAGCACGUCCCUGUACACUCUUGAGAGACCAAAAGUAAAA
.........-....((((((((((-((((((((((...(((....))).))))))).(.((((((...(((.((....))..))).......)))))).).......))))))))))))) ( -30.00)
>sp_mu.0 333916 118 + 2030921/56-176
UUCUCCUGU-AUUUUUUUAUUUUUGGGUGAUUAGGCACUUGGUGACAGUCCUAAUCUGUGUGUAC-UUUGCAACAUUUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGUAAAA
.........-....((((((((((((..(((((((.(((.(....)))))))))))...((((((-..(((.((....))..))).......))))))..........)))))))))))) ( -31.60)
>sp_ag.0 393162 119 - 2160267/56-176
UUCUCCUGUAAGUUUUUUAUUUUUGGUUGAUAUAGCACUUGGUGACAGCCUAUAUCUGCGUGUACUUUUGCAACAAUUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGU-AAA
...............((((((((((((((((((((...(((....))).)))))))...((((((...(((.((....))..))).......))))))........))))))))))-))) ( -29.90)
>consensus
UUCUCCUGU_AUUUUUUUAUUUUUGGGUGAUAAAGCACUUGGUGACAGACAUAAUCUGUGUGUACUUUUGCAACAUUUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGUAAAA
..............((((((((((((..(((((((...(((....))).)))))))...((((((...(((.((....))..))).......))))))..........)))))))))))) (-27.69 = -26.13 +  -1.55) 
# Strand winner: reverse (0.88)

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 19:01:49 2006