Locus 5

Sequence ID sp_mu.0
Location 1,839,762 – 1,839,882
Length 120
Max. P 0.991808
window55 window56 window57 window58 window59 window60 window61 window62 window63

overview

Window 5

Location 1,839,762 – 1,839,879
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.56
Mean single sequence MFE -34.40
Consensus MFE -29.20
Energy contribution -29.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.85
SVM decision value 1.54
SVM RNA-class probability 0.962383
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 117 - 2030921/0-120
AUAUACUAUAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACGCGCCCAAGCCUAUG-CUUGGUUUAU-CUUUUAUA-AAAGAA
.((.(((((((((((..(((((((.(((......)))..)).)))))....((((((.((((.........))))..))))))...)))))))-..)))).))(-((((....-))))). ( -34.10)
>sp_ag.0 1904703 119 - 2160267/0-120
AUAUUCUUGAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCAAGCUAUUG-CUUGGUUUUUACUUUCUUAUAAAGUA
......(((((((((....((((..(((......)))..)))))))))))))(((((.((((.........)))))))))..((((((....)-)))))....((((((.....)))))) ( -37.50)
>sp_pn.0 1851494 117 + 2038615/0-120
CUAAACACUAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCAAGUCAAAAACUUGGUACAA---AGAACAAAGUUCA
......(((.(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))))))....(((((.((....---...)).))))).. ( -31.60)
>consensus
AUAUACUAUAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCAAGCCAAUG_CUUGGUUUAU_CUUUAAUA_AAAGAA
..........(((((..(((((((.(((......)))..)).))))).....(((((.((((.........))))))))))))))................................... (-29.20 = -29.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,839,762 – 1,839,879
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.56
Mean single sequence MFE -39.53
Consensus MFE -32.39
Energy contribution -32.50
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.82
SVM decision value 0.65
SVM RNA-class probability 0.811778
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 117 - 2030921/0-120
UUCUUU-UAUAAAAG-AUAAACCAAG-CAUAGGCUUGGGCGCGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUAUAGUAUAU
.(((((-....))))-)......(((-(....))))(((((((...(((((((.(((((.((....))))))).))).))))...(((((.......))))))))))))........... ( -38.60)
>sp_ag.0 1904703 119 - 2160267/0-120
UACUUUAUAAGAAAGUAAAAACCAAG-CAAUAGCUUGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUCAAGAAUAU
((((((.....))))))....(((((-(....)))))).(((((...(((((((((......)).)))))))...))))).....(((((..((((....))))...)))))........ ( -41.30)
>sp_pn.0 1851494 117 + 2038615/0-120
UGAACUUUGUUCU---UUGUACCAAGUUUUUGACUUGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUAGUGUUUAG
.((((((.((...---....)).))))))...(((((((((((..(((((((((((......)).)))))))...))(((.(.((((....)))).).))).)))))))).)))...... ( -38.70)
>consensus
UACUUU_UAUAAAAG_AUAAACCAAG_CAUUGGCUUGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUAAAGUAUAU
....................(((.........((((((((.....)))))))).....((.(.(((((.......))))).).)))))(((.((((....)))).)))............ (-32.39 = -32.50 +   0.11) 
# Strand winner: reverse (0.99)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,839,762 – 1,839,879
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.20
Mean single sequence MFE -37.40
Consensus MFE -31.12
Energy contribution -30.13
Covariance contribution -0.99
Combinations/Pair 1.21
Mean z-score -2.00
Structure conservation index 0.83
SVM decision value 0.61
SVM RNA-class probability 0.800101
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 117 - 2030921/40-160
CACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACGCGCCCAAGCCUAUG-CUUGGUUUAU-CUUUUAUA-AAAGAAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGA
((((((.....))))))........(((((((...(((.(((((((((....)-)))))....(-((((....-)))))...))).))).((((.......))))......)))).))). ( -37.50)
>sp_ag.0 1904703 119 - 2160267/40-160
CACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCAAGCUAUUG-CUUGGUUUUUACUUUCUUAUAAAGUAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGA
((((((.....)))))).((((.........)))).......(((((((.(((-(......((((((((.....))))))))((((((..((.....)).))))))).))).))))))). ( -40.40)
>sp_pn.0 1851494 117 + 2038615/40-160
CACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCAAGUCAAAAACUUGGUACAA---AGAACAAAGUUCAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGA
((.(((.....((((((.((((.........))))..))))))...(((...(((((.((....---...)).)))))....((((((..((.....)).)))))))))...))).)).. ( -34.30)
>consensus
CACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCAAGCCAAUG_CUUGGUUUAU_CUUUAAUA_AAAGAAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGA
((((((.....)))))).((((.........)))).......((((((....................((((...))))...((((((..((.....)).)))))).......)))))). (-31.12 = -30.13 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,839,762 – 1,839,879
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.80
Mean single sequence MFE -38.57
Consensus MFE -32.73
Energy contribution -33.07
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.51
Structure conservation index 0.85
SVM decision value 2.29
SVM RNA-class probability 0.991808
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 117 - 2030921/80-200
GCCCAAGCCUAUG-CUUGGUUUAU-CUUUUAUA-AAAGAAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUUAGAUGG
..((((((....)-)))))....(-((((....-))))).(((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))))...... ( -38.90)
>sp_ag.0 1904703 119 - 2160267/80-200
GCCCAAGCUAUUG-CUUGGUUUUUACUUUCUUAUAAAGUAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUUCUAUGG
..((((((....)-)))))..((((((((.....))))))))(((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))........ ( -40.50)
>sp_pn.0 1851494 117 + 2038615/80-200
GCCCAAGUCAAAAACUUGGUACAA---AGAACAAAGUUCAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUAAAAUGG
..((((((.....)))))).....---.((((...))))..((((((((.((((.......)))).(((.((((((.....)))))).)))..............))))))))....... ( -36.30)
>consensus
GCCCAAGCCAAUG_CUUGGUUUAU_CUUUAAUA_AAAGAAAAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUUAAAUGG
..(((((.......))))).....................(((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))))...... (-32.73 = -33.07 +   0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,839,762 – 1,839,879
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.80
Mean single sequence MFE -37.53
Consensus MFE -31.11
Energy contribution -31.00
Covariance contribution -0.11
Combinations/Pair 1.04
Mean z-score -2.73
Structure conservation index 0.83
SVM decision value 1.70
SVM RNA-class probability 0.972981
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 117 - 2030921/80-200
CCAUCUAAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCUUUUCUUU-UAUAAAAG-AUAAACCAAG-CAUAGGCUUGGGC
......(((((((((...............((.(((((.......))))).)).(((((.......)))))))))))))).(((((-....))))-)....(((((-(....)))))).. ( -37.10)
>sp_ag.0 1904703 119 - 2160267/80-200
CCAUAGAAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCUUUACUUUAUAAGAAAGUAAAAACCAAG-CAAUAGCUUGGGC
........((((.((((((((.......)))))))).))..((((((((((((.(((.((.((.....))..)).)))((((((((.....))))))))......)-))))))))))))) ( -41.50)
>sp_pn.0 1851494 117 + 2038615/80-200
CCAUUUUAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCUUUGAACUUUGUUCU---UUGUACCAAGUUUUUGACUUGGGC
...((..((((((((...............((.(((((.......))))).)).(((((.......)))))))))))))..))..........---.....(((((((...))))))).. ( -34.00)
>consensus
CCAUAUAAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCUUCCAAGCUGUUGUCGCGAGUUCGAUUCUCGUCACCCGCUUUACUUU_UAUAAAAG_AUAAACCAAG_CAUUGGCUUGGGC
......(((((((((...............((.(((((.......))))).)).(((((.......)))))))))))))).....................(((((.(....)))))).. (-31.11 = -31.00 +  -0.11) 
# Strand winner: forward (0.80)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,839,762 – 1,839,882
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.50
Mean single sequence MFE -39.07
Consensus MFE -38.40
Energy contribution -38.40
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.98
SVM decision value 0.01
SVM RNA-class probability 0.538371
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 120 - 2030921/120-240
AAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUUAGAUGGGAGUUAACGGGCUCGAACCGCUGACCCUCUGCUUGUAAGG
(((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))))((..(((.((((.(((.......))).)))))))...))....... ( -39.60)
>sp_ag.0 1904703 120 - 2160267/120-240
AAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUUCUAUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGG
(((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))))....(((.((((.(((.......))).)))))))............ ( -38.80)
>sp_pn.0 1851494 120 + 2038615/120-240
AAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUAAAAUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGG
.((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))).....(((.((((.(((.......))).)))))))............ ( -38.80)
>consensus
AAGCGGGUGACGAGAAUCGAACUCGCGACAACAGCUUGGAAGGCUGUAGUUUUACCACUAAACUACACCCGCUUAAAUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGG
.((((((((.((((.......)))).(((.((((((.....)))))).)))..............)))))))).....(((.((((.(((.......))).)))))))............ (-38.40 = -38.40 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,839,762 – 1,839,882
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -42.90
Consensus MFE -41.17
Energy contribution -41.17
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.68
Structure conservation index 0.96
SVM decision value 2.28
SVM RNA-class probability 0.991696
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 120 - 2030921/160-280
AGGCUGUAGUUUUACCACUAAACUACACCCGCUUAGAUGGGAGUUAACGGGCUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAACUGAGCUAAACUCCCUCUUGCUAAG
.((.((((((((.......)))))))).))((..(((.(((((((...(((.(((......))))))((((((.....)))))).((((........))))..)))))))))).)).... ( -44.30)
>sp_ag.0 1904703 119 - 2160267/160-280
AGGCUGUAGUUUUACCACUAAACUACACCCGCUUCUAUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCU-UUGCUAAG
.((.((((((((.......)))))))).))((......(((((((...(((.(((......))))))((((((.....)))))).((((........))))..))))))).-..)).... ( -41.00)
>sp_pn.0 1851494 120 + 2038615/160-280
AGGCUGUAGUUUUACCACUAAACUACACCCGCUAAAAUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCUAGAGCUAAG
.((.((((((((.......)))))))).))(((.....(((((((...(((.(((......))))))((((((.....)))))).((((........))))..)))))))...))).... ( -43.40)
>consensus
AGGCUGUAGUUUUACCACUAAACUACACCCGCUUAAAUGGGAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCU_UUGCUAAG
.((.((((((((.......)))))))).))((......(((((((...(((.(((......))))))((((((.....)))))).((((........))))..)))))))....)).... (-41.17 = -41.17 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,839,762 – 1,839,882
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -41.60
Consensus MFE -39.60
Energy contribution -39.60
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.95
SVM decision value 0.66
SVM RNA-class probability 0.815195
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 120 - 2030921/160-280
CUUAGCAAGAGGGAGUUUAGCUCAGUUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCAGCGGUUCGAGCCCGUUAACUCCCAUCUAAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCU
....((.((((((((((..((((........)))).(((((.......)))))((((...((...)).))))...))))))).)))..))((.((((((((.......)))))))).)). ( -42.80)
>sp_ag.0 1904703 119 - 2160267/160-280
CUUAGCAA-AGGGAGUUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCAGCGGUUCGAUCCCGUUAACUCCCAUAGAAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCU
........-.(((((((.(((...)))((((((((..(((((((........)))).)))..))))..))))...)))))))........((.((((((((.......)))))))).)). ( -40.10)
>sp_pn.0 1851494 120 + 2038615/160-280
CUUAGCUCUAGGGAGUUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCAGCGGUUCGAUCCCGUUAACUCCCAUUUUAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCU
...(((((....)))))..(((.((.(((((((((.(((((.......)))))(((((........))))).)))..)))))).)).)))((.((((((((.......)))))))).)). ( -41.90)
>consensus
CUUAGCAA_AGGGAGUUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCAGCGGUUCGAUCCCGUUAACUCCCAUAUAAGCGGGUGUAGUUUAGUGGUAAAACUACAGCCU
..........(((((((..((((........)))).(((((.......)))))(((((........)).)))...)))))))........((.((((((((.......)))))))).)). (-39.60 = -39.60 +   0.00) 
# Strand winner: reverse (0.92)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,839,762 – 1,839,882
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.28
Mean single sequence MFE -36.13
Consensus MFE -33.46
Energy contribution -32.80
Covariance contribution -0.66
Combinations/Pair 1.08
Mean z-score -2.04
Structure conservation index 0.93
SVM decision value 0.68
SVM RNA-class probability 0.822154
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1839762 120 - 2030921/200-320
GAGUUAACGGGCUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAACUGAGCUAAACUCCCUCUUGCUAAGCGACGACCCUAUCUCACAGGGGGCAACCCCCAACUACUUC
(((.....(((.(((...((((.....((((((.....)))))).((((........)))).................)))).))))))...)))...((((....)))).......... ( -37.50)
>sp_ag.0 1904703 119 - 2160267/200-320
GAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCU-UUGCUAAGCGACUACCUUAUCUCACAGGGGGCAACCCCCAACUACUUC
(((.(((.(((.(((......))))))..(((((((((((.((..((((........))))....)).)).-)))).)))))......))).)))...((((....)))).......... ( -34.00)
>sp_pn.0 1851494 120 + 2038615/200-320
GAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCUAGAGCUAAGCGACUUCCCUAUCUCACAGGGGGCAACCCCCAACUACUUC
(((.....(((((((....(((.....((((((.....)))))).((((........))))............)))....)))..))))...)))...((((....)))).......... ( -36.90)
>consensus
GAGUUAACGGGAUCGAACCGCUGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAACUCCCU_UUGCUAAGCGACUACCCUAUCUCACAGGGGGCAACCCCCAACUACUUC
(((.....(((((((....((......((((((.....)))))).((((........)))).............))....))).).)))...)))...((((....)))).......... (-33.46 = -32.80 +  -0.66)

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 18:51:15 2006