Locus 103

Sequence ID sp_mu.0
Location 1,654,783 – 1,654,903
Length 120
Max. P 0.997708
window586 window587 window588 window589 window590 window591

overview

Window 6

Location 1,654,783 – 1,654,903
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.52
Mean single sequence MFE -25.23
Consensus MFE -24.07
Energy contribution -24.40
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.95
SVM decision value 2.76
SVM RNA-class probability 0.996872
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1654783 120 + 2030921/0-120
AUCGGGAAGACAGGAUUCGAACCUGCGACCCCUUGGUCCCAAACCAAGUACUCUACCAAGCUGAGCUACUUCCCGUAAAACCUCUCCUCAUCAUUAAAGUGUGCUAGUCCUUUACUAACC
..(((((((.((((.......))))......((((((.....))))))..(((.........)))...)))))))...................(((((..(....)..)))))...... ( -23.50)
>sy_ha.0 2500550 107 + 2685015/0-120
GUCGGGAAGACAGGAUUCGAACCUGCGACCCCUUGGUCCCAAACCAAGUGCUCUACCAAGCUGAGCUACUUCCCGUAUGUAAU-------UAAAUAAGAAAUAAAA------UUUAAAUG
..(((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))........-------................------........ ( -26.10)
>sy_sa.0 2311725 104 + 2516575/0-120
GUCGGGAAGACAGGAUUCGAACCUGCGACCCCUUGGUCCCAAACCAAGUGCUCUACCAAGCUGAGCUACUUCCCGUAUAUA---------UAAUUAACAUGCAUU-------UUAAAAUG
..(((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))......---------...............-------........ ( -26.10)
>consensus
GUCGGGAAGACAGGAUUCGAACCUGCGACCCCUUGGUCCCAAACCAAGUGCUCUACCAAGCUGAGCUACUUCCCGUAUAUA_U_______UAAUUAAAAUGUAAUA______UUAAAAUG
..(((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))............................................. (-24.07 = -24.40 +   0.33)

alignment

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secondary structure

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Window 7

Location 1,654,783 – 1,654,903
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.52
Mean single sequence MFE -33.57
Consensus MFE -31.55
Energy contribution -31.33
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.64
Structure conservation index 0.94
SVM decision value 2.83
SVM RNA-class probability 0.997302
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1654783 120 + 2030921/0-120
GGUUAGUAAAGGACUAGCACACUUUAAUGAUGAGGAGAGGUUUUACGGGAAGUAGCUCAGCUUGGUAGAGUACUUGGUUUGGGACCAAGGGGUCGCAGGUUCGAAUCCUGUCUUCCCGAU
.((((((.....))))))...(((((....)))))..........(((((((..((((.((((....)))).(((((((...))))))))))).(((((.......)))))))))))).. ( -36.50)
>sy_ha.0 2500550 107 + 2685015/0-120
CAUUUAAA------UUUUAUUUCUUAUUUA-------AUUACAUACGGGAAGUAGCUCAGCUUGGUAGAGCACUUGGUUUGGGACCAAGGGGUCGCAGGUUCGAAUCCUGUCUUCCCGAC
........------................-------........(((((((..((((.((((....)))).(((((((...))))))))))).(((((.......)))))))))))).. ( -32.10)
>sy_sa.0 2311725 104 + 2516575/0-120
CAUUUUAA-------AAUGCAUGUUAAUUA---------UAUAUACGGGAAGUAGCUCAGCUUGGUAGAGCACUUGGUUUGGGACCAAGGGGUCGCAGGUUCGAAUCCUGUCUUCCCGAC
........-------...............---------......(((((((..((((.((((....)))).(((((((...))))))))))).(((((.......)))))))))))).. ( -32.10)
>consensus
CAUUUAAA______UAAUACAUCUUAAUUA_______A_UAUAUACGGGAAGUAGCUCAGCUUGGUAGAGCACUUGGUUUGGGACCAAGGGGUCGCAGGUUCGAAUCCUGUCUUCCCGAC
.............................................(((((((..((((.((((....)))).(((((((...))))))))))).(((((.......)))))))))))).. (-31.55 = -31.33 +  -0.22) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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Window 8

Location 1,654,783 – 1,654,903
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 64.22
Mean single sequence MFE -26.20
Consensus MFE -22.22
Energy contribution -20.67
Covariance contribution -1.55
Combinations/Pair 1.25
Mean z-score -1.14
Structure conservation index 0.85
SVM decision value 2.91
SVM RNA-class probability 0.997708
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1654783 120 + 2030921/80-200
CCUCUCCUCAUCAUUAAAGUGUGCUAGUCCUUUACUAACCCCACUCAUGCACCCUGCAGGAUUCGAACCUGCAACCGCCUGAUUCGUAGUCAGGUACUCUAUCCAGUUGAGCCAAGGGUG
.................((((.(.((((.....)))).)..))))....(((((((((((.......)))))....(((((((.....))))))).(((.........)))...)))))) ( -29.80)
>sy_ha.0 2500550 101 + 2685015/80-200
AAU-------UAAAUAAGAAAUAAAA------UUUAAAUG------ACGCGCCCGAUAGGAGUCGAACCCAUAACCUCUUGAUCCGUAGUCAAACGCUCUAUCCAGUUGAGCUACGGGCG
...-------................------........------...(((((....(((.((((............)))))))(((((..(((..........)))..)))))))))) ( -21.40)
>sy_sa.0 2311725 98 + 2516575/80-200
A---------UAAUUAACAUGCAUU-------UUAAAAUG------GUGCGCCCGACAGGGGUCGAACCUGUAACCUCUUGAUUCGUAGUCAAGUACUCUAUCCAGUUGAGCUACGGGCG
.---------..........(((((-------.......)------))))((((((((((.......))))).....((((((.....))))))..(((.........)))...))))). ( -27.40)
>consensus
A_U_______UAAUUAAAAUGUAAUA______UUAAAAUG______AUGCGCCCGACAGGAGUCGAACCUGUAACCUCUUGAUUCGUAGUCAAGUACUCUAUCCAGUUGAGCUACGGGCG
.................................................(((((((((((.......))))).....((((((.....))))))..(((.........)))...)))))) (-22.22 = -20.67 +  -1.55)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,654,783 – 1,654,903
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 64.22
Mean single sequence MFE -27.93
Consensus MFE -24.54
Energy contribution -21.67
Covariance contribution -2.88
Combinations/Pair 1.40
Mean z-score -0.45
Structure conservation index 0.88
SVM decision value 1.47
SVM RNA-class probability 0.956700
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1654783 120 + 2030921/80-200
CACCCUUGGCUCAACUGGAUAGAGUACCUGACUACGAAUCAGGCGGUUGCAGGUUCGAAUCCUGCAGGGUGCAUGAGUGGGGUUAGUAAAGGACUAGCACACUUUAAUGAUGAGGAGAGG
...((((..((((..........((((((((((.(......)..))))(((((.......))))).))))))..(((((..((((((.....)))))).)))))......))))..)))) ( -38.20)
>sy_ha.0 2500550 101 + 2685015/80-200
CGCCCGUAGCUCAACUGGAUAGAGCGUUUGACUACGGAUCAAGAGGUUAUGGGUUCGACUCCUAUCGGGCGCGU------CAUUUAAA------UUUUAUUUCUUAUUUA-------AUU
((((((..((((.........))))(((.((((...((((....))))...)))).)))......))))))...------........------................-------... ( -24.00)
>sy_sa.0 2311725 98 + 2516575/80-200
CGCCCGUAGCUCAACUGGAUAGAGUACUUGACUACGAAUCAAGAGGUUACAGGUUCGACCCCUGUCGGGCGCAC------CAUUUUAA-------AAUGCAUGUUAAUUA---------U
.(((((..((((.........)))).(((((.......))))).....(((((.......))))))))))(((.------........-------..)))..........---------. ( -21.60)
>consensus
CGCCCGUAGCUCAACUGGAUAGAGUACUUGACUACGAAUCAAGAGGUUACAGGUUCGACUCCUGUCGGGCGCAU______CAUUUAAA______UAAUACAUCUUAAUUA_______A_U
((((((..((((.........)))).(((((.......))))).....(((((.......)))))))))))................................................. (-24.54 = -21.67 +  -2.88) 
# Strand winner: reverse (0.75)

alignment

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secondary structure

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Window 0

Location 1,654,783 – 1,654,896
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.77
Mean single sequence MFE -35.28
Consensus MFE -32.08
Energy contribution -31.84
Covariance contribution -0.24
Combinations/Pair 1.14
Mean z-score -1.32
Structure conservation index 0.91
SVM decision value 0.12
SVM RNA-class probability 0.592833
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1654783 113 + 2030921/200-320
CUCCUUCUUA---UUUAUGCCGAGGACCGGAAUCGAACCGGUACGAAGGUUCCCCUUCGCAGGAUUUUAAGUCCUGUGCGUCUGCCAGUUCCGCCACCCCGGCCUCC---UA-AAGCGAA
..........---....(((.((((.((((....((((.((((.(((((....)))))(((((((.....))))))).....)))).)))).......)))))))).---..-..))).. ( -36.50)
>sp_pn.0 1789053 109 + 2038615/200-320
CUCCAUAUUA---U----GCCGAGGACCGGAAUCGAACCGGUACGAUCGUUACCAAUCGCAGGAUUUUAAGUCCUGUGCGUCUGCCAGUUCCGCCACCCCGGCCUCU---CU-AAGCGAA
..........---.----...((((.((((....((((.((((.((.(((........(((((((.....)))))))))))))))).)))).......)))))))).---..-....... ( -32.80)
>sp_ag.0 2138176 111 - 2160267/200-320
CUAAAUAUUA---U--AUGCCGAGGACCGGAAUCGAACCGGUACGAUGUUUACCA-UCGCAGGAUUUUAAGUCCUGUGCGUCUGCCAGUUCCGCCACCCCGGCCUCU---AACAAGCGAA
..........---.--.....((((.((((....((((.((((.(((((......-..(((((((.....)))))))))))))))).)))).......)))))))).---.......... ( -34.80)
>sy_ha.0 2500550 117 + 2685015/200-320
CUUUAUUUAA--GAUGGUGCCGAGGACCGGAAUCGAACCGGUACGGUGAUCUCUCACCGCAGGAUUUUAAGUCCUGUGCGUCUGCCAGUUCCGCCACCCCGGCAAUA-UAAUGGAGCGGA
(((((((...--.(((.(((((.((...((....((((.((((.(((((....)))))(((((((.....))))))).....)))).))))..))..))))))).))-)))))))).... ( -39.60)
>sy_sa.0 2311725 120 + 2516575/200-320
CUAUAUUAAAAUGAUGGUGCCGAGGACCGGAAUCGAACCGGUACGAUAAUCACUUAUCGCAGGAUUUUAAGUCCUGUGCGUCUGCCAGUUCCGCCACCCCGGCAAAAAUAAUGGAGCAGA
.................(((((.((...((....((((.((((.(((((....)))))(((((((.....))))))).....)))).))))..))..)))))))................ ( -32.70)
>consensus
CUACAUAUUA___UU_AUGCCGAGGACCGGAAUCGAACCGGUACGAUGAUUACCAAUCGCAGGAUUUUAAGUCCUGUGCGUCUGCCAGUUCCGCCACCCCGGCCUCA___AU_AAGCGAA
..................((((.((...((....((((.((((.(((((....)))))(((((((.....))))))).....)))).))))..))..))))))................. (-32.08 = -31.84 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,654,783 – 1,654,896
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.77
Mean single sequence MFE -39.38
Consensus MFE -36.34
Energy contribution -35.66
Covariance contribution -0.68
Combinations/Pair 1.18
Mean z-score -1.48
Structure conservation index 0.92
SVM decision value 0.49
SVM RNA-class probability 0.756741
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1654783 113 + 2030921/200-320
UUCGCUU-UA---GGAGGCCGGGGUGGCGGAACUGGCAGACGCACAGGACUUAAAAUCCUGCGAAGGGGAACCUUCGUACCGGUUCGAUUCCGGUCCUCGGCAUAAA---UAAGAAGGAG
...(((.-..---.(((((((((((....(((((((........(((((.......)))))((((((....))))))..))))))).))))))).))))))).....---.......... ( -43.00)
>sp_pn.0 1789053 109 + 2038615/200-320
UUCGCUU-AG---AGAGGCCGGGGUGGCGGAACUGGCAGACGCACAGGACUUAAAAUCCUGCGAUUGGUAACGAUCGUACCGGUUCGAUUCCGGUCCUCGGC----A---UAAUAUGGAG
...(((.-.(---((.(((((((((....(((((((........(((((.......)))))((((((....))))))..))))))).)))))))))))))))----.---.......... ( -40.40)
>sp_ag.0 2138176 111 - 2160267/200-320
UUCGCUUGUU---AGAGGCCGGGGUGGCGGAACUGGCAGACGCACAGGACUUAAAAUCCUGCGA-UGGUAAACAUCGUACCGGUUCGAUUCCGGUCCUCGGCAU--A---UAAUAUUUAG
......((((---(...(((((((.(.(((((((((........(((((.......)))))(((-((.....)))))..))))).....)))).))))))))..--.---)))))..... ( -38.10)
>sy_ha.0 2500550 117 + 2685015/200-320
UCCGCUCCAUUA-UAUUGCCGGGGUGGCGGAACUGGCAGACGCACAGGACUUAAAAUCCUGCGGUGAGAGAUCACCGUACCGGUUCGAUUCCGGUCCUCGGCACCAUC--UUAAAUAAAG
............-...((((((((.(.(((((((((........(((((.......)))))((((((....))))))..))))).....)))).))))))))).....--.......... ( -39.10)
>sy_sa.0 2311725 120 + 2516575/200-320
UCUGCUCCAUUAUUUUUGCCGGGGUGGCGGAACUGGCAGACGCACAGGACUUAAAAUCCUGCGAUAAGUGAUUAUCGUACCGGUUCGAUUCCGGUCCUCGGCACCAUCAUUUUAAUAUAG
................((((((((.(.(((((((((........(((((.......)))))((((((....))))))..))))).....)))).)))))))))................. ( -36.30)
>consensus
UUCGCUU_AU___AGAGGCCGGGGUGGCGGAACUGGCAGACGCACAGGACUUAAAAUCCUGCGAUGGGUAACCAUCGUACCGGUUCGAUUCCGGUCCUCGGCAC_AA___UAAAAUAGAG
.................(((((((.(.(((((((((........(((((.......)))))((((((....))))))..))))).....)))).)))))))).................. (-36.34 = -35.66 +  -0.68) 
# Strand winner: reverse (1.00)

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 18:58:44 2006