Locus 28

Sequence ID Bhalo.0
Location 3,183,479 – 3,183,594
Length 115
Max. P 0.993339
window155 window156 window157 window158 window159

overview

Window 5

Location 3,183,479 – 3,183,587
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 59.77
Mean single sequence MFE -38.22
Consensus MFE -12.70
Energy contribution -15.57
Covariance contribution 2.88
Combinations/Pair 1.24
Mean z-score -3.97
Structure conservation index 0.33
SVM decision value 0.93
SVM RNA-class probability 0.883208
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3183479 108 + 4202352/0-120
AAAAAAAUCUUUUUACCCAC------GC-UGCCAGAAUUUC--UAGC--AAAGGGGCAAAAAGAUUUCUCUUUUCACGGUACCACCCUCAUUCG-UAGCAUUUUUACAAAUGCUACCUCA
....((((((((((.(((.(------..-(((.((.....)--).))--)..)))).))))))))))..........((.....)).......(-((((((((....))))))))).... ( -28.30)
>Bclau.0 2774870 102 + 4303871/0-120
AAAAAAGACUUUCUGCGCGC------CCAUGCUGGGAU--C--CAGC--AAGGGGCGAGAAAG-----UCUUCACGCGGUACCACCCUUUUUCGCUAACAAUGGU-UAGCCUCUAGCAAG
....((((((((((.(((.(------((.((((((...--)--))))--).))))))))))))-----))))...((((.....)).......((((((....))-)))).....))... ( -42.80)
>Bsubt.0 2896109 117 + 4214630/0-120
AAAAAAGCCCUUCCGCCCACAAUCAGCCGCGCAGUAACUGCGAUAGCUAAAAGGGGCGAAAAGGCUUUUCUUUCCGCGGUACCACCCUUGUUUA-CGGC--CUGUUAAUCGGCCGUCUCA
..(((((((.((.(((((......(((..(((((...)))))...))).....))))).)).)))))))........((.....)).......(-((((--(........)))))).... ( -39.30)
>Blich.0 2850042 112 + 4222334/0-120
AAAAAAGCCUUCCCGCCCACUGUUGACGCUGCACACCUUGC---AGGCCAAAGGGGCGAAAAGGCUUUUCUUUCCGCGGUACCACCCUUGUUCG-CGGC--UUUUGAA--AGCCGCCUUA
..(((((((((..(((((.((.(((.(.(((((.....)))---))).))))))))))..)))))))))........((.....)).......(-((((--((....)--)))))).... ( -42.50)
>consensus
AAAAAAGCCUUUCCGCCCAC______CC_UGCAGGAAUUGC__UAGC__AAAGGGGCAAAAAGGCUUUUCUUUCCGCGGUACCACCCUUGUUCG_CAGC__UUGU_AA_CAGCCACCUCA
..((((((((((((((((............(((.....)))............))))))))))))))))........((.....)).........((((............))))..... (-12.70 = -15.57 +   2.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,183,479 – 3,183,587
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 59.77
Mean single sequence MFE -50.80
Consensus MFE -23.05
Energy contribution -22.55
Covariance contribution -0.50
Combinations/Pair 1.54
Mean z-score -5.62
Structure conservation index 0.45
SVM decision value 1.30
SVM RNA-class probability 0.938827
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3183479 108 + 4202352/0-120
UGAGGUAGCAUUUGUAAAAAUGCUA-CGAAUGAGGGUGGUACCGUGAAAAGAGAAAUCUUUUUGCCCCUUU--GCUA--GAAAUUCUGGCA-GC------GUGGGUAAAAAGAUUUUUUU
....(((((((((....))))))))-)......((......))......(((((((((((((((((((.((--((((--(.....))))))-).------).)))))))))))))))))) ( -44.60)
>Bclau.0 2774870 102 + 4303871/0-120
CUUGCUAGAGGCUA-ACCAUUGUUAGCGAAAAAGGGUGGUACCGCGUGAAGA-----CUUUCUCGCCCCUU--GCUG--G--AUCCCAGCAUGG------GCGCGCAGAAAGUCUUUUUU
...((.....((((-((....))))))......((......))))..(((((-----((((((((((((.(--((((--(--...)))))).))------).))).)))))))))))... ( -44.80)
>Bsubt.0 2896109 117 + 4214630/0-120
UGAGACGGCCGAUUAACAG--GCCG-UAAACAAGGGUGGUACCGCGGAAAGAAAAGCCUUUUCGCCCCUUUUAGCUAUCGCAGUUACUGCGCGGCUGAUUGUGGGCGGAAGGGCUUUUUU
....((((((........)--))))-)........(((....)))....(((((((((((((((((((..((((((..(((((...))))).))))))..).)))))))))))))))))) ( -57.30)
>Blich.0 2850042 112 + 4222334/0-120
UAAGGCGGCU--UUCAAAA--GCCG-CGAACAAGGGUGGUACCGCGGAAAGAAAAGCCUUUUCGCCCCUUUGGCCU---GCAAGGUGUGCAGCGUCAACAGUGGGCGGGAAGGCUUUUUU
....((((((--(....))--))))-)........(((....)))....(((((((((((..((((((((((((((---(((.....))))).))))).)).)))))..))))))))))) ( -56.50)
>consensus
UGAGGCAGCAG_UU_AAAA__GCCA_CGAACAAGGGUGGUACCGCGGAAAGAAAAGCCUUUUCGCCCCUUU__GCUA__GCAAUUCCUGCA_GG______GUGGGCAGAAAGGCUUUUUU
...(.((((((........)))))).)......((......))......(((((((((((((((((((................................).)))))))))))))))))) (-23.05 = -22.55 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,183,479 – 3,183,594
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 60.06
Mean single sequence MFE -37.88
Consensus MFE -17.01
Energy contribution -16.82
Covariance contribution -0.19
Combinations/Pair 1.56
Mean z-score -2.83
Structure conservation index 0.45
SVM decision value 2.39
SVM RNA-class probability 0.993339
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3183479 115 + 4202352/40-160
CACUACACCCGUUAUCAAAAUGAGACGAUUUGAUCGUCCAUGAGGUAGCAUUUGUAAAAAUGCUA-CGAAUGAGGGUGGUACCGUGAAAAGAGAAAUCUUUUUGCCCCUUU--GCUA--G
.....(((((....((...(((.((((((...)))))))))...(((((((((....))))))))-)))....))))).....(..((((((....))))))..)......--....--. ( -39.30)
>Bclau.0 2774870 108 + 4303871/40-160
GAACGCAUUCGUUAUAAAAAC--UGCAAGCCGGAUUUCGGCUUGCUAGAGGCUA-ACCAUUGUUAGCGAAAAAGGGUGGUACCGCGUGAAGA-----CUUUCUCGCCCCUU--GCUG--G
....((.(((..........(--(((((((((.....)))))))).))..((((-((....))))))))).(((((.(....)(((.(((..-----..))).))))))))--))..--. ( -35.40)
>Bsubt.0 2896109 112 + 4214630/40-160
-GAUUCACUCGUUACUAAAGC--GGAUAG--AAAUAUCCAUGAGACGGCCGAUUAACAG--GCCG-UAAACAAGGGUGGUACCGCGGAAAGAAAAGCCUUUUCGCCCCUUUUAGCUAUCG
-......((((((.....)))--(((((.--...)))))..)))((((((........)--))))-)....(((((.(....)((((((((......))))))))))))).......... ( -37.10)
>Blich.0 2850042 110 + 4222334/40-160
AGGUUCACUCGUUAUUAAACC--GGAUAAGCGAUUAUCCAUAAGGCGGCU--UUCAAAA--GCCG-CGAACAAGGGUGGUACCGCGGAAAGAAAAGCCUUUUCGCCCCUUUGGCCU---G
.(((((((((...........--((((((....)))))).....((((((--(....))--))))-)......)))))).)))((((((((......))))))))...........---. ( -39.70)
>consensus
_AAUUCACUCGUUAUUAAAAC__GGAUAG_CGAAUAUCCAUGAGGCAGCAG_UU_AAAA__GCCA_CGAACAAGGGUGGUACCGCGGAAAGAAAAGCCUUUUCGCCCCUUU__GCUA__G
.....(((((.............(((((......)))))....(.((((((........)))))).)......))))).....((((((((......))))))))............... (-17.01 = -16.82 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,183,479 – 3,183,593
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 53.87
Mean single sequence MFE -36.25
Consensus MFE -12.15
Energy contribution -11.71
Covariance contribution -0.44
Combinations/Pair 1.50
Mean z-score -2.75
Structure conservation index 0.34
SVM decision value 0.88
SVM RNA-class probability 0.874319
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3183479 114 + 4202352/80-200
CAGCCUGCUUUAGUAGAUG-UUGCCGGGUGGUUUUU----CACUACACCCGUUAUCAAAAUGAGACGAUUUGAUCGUCCAUGAGGUAGCAUUUGUAAAAAUGCUA-CGAAUGAGGGUGGU
((((((((....))))..)-)))...(((((....)----)))).(((((....((...(((.((((((...)))))))))...(((((((((....))))))))-)))....))))).. ( -38.10)
>Bclau.0 2774870 102 + 4303871/80-200
-------UUGUAGUAAGAG--CGCCGGAUG--CUGU----GAACGCAUUCGUUAUAAAAAC--UGCAAGCCGGAUUUCGGCUUGCUAGAGGCUA-ACCAUUGUUAGCGAAAAAGGGUGGU
-------............--(((((((((--(.(.----...)))))))..........(--(((((((((.....)))))))).))..((((-((....)))))).......)))).. ( -35.20)
>Bsubt.0 2896109 101 + 4214630/80-200
-----AUG-ACAGUAGGACUUGGCCGGGUGAACUU------GAUUCACUCGUUACUAAAGC--GGAUAG--AAAUAUCCAUGAGACGGCCGAUUAACAG--GCCG-UAAACAAGGGUGGU
-----...-.........((((..((((((((...------..))))))))..........--(((((.--...))))).....((((((........)--))))-)...))))...... ( -32.10)
>Blich.0 2850042 110 + 4222334/80-200
--UCCAUGUUUAGUAGGGC-UGGCCGGGUGAACAUUACGAAGGUUCACUCGUUAUUAAACC--GGAUAAGCGAUUAUCCAUAAGGCGGCU--UUCAAAA--GCCG-CGAACAAGGGUGGU
--.((((.((((((((((.-...))((((((((.........)))))))).))))))))((--((((((....)))))).....((((((--(....))--))))-)......)))))). ( -39.60)
>consensus
_____AUGUUUAGUAGGAC_UGGCCGGGUGAACUUU_____AAUUCACUCGUUAUUAAAAC__GGAUAG_CGAAUAUCCAUGAGGCAGCAG_UU_AAAA__GCCA_CGAACAAGGGUGGU
......................((((((((...............))))).............(((((......)))))....(.((((((........)))))).).......)))... (-12.15 = -11.71 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,183,479 – 3,183,593
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 56.18
Mean single sequence MFE -30.07
Consensus MFE -17.05
Energy contribution -15.30
Covariance contribution -1.75
Combinations/Pair 1.57
Mean z-score -1.12
Structure conservation index 0.57
SVM decision value 0.74
SVM RNA-class probability 0.838833
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3183479 114 + 4202352/120-240
UG-AAGCUCACCUCGGAGUGCGACUUCGAACAAUCGGGCACAGCCUGCUUUAGUAGAUG-UUGCCGGGUGGUUUUU----CACUACACCCGUUAUCAAAAUGAGACGAUUUGAUCGUCCA
((-((((.....((((((.....)))))).......((((((..((((....)))).))-.))))(((((......----.....)))))))).)))...((.((((((...)))))))) ( -33.60)
>Bclau.0 2774870 94 + 4303871/120-240
UG-AAACUCACCUCUGAGUGCGUCUCUGAACA---------------UUGUAGUAAGAG--CGCCGGAUG--CUGU----GAACGCAUUCGUUAUAAAAAC--UGCAAGCCGGAUUUCGG
..-..(((((....))))).((..((((....---------------(((((((.....--...((((((--(.(.----...))))))))........))--)))))..))))...)). ( -24.09)
>Bsubt.0 2896109 94 + 4214630/120-240
GGUGAACUCGCCUCAGAGUGCCAGUCUGAA---------------AUG-ACAGUAGGACUUGGCCGGGUGAACUU------GAUUCACUCGUUACUAAAGC--GGAUAG--AAAUAUCCA
(((((((((......))))((((((((...---------------...-......)))).))))((((((((...------..))))))))))))).....--(((((.--...))))). ( -31.60)
>Blich.0 2850042 110 + 4222334/120-240
UGUGAACUCCCCUCUGAGUGUCAGUCUGAACGAUU-------UCCAUGUUUAGUAGGGC-UGGCCGGGUGAACAUUACGAAGGUUCACUCGUUAUUAAACC--GGAUAAGCGAUUAUCCA
.....((((......))))(((((((((((((...-------....)))))....))))-))))(((((((((.........)))))))))..........--((((((....)))))). ( -31.00)
>consensus
UG_AAACUCACCUCUGAGUGCCACUCUGAACA_____________AUGUUUAGUAGGAC_UGGCCGGGUGAACUUU_____AAUUCACUCGUUAUUAAAAC__GGAUAG_CGAAUAUCCA
.....((((......))))((((((((............................)))).))))((((((...............))))))............(((((......))))). (-17.05 = -15.30 +  -1.75)

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 17:17:37 2006