Locus 96

Sequence ID sy_ha.0
Location 70,651 – 1,996,193
Length 1925542
Max. P 0.999998
window493 window494 window495 window496 window497 window498

overview

Window 3

Location 1,996,134 – 1,996,193
Length 59
Sequences 3
Columns 59
Reading direction reverse
Mean pairwise identity 72.32
Mean single sequence MFE -17.03
Consensus MFE -13.24
Energy contribution -13.81
Covariance contribution 0.56
Combinations/Pair 1.33
Mean z-score -3.29
Structure conservation index 0.78
SVM decision value 6.34
SVM RNA-class probability 0.999998
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1996134 59 + 2685015
UCUGGGAGUGGGACAGAAAUAAUAUUUUCUCAAAAUUUAUUUCGUUGUACUACCACGGC
.(((((((((.(((.(((((((.((((.....)))))))))))))).)))).)).))). ( -15.40)
>sy_au.0 317802 59 - 2809422
UCUGGGAGUGGGACAGAAAUGAUAUUUUCACAAAAUUUAUUUCGUCGUCCCACCCCAAC
..((((.(((((((.(((((((.((((.....)))))))))))...))))))))))).. ( -24.80)
>sy_sa.0 2503671 58 + 2516575
UAACGGAGAGGGACAAAAAUCCAAUUUUC-UAAUAGAGAUUUUGUAGUCCUACCUACGC
....((...(((((.(((((((.(((...-.))).).))))))...))))).))..... ( -10.90)
>consensus
UCUGGGAGUGGGACAGAAAUAAUAUUUUC_CAAAAUUUAUUUCGUAGUCCUACCACAGC
..((((.(((((((.(((((((..............)))))))...))))))))))).. (-13.24 = -13.81 +   0.56) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,996,134 – 1,996,193
Length 59
Sequences 3
Columns 59
Reading direction reverse
Mean pairwise identity 72.32
Mean single sequence MFE -17.03
Consensus MFE -13.24
Energy contribution -13.81
Covariance contribution 0.56
Combinations/Pair 1.33
Mean z-score -3.29
Structure conservation index 0.78
SVM decision value 6.34
SVM RNA-class probability 0.999998
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1996134 59 + 2685015/0-59
UCUGGGAGUGGGACAGAAAUAAUAUUUUCUCAAAAUUUAUUUCGUUGUACUACCACGGC
.(((((((((.(((.(((((((.((((.....)))))))))))))).)))).)).))). ( -15.40)
>sy_au.0 317802 59 - 2809422/0-59
UCUGGGAGUGGGACAGAAAUGAUAUUUUCACAAAAUUUAUUUCGUCGUCCCACCCCAAC
..((((.(((((((.(((((((.((((.....)))))))))))...))))))))))).. ( -24.80)
>sy_sa.0 2503671 58 + 2516575/0-59
UAACGGAGAGGGACAAAAAUCCAAUUUUC-UAAUAGAGAUUUUGUAGUCCUACCUACGC
....((...(((((.(((((((.(((...-.))).).))))))...))))).))..... ( -10.90)
>consensus
UCUGGGAGUGGGACAGAAAUAAUAUUUUC_CAAAAUUUAUUUCGUAGUCCUACCACAGC
..((((.(((((((.(((((((..............)))))))...))))))))))).. (-13.24 = -13.81 +   0.56) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 70,651 – 70,765
Length 114
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 72.83
Mean single sequence MFE -36.53
Consensus MFE -24.30
Energy contribution -24.97
Covariance contribution 0.67
Combinations/Pair 1.09
Mean z-score -4.41
Structure conservation index 0.67
SVM decision value 5.89
SVM RNA-class probability 0.999995
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 70651 114 - 2685015
AUUUUGCAUUCCUCUACACUAUGAU-GUUAUAAUGCACUUAACAAGGAAUCCA-GCAUGGAUACACCAAUCCCCUCACUACCGCAAAUAGUGAGGGGAUUGUUGUAGGUGUGGCUA
.............(((((((....(-((((.........))))).....(((.-....)))((((.((((((((((((((.......)))))))))))))).)))))))))))... ( -39.70)
>sy_au.0 219278 113 - 2809422
AUUUUGCAUUUUUUUGCUGUAAAGUUGUUAUAAUACAGUUAACAGGAAUU--A-GCAUAGAUACACCAAUCCCCUCACUACUCGCAAUAGUGAGGGGAUUUUUUUCGGUGUAGCUA
.....((...(((.(((((.....((((((.........))))))....)--)-))).)))(((((((((((((((((((.......)))))))))))))......)))))))).. ( -36.90)
>sy_sa.0 2506858 115 + 2516575
AUUUUGCAUUCCUACCCACUAUGAU-GUUAUAAUUCAAUUAACGAAGGUUAUAUGCAUAUAAGCACCAAUCCCCUCACUAUUUGCGGUAGUGAGGGGAUUUUUUGAUGCGUCUUAA
....(((((............(((.-........)))..((((....)))).))))).....(((.(((((((((((((((.....)))))))))))))....)).)))....... ( -33.00)
>consensus
AUUUUGCAUUCCUAUACACUAUGAU_GUUAUAAUACAAUUAACAAGGAUU__A_GCAUAGAUACACCAAUCCCCUCACUACUCGCAAUAGUGAGGGGAUUUUUUUAGGUGUAGCUA
..........................((((.........))))..................(((((((((((((((((((.......)))))))))))))......)))))).... (-24.30 = -24.97 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 70,651 – 70,765
Length 114
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 72.83
Mean single sequence MFE -38.77
Consensus MFE -25.02
Energy contribution -26.13
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -5.29
Structure conservation index 0.65
SVM decision value 4.42
SVM RNA-class probability 0.999895
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 70651 114 - 2685015
UAGCCACACCUACAACAAUCCCCUCACUAUUUGCGGUAGUGAGGGGAUUGGUGUAUCCAUGC-UGGAUUCCUUGUUAAGUGCAUUAUAAC-AUCAUAGUGUAGAGGAAUGCAAAAU
.(((......((((.(((((((((((((((.....))))))))))))))).)))).....))-)(.(((((((......((((((((...-...))))))))))))))).)..... ( -44.90)
>sy_au.0 219278 113 - 2809422
UAGCUACACCGAAAAAAAUCCCCUCACUAUUGCGAGUAGUGAGGGGAUUGGUGUAUCUAUGC-U--AAUUCCUGUUAACUGUAUUAUAACAACUUUACAGCAAAAAAAUGCAAAAU
(((.((((((((......((((((((((((.....)))))))))))))))))))).)))(((-(--(((....)))).(((((............))))).........))).... ( -36.60)
>sy_sa.0 2506858 115 + 2516575
UUAAGACGCAUCAAAAAAUCCCCUCACUACCGCAAAUAGUGAGGGGAUUGGUGCUUAUAUGCAUAUAACCUUCGUUAAUUGAAUUAUAAC-AUCAUAGUGGGUAGGAAUGCAAAAU
.......((((((....((((((((((((.......)))))))))))))))))).....(((((...(((((((.....)))(((((...-...)))))))))....))))).... ( -34.80)
>consensus
UAGCCACACCUAAAAAAAUCCCCUCACUAUUGCAAGUAGUGAGGGGAUUGGUGUAUCUAUGC_U__AAUCCUUGUUAACUGAAUUAUAAC_AUCAUAGUGCAAAGGAAUGCAAAAU
....((((((......((((((((((((((.....))))))))))))))))))))........................((((((.....................)))))).... (-25.02 = -26.13 +   1.12) 
# Strand winner: reverse (0.65)

alignment

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secondary structure

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dotplot

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Window 7

Location 70,651 – 70,765
Length 114
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 72.83
Mean single sequence MFE -36.53
Consensus MFE -24.30
Energy contribution -24.97
Covariance contribution 0.67
Combinations/Pair 1.09
Mean z-score -4.41
Structure conservation index 0.67
SVM decision value 5.89
SVM RNA-class probability 0.999995
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 70651 114 - 2685015/0-116
AUUUUGCAUUCCUCUACACUAUGAU-GUUAUAAUGCACUUAACAAGGAAUCCA-GCAUGGAUACACCAAUCCCCUCACUACCGCAAAUAGUGAGGGGAUUGUUGUAGGUGUGGCUA
.............(((((((....(-((((.........))))).....(((.-....)))((((.((((((((((((((.......)))))))))))))).)))))))))))... ( -39.70)
>sy_au.0 219278 113 - 2809422/0-116
AUUUUGCAUUUUUUUGCUGUAAAGUUGUUAUAAUACAGUUAACAGGAAUU--A-GCAUAGAUACACCAAUCCCCUCACUACUCGCAAUAGUGAGGGGAUUUUUUUCGGUGUAGCUA
.....((...(((.(((((.....((((((.........))))))....)--)-))).)))(((((((((((((((((((.......)))))))))))))......)))))))).. ( -36.90)
>sy_sa.0 2506858 115 + 2516575/0-116
AUUUUGCAUUCCUACCCACUAUGAU-GUUAUAAUUCAAUUAACGAAGGUUAUAUGCAUAUAAGCACCAAUCCCCUCACUAUUUGCGGUAGUGAGGGGAUUUUUUGAUGCGUCUUAA
....(((((............(((.-........)))..((((....)))).))))).....(((.(((((((((((((((.....)))))))))))))....)).)))....... ( -33.00)
>consensus
AUUUUGCAUUCCUAUACACUAUGAU_GUUAUAAUACAAUUAACAAGGAUU__A_GCAUAGAUACACCAAUCCCCUCACUACUCGCAAUAGUGAGGGGAUUUUUUUAGGUGUAGCUA
..........................((((.........))))..................(((((((((((((((((((.......)))))))))))))......)))))).... (-24.30 = -24.97 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 70,651 – 70,765
Length 114
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 72.83
Mean single sequence MFE -38.77
Consensus MFE -25.02
Energy contribution -26.13
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -5.29
Structure conservation index 0.65
SVM decision value 4.42
SVM RNA-class probability 0.999895
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 70651 114 - 2685015/0-116
UAGCCACACCUACAACAAUCCCCUCACUAUUUGCGGUAGUGAGGGGAUUGGUGUAUCCAUGC-UGGAUUCCUUGUUAAGUGCAUUAUAAC-AUCAUAGUGUAGAGGAAUGCAAAAU
.(((......((((.(((((((((((((((.....))))))))))))))).)))).....))-)(.(((((((......((((((((...-...))))))))))))))).)..... ( -44.90)
>sy_au.0 219278 113 - 2809422/0-116
UAGCUACACCGAAAAAAAUCCCCUCACUAUUGCGAGUAGUGAGGGGAUUGGUGUAUCUAUGC-U--AAUUCCUGUUAACUGUAUUAUAACAACUUUACAGCAAAAAAAUGCAAAAU
(((.((((((((......((((((((((((.....)))))))))))))))))))).)))(((-(--(((....)))).(((((............))))).........))).... ( -36.60)
>sy_sa.0 2506858 115 + 2516575/0-116
UUAAGACGCAUCAAAAAAUCCCCUCACUACCGCAAAUAGUGAGGGGAUUGGUGCUUAUAUGCAUAUAACCUUCGUUAAUUGAAUUAUAAC-AUCAUAGUGGGUAGGAAUGCAAAAU
.......((((((....((((((((((((.......)))))))))))))))))).....(((((...(((((((.....)))(((((...-...)))))))))....))))).... ( -34.80)
>consensus
UAGCCACACCUAAAAAAAUCCCCUCACUAUUGCAAGUAGUGAGGGGAUUGGUGUAUCUAUGC_U__AAUCCUUGUUAACUGAAUUAUAAC_AUCAUAGUGCAAAGGAAUGCAAAAU
....((((((......((((((((((((((.....))))))))))))))))))))........................((((((.....................)))))).... (-25.02 = -26.13 +   1.12) 
# Strand winner: reverse (0.65)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:57:27 2006