Locus 34

Sequence ID sy_ha.0
Location 1,218,105 – 1,218,217
Length 112
Max. P 0.999291
window177 window178 window179

overview

Window 7

Location 1,218,105 – 1,218,217
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 68.18
Mean single sequence MFE -35.63
Consensus MFE -16.18
Energy contribution -17.30
Covariance contribution 1.12
Combinations/Pair 1.22
Mean z-score -4.68
Structure conservation index 0.45
SVM decision value 3.49
SVM RNA-class probability 0.999291
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1218105 112 + 2685015/200-320
-CGUUU--AUUAAUGAACGUAUCAUUGAUAGAGUGAAUAGCAAUAUGC-----UAUUUAAGUAUGGUGGUAACGUGCUCAAGCGCCCUUACAUUUAACGAUGUAUGGGUGCUUUUUAUUU
-..(((--((((((((.....))))))))))).((((((((.....))-----))))))((((((.......)))))).((((((((.((((((....)))))).))))))))....... ( -39.10)
>sy_au.0 989159 116 - 2809422/200-320
-CGUUU--AUUAAUGAACGUAUCAUUAAUAGAGUGAACAUUAUCUUAUGAUUAUGUUUAAGUUUGGUGGUAACGUGCAAUCGCGCCCUUACAUAUU-UGUUGUAAGGGUUUUUUUUACGU
-(((((--(....))))))(((((((((.....(((((((.(((....))).)))))))...)))))))))(((((.((....(((((((((....-...)))))))))...)).))))) ( -33.80)
>sy_sa.0 1070124 107 + 2516575/200-320
ACGUUUUAGUUAAUGAACGUAUCAUUAAUAAAGU------UAUUUGAC-------UUAAAGUAUGGUGGUACCGUGCGCAUGCGCCCUUACAUUAAUUUGUAAGGGCGUUUUUCUAUUUU
........((((((((.....)))))))).((((------(....)))-------))...((((((.....))))))....(((((((((((......)))))))))))........... ( -34.00)
>consensus
_CGUUU__AUUAAUGAACGUAUCAUUAAUAGAGUGAA_A_UAUUUUAC_____U_UUUAAGUAUGGUGGUAACGUGCACAAGCGCCCUUACAUUUA_UGAUGUAAGGGUUUUUUUUAUUU
........((((((((.....))))))))...............................(((((.......)))))......((((((((((......))))))))))........... (-16.18 = -17.30 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,218,105 – 1,218,217
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 68.18
Mean single sequence MFE -24.50
Consensus MFE -7.63
Energy contribution -8.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.86
Structure conservation index 0.31
SVM decision value -0.02
SVM RNA-class probability 0.521987
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1218105 112 + 2685015/200-320
AAAUAAAAAGCACCCAUACAUCGUUAAAUGUAAGGGCGCUUGAGCACGUUACCACCAUACUUAAAUA-----GCAUAUUGCUAUUCACUCUAUCAAUGAUACGUUCAUUAAU--AAACG-
.......((((.(((.(((((......))))).))).)))).....((((.............((((-----((.....)))))).....(((.(((((.....))))).))--)))))- ( -24.20)
>sy_au.0 989159 116 - 2809422/200-320
ACGUAAAAAAAACCCUUACAACA-AAUAUGUAAGGGCGCGAUUGCACGUUACCACCAAACUUAAACAUAAUCAUAAGAUAAUGUUCACUCUAUUAAUGAUACGUUCAUUAAU--AAACG-
..((((......((((((((...-....)))))))).....)))).((((.............(((((.(((....))).))))).....(((((((((.....))))))))--)))))- ( -25.00)
>sy_sa.0 1070124 107 + 2516575/200-320
AAAAUAGAAAAACGCCCUUACAAAUUAAUGUAAGGGCGCAUGCGCACGGUACCACCAUACUUUAA-------GUCAAAUA------ACUUUAUUAAUGAUACGUUCAUUAACUAAAACGU
............((((((((((......))))))))))...(((...((.....)).........-------........------..(((((((((((.....))))))).)))).))) ( -24.30)
>consensus
AAAUAAAAAAAACCCAUACAACA_UAAAUGUAAGGGCGCAUGAGCACGUUACCACCAUACUUAAA_A_____GUAAAAUA_U_UUCACUCUAUUAAUGAUACGUUCAUUAAU__AAACG_
.............................((((.(((......)).).))))........................................(((((((.....)))))))......... ( -7.63 =  -8.30 +   0.67) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,218,105 – 1,218,214
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 58.00
Mean single sequence MFE -32.10
Consensus MFE -10.81
Energy contribution -12.37
Covariance contribution 1.56
Combinations/Pair 1.20
Mean z-score -4.21
Structure conservation index 0.34
SVM decision value 2.46
SVM RNA-class probability 0.994272
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1218105 109 + 2685015/237-357
UAGCAAUAUGC-----UAUUUAAGUAUGGUGGUAACGUGCUCAAGCGCCCUUACAUUUAACGAUGUAUGGGUGCUUUUUAUUUUUCAUAAA------UAGAGUAUAGAUCACUAAAUAUU
((((.....))-----))........(((((((...((((((((((((((.((((((....)))))).))))))))..(((((.....)))------))))))))..)))))))...... ( -36.20)
>sy_au.0 989159 114 - 2809422/237-357
CAUUAUCUUAUGAUUAUGUUUAAGUUUGGUGGUAACGUGCAAUCGCGCCCUUACAUAUU-UGUUGUAAGGGUUUUUUUUACGUUCAAAAAAC-----UUUAAAGUAUUUUAACAAGUAUU
(((.(((....))).)))...((((((..(((..(((((.((....(((((((((....-...)))))))))...)).))))))))..))))-----))...(((((((....))))))) ( -25.00)
>sy_sa.0 1070124 110 + 2516575/237-357
---UAUUUGAC-------UUAAAGUAUGGUGGUACCGUGCGCAUGCGCCCUUACAUUAAUUUGUAAGGGCGUUUUUCUAUUUUUUUAGAAAUCUAUAUAUGUUGCAAUUUAACACAUACU
---........-------....((((((.((......((((((((((((((((((......))))))))))).((((((......)))))).......))).))))......)))))))) ( -35.10)
>consensus
_A_UAUUUUAC_____U_UUUAAGUAUGGUGGUAACGUGCACAAGCGCCCUUACAUUUA_UGAUGUAAGGGUUUUUUUUAUUUUUAAAAAA______UAUAAUGUAAUUUAACAAAUAUU
.......................(((((.......)))))......((((((((((......))))))))))................................................ (-10.81 = -12.37 +   1.56)

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 18:53:05 2006