Locus 110

Sequence ID Blich.0
Location 3,068,831 – 3,068,932
Length 101
Max. P 0.999976
window746 window747 window748 window749

overview

Window 6

Location 3,068,831 – 3,068,932
Length 101
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 62.40
Mean single sequence MFE -23.73
Consensus MFE -11.86
Energy contribution -14.55
Covariance contribution 2.69
Combinations/Pair 1.12
Mean z-score -3.22
Structure conservation index 0.50
SVM decision value 3.54
SVM RNA-class probability 0.999357
Prediction RNA
WARNING Sequence 2: Base composition out of range.

Download alignment: ClustalW | MAF

>Blich.0 3068831 101 + 4222334
UUGCUC-CUUUACAUGUGUGUGUUA--ACUGUAUUACUCGAUGUAGUACACUUAAUACAAUAUAGACAUCGUCCUUUUUUGUCAAUCGCUUUUUU-CAAAAAAAU
..((..-.......(((((((((((--(.((((((((.....)))))))).))))))).)))))((((...........))))....))......-......... ( -21.80)
>Bsubt.0 3118473 103 + 4214630
UAAAUGAUUUUAUAUUAGUGUCUAU--AGUGUAUUACUUCAAUUAGUACACUUAAUACAAUAAAUACUUUGACUCACAAAGUCAAUCCUUUUUUUACAAAAAAAC
............((((.((((....--(((((((((.......)))))))))..))))))))......((((((.....)))))).................... ( -15.20)
>Bcere.0 1352861 104 - 5224283
GCAAUGUCUCCUUUCUGACUUGUAUUAAGUGUACUACUAUGUGUAAUACACUUAAUACAAUAAAGGUGAUGAAUGUGUUUGUCAACUGAAAAUGU-UAGAAAAAU
...........((((((((((((((((((((((.(((.....))).))))))))))))))...((.(((..((....))..))).))......))-))))))... ( -31.20)
>Banth.0 1299781 104 - 5227293
GCAAUGUCUCCUUCCUGACAUGUAUUAAUUGUACUAAUGUGUGUAGUACACUUAAUACGAUAUAGGUGAUAAAUGUGUUUGUCAACUGAAAAUGU-UAGAAAAAU
..............((((((((((((((.(((((((.......))))))).)))))))....(((.(((((((....))))))).)))...))))-)))...... ( -26.70)
>consensus
GCAAUGUCUCCAUACUGACGUGUAU__AGUGUACUACUAUAUGUAGUACACUUAAUACAAUAAAGACGAUGAAUGUGUUUGUCAACCGAAAAUGU_CAAAAAAAU
....................(((((((((((((((((.....))))))))))))))))).............................................. (-11.86 = -14.55 +   2.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,068,831 – 3,068,932
Length 101
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 62.40
Mean single sequence MFE -20.77
Consensus MFE -10.30
Energy contribution -13.43
Covariance contribution 3.12
Combinations/Pair 1.27
Mean z-score -2.46
Structure conservation index 0.50
SVM decision value 2.64
SVM RNA-class probability 0.995969
Prediction RNA
WARNING Sequence 2: Base composition out of range.

Download alignment: ClustalW | MAF

>Blich.0 3068831 101 + 4222334
AUUUUUUUG-AAAAAAGCGAUUGACAAAAAAGGACGAUGUCUAUAUUGUAUUAAGUGUACUACAUCGAGUAAUACAGU--UAACACACACAUGUAAAG-GAGCAA
.........-......((..((.(((.....((((...))))....(((.((((.((((.(((.....))).)))).)--))).)))....))).)).-..)).. ( -15.10)
>Bsubt.0 3118473 103 + 4214630
GUUUUUUUGUAAAAAAAGGAUUGACUUUGUGAGUCAAAGUAUUUAUUGUAUUAAGUGUACUAAUUGAAGUAAUACACU--AUAGACACUAAUAUAAAAUCAUUUA
..((((((....))))))((((.((((((.....)))))).....((((((((.((((.(((..((.(....).))..--.)))))))))))))))))))..... ( -16.80)
>Bcere.0 1352861 104 - 5224283
AUUUUUCUA-ACAUUUUCAGUUGACAAACACAUUCAUCACCUUUAUUGUAUUAAGUGUAUUACACAUAGUAGUACACUUAAUACAAGUCAGAAAGGAGACAUUGC
...(((((.-((.......(((....)))................((((((((((((((((((.....)))))))))))))))))))).)))))(....)..... ( -29.70)
>Banth.0 1299781 104 - 5227293
AUUUUUCUA-ACAUUUUCAGUUGACAAACACAUUUAUCACCUAUAUCGUAUUAAGUGUACUACACACAUUAGUACAAUUAAUACAUGUCAGGAAGGAGACAUUGC
..((((((.-.........(((....)))..........(((((((.(((((((.(((((((.......))))))).))))))))))).))).))))))...... ( -21.50)
>consensus
AUUUUUCUA_AAAAAAUCAAUUGACAAACACAGUCAACACCUAUAUUGUAUUAAGUGUACUACACAAAGUAAUACACU__AUACACACCAAUAAAAAGACAUUGA
....((((...........((((((.......)))))).........((((((((((((((((.....))))))))))))))))..........))))....... (-10.30 = -13.43 +   3.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,068,831 – 3,068,932
Length 101
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 66.67
Mean single sequence MFE -26.57
Consensus MFE -13.46
Energy contribution -16.03
Covariance contribution 2.57
Combinations/Pair 1.27
Mean z-score -3.61
Structure conservation index 0.51
SVM decision value 5.14
SVM RNA-class probability 0.999976
Prediction RNA

Download alignment: ClustalW | MAF

>Blich.0 3068831 101 + 4222334/0-105
UUGCUC-CUUUACAUGUGUGUGUUA--ACUGUAUUACUCGAUGUAGUACACUUAAUACAAUAUAGACAUCGUCCUUUUUUGUCAAUCGCUUUUUUCAAAAAAAU
..((..-.......(((((((((((--(.((((((((.....)))))))).))))))).)))))((((...........))))....))............... ( -21.80)
>Bcere.0 1352861 104 - 5224283/0-105
GCAAUGUCUCCUUUCUGACUUGUAUUAAGUGUACUACUAUGUGUAAUACACUUAAUACAAUAAAGGUGAUGAAUGUGUUUGUCAACUGAAAAUGUUAGAAAAAU
...........((((((((((((((((((((((.(((.....))).))))))))))))))...((.(((..((....))..))).))......))))))))... ( -31.20)
>Banth.0 1299781 104 - 5227293/0-105
GCAAUGUCUCCUUCCUGACAUGUAUUAAUUGUACUAAUGUGUGUAGUACACUUAAUACGAUAUAGGUGAUAAAUGUGUUUGUCAACUGAAAAUGUUAGAAAAAU
..............((((((((((((((.(((((((.......))))))).)))))))....(((.(((((((....))))))).)))...)))))))...... ( -26.70)
>consensus
GCAAUGUCUCCUUACUGACAUGUAUUAACUGUACUACUAUGUGUAGUACACUUAAUACAAUAUAGGUGAUGAAUGUGUUUGUCAACUGAAAAUGUUAGAAAAAU
..............(((((.((((((((.((((((((.....)))))))).)))))))).....(((((((((....)))))).)))......)))))...... (-13.46 = -16.03 +   2.57)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,068,831 – 3,068,932
Length 101
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 66.67
Mean single sequence MFE -22.10
Consensus MFE -11.02
Energy contribution -13.03
Covariance contribution 2.01
Combinations/Pair 1.24
Mean z-score -2.99
Structure conservation index 0.50
SVM decision value 4.08
SVM RNA-class probability 0.999787
Prediction RNA

Download alignment: ClustalW | MAF

>Blich.0 3068831 101 + 4222334/0-105
AUUUUUUUGAAAAAAGCGAUUGACAAAAAAGGACGAUGUCUAUAUUGUAUUAAGUGUACUACAUCGAGUAAUACAGU--UAACACACACAUGUAAAG-GAGCAA
...............((..((.(((.....((((...))))....(((.((((.((((.(((.....))).)))).)--))).)))....))).)).-..)).. ( -15.10)
>Bcere.0 1352861 104 - 5224283/0-105
AUUUUUCUAACAUUUUCAGUUGACAAACACAUUCAUCACCUUUAUUGUAUUAAGUGUAUUACACAUAGUAGUACACUUAAUACAAGUCAGAAAGGAGACAUUGC
...(((((.((.......(((....)))................((((((((((((((((((.....)))))))))))))))))))).)))))(....)..... ( -29.70)
>Banth.0 1299781 104 - 5227293/0-105
AUUUUUCUAACAUUUUCAGUUGACAAACACAUUUAUCACCUAUAUCGUAUUAAGUGUACUACACACAUUAGUACAAUUAAUACAUGUCAGGAAGGAGACAUUGC
..((((((..........(((....)))..........(((((((.(((((((.(((((((.......))))))).))))))))))).))).))))))...... ( -21.50)
>consensus
AUUUUUCUAACAUUUUCAGUUGACAAACACAUUCAUCACCUAUAUUGUAUUAAGUGUACUACACACAGUAGUACAAUUAAUACAAGUCAGAAAGGAGACAUUGC
.(((((((..........(((....)))..................(((((((.((((((((.....)))))))).))))))).....)))))))......... (-11.02 = -13.03 +   2.01)

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 17:25:23 2006