Locus 116

Sequence ID Blich.0
Location 4,014,275 – 4,014,389
Length 114
Max. P 0.995082
window815 window816 window817 window818

overview

Window 5

Location 4,014,275 – 4,014,389
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 60.17
Mean single sequence MFE -43.13
Consensus MFE -8.43
Energy contribution -11.43
Covariance contribution 3.01
Combinations/Pair 1.18
Mean z-score -4.45
Structure conservation index 0.20
SVM decision value 0.09
SVM RNA-class probability 0.579344
Prediction RNA

Download alignment: ClustalW | MAF

>Blich.0 4014275 114 + 4222334/0-120
UGAAACCCGGCAACCGCUGUCUAUGACAGAAUG--GUGCUAAAUCCUUAAGAGCAUGUUCGUGCUCU-UGAAGAUAAGGAGGAGAUUGAAUAUAUCAAGCUCUUCCUUAUC---GGGAAG
.....(((((((.((.(((((...)))))...)--)))))......((((((((((....)))))))-))).((((((((((((.((((.....)))).))))))))))))---)))... ( -50.80)
>Bsubt.0 3998216 112 + 4214630/0-120
CGAUACCCGGCAACCGCUGUUUA--ACAGAAUG--GUGCUAAAUCCUUUAGAGCA-AUGAUUGCUCU-UGAAGAUAAGGUUGAGAUUG--UCACGCAAGCUCUUCCUUAUCCAAAGGAAG
........((((.((.(((....--.)))...)--)))))...((((((((((((-.....))))))-....(((((((..(((.(((--.....))).)))..))))))).)))))).. ( -35.90)
>Banth.0 1375383 115 + 5227293/0-120
CGAUGCCUCGGCAGCGGACUCGAUUUUAGAGUGCUGUGCCAAAUCCAGCA-AGCAUGUGCUUGAAAGAUGAGAAGAGCGUUUCUUAUAGAUGUAUAAGACCUCUUCUCGUU----GGAAG
.........((((.(((((((.......)))).)))))))...(((..((-(((....)))))...(((((((((((.((((..(((....)))..)))))))))))))))----))).. ( -42.70)
>consensus
CGAUACCCGGCAACCGCUGUCUAU_ACAGAAUG__GUGCUAAAUCCUUAAGAGCAUGUGCUUGCUCU_UGAAGAUAAGGUUGAGAUUG_AUAUAUCAAGCUCUUCCUUAUC____GGAAG
...........................................(((....(((((......)))))......(((((((..(((.((((.....)))).)))..)))))))....))).. ( -8.43 = -11.43 +   3.01)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,014,275 – 4,014,389
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 60.17
Mean single sequence MFE -37.50
Consensus MFE -8.70
Energy contribution -8.50
Covariance contribution -0.20
Combinations/Pair 1.45
Mean z-score -3.79
Structure conservation index 0.23
SVM decision value 0.11
SVM RNA-class probability 0.589769
Prediction RNA

Download alignment: ClustalW | MAF

>Blich.0 4014275 114 + 4222334/0-120
CUUCCC---GAUAAGGAAGAGCUUGAUAUAUUCAAUCUCCUCCUUAUCUUCA-AGAGCACGAACAUGCUCUUAAGGAUUUAGCAC--CAUUCUGUCAUAGACAGCGGUUGCCGGGUUUCA
...(((---(.((((((.(((.((((.....)))).))).))))))((((.(-((((((......))))))).))))....((((--(...(((((...))))).)).)))))))..... ( -39.80)
>Bsubt.0 3998216 112 + 4214630/0-120
CUUCCUUUGGAUAAGGAAGAGCUUGCGUGA--CAAUCUCAACCUUAUCUUCA-AGAGCAAUCAU-UGCUCUAAAGGAUUUAGCAC--CAUUCUGU--UAAACAGCGGUUGCCGGGUAUCG
...(((((((((((((..(((.(((.....--))).)))..))))))))...-((((((.....-)))))))))))(((..((((--(...(((.--....))).)).)))..))).... ( -34.30)
>Banth.0 1375383 115 + 5227293/0-120
CUUCC----AACGAGAAGAGGUCUUAUACAUCUAUAAGAAACGCUCUUCUCAUCUUUCAAGCACAUGCU-UGCUGGAUUUGGCACAGCACUCUAAAAUCGAGUCCGCUGCCGAGGCAUCG
..(((----(..((((((((.(((((((....)))))))....))))))))......(((((....)))-)).))))(((((((..(.((((.......)))).)..)))))))...... ( -38.40)
>consensus
CUUCC____GAUAAGGAAGAGCUUGAUACAU_CAAUCUCAACCUUAUCUUCA_AGAGCAAGCACAUGCUCUAAAGGAUUUAGCAC__CAUUCUGU_AUAGACAGCGGUUGCCGGGUAUCG
(((((.........))))).(((((.....................(((....((((((......))))))...)))......................(((....)))..))))).... ( -8.70 =  -8.50 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,014,275 – 4,014,389
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 61.02
Mean single sequence MFE -38.50
Consensus MFE -10.77
Energy contribution -12.67
Covariance contribution 1.90
Combinations/Pair 1.25
Mean z-score -3.90
Structure conservation index 0.28
SVM decision value 0.87
SVM RNA-class probability 0.870014
Prediction RNA

Download alignment: ClustalW | MAF

>Blich.0 4014275 114 + 4222334/14-134
CGCUGUCUAUGACAGAAUG--GUGCUAAAUCCUUAAGAGCAUGUUCGUGCUCU-UGAAGAUAAGGAGGAGAUUGAAUAUAUCAAGCUCUUCCUUAUC---GGGAAGAGCUUUUUUAUGUC
..(((((...)))))....--..(((...(((((((((((((....)))))))-))).((((((((((((.((((.....)))).))))))))))))---.)))..)))........... ( -45.10)
>Bsubt.0 3998216 112 + 4214630/14-134
CGCUGUUUA--ACAGAAUG--GUGCUAAAUCCUUUAGAGCA-AUGAUUGCUCU-UGAAGAUAAGGUUGAGAUUG--UCACGCAAGCUCUUCCUUAUCCAAAGGAAGAGCUUUUUUAUAUU
.(((((((.--...)))))--))(((...((((((((((((-.....))))))-....(((((((..(((.(((--.....))).)))..))))))).))))))..)))........... ( -34.00)
>Banth.0 1375383 115 + 5227293/14-134
CGGACUCGAUUUUAGAGUGCUGUGCCAAAUCCAGCA-AGCAUGUGCUUGAAAGAUGAGAAGAGCGUUUCUUAUAGAUGUAUAAGACCUCUUCUCGUU----GGAAGAGGUCUUUUGUUAU
(((((((.......)))).))).(((...(((..((-(((....)))))...(((((((((((.((((..(((....)))..)))))))))))))))----)))...))).......... ( -36.40)
>consensus
CGCUGUCUAU_ACAGAAUG__GUGCUAAAUCCUUAAGAGCAUGUGCUUGCUCU_UGAAGAUAAGGUUGAGAUUG_AUAUAUCAAGCUCUUCCUUAUC____GGAAGAGCUUUUUUAUAUU
....................................(((((......)))))..............................(((((((((((.......)))))))))))......... (-10.77 = -12.67 +   1.90)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,014,275 – 4,014,389
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 61.02
Mean single sequence MFE -34.53
Consensus MFE -12.54
Energy contribution -13.67
Covariance contribution 1.12
Combinations/Pair 1.26
Mean z-score -4.76
Structure conservation index 0.36
SVM decision value 2.54
SVM RNA-class probability 0.995082
Prediction RNA

Download alignment: ClustalW | MAF

>Blich.0 4014275 114 + 4222334/14-134
GACAUAAAAAAGCUCUUCCC---GAUAAGGAAGAGCUUGAUAUAUUCAAUCUCCUCCUUAUCUUCA-AGAGCACGAACAUGCUCUUAAGGAUUUAGCAC--CAUUCUGUCAUAGACAGCG
...........(((..(((.---((((((((.(((.((((.....)))).))).))))))))...(-((((((......)))))))..)))...)))..--....(((((...))))).. ( -36.50)
>Bsubt.0 3998216 112 + 4214630/14-134
AAUAUAAAAAAGCUCUUCCUUUGGAUAAGGAAGAGCUUGCGUGA--CAAUCUCAACCUUAUCUUCA-AGAGCAAUCAU-UGCUCUAAAGGAUUUAGCAC--CAUUCUGU--UAAACAGCG
.........((((((((((((.....))))))))))))((.(((--((........((.(((((..-((((((.....-))))))..)))))..))...--.....)))--))....)). ( -34.59)
>Banth.0 1375383 115 + 5227293/14-134
AUAACAAAAGACCUCUUCC----AACGAGAAGAGGUCUUAUACAUCUAUAAGAAACGCUCUUCUCAUCUUUCAAGCACAUGCU-UGCUGGAUUUGGCACAGCACUCUAAAAUCGAGUCCG
.........(.((...(((----(..((((((((.(((((((....)))))))....))))))))......(((((....)))-)).))))...)))...(.((((.......)))).). ( -32.50)
>consensus
AAAAUAAAAAAGCUCUUCC____GAUAAGGAAGAGCUUGAUACAU_CAAUCUCAACCUUAUCUUCA_AGAGCAAGCACAUGCUCUAAAGGAUUUAGCAC__CAUUCUGU_AUAGACAGCG
....((((.((((((((((.........))))))))))......................(((....((((((......))))))...)))))))......................... (-12.54 = -13.67 +   1.12)

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 17:26:17 2006