Locus 3

Sequence ID hg18.chr11
Location 93,103,792 – 93,103,915
Length 123
Max. P 0.914876
window5 window6

overview

Window 5

Location 93,103,792 – 93,103,904
Length 112
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.70
Mean single sequence MFE -30.59
Consensus MFE -21.31
Energy contribution -21.37
Covariance contribution 0.06
Combinations/Pair 1.27
Mean z-score -2.40
Structure conservation index 0.70
SVM decision value 1.10
SVM RNA-class probability 0.914876
Prediction RNA

Download alignment: ClustalW | MAF

>hg18.chr11 93103792 112 - 134452384
CCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAA-AAUUUC--CCAGUAGGUUUU-C-UAUCUGCUACUUUGCUAGCAAUCAGCUUAUUGGGAACAGUU
(((.(((....((((......)))).....))).)))...............-...(((--((((((((((..-.-....(((((......)))))...)))))))))))))..... ( -27.60)
>rn4.chr8 116925096 113 + 129041809
CCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAGAAAAAUUC--CCAUUAGGUUUU-C-CAUAUGCUACUUGAGUAGCACUUAACCUGUUGGGAACAUUU
(((.(((....((((......)))).....))).)))...................(((--(((.((((((..-.-....((((((....))))))...)))))).))))))..... ( -30.60)
>bosTau2.chr29 547350 114 - 45822729
CCAAGGCUUUUAGAACGCAGUUUCUAAUUUGCUGUGGACAUGACCGUAAAACAAAAUCC--CAACUAGGUUUUUC-UUCCUGCUACUUUGUUAGCAUACAGCCUGUUGGGAACAUUU
(((.(((..((((((......))))))...))).)))...................(((--((((.(((((....-....(((((......)))))...))))))))))))...... ( -29.90)
>dasNov1.scaffold_2894 17074 112 - 85457
CCAAGGCUUUUAGAAUGCAGUUUCUGAUUUGCUGUGGAGUUGACCAUAAAAAAAACUCU--CCACUGGGCUUU-C-U-UUUGCUACCUUGCUAGCCUUCAGCCUGUUGGGAACAUUC
.....((.........)).(((((..((..(((((((((..................))--)))).(((((..-.-.-...((......)).)))))..)))..))..))))).... ( -27.37)
>echTel1.scaffold_316886 80434 112 + 105239
CCAAGGCUUUUAGAAUGUGGUUUCUGAUUUGCUGUGGACAUGACCAUAG--ACAAUUUC--CCAGGAGGUUUU-UGUUUUUGCUACCUUGCUAGCAUAUAACCGAUUGGGGACAUUG
(((.(((..((((((......))))))...))).)))............--.(((((((--((((..((((..-((((...((......)).))))...))))..))))))).)))) ( -33.40)
>monDom4.chr4 174693365 113 + 430141050
CCAAGGCUUUUAGAAUGCAGUUUCUGAUU-GCUGUGGACAUGACCAUAAAAAAAAUUAUAUCCAACAGGUUU--A-UAUUUGCUAUCUUACUAGCAUCUAACCUGUUGGGAACAGUU
(((.(((..((((((......))))))..-))).))).......................(((((((((((.--.-....(((((......)))))...)))))))))))....... ( -34.70)
>consensus
CCAAGGCUUUUAGAAUGCAGUUUCUGAUUUGCUGUGGACAUGACCAUAAAAAAAAUUUC__CCACUAGGUUUU_C_UAUUUGCUACCUUGCUAGCAUUCAACCUGUUGGGAACAUUU
(((.(((..((((((......))))))...))).)))........................(((.((((((.........(((((......)))))...)))))).)))........ (-21.31 = -21.37 +   0.06) 

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 93,103,815 – 93,103,915
Length 100
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 82.27
Mean single sequence MFE -25.55
Consensus MFE -17.72
Energy contribution -18.97
Covariance contribution 1.25
Combinations/Pair 1.10
Mean z-score -1.77
Structure conservation index 0.69
SVM decision value 0.26
SVM RNA-class probability 0.657153
Prediction RNA

Download alignment: ClustalW | MAF

>hg18.chr11 93103815 100 - 134452384
AAUGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAA-AAUUUCCCAGUAGGUUUU----C-UAUCUGCUACUUUGCUAG
.((((((((..(((.(((....((((......)))).....))).)))..)))))))).....-........(((((((...----.-.))))))).......... ( -25.80)
>rn4.chr8 116925119 98 + 129041809
---GGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAGAAAAAUUCCCAUUAGGUUUU----C-CAUAUGCUACUUGAGUAG
---((((((..(((.(((....((((......)))).....))).)))..)))))).....(((((....((....))))))----)-......((((....)))) ( -20.60)
>canFam2.chr21 44003445 105 + 54024781
AAUGGUCAUUACCAAGGCUUUGAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAAAAUUUUCCCGUUAGGUUUUCUUCC-UUUUUGCUAGUUUGCUAG
.((((((((..(((.(((..((((((......))))))...))).)))..))))))))............((....)).........-......((((....)))) ( -28.40)
>dasNov1.scaffold_2894 17097 100 - 85457
GCUGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUGAUUUGCUGUGGAGUUGACCAUAAAAAAAACUCUCCACUGGGCUUU----C-U-UUUGCUACCUUGCUAG
((((((((...(((.(((..((((((......))))))...))).)))...))))))(((((.((((((......))).)))----.-)-)))).......))... ( -25.20)
>loxAfr1.scaffold_17974 29100 99 - 49915
AAAGGUCAUUACCAAGGCUUUUAGAAUGCAGUUU--GAUUUGCUGUGGACUUGACGGUAAUAAAAACCUCCCACUAGGUUUU----C-UCUUUGCGACCUUGCUAG
.((((((....(((.(((..(((((......)))--))...))).)))........((((..(((((((......)))))))----.-...))))))))))..... ( -24.40)
>echTel1.scaffold_316886 80457 100 + 105239
AGUGGUCAUUACCAAGGCUUUUAGAAUGUGGUUUCUGAUUUGCUGUGGACAUGACCAUAG--ACAAUUUCCCAGGAGGUUUU----UGUUUUUGCUACCUUGCUAG
.((((((((..(((.(((..((((((......))))))...))).)))..))))))))((--((((...((.....))...)----)))))..((......))... ( -28.90)
>consensus
AAUGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAAAAAUUUCCCACUAGGUUUU____C_UAUUUGCUACCUUGCUAG
.(((((((...(((.(((..((((((......))))))...))).)))...)))))))............((....))............................ (-17.72 = -18.97 +   1.25) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Nov 24 16:48:58 2006