Locus 7

Sequence ID hg18.chr11
Location 93,107,925 – 93,108,000
Length 75
Max. P 0.996688
window12 window13

overview

Window 2

Location 93,107,925 – 93,108,000
Length 75
Sequences 6
Columns 76
Reading direction forward
Mean pairwise identity 86.01
Mean single sequence MFE -18.02
Consensus MFE -13.71
Energy contribution -13.74
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -2.12
Structure conservation index 0.76
SVM decision value 0.01
SVM RNA-class probability 0.538812
Prediction RNA

Download alignment: ClustalW | MAF

>hg18.chr11 93107925 75 + 134452384
AUAUCCCUUCUUAUAUGUAUCAAAACUCAUACUGAACAAUGAGUUCUGGGUUGCAAAAGAGGAUUUAU-UUUUUGC
......((((((...(((((((.(((((((........))))))).)))..)))).))))))......-....... ( -14.80)
>mm8.chr9 108937603 74 - 124000669
AUAUUCCUUCUUGUAUAUAUCAAAACUCAUACUGAGCAAUGAGUUCUGGGUUGC--AAGAGGAUUUAUAUUUUUGC
....((((.((((((....(((.(((((((........))))))).)))..)))--)))))))............. ( -20.30)
>oryCun1.scaffold_94908 1068 74 + 5219
-UGUUCCUGCUUGUAUGUAUCAAAACUCAUACUGAGCCAUGAGUUCUGGGUUGCAAAAGAGGAUUUAU-UUUUUGC
-...((((.(((...(((((((.(((((((........))))))).)))..)))).))))))).....-....... ( -15.90)
>bosTau2.chr29 551396 74 + 45822729
AUGUUCCUUCUUAUCUGUAUCAAAACUCAUACUGAACAAUGAGUUGUGGGUUGCAAAAGAGGAUUUA--CUUUCGC
....((((.(((...((((((..(((((((........)))))))...)).)))).)))))))....--....... ( -15.20)
>echTel1.scaffold_316886 84615 74 - 105239
AUGUCCCUUCUUAUCUGUAUCAAAACUCAUACUGCACAAUGAGUUUUGGGUUGCAAAAGAGGAUUUA--UUCUUGC
......((((((...(((((((((((((((........)))))))))))..)))).)))))).....--....... ( -18.30)
>monDom4.chr4 174696894 75 - 430141050
UUGUCCCUUCUUGUAUGUAUCACAACUCAUACAAAACCAUGGGUUGUGGGUUGCAAAAGAGGGUUUGU-UCUUUGC
.....(((((((...(((((((((((((((........)))))))))))..)))).))))))).....-....... ( -23.60)
>consensus
AUGUCCCUUCUUAUAUGUAUCAAAACUCAUACUGAACAAUGAGUUCUGGGUUGCAAAAGAGGAUUUAU_UUUUUGC
......((((((.......(((.(((((((........))))))).))).......)))))).............. (-13.71 = -13.74 +   0.03) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 93,107,925 – 93,108,000
Length 75
Sequences 6
Columns 76
Reading direction reverse
Mean pairwise identity 86.01
Mean single sequence MFE -16.99
Consensus MFE -16.25
Energy contribution -15.89
Covariance contribution -0.36
Combinations/Pair 1.24
Mean z-score -2.58
Structure conservation index 0.96
SVM decision value 2.73
SVM RNA-class probability 0.996688
Prediction RNA

Download alignment: ClustalW | MAF

>hg18.chr11 93107925 75 - 134452384
GCAAAAA-AUAAAUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGGAUAU
.......-....((((.(((((......((((((((((........)))))))))).........))))))))).. ( -17.66)
>mm8.chr9 108937603 74 + 124000669
GCAAAAAUAUAAAUCCUCUU--GCAACCCAGAACUCAUUGCUCAGUAUGAGUUUUGAUAUAUACAAGAAGGAAUAU
.............(((((((--(.....((((((((((........)))))))))).......)))).)))).... ( -18.40)
>oryCun1.scaffold_94908 1068 74 - 5219
GCAAAAA-AUAAAUCCUCUUUUGCAACCCAGAACUCAUGGCUCAGUAUGAGUUUUGAUACAUACAAGCAGGAACA-
.......-.....(((((((........(((((((((((......)))))))))))........))).))))...- ( -16.99)
>bosTau2.chr29 551396 74 - 45822729
GCGAAAG--UAAAUCCUCUUUUGCAACCCACAACUCAUUGUUCAGUAUGAGUUUUGAUACAGAUAAGAAGGAACAU
((....)--)...(((((((........((.(((((((........))))))).))........))).)))).... ( -15.69)
>echTel1.scaffold_316886 84615 74 + 105239
GCAAGAA--UAAAUCCUCUUUUGCAACCCAAAACUCAUUGUGCAGUAUGAGUUUUGAUACAGAUAAGAAGGGACAU
.......--....(((..((((((....((((((((((........)))))))))).....).)))))..)))... ( -16.30)
>monDom4.chr4 174696894 75 + 430141050
GCAAAGA-ACAAACCCUCUUUUGCAACCCACAACCCAUGGUUUUGUAUGAGUUGUGAUACAUACAAGAAGGGACAA
.......-.....((((.(((((.....((((((.((((......)))).)))))).......))))))))).... ( -16.90)
>consensus
GCAAAAA_AUAAAUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUACAAGAAGGAACAU
.............(((((((........((((((((((........))))))))))........))).)))).... (-16.25 = -15.89 +  -0.36) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Nov 24 16:49:09 2006