Locus 10

Sequence ID 3R_DroMel_CAF1
Location 138,643 – 138,748
Length 105
Max. P 0.646443
window22 window23

overview

Window 2

Location 138,643 – 138,748
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 81.43
Mean single sequence MFE -31.42
Consensus MFE -20.90
Energy contribution -22.12
Covariance contribution 1.22
Combinations/Pair 1.22
Mean z-score -1.50
Structure conservation index 0.67
SVM decision value 0.08
SVM RNA-class probability 0.572223
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 138643 105 + 27905053
UCAUUAUUUUCAACUGAUCCCUAAAACUAUUUU-UUUUAGAGGGAAGGAGGUAGCUGUGAUAUAUGGGGGCCUACCCCCAGGUACCAAGCUAGCCCAGGCUGCUAA
.................(((((....(((....-...)))))))).((.(.(((((.((.(((.((((((....)))))).))).))))))).))).......... ( -30.70)
>DroSec_CAF1 1267 103 + 1
UCAUCAUUUUCAACUGAUCCCUAAUACUAUUU---UCUAGAGGGAAGGAGGUAGCUGUGAUAUAUGGGGGCCUGCCCCCAGGUACCAAGCUAGCCCAGGCUGCUAA
.................(((((....(((...---..)))))))).((.(.(((((.((.(((.((((((....)))))).))).))))))).))).......... ( -31.50)
>DroSim_CAF1 2221 103 + 1
UCAUCAUUUUCAACUGAUGCCUAAUACUAUUU---UCUAGAGGGAAGGAGGUAGCUGUGAUAUAUGGGGGCCUGCCCCCAGGUACCAAGCUAGCCCAGGCUGCUAA
..((((........))))((((.......((.---.(....)..))((.(.(((((.((.(((.((((((....)))))).))).))))))).)))))))...... ( -33.60)
>DroEre_CAF1 2152 105 + 1
UCCCUGUUUCCAACUGAUCCCUGACCCAAUUUU-UUUUAGGGGGAAGGAGGUAGCAGUAAUAUAUGGUGGCCUGCCCCCAGGUACUAAGCUAGCCCAGGCGGCUAA
...(((((.((..((..(((((((.........-..)))))))..))..)).))))).......(((((.((((....)))))))))((((.((....)))))).. ( -33.00)
>DroYak_CAF1 2411 106 + 1
UAAUUGUUUCCUACUGAUCCCUGACACAAUUUUUUUUUAGAGGGAAGGAGGUAGCCGUCAUAUAUGGGGGCCUGCCCCCUGGUACUAAGUUAGCCCAGGCUGCUAA
...((.((((((.((((...................)))))))))).))(((((((.........(((((....))))).(((.........)))..))))))).. ( -32.41)
>DroPer_CAF1 1444 97 + 1
UCAAGAUACUCAUCUAUUG--------AAUUCC-GUUCAGAGGAAAGGAGGUUGCUGUAAUCUAUGGCGGCCUGCCACCAGGCACCAAGCUAGCCCAAGCUGCCAA
(((((((....))))..))--------).((((-.......)))).(((((((((((((...))))))))))).))....((((....(((......))))))).. ( -27.30)
>consensus
UCAUUAUUUUCAACUGAUCCCUAACACAAUUUU_UUUUAGAGGGAAGGAGGUAGCUGUGAUAUAUGGGGGCCUGCCCCCAGGUACCAAGCUAGCCCAGGCUGCUAA
.............((..(((((..................))))).)).(((((((........((((((....))))))(((.........)))..))))))).. (-20.90 = -22.12 +   1.22)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 138,643 – 138,748
Length 105
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 81.43
Mean single sequence MFE -31.27
Consensus MFE -21.27
Energy contribution -22.50
Covariance contribution 1.23
Combinations/Pair 1.21
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value 0.23
SVM RNA-class probability 0.646443
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 138643 105 - 27905053
UUAGCAGCCUGGGCUAGCUUGGUACCUGGGGGUAGGCCCCCAUAUAUCACAGCUACCUCCUUCCCUCUAAAA-AAAAUAGUUUUAGGGAUCAGUUGAAAAUAAUGA
....((((.((((.((((((((((..((((((....))))))..))))).))))))).......((((((((-.......))))))))..)))))).......... ( -34.10)
>DroSec_CAF1 1267 103 - 1
UUAGCAGCCUGGGCUAGCUUGGUACCUGGGGGCAGGCCCCCAUAUAUCACAGCUACCUCCUUCCCUCUAGA---AAAUAGUAUUAGGGAUCAGUUGAAAAUGAUGA
....((((.((((.((((((((((..((((((....))))))..))))).)))))))....((((((((..---...)))....))))).)))))).......... ( -35.00)
>DroSim_CAF1 2221 103 - 1
UUAGCAGCCUGGGCUAGCUUGGUACCUGGGGGCAGGCCCCCAUAUAUCACAGCUACCUCCUUCCCUCUAGA---AAAUAGUAUUAGGCAUCAGUUGAAAAUGAUGA
......(((((((.((((((((((..((((((....))))))..))))).))))))).........(((..---...)))...)))))((((........)))).. ( -33.90)
>DroEre_CAF1 2152 105 - 1
UUAGCCGCCUGGGCUAGCUUAGUACCUGGGGGCAGGCCACCAUAUAUUACUGCUACCUCCUUCCCCCUAAAA-AAAAUUGGGUCAGGGAUCAGUUGGAAACAGGGA
.......((((..((((((........((..((((..............))))..))(((((..(((.....-......)))..)))))..))))))...)))).. ( -31.44)
>DroYak_CAF1 2411 106 - 1
UUAGCAGCCUGGGCUAACUUAGUACCAGGGGGCAGGCCCCCAUAUAUGACGGCUACCUCCUUCCCUCUAAAAAAAAAUUGUGUCAGGGAUCAGUAGGAAACAAUUA
.....(((((((((((...)))).)))(((((....))))).........)))).(((.(((((((..................)))))..)).)))......... ( -29.57)
>DroPer_CAF1 1444 97 - 1
UUGGCAGCUUGGGCUAGCUUGGUGCCUGGUGGCAGGCCGCCAUAGAUUACAGCAACCUCCUUUCCUCUGAAC-GGAAUU--------CAAUAGAUGAGUAUCUUGA
..((((((....))).)))(((((((((....)))).))))).((((..........(((.(((....))).-)))(((--------((.....)))))))))... ( -23.60)
>consensus
UUAGCAGCCUGGGCUAGCUUGGUACCUGGGGGCAGGCCCCCAUAUAUCACAGCUACCUCCUUCCCUCUAAAA_AAAAUAGUAUUAGGGAUCAGUUGAAAAUAAUGA
(((((.....(((.((((((((((..((((((....))))))..))))).))))))))...((((....................))))...)))))......... (-21.27 = -22.50 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:09 2006