Locus 6105

Sequence ID 3R_DroMel_CAF1
Location 16,006,282 – 16,006,417
Length 135
Max. P 0.852076
window9953 window9954

overview

Window 3

Location 16,006,282 – 16,006,402
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.93
Mean single sequence MFE -27.95
Consensus MFE -18.24
Energy contribution -18.30
Covariance contribution 0.06
Combinations/Pair 1.21
Mean z-score -1.65
Structure conservation index 0.65
SVM decision value 0.08
SVM RNA-class probability 0.571659
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16006282 120 + 27905053
CACUGUUUACACUUCAGCGUUUUCGAGUCAGUUCUGGCUUUCUGUACCCUUGCAAAUGGUAUACUGCCUUCUGGCAGAAGCUUGUAAGCAAGGAAAGAAAACAUAUCCGAGCAUAUAAAG
..(((.........))).((((((((((((....)))))).......((((((....(((...(((((....)))))..))).....))))))...)))))).................. ( -31.00)
>DroSec_CAF1 22642 112 + 1
CACUGUUUACACUUU------U--CCGUCAAUUCUGGCUUUCUAUACCCUUGCAAAUGGUAUACUGCCUUCAGGCAGGAGUUUGUAAGCCAGAAAGGAAGACAUAUCCGAGCAUAUCAAG
...(((((....(((------(--((.....(((((((((.(((((((.........))))))(((((....)))))......).))))))))).)))))).......)))))....... ( -31.30)
>DroSim_CAF1 6284 110 + 1
CACUGUUUACACUUU------U--CCGUCAAUUCUGGCUUUCUAUACCCUUGCAAAUGGUAUACUGCUUUCAGACAGAAGUUUGUAAGCCAGGAAAGAAGACAUAUCCGAUCAUA--AAG
..(((((((((..((------(--(.(((......(((....((((((.........))))))..)))....))).))))..)))))).))).......................--... ( -21.10)
>DroYak_CAF1 7111 119 + 1
CUCUGUUGACAUUUCUGUUUUUUUCCGUCAUUUCUGGCUUUCUGUAC-CUUGCAGAUGGCAUUCUGACUUUUAUCAGAAGUUUGCAACGCAGAAAAGAAGACAUUUCUGAUCAAAUUAAC
.....((((((....(((((((((..((((....)))).((((((..-.((((((((....((((((......)))))))))))))).)))))))))))))))....)).))))...... ( -28.40)
>consensus
CACUGUUUACACUUC______U__CCGUCAAUUCUGGCUUUCUAUACCCUUGCAAAUGGUAUACUGCCUUCAGGCAGAAGUUUGUAAGCCAGAAAAGAAGACAUAUCCGAGCAUAU_AAG
...(((((.(................((((....))))(((((.....(((((((((......(((((....)))))..)))))))))..))))).).)))))................. (-18.24 = -18.30 +   0.06)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 16,006,322 – 16,006,417
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 65.38
Mean single sequence MFE -20.85
Consensus MFE -11.89
Energy contribution -11.95
Covariance contribution 0.06
Combinations/Pair 1.29
Mean z-score -1.42
Structure conservation index 0.57
SVM decision value 0.79
SVM RNA-class probability 0.852076
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16006322 95 + 27905053
UCUGUACCCUUGCAAAUGGUAUACUGCCUUCUGGCAGAAGCUUGUAAGCAAGGAAAGAAAACAUAUCCGAGCAUAUAAAGUAUAUAUAUCGUUAA-------------------------
..((((....))))((((((((((((((....)))))..(((((((.((..(((...........)))..)).))).))))...)))))))))..------------------------- ( -23.30)
>DroSec_CAF1 22674 98 + 1
UCUAUACCCUUGCAAAUGGUAUACUGCCUUCAGGCAGGAGUUUGUAAGCCAGAAAGGAAGACAUAUCCGAGCAUAUCAAGUAUA--UAUCGGUAAAUAAG--------------------
....(((((((((((((......(((((....)))))..)))))))))...(...(((.......)))...)............--....))))......-------------------- ( -22.80)
>DroSim_CAF1 6316 80 + 1
UCUAUACCCUUGCAAAUGGUAUACUGCUUUCAGACAGAAGUUUGUAAGCCAGGAAAGAAGACAUAUCCGAUCAUA--AAGUA--------------------------------------
..((((((.........))))))((((((.(((((....))))).))).))).......................--.....-------------------------------------- ( -13.30)
>DroYak_CAF1 7151 115 + 1
UCUGUAC-CUUGCAGAUGGCAUUCUGACUUUUAUCAGAAGUUUGCAACGCAGAAAAGAAGACAUUUCUGAUCAAAUUAACCAUC----UUAGUAAGUAACGUUUCCAAAAUUUGUUUUUU
...((..-(((((((((((...(((((......)))))((((((.....((((((........))))))..))))))..)))))----)..)))))..)).................... ( -24.00)
>consensus
UCUAUACCCUUGCAAAUGGUAUACUGCCUUCAGGCAGAAGUUUGUAAGCCAGAAAAGAAGACAUAUCCGAGCAUAU_AAGUAUA____UCGGUAA_________________________
(((.....(((((((((......(((((....)))))..))))))))).......))).............................................................. (-11.89 = -11.95 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:47 2006