Locus 9456

Sequence ID 3R_DroMel_CAF1
Location 25,039,465 – 25,039,565
Length 100
Max. P 0.922768
window15141 window15142

overview

Window 1

Location 25,039,465 – 25,039,565
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 87.33
Mean single sequence MFE -22.84
Consensus MFE -18.37
Energy contribution -18.50
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -2.14
Structure conservation index 0.80
SVM decision value 1.15
SVM RNA-class probability 0.922768
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25039465 100 + 27905053
GUAUGUUUGUAUAUAAUGGACAAGAAGAAGAAUAAGCAGAAGAAGGGCGAGCAACAGCUGCGCAAGCGCUUUAUGAAGAAUGAGGGUAGCGCAAGGAAAG
...((((..(.....)..)))).............((.........((((((....))).)))..((.((((((.....))))))...))))........ ( -19.40)
>DroSec_CAF1 60225 100 + 1
GUAUGUUUGUAUAUAAUGGGCAAGAAGAAGAACAAGCAGAAGAAGGGCGAGCAACAGCUGCGCAAGCGCUUUAUGAAUAGGGAGGGAAGCGCAUGGAAAG
...(((((((.....................)))))))........((((((....))).)))..(((((((.............)))))))........ ( -20.92)
>DroSim_CAF1 54607 100 + 1
GUAUGUUUGUAUAUAAUGGGCAAGAAGAAGAACAAGCAGAAGAAGGGCGAGCAACAGCUGCGCAAGCGCUUUAAGAAUAGGGAGGGAAGCGAAUGGAAAG
...(((((((.....................)))))))........((((((....))).)))...((((((.............))))))......... ( -16.92)
>DroEre_CAF1 62671 92 + 1
-UAUGUCUGUAUAUAAUGGGCAAGAAGA------AGCAGCUGAAGGGCGAGCAACAGCUGCGCAAGCGCUUUGCAAAGAGGGUGCGAAGCGCAGGG-AAG
-..(((((((.....)))))))......------.(((((((..(......)..)))))))....((((((((((.......))))))))))....-... ( -34.10)
>consensus
GUAUGUUUGUAUAUAAUGGGCAAGAAGAAGAACAAGCAGAAGAAGGGCGAGCAACAGCUGCGCAAGCGCUUUAUGAAGAGGGAGGGAAGCGCAUGGAAAG
...((((..(.....)..))))........................((((((....))).)))..(((((((.............)))))))........ (-18.37 = -18.50 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 25,039,465 – 25,039,565
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 87.33
Mean single sequence MFE -15.26
Consensus MFE -11.71
Energy contribution -12.21
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.77
SVM decision value 0.71
SVM RNA-class probability 0.829419
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25039465 100 - 27905053
CUUUCCUUGCGCUACCCUCAUUCUUCAUAAAGCGCUUGCGCAGCUGUUGCUCGCCCUUCUUCUGCUUAUUCUUCUUCUUGUCCAUUAUAUACAAACAUAC
........(((((.................)))))..(((.(((....)))))).............................................. ( -13.03)
>DroSec_CAF1 60225 100 - 1
CUUUCCAUGCGCUUCCCUCCCUAUUCAUAAAGCGCUUGCGCAGCUGUUGCUCGCCCUUCUUCUGCUUGUUCUUCUUCUUGCCCAUUAUAUACAAACAUAC
........((((((...............))))))..(((.(((....)))))).........((..(........)..))................... ( -14.26)
>DroSim_CAF1 54607 100 - 1
CUUUCCAUUCGCUUCCCUCCCUAUUCUUAAAGCGCUUGCGCAGCUGUUGCUCGCCCUUCUUCUGCUUGUUCUUCUUCUUGCCCAUUAUAUACAAACAUAC
.........(((((...............)))))...(((.(((....)))))).........((..(........)..))................... ( -10.16)
>DroEre_CAF1 62671 92 - 1
CUU-CCCUGCGCUUCGCACCCUCUUUGCAAAGCGCUUGCGCAGCUGUUGCUCGCCCUUCAGCUGCU------UCUUCUUGCCCAUUAUAUACAGACAUA-
...-....((((((.(((.......))).))))))....(((((((............))))))).------...........................- ( -23.60)
>consensus
CUUUCCAUGCGCUUCCCUCCCUAUUCAUAAAGCGCUUGCGCAGCUGUUGCUCGCCCUUCUUCUGCUUGUUCUUCUUCUUGCCCAUUAUAUACAAACAUAC
........((((((...............))))))..(((.(((....)))))).............................................. (-11.71 = -12.21 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:35:02 2006