Locus 720

Sequence ID 3L_DroMel_CAF1
Location 2,193,274 – 2,193,366
Length 92
Max. P 0.988236
window1104 window1105

overview

Window 4

Location 2,193,274 – 2,193,366
Length 92
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 81.14
Mean single sequence MFE -29.00
Consensus MFE -18.75
Energy contribution -19.35
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.65
SVM decision value 1.73
SVM RNA-class probability 0.974271
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2193274 92 + 23771897
UUCAGCUACGAUGCUGUCUGGCAGUUUAUGAAAACUGCAGCGGCUGUUUGUUUGGAUUUUCCUCUCUCUCUCUCUCUCUCGCACGAGGGAAA-------
(((((..((((.(((((...(((((((....))))))).)))))...)))))))))..................((((((....))))))..------- ( -25.60)
>DroSec_CAF1 245221 77 + 1
UUCAGCUGCUGUGCUGUCUGGCAGUUUAUGAAAACUGCAGCGGAAAA-U----GGAUUUUCCUCUCGCUCUCU----------CGAGGGAAA-------
((((.((((((((((....)))(((((....))))))))))))....-)----))).(((((.((((......----------)))))))))------- ( -25.10)
>DroSim_CAF1 245718 81 + 1
UUCAGCUGCUGUGCUGUCUGGCAGUUUAUGAAAACUGCAGCGGCAAA-UGUUUGGAUUUUCCUCUCGCUCUCU----------CGAGGGAAA-------
(((((..((..((((((...(((((((....))))))).))))))..-.))))))).(((((.((((......----------)))))))))------- ( -27.50)
>DroEre_CAF1 250494 77 + 1
UUCAGCUGCUGCGCUGUCUGCCAGUUUAUGAAAACUGCAGCGGCAAA-UGUUUGGCUCUUCC--UCGCU--CU----------CGAGGGAAC-------
....((((((((((.....)).(((((....)))))))))))))...-..........((((--(((..--..----------)))))))..------- ( -27.60)
>DroYak_CAF1 244149 86 + 1
UUCAGCUGCUGUGCUGGCUGGCAGUUUAUGAAAACUGCAGCGGCAAA-UGUUUGGCUUUUCCUCUCGCU--CU----------CGAGGGAAAGCCAGGG
....(((((((((((....)))(((((....)))))))))))))...-..((((((((((((((.....--..----------.)))))))))))))). ( -39.20)
>consensus
UUCAGCUGCUGUGCUGUCUGGCAGUUUAUGAAAACUGCAGCGGCAAA_UGUUUGGAUUUUCCUCUCGCUCUCU__________CGAGGGAAA_______
............((((.(((.((((((....)))))))))))))..............((((.((((................))))))))........ (-18.75 = -19.35 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,193,274 – 2,193,366
Length 92
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 81.14
Mean single sequence MFE -26.46
Consensus MFE -18.67
Energy contribution -19.07
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 0.71
SVM decision value 2.11
SVM RNA-class probability 0.988236
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2193274 92 - 23771897
-------UUUCCCUCGUGCGAGAGAGAGAGAGAGAGAGGAAAAUCCAAACAAACAGCCGCUGCAGUUUUCAUAAACUGCCAGACAGCAUCGUAGCUGAA
-------((((.(((...(....)...))).))))..((.....)).......((((..(.(((((((....)))))))..((.....)))..)))).. ( -23.70)
>DroSec_CAF1 245221 77 - 1
-------UUUCCCUCG----------AGAGAGCGAGAGGAAAAUCC----A-UUUUCCGCUGCAGUUUUCAUAAACUGCCAGACAGCACAGCAGCUGAA
-------((((.(((.----------...))).))))((((((...----.-)))))).(((((((((....)))))).))).((((......)))).. ( -26.00)
>DroSim_CAF1 245718 81 - 1
-------UUUCCCUCG----------AGAGAGCGAGAGGAAAAUCCAAACA-UUUGCCGCUGCAGUUUUCAUAAACUGCCAGACAGCACAGCAGCUGAA
-------(((((((((----------......)))).))))).........-.......(((((((((....)))))).))).((((......)))).. ( -23.90)
>DroEre_CAF1 250494 77 - 1
-------GUUCCCUCG----------AG--AGCGA--GGAAGAGCCAAACA-UUUGCCGCUGCAGUUUUCAUAAACUGGCAGACAGCGCAGCAGCUGAA
-------(((((((((----------..--..)))--))..))))......-...((.((((((((((....))))).((.....))))))).)).... ( -24.80)
>DroYak_CAF1 244149 86 - 1
CCCUGGCUUUCCCUCG----------AG--AGCGAGAGGAAAAGCCAAACA-UUUGCCGCUGCAGUUUUCAUAAACUGCCAGCCAGCACAGCAGCUGAA
...(((((((((((((----------..--..)))).)).)))))))....-......((((((((((....)))))).))))((((......)))).. ( -33.90)
>consensus
_______UUUCCCUCG__________AGAGAGCGAGAGGAAAAUCCAAACA_UUUGCCGCUGCAGUUUUCAUAAACUGCCAGACAGCACAGCAGCUGAA
.......((((((((..................))).))))).................(((((((((....)))))).))).((((......)))).. (-18.67 = -19.07 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:25 2006