Locus 5839

Sequence ID 2L_DroMel_CAF1
Location 16,557,565 – 16,557,657
Length 92
Max. P 0.698312
window9267 window9268

overview

Window 7

Location 16,557,565 – 16,557,657
Length 92
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 68.07
Mean single sequence MFE -6.83
Consensus MFE -5.06
Energy contribution -5.06
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.65
Structure conservation index 0.74
SVM decision value 0.35
SVM RNA-class probability 0.698312
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16557565 92 + 22407834
----------------UUUUUUUUUU-UUUUGUUUCCAUGCCCGGCUAUUUGCCAAAAACAUUU-UUUAUCUCCGUUUAGCUAUAUUUCUCUCUACACCAUAUUUUUCGC
----------------..........-............((..(((.....)))..((((....-.........)))).))............................. (  -5.32)
>DroVir_CAF1 9536 101 + 1
AUUCCCCACAGCAAAGUU--C-UUAAUUUCUGUUUUGCAACAAGGCUUUUUGCCAAAAAAUAUU-CUGAUUCCCGUAUGAUGCU---UCUU--CCCUUCAUAUAUUUAAU
..........((((((..--.-..........)))))).....(((.....)))..........-.........((((((....---....--....))))))....... ( -11.62)
>DroSec_CAF1 12109 89 + 1
--------------------UUUUUU-UUUUGUUUCCAUACCCGGCUAUUUGCCAAAAACAUUUUUUUAUCUCCGUUUAGCUAUAUUUCUCUCUACACCAUAUUUUUCGC
--------------------......-................(((.....)))........................................................ (  -5.10)
>DroEre_CAF1 11923 88 + 1
--------------------U-UUUA-UUUCGUUUCCAUGCCAGGCUAUUUGCCAAAAACAUUUUUUUAUCUUCGUUUAGCUAUAUUUGUCUCUACACCAUAUUUAUAUA
--------------------.-....-................(((.....)))....................((..(((.......).))..)).............. (  -5.40)
>DroYak_CAF1 11942 81 + 1
--------------------U-UUUA-UUUCGUUUCCAAGCCCGGCUAUUUGCCAAAAACAUUU-UUUAUCUUCGUUUAGCUAUAUUUGUCUCUACACCAUAUU------
--------------------.-....-...........(((..(((.....)))..((((....-.........)))).)))......................------ (  -6.72)
>consensus
____________________U_UUUA_UUUUGUUUCCAUGCCCGGCUAUUUGCCAAAAACAUUU_UUUAUCUCCGUUUAGCUAUAUUUCUCUCUACACCAUAUUUUUAGC
...........................................(((.....)))........................................................ ( -5.06 =  -5.06 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,557,565 – 16,557,657
Length 92
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 68.07
Mean single sequence MFE -12.23
Consensus MFE -7.24
Energy contribution -6.96
Covariance contribution -0.28
Combinations/Pair 1.47
Mean z-score -1.42
Structure conservation index 0.59
SVM decision value 0.27
SVM RNA-class probability 0.660321
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16557565 92 - 22407834
GCGAAAAAUAUGGUGUAGAGAGAAAUAUAGCUAAACGGAGAUAAA-AAAUGUUUUUGGCAAAUAGCCGGGCAUGGAAACAAAA-AAAAAAAAAA----------------
.............................(((....(((((((..-...)))))))(((.....))).))).((....))...-..........---------------- ( -11.50)
>DroVir_CAF1 9536 101 - 1
AUUAAAUAUAUGAAGGG--AAGA---AGCAUCAUACGGGAAUCAG-AAUAUUUUUUGGCAAAAAGCCUUGUUGCAAAACAGAAAUUAA-G--AACUUUGCUGUGGGGAAU
........(((((.(..--....---..).)))))......((((-((....)))))).......(((..(.(((((...........-.--...))))).)..)))... ( -13.06)
>DroSec_CAF1 12109 89 - 1
GCGAAAAAUAUGGUGUAGAGAGAAAUAUAGCUAAACGGAGAUAAAAAAAUGUUUUUGGCAAAUAGCCGGGUAUGGAAACAAAA-AAAAAA--------------------
((.........(.((((........)))).)....((((((((......)))))))))).............((....))...-......-------------------- ( -10.30)
>DroEre_CAF1 11923 88 - 1
UAUAUAAAUAUGGUGUAGAGACAAAUAUAGCUAAACGAAGAUAAAAAAAUGUUUUUGGCAAAUAGCCUGGCAUGGAAACGAAA-UAAA-A--------------------
.......((((..(((....))).)))).((((...(((((((......)))))))(((.....))))))).((....))...-....-.-------------------- ( -13.10)
>DroYak_CAF1 11942 81 - 1
------AAUAUGGUGUAGAGACAAAUAUAGCUAAACGAAGAUAAA-AAAUGUUUUUGGCAAAUAGCCGGGCUUGGAAACGAAA-UAAA-A--------------------
------.((((..(((....))).)))).(((....(((((((..-...)))))))(((.....))).)))(((....)))..-....-.-------------------- ( -13.20)
>consensus
GCGAAAAAUAUGGUGUAGAGAGAAAUAUAGCUAAACGGAGAUAAA_AAAUGUUUUUGGCAAAUAGCCGGGCAUGGAAACAAAA_UAAA_A____________________
.............................(((....(((((((......)))))))(((.....))).))).((....)).............................. ( -7.24 =  -6.96 +  -0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:18 2006