Locus 2931

Sequence ID 2R_DroMel_CAF1
Location 10,159,614 – 10,159,746
Length 132
Max. P 0.999993
window4831 window4832 window4833

overview

Window 1

Location 10,159,614 – 10,159,726
Length 112
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 71.45
Mean single sequence MFE -30.88
Consensus MFE -22.71
Energy contribution -22.96
Covariance contribution 0.25
Combinations/Pair 1.25
Mean z-score -3.80
Structure conservation index 0.74
SVM decision value 5.78
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10159614 112 + 20766785
UACUACUUGAAUUAAAUUAUUCAAA-AAAACAUUUGAUCGCGGCUUAUCGAUAAGCUGAUUACUGUGCUAUCGAUAGGUCAUGAUCAGUAAGUAGCUGCACACGAUAGCAAGA--
..((((((((((......))))...-.......(((((((.((((((((((((.((..........)))))))))))))).))))))).)))))).(((........)))...-- ( -33.70)
>DroSec_CAF1 21789 113 + 1
UGCAAUUUGAAUUAAAUUAUACAAAAAAAACAUUUGAUCGUGUCUUAUCGAUAAAAUGAGUACUGCGCUAUCGAUAGGUCACGAUCAGUGAGUUUGUGCACACGAUAGUGAGA--
((((.((((.((......)).))))..((((..(((((((((.((((((((((...............)))))))))).)))))))))...)))).))))(((....)))...-- ( -32.36)
>DroSim_CAF1 15063 102 + 1
----------UAUAUAAUAUACAAA-ACAAUAUUUGAUCGUGUCUUAUCGAUAAAAUGAGUACUGCGCUAUCGAUAGGUCACGAUCAGUGAGUUUGUGCACACGAUAGUGAGA--
----------.........((((((-.......(((((((((.((((((((((...............)))))))))).)))))))))....))))))..(((....)))...-- ( -30.46)
>DroYak_CAF1 16804 99 + 1
AAGAGUUUAAAUUAAAUUAUUCAAAAGCAAUAUUUGAUCGCGGUAUAUCGAUAAGCUGAUAACUGUGCUAUCGACAUGCCACGAUCGGUGAGU----------------AAGUAU
................(((((((..........(((((((.(((((.((((((.((..........)))))))).))))).))))))))))))----------------)).... ( -27.00)
>consensus
UACAAUUUGAAUUAAAUUAUACAAA_AAAACAUUUGAUCGCGGCUUAUCGAUAAAAUGAGUACUGCGCUAUCGAUAGGUCACGAUCAGUGAGUUUGUGCACACGAUAGUAAGA__
.................................((((((((((((((((((((...............))))))))))))))))))))........................... (-22.71 = -22.96 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,159,614 – 10,159,726
Length 112
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 71.45
Mean single sequence MFE -26.31
Consensus MFE -16.88
Energy contribution -16.95
Covariance contribution 0.06
Combinations/Pair 1.12
Mean z-score -3.34
Structure conservation index 0.64
SVM decision value 5.31
SVM RNA-class probability 0.999983
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10159614 112 - 20766785
--UCUUGCUAUCGUGUGCAGCUACUUACUGAUCAUGACCUAUCGAUAGCACAGUAAUCAGCUUAUCGAUAAGCCGCGAUCAAAUGUUUU-UUUGAAUAAUUUAAUUCAAGUAGUA
--...(((........)))(((((((..(((((.((.(.((((((((((..........)).)))))))).).)).)))))........-...((((......))))))))))). ( -27.00)
>DroSec_CAF1 21789 113 - 1
--UCUCACUAUCGUGUGCACAAACUCACUGAUCGUGACCUAUCGAUAGCGCAGUACUCAUUUUAUCGAUAAGACACGAUCAAAUGUUUUUUUUGUAUAAUUUAAUUCAAAUUGCA
--...........((((((.((((....((((((((.(.(((((((((.............))))))))).).))))))))...))))....))))))................. ( -23.92)
>DroSim_CAF1 15063 102 - 1
--UCUCACUAUCGUGUGCACAAACUCACUGAUCGUGACCUAUCGAUAGCGCAGUACUCAUUUUAUCGAUAAGACACGAUCAAAUAUUGU-UUUGUAUAUUAUAUA----------
--......(((.(((((((.((((....((((((((.(.(((((((((.............))))))))).).))))))))......))-))))))))).)))..---------- ( -26.72)
>DroYak_CAF1 16804 99 - 1
AUACUU----------------ACUCACCGAUCGUGGCAUGUCGAUAGCACAGUUAUCAGCUUAUCGAUAUACCGCGAUCAAAUAUUGCUUUUGAAUAAUUUAAUUUAAACUCUU
......----------------.......((((((((.(((((((((((..........)).))))))))).))))))))..........(((((((......)))))))..... ( -27.60)
>consensus
__UCUCACUAUCGUGUGCACAAACUCACUGAUCGUGACCUAUCGAUAGCACAGUAAUCAGCUUAUCGAUAAGACACGAUCAAAUAUUGU_UUUGAAUAAUUUAAUUCAAAUUGUA
.............................(((((((.(.(((((((((.............))))))))).).)))))))................................... (-16.88 = -16.95 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,159,648 – 10,159,746
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.34
Mean single sequence MFE -30.78
Consensus MFE -21.92
Energy contribution -24.36
Covariance contribution 2.44
Combinations/Pair 1.10
Mean z-score -2.63
Structure conservation index 0.71
SVM decision value 3.27
SVM RNA-class probability 0.998893
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10159648 98 + 20766785
GAUCGCGGCUUAUCGAUAAGCUGAUUACUGUGCUAUCGAUAGGUCAUGAUCAGUAAGUAGCUGCACACGAUAGCAAGA----------------AUUC------AUCUAGAGAUGACAAU
(((((.((((((((((((.((..........)))))))))))))).)))))........(((((....).))))....----------------..((------(((....))))).... ( -31.10)
>DroSec_CAF1 21824 104 + 1
GAUCGUGUCUUAUCGAUAAAAUGAGUACUGCGCUAUCGAUAGGUCACGAUCAGUGAGUUUGUGCACACGAUAGUGAGA----------------GUCUAGAGAUAUUUAGAGAUGACAAU
(((((((.((((((((((...............)))))))))).))))))).(((.((....)).)))....((.(..----------------.((((((....))))))..).))... ( -31.86)
>DroSim_CAF1 15087 104 + 1
GAUCGUGUCUUAUCGAUAAAAUGAGUACUGCGCUAUCGAUAGGUCACGAUCAGUGAGUUUGUGCACACGAUAGUGAGA----------------GUCUAGAGAUAUUUAGAGAUGACAAU
(((((((.((((((((((...............)))))))))).))))))).(((.((....)).)))....((.(..----------------.((((((....))))))..).))... ( -31.86)
>DroEre_CAF1 21408 120 + 1
GAUCGCGGCUUAUUGAUAACUUGAUUACUUUACUAUCGAUAUGUCACGAUCAGUGAGUGGUCGCAAACGAUAACAAGUACUUAUCGCAUCACAGAUCUAGCGAUAUUUAGAGAUGACAAU
.((((((((.((((((((...(((.....))).)))))))).)))..((((.(((((((((.....((........))....))))).)))).))))..)))))................ ( -28.30)
>consensus
GAUCGCGGCUUAUCGAUAAAAUGAGUACUGCGCUAUCGAUAGGUCACGAUCAGUGAGUUGGUGCACACGAUAGCAAGA________________AUCUAGAGAUAUUUAGAGAUGACAAU
((((((((((((((((((...............)))))))))))))))))).(((.((....)).)))...........................((((((....))))))......... (-21.92 = -24.36 +   2.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:02 2006