Locus 3351

Sequence ID 3R_DroMel_CAF1
Location 9,037,733 – 9,037,823
Length 90
Max. P 0.835203
window5397 window5398

overview

Window 7

Location 9,037,733 – 9,037,823
Length 90
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 75.86
Mean single sequence MFE -31.95
Consensus MFE -24.21
Energy contribution -23.87
Covariance contribution -0.34
Combinations/Pair 1.28
Mean z-score -0.92
Structure conservation index 0.76
SVM decision value 0.36
SVM RNA-class probability 0.705347
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9037733 90 + 27905053
---UUGACCAUGGCUUU-U-GCCGGCCGGUCAAGUGCCGGGACGUGUCUGUCGGAAUC---------AGAUUUAAAGUCAGACAACUUGACGCGCCCCAAGUUG
---((((((.((((...-.-))))...)))))).....(((.(((((((((((....)---------.(((.....))).))))....)))))).)))...... ( -30.70)
>DroPse_CAF1 155116 101 + 1
GGAGUGGCCAUGGCAUC-UCCCCGACCGGUCAAGUGCCGGGACGUGUCUGUCAGAGUCGUCGGAUCGAGACUCAAAGUCAGACAACUUGACGCGCCC--AGUCG
((((..((....))..)-))).((((.(((.....)))(((.((((((.....(((((.(((...)))))))).((((......)))))))))))))--.)))) ( -38.90)
>DroSec_CAF1 151593 90 + 1
---UUGACCAUGGCUUU-U-GCCGGCCGGUCAAGUGCCGGGACGUGUCUGUCGCAAUC---------AGAUUUAAAGUCAGACAACUUGACGCGCCCCAAGUUA
---((((((.((((...-.-))))...)))))).....(((.((((((((((......---------.............))))....)))))).)))...... ( -30.11)
>DroWil_CAF1 155015 80 + 1
GGCUUGGCCAUGGCAUCAU-GUUGGCCGGUCAAGUGCCGGGACGUGUCUGUC---------------------AAAAUCAGACAACUUGACGCACCCAAUGG--
.((((((((..(((.....-....)))))))))))...(((..(((((((((---------------------.......))))....))))).))).....-- ( -27.50)
>DroAna_CAF1 162503 89 + 1
CUUUUGACCAUGGCUUU-U-GCCGGCCGGUCAAGUGCUGAGACGUGUCGGUCGGAAUC---------AGAUUUAAAGUCAGACAACUUGACGCGCCCCGA----
...((((((.((((...-.-))))...))))))((((...(((......)))......---------.........(((((.....))))))))).....---- ( -25.60)
>DroPer_CAF1 156351 101 + 1
GGAGUGGCCAUGGCAUC-UCCCCGACCGGUCAAGUGCCGGGACGUGUCUGUCAGAGUCGUCGGAUCGAGACUCAAAGUCAGACAACUUGACGCGCCC--AGUCG
((((..((....))..)-))).((((.(((.....)))(((.((((((.....(((((.(((...)))))))).((((......)))))))))))))--.)))) ( -38.90)
>consensus
GG_UUGACCAUGGCAUC_U_GCCGGCCGGUCAAGUGCCGGGACGUGUCUGUCGGAAUC_________AGAUUUAAAGUCAGACAACUUGACGCGCCCCAAGU_G
....(((((.((((......))))...))))).((((((((...((((((.(.(((((..........)))))...).)))))).))))..))))......... (-24.21 = -23.87 +  -0.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,037,733 – 9,037,823
Length 90
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.86
Mean single sequence MFE -32.52
Consensus MFE -21.67
Energy contribution -20.92
Covariance contribution -0.75
Combinations/Pair 1.19
Mean z-score -1.43
Structure conservation index 0.67
SVM decision value 0.73
SVM RNA-class probability 0.835203
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9037733 90 - 27905053
CAACUUGGGGCGCGUCAAGUUGUCUGACUUUAAAUCU---------GAUUCCGACAGACACGUCCCGGCACUUGACCGGCCGGC-A-AAAGCCAUGGUCAA---
....((((((((.(((....((((.((.((.......---------)).)).))))))).))))))))....((((((...(((-.-...))).)))))).--- ( -31.30)
>DroPse_CAF1 155116 101 - 1
CGACU--GGGCGCGUCAAGUUGUCUGACUUUGAGUCUCGAUCCGACGACUCUGACAGACACGUCCCGGCACUUGACCGGUCGGGGA-GAUGCCAUGGCCACUCC
...((--((.((.(((((((((((((.(...((((((((...))).))))).).)))))).((....))))))))))).))))(((-(..((....))..)))) ( -39.50)
>DroSec_CAF1 151593 90 - 1
UAACUUGGGGCGCGUCAAGUUGUCUGACUUUAAAUCU---------GAUUGCGACAGACACGUCCCGGCACUUGACCGGCCGGC-A-AAAGCCAUGGUCAA---
....((((((((.(((..((.(((.((.......)).---------))).))....))).))))))))....((((((...(((-.-...))).)))))).--- ( -31.10)
>DroWil_CAF1 155015 80 - 1
--CCAUUGGGUGCGUCAAGUUGUCUGAUUUU---------------------GACAGACACGUCCCGGCACUUGACCGGCCAAC-AUGAUGCCAUGGCCAAGCC
--...((((.((.(((((((((((((.....---------------------..)))))).((....))))))))))).))))(-(((....))))........ ( -25.60)
>DroAna_CAF1 162503 89 - 1
----UCGGGGCGCGUCAAGUUGUCUGACUUUAAAUCU---------GAUUCCGACCGACACGUCUCAGCACUUGACCGGCCGGC-A-AAAGCCAUGGUCAAAAG
----..((((((.(((..(..(((.((.......)).---------)))..)....))).)))))).....(((((((...(((-.-...))).)))))))... ( -28.10)
>DroPer_CAF1 156351 101 - 1
CGACU--GGGCGCGUCAAGUUGUCUGACUUUGAGUCUCGAUCCGACGACUCUGACAGACACGUCCCGGCACUUGACCGGUCGGGGA-GAUGCCAUGGCCACUCC
...((--((.((.(((((((((((((.(...((((((((...))).))))).).)))))).((....))))))))))).))))(((-(..((....))..)))) ( -39.50)
>consensus
C_ACUUGGGGCGCGUCAAGUUGUCUGACUUUAAAUCU_________GAUUCCGACAGACACGUCCCGGCACUUGACCGGCCGGC_A_AAAGCCAUGGCCAA_CC
.......((.((.(((((((((((((.(....((((..........))))..).)))))).((....))))))))))).)).........((....))...... (-21.67 = -20.92 +  -0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:03 2006