Locus 2005

Sequence ID 3R_DroMel_CAF1
Location 5,695,440 – 5,695,632
Length 192
Max. P 0.698039
window3284 window3285

overview

Window 4

Location 5,695,440 – 5,695,553
Length 113
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.23
Mean single sequence MFE -31.30
Consensus MFE -19.15
Energy contribution -18.60
Covariance contribution -0.55
Combinations/Pair 1.19
Mean z-score -1.30
Structure conservation index 0.61
SVM decision value 0.27
SVM RNA-class probability 0.662840
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5695440 113 + 27905053
AUUCCGCCAGCAAAAAAAAAAAAAAAACUCGA-AAGUAGGUCAGUAAGUGACG----UGGCUGGUUGACCCAUUUGCGAC--CUGAAGUUUGCCUAGUUGCAAAGUUGCCAAGGUUGGUU
..((.((((((................(((..-..).))((((.....)))).----..)))))).))........((((--((.((.(((((......))))).))....))))))... ( -29.30)
>DroPse_CAF1 12097 98 + 1
UUUUCCA--------------------UGCCA-AAGUAGGUCAGCAAGUGACGUUCGUCGCCGGUUGACCCAUUUGUUGCCCCCAAAAGCUGCAGAGUUGCAAAGUUGGCAAGGCUGCC-
....((.--------------------(((((-(.((((((((((..(((((....)))))..)))))))..(((((.((........)).)))))..)))....)))))).)).....- ( -34.60)
>DroPer_CAF1 14502 99 + 1
UUUUCCA--------------------UGCCAAAAGUAGGUCAGCAAGUGACGUUCGUCGCCGGUUGACCCAUUUGUUGCCCCCAAAAGCUGCAGAGUUGCAAAGUUGCCAAGGCUGCC-
.......--------------------.((...((((.(((((((..(((((....)))))..))))))).))))...))...........((((..(((((....)).)))..)))).- ( -30.00)
>consensus
UUUUCCA____________________UGCCA_AAGUAGGUCAGCAAGUGACGUUCGUCGCCGGUUGACCCAUUUGUUGCCCCCAAAAGCUGCAGAGUUGCAAAGUUGCCAAGGCUGCC_
............................((...((((.(((((((..(((((....)))))..))))))).))))...(((..(((....(((......)))...)))....))).)).. (-19.15 = -18.60 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,695,515 – 5,695,632
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 68.05
Mean single sequence MFE -25.37
Consensus MFE -12.50
Energy contribution -15.06
Covariance contribution 2.56
Combinations/Pair 1.08
Mean z-score -1.86
Structure conservation index 0.49
SVM decision value 0.34
SVM RNA-class probability 0.698039
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5695515 117 - 27905053
CAUAAACAAGAGGCAAUCAAAGGGAACUACCCCCCGGCUGCAAAAUC-CCAGACCCAAUAUUCAGGCCAAAGACGCCACCAACCAACCUUGGCAACUUUGCAACUAGGCAAACUUCAG--
.........((((........(((.....)))((..(.((((((...-................(((.......))).((((......))))....)))))).)..))....))))..-- ( -21.60)
>DroPse_CAF1 12156 98 - 1
-----------AACAAUCAA-----ACAACCCCCCGAUUGAAGACUUUCUUUACCCCGAAAUCGGGCCAA----GCCUC--GGCAGCCUUGCCAACUUUGCAACUCUGCAGCUUUUGGGG
-----------.........-----......((((((.(((((.....))))).((((....))))..((----((...--.((((..((((.......))))..)))).)))))))))) ( -27.80)
>DroPer_CAF1 14562 98 - 1
-----------AACAAUCAA-----ACAACCCCCCGAUUGAAGACUUUCUUUACCCCGAAAUCGGGCCAA----GCCUC--GGCAGCCUUGGCAACUUUGCAACUCUGCAGCUUUUGGGG
-----------..(((((..-----..........))))).............((((((((.(..(((((----(.((.--...)).)))))).....((((....))))).)))))))) ( -26.70)
>consensus
___________AACAAUCAA_____ACAACCCCCCGAUUGAAGACUUUCUUUACCCCGAAAUCGGGCCAA____GCCUC__GGCAGCCUUGGCAACUUUGCAACUCUGCAGCUUUUGGGG
.............(((((.................))))).............(((((((.....(((((....(((....)))....)))))....((((......))))..))))))) (-12.50 = -15.06 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:59 2006