Locus 720

Sequence ID 2R_DroMel_CAF1
Location 3,533,672 – 3,533,815
Length 143
Max. P 0.917705
window1268 window1269 window1270 window1271

overview

Window 8

Location 3,533,672 – 3,533,781
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 88.17
Mean single sequence MFE -38.91
Consensus MFE -29.20
Energy contribution -31.20
Covariance contribution 2.00
Combinations/Pair 1.03
Mean z-score -2.14
Structure conservation index 0.75
SVM decision value 0.84
SVM RNA-class probability 0.863220
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3533672 109 + 20766785
AUUCCAAGGGGGCAGGCGCACGCCCUUCGGAAGGCAAUGUAAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUUGCCUCCCUCCUAUCCAGAGCCCAG
.((((((((((((....)).).))))).))))(((..(((....)))..((((((((......(((((((((.....)))))))))........)))))))).)))... ( -39.04)
>DroSec_CAF1 5000 108 + 1
AUUCCA-GGGGGCAGGCUCACGCCCUUCGGAUGGCAAUGUAAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUCGCCUCCCUCCCAUCCAGAGCCCAG
......-((((((.(((....)))....((((((((((.(((((...(((.....)))..)))))..((....))))))))))))))))))(((.......)))..... ( -40.30)
>DroSim_CAF1 1394 108 + 1
AUUCCG-GGGGACAGGCUCACGCCCUUCGGAUGGCAAUGUAAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUCGCCUCCCUCCCAUCCAGAGCCCAG
.....(-(((((..(((....)))...(((((((((((.(((((...(((.....)))..)))))..((....)))))))))))))..))))))............... ( -38.10)
>DroEre_CAF1 1363 97 + 1
GUUCCA-G-GGGCAGGCCCUCGCCCCUCGGAGGGCAAUGUAAUGGCAGCCAGGAUGGCCACAUUAAAUGGCAACAAU------UUGCCUCCCUCCCGCCCAG----CAG
..((((-(-((((........)))))).)))((((....(((((...(((.....)))..)))))...(((((....------)))))........))))..----... ( -38.20)
>consensus
AUUCCA_GGGGGCAGGCUCACGCCCUUCGGAUGGCAAUGUAAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUCGCCUCCCUCCCAUCCAGAGCCCAG
.......((((((.(((....)))....((((((((((.(((((...(((.....)))..)))))..((....)))))))))))))))))).................. (-29.20 = -31.20 +   2.00) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,533,672 – 3,533,781
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 88.17
Mean single sequence MFE -45.67
Consensus MFE -33.91
Energy contribution -36.35
Covariance contribution 2.44
Combinations/Pair 1.09
Mean z-score -2.47
Structure conservation index 0.74
SVM decision value 1.12
SVM RNA-class probability 0.917705
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3533672 109 - 20766785
CUGGGCUCUGGAUAGGAGGGAGGCAAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUUACAUUGCCUUCCGAAGGGCGUGCGCCUGCCCCCUUGGAAU
..((((...........(((((((((((((((.....)))))).(((((..(((.....)))..).))))..)))))))))...((((....))))))))......... ( -44.30)
>DroSec_CAF1 5000 108 - 1
CUGGGCUCUGGAUGGGAGGGAGGCGAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUUACAUUGCCAUCCGAAGGGCGUGAGCCUGCCCCC-UGGAAU
..((((..(((((((.((.(((((((((((((.....)))))))).....((((.....))))))).))...)).)))))))..((((....))))))))..-...... ( -47.90)
>DroSim_CAF1 1394 108 - 1
CUGGGCUCUGGAUGGGAGGGAGGCGAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUUACAUUGCCAUCCGAAGGGCGUGAGCCUGUCCCC-CGGAAU
(((((....((((((.((.(((((((((((((.....)))))))).....((((.....))))))).))...)).))))))((.((((....)))).)).))-)))... ( -49.00)
>DroEre_CAF1 1363 97 - 1
CUG----CUGGGCGGGAGGGAGGCAA------AUUGUUGCCAUUUAAUGUGGCCAUCCUGGCUGCCAUUACAUUGCCCUCCGAGGGGCGAGGGCCUGCCC-C-UGGAAC
...----..((((.((((((.(((((------....)))))...(((((..(((.....)))..).)))).....))))))...((((....))))))))-.-...... ( -41.50)
>consensus
CUGGGCUCUGGAUGGGAGGGAGGCAAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUUACAUUGCCAUCCGAAGGGCGUGAGCCUGCCCCC_UGGAAU
..((((..(((((((.((.(((((((((((((.....)))))))).....((((.....))))))).))...)).)))))))..((((....))))))))......... (-33.91 = -36.35 +   2.44) 

alignment

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secondary structure

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dotplot

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Window 0

Location 3,533,712 – 3,533,815
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 92.07
Mean single sequence MFE -31.20
Consensus MFE -25.44
Energy contribution -27.57
Covariance contribution 2.12
Combinations/Pair 1.07
Mean z-score -2.19
Structure conservation index 0.82
SVM decision value 0.96
SVM RNA-class probability 0.890187
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3533712 103 + 20766785
AAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUUGCCUCCCUCCUAUCCAGAGCCCAGAUCCCUGCCUGCCUUCGGAUCCUGCCCAACGGGU
...((((((((((((((......(((((((((.....)))))))))........)))))))).))...(((((............))))).))))........ ( -32.74)
>DroSec_CAF1 5039 103 + 1
AAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUCGCCUCCCUCCCAUCCAGAGCCCAGAUCCCUGCCUGCCUUCGGAUCCUGCCCAACGGGU
...((((((((((((((........(((((((.....)))))))..........)))))))).))...(((((............))))).))))........ ( -32.87)
>DroSim_CAF1 1433 103 + 1
AAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUCGCCUCCCUCCCAUCCAGAGCCCAGAUCCCUGCCUGCCUUCGGAUCCUGCCCAACGGGU
...((((((((((((((........(((((((.....)))))))..........)))))))).))...(((((............))))).))))........ ( -32.87)
>DroEre_CAF1 1401 93 + 1
AAUGGCAGCCAGGAUGGCCACAUUAAAUGGCAACAAU------UUGCCUCCCUCCCGCCCAG----CAGAUCCCUGCCUGCCUUCAGAUCCUGCCCAACGGGU
...(((((.((((...((((.......))))....((------((((..............)----))))).)))).)))))..........((((...)))) ( -26.34)
>consensus
AAUGGCAGCCUGGAUGGCCACAUUAAAUGGCAACAAUUGCCAUUCGCCUCCCUCCCAUCCAGAGCCCAGAUCCCUGCCUGCCUUCGGAUCCUGCCCAACGGGU
...(((((.((((((((......(((((((((.....)))))))))........))))))))....(((....))).)))))..........((((...)))) (-25.44 = -27.57 +   2.12) 

alignment

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secondary structure

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dotplot

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Window 1

Location 3,533,712 – 3,533,815
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 92.07
Mean single sequence MFE -39.40
Consensus MFE -32.21
Energy contribution -33.15
Covariance contribution 0.94
Combinations/Pair 1.13
Mean z-score -1.81
Structure conservation index 0.82
SVM decision value 0.49
SVM RNA-class probability 0.754901
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3533712 103 - 20766785
ACCCGUUGGGCAGGAUCCGAAGGCAGGCAGGGAUCUGGGCUCUGGAUAGGAGGGAGGCAAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUU
........(((.((((((............)))))).(((.((((((.((..(.(...((((((((.....))))))))..).)..))))))))))))))... ( -36.60)
>DroSec_CAF1 5039 103 - 1
ACCCGUUGGGCAGGAUCCGAAGGCAGGCAGGGAUCUGGGCUCUGGAUGGGAGGGAGGCGAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUU
.((((((((((.((((((............))))))..))))..)))))).....(((((((((((.....)))))))).....((((.....)))))))... ( -41.20)
>DroSim_CAF1 1433 103 - 1
ACCCGUUGGGCAGGAUCCGAAGGCAGGCAGGGAUCUGGGCUCUGGAUGGGAGGGAGGCGAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUU
.((((((((((.((((((............))))))..))))..)))))).....(((((((((((.....)))))))).....((((.....)))))))... ( -41.20)
>DroEre_CAF1 1401 93 - 1
ACCCGUUGGGCAGGAUCUGAAGGCAGGCAGGGAUCUG----CUGGGCGGGAGGGAGGCAA------AUUGUUGCCAUUUAAUGUGGCCAUCCUGGCUGCCAUU
.((((((.((((((.((((........))))..))))----)).)))))).((.((.((.------..((..(((((.....)))))))...)).)).))... ( -38.60)
>consensus
ACCCGUUGGGCAGGAUCCGAAGGCAGGCAGGGAUCUGGGCUCUGGAUGGGAGGGAGGCAAAUGGCAAUUGUUGCCAUUUAAUGUGGCCAUCCAGGCUGCCAUU
.((((((.((..((((((....(....)..)))))).....)).)))))).....(((((((((((.....)))))))).....((((.....)))))))... (-32.21 = -33.15 +   0.94) 

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 09:45:36 2006