Locus 2410

Sequence ID 3R_DroMel_CAF1
Location 6,756,929 – 6,757,117
Length 188
Max. P 0.999979
window3915 window3916 window3917 window3918 window3919

overview

Window 5

Location 6,756,929 – 6,757,048
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.16
Mean single sequence MFE -33.80
Consensus MFE -32.50
Energy contribution -32.90
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.96
SVM decision value 3.90
SVM RNA-class probability 0.999696
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756929 119 + 27905053
GAAUGCAGUUUGCAACGUAUCUACCAGUUGGCAAAUAGCCUUAGACGCCCGGCC-CCCAAAAGUCUGUGCAUAAAAUAACAAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGA
...(((.....))).........((((((((((....(((.(((((....((..-.))....)))))(((((..............)))))..))).....))))))))))......... ( -33.44)
>DroSec_CAF1 21088 120 + 1
GAAUGCAGUUUGCAACGUAUCUACCAGUUGGCAAAUAGCCUUAGACGCCCGGCUCCCCAAAAGUCUGUGCAUAAAAUAACAAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGA
...(((.....))).........((((((((((....(((.(((((....((....))....)))))(((((..............)))))..))).....))))))))))......... ( -34.24)
>DroSim_CAF1 25454 120 + 1
GAAUGCAGUUUGCAACGUAUCUACCAGUUGGCAAAUAGCCUUAGACGCCCGGCCCCCCAAAAGUCUGUGCAUAAAAUAACAAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGA
...(((.....))).........((((((((((....(((.(((((....((....))....)))))(((((..............)))))..))).....))))))))))......... ( -34.24)
>DroEre_CAF1 5539 118 + 1
GAAUGCAGU-UGCAACGUAUCUUCCAGCUGGCAAAUAGCCUUAGACGCUCGGCC-CCCAAAAGUCUGUGCAUAAAAUAACAAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGA
...(((...-.)))......(((((((.(((((....(((.(((((....((..-.))....)))))(((((..............)))))..))).....))))).)))))))...... ( -33.54)
>DroYak_CAF1 17493 118 + 1
GAAUGCAGU-UGCAACGUAUCUUCCAGCUGGCAAAUAGCCUUAGACGCUCGGCC-CCCAAAAGUCUGUGCAUAAAAUAACAAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGA
...(((...-.)))......(((((((.(((((....(((.(((((....((..-.))....)))))(((((..............)))))..))).....))))).)))))))...... ( -33.54)
>consensus
GAAUGCAGUUUGCAACGUAUCUACCAGUUGGCAAAUAGCCUUAGACGCCCGGCC_CCCAAAAGUCUGUGCAUAAAAUAACAAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGA
...(((.....)))......((.((((((((((....(((.(((((....((....))....)))))(((((..............)))))..))).....)))))))))).))...... (-32.50 = -32.90 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,756,929 – 6,757,048
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.16
Mean single sequence MFE -42.42
Consensus MFE -42.04
Energy contribution -41.56
Covariance contribution -0.48
Combinations/Pair 1.05
Mean z-score -3.34
Structure conservation index 0.99
SVM decision value 5.21
SVM RNA-class probability 0.999979
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756929 119 - 27905053
UCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG-GGCCGGGCGUCUAAGGCUAUUUGCCAACUGGUAGAUACGUUGCAAACUGCAUUC
......((.((((((((((...(((((..(((((.(((....)))...))))).((((.(((((.-..))))).))))..)))))..)))))))))).))......(((.....)))... ( -39.40)
>DroSec_CAF1 21088 120 - 1
UCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGGGAGCCGGGCGUCUAAGGCUAUUUGCCAACUGGUAGAUACGUUGCAAACUGCAUUC
......((.((((((((((...(((((..(((((.(((....)))...))))).((((.(((((....))))).))))..)))))..)))))))))).))......(((.....)))... ( -42.40)
>DroSim_CAF1 25454 120 - 1
UCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGGGGGCCGGGCGUCUAAGGCUAUUUGCCAACUGGUAGAUACGUUGCAAACUGCAUUC
......((.((((((((((...(((((..(((((.(((....)))...))))).((((.(((((....))))).))))..)))))..)))))))))).))......(((.....)))... ( -40.90)
>DroEre_CAF1 5539 118 - 1
UCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG-GGCCGAGCGUCUAAGGCUAUUUGCCAGCUGGAAGAUACGUUGCA-ACUGCAUUC
......(((((((((((((...(((((..(((((.(((....)))...))))).((((.(((((.-..))))).))))..)))))..)))))))))))))......(((.-...)))... ( -44.70)
>DroYak_CAF1 17493 118 - 1
UCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG-GGCCGAGCGUCUAAGGCUAUUUGCCAGCUGGAAGAUACGUUGCA-ACUGCAUUC
......(((((((((((((...(((((..(((((.(((....)))...))))).((((.(((((.-..))))).))))..)))))..)))))))))))))......(((.-...)))... ( -44.70)
>consensus
UCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG_GGCCGGGCGUCUAAGGCUAUUUGCCAACUGGUAGAUACGUUGCAAACUGCAUUC
......((.((((((((((...(((((..(((((.(((....)))...))))).((((.(((((....))))).))))..)))))..)))))))))).))......(((.....)))... (-42.04 = -41.56 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,756,969 – 6,757,077
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.33
Mean single sequence MFE -30.76
Consensus MFE -25.48
Energy contribution -25.08
Covariance contribution -0.40
Combinations/Pair 1.08
Mean z-score -1.38
Structure conservation index 0.83
SVM decision value 0.23
SVM RNA-class probability 0.643925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6756969 108 - 27905053
GCCAAUCCUUGCUUAUACCAGC-----------CCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG-GGCCGGGCGUCUAA
(((.......(((......)))-----------..........((((((((((.((((......)))).(((((.(((....)))...))))).......)))))-))))))))...... ( -30.10)
>DroSec_CAF1 21128 112 - 1
GCCAAUCCUUGCUUAUACCAGCCG--------CCCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGGGAGCCGGGCGUCUAA
...................((.((--------(((.........(((((((...((((......)))).(((((.(((....)))...)))))..........)))))))))))).)).. ( -31.00)
>DroSim_CAF1 25494 112 - 1
GCCAAUCCUUGCUUAUACCAGCCG--------CCCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGGGGGCCGGGCGUCUAA
.................((.(((.--------(((((..(((((((((...(((....)))..))))).(((((.(((....)))...))))).))))...)))))))).))........ ( -33.70)
>DroEre_CAF1 5578 108 - 1
GCCAAUCCUUGCUUAUACCAACCC-----------CAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG-GGCCGAGCGUCUAA
........................-----------...((.((((((((((((.((((......)))).(((((.(((....)))...))))).......)))))-)))))))))..... ( -29.20)
>DroYak_CAF1 17532 119 - 1
GCCAAUCCUUGCUUAUGCCAACCCAACCCAACCCCAAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG-GGCCGAGCGUCUAA
..........((....))....................((.((((((((((((.((((......)))).(((((.(((....)))...))))).......)))))-)))))))))..... ( -29.80)
>consensus
GCCAAUCCUUGCUUAUACCAGCCC________CCCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUUGUUAUUUUAUGCACAGACUUUUGGG_GGCCGGGCGUCUAA
......................................((.((((((((((((.((((......)))).(((((.(((....)))...))))).......))))).)))))))))..... (-25.48 = -25.08 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,757,008 – 6,757,117
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.74
Mean single sequence MFE -33.30
Consensus MFE -28.07
Energy contribution -27.83
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.84
SVM decision value 1.73
SVM RNA-class probability 0.974354
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6757008 109 + 27905053
AAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGACGAUGGG-----------GCUGGUAUAAGCAAGGAUUGGCAACUGAGUGCUGGCCAAGAAAGCGGGAGUAUUGUACUUUG
..((((((((..((((((((((....)))((..(((((..(......-----------(((......)))..)..)))))..)).....))))))).(....)....))))))))..... ( -30.90)
>DroSec_CAF1 21168 112 + 1
AAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGACGAUGGGG--------CGGCUGGUAUAAGCAAGGAUUGGCAACUGAGUGCUGGCCAAGAAAGCGGGAGUAUUGUACUUUG
..((((((((..(((((((((((((((((....(((..........))--------).(((......)))..)).))))).))).....))))))).(....)....))))))))..... ( -32.20)
>DroSim_CAF1 25534 112 + 1
AAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGACGAUGGGG--------CGGCUGGUAUAAGCAAGGAUUGGCAACUGAGUGCUGGCCAAGAAAGCGGGAGUAUUGUACUUUG
..((((((((..(((((((((((((((((....(((..........))--------).(((......)))..)).))))).))).....))))))).(....)....))))))))..... ( -32.20)
>DroEre_CAF1 5617 109 + 1
AAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGACGAUG-----------GGGUUGGUAUAAGCAAGGAUUGGCAACUGAGUGCUGGCCAAGAAAGCGGGAGUAUUGUACUUUG
..((((((((..(((((...(((((((((.....(((......))-----------)))))))))).((((......(....)....))))))))).(....)....))))))))..... ( -31.00)
>DroYak_CAF1 17571 120 + 1
AAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGACGAUUGGGGUUGGGUUGGGUUGGCAUAAGCAAGGAUUGGCAACUGAGUGCUGGCCAAGAAAGCGGGAGUAUUGUACUUUG
..((((((((..(((((...(((((((((.((..((((..(.....)..)))).)).))))))))).((((......(....)....))))))))).(....)....))))))))..... ( -40.20)
>consensus
AAUAUAAUGCAAUGGCCAGAGUGCCAACUGGAAGCCAAGACGAUGGGG________CGGCUGGUAUAAGCAAGGAUUGGCAACUGAGUGCUGGCCAAGAAAGCGGGAGUAUUGUACUUUG
..((((((((..((((((((((....)))((..(((((..(.................(((......)))..)..)))))..)).....))))))).(....)....))))))))..... (-28.07 = -27.83 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,757,008 – 6,757,117
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.74
Mean single sequence MFE -26.13
Consensus MFE -23.82
Energy contribution -23.66
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.57
Structure conservation index 0.91
SVM decision value 4.17
SVM RNA-class probability 0.999822
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6757008 109 - 27905053
CAAAGUACAAUACUCCCGCUUUCUUGGCCAGCACUCAGUUGCCAAUCCUUGCUUAUACCAGC-----------CCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUU
.................((.....(((((((.....(((.((((((....(((......)))-----------.(((......)))......))))))))))))))))..))........ ( -26.00)
>DroSec_CAF1 21168 112 - 1
CAAAGUACAAUACUCCCGCUUUCUUGGCCAGCACUCAGUUGCCAAUCCUUGCUUAUACCAGCCG--------CCCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUU
.................((.....(((((((.....(((.((((((....(((......))).(--------((..........))).....))))))))))))))))..))........ ( -26.70)
>DroSim_CAF1 25534 112 - 1
CAAAGUACAAUACUCCCGCUUUCUUGGCCAGCACUCAGUUGCCAAUCCUUGCUUAUACCAGCCG--------CCCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUU
.................((.....(((((((.....(((.((((((....(((......))).(--------((..........))).....))))))))))))))))..))........ ( -26.70)
>DroEre_CAF1 5617 109 - 1
CAAAGUACAAUACUCCCGCUUUCUUGGCCAGCACUCAGUUGCCAAUCCUUGCUUAUACCAACCC-----------CAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUU
.................((.....(((((((.....(((.((((((....(((...((......-----------....))...))).....))))))))))))))))..))........ ( -24.40)
>DroYak_CAF1 17571 120 - 1
CAAAGUACAAUACUCCCGCUUUCUUGGCCAGCACUCAGUUGCCAAUCCUUGCUUAUGCCAACCCAACCCAACCCCAAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUU
.................((.....(((((((.....(((.((((((...((.....(((((..(...............)..)))))...))))))))))))))))))..))........ ( -26.86)
>consensus
CAAAGUACAAUACUCCCGCUUUCUUGGCCAGCACUCAGUUGCCAAUCCUUGCUUAUACCAGCCC________CCCCAUCGUCUUGGCUUCCAGUUGGCACUCUGGCCAUUGCAUUAUAUU
.................((.....(((((((.....(((.((((((....(((...((.....................))...))).....))))))))))))))))..))........ (-23.82 = -23.66 +  -0.16)

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 10:35:07 2006