Locus 3194

Sequence ID X_DroMel_CAF1
Location 8,466,395 – 8,466,545
Length 150
Max. P 0.804699
window5238 window5239 window5240

overview

Window 8

Location 8,466,395 – 8,466,507
Length 112
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -40.85
Consensus MFE -29.38
Energy contribution -30.75
Covariance contribution 1.38
Combinations/Pair 1.06
Mean z-score -1.98
Structure conservation index 0.72
SVM decision value 0.63
SVM RNA-class probability 0.804699
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466395 112 + 22224390
GUCCGGAUUUGCAGGUUGCUAGUUGGGCAAAGCGGCUUGAGAUGU------UGCUCUUGGCAUUGCUGAGUGUUGCAGCUGCAACUUGCAAUGGAUUUCCUUCAGUUCUUAGAGAACU
(((((...(((((((((((.(((((((((.(((.(((.(((....------..)))..)))...)))...)))).))))))))))))))))))))).......(((((.....))))) ( -41.50)
>DroSec_CAF1 9176 112 + 1
GUGCGGAUUUGCAGGUUGCUAGUUGGGCAAAGCUGCUUGAGAUGU------UGCUCUUGGCAUUGGUGAGUGUUGCAGCUGCAACUUGCAACGGAUUUCCAUCACCUUUUAGGGAACU
.....((((((((((((((.(((((((((..((((((.(((....------..)))..)))...)))...)))).)))))))))))))))).((....))))).(((....))).... ( -36.00)
>DroSim_CAF1 17981 112 + 1
GUCCGGAUUUGCAGGUUGCUAGUUGGGCAAAGCUGCUUGAGAUGU------UGCUCUUGGCAUUGGUGAGUGUUGCAGCUGCAACUUGCAACGGAUUUCCAUCACUUUUUAGGGAACU
(((((...(((((((((((.(((((((((..((((((.(((....------..)))..)))...)))...)))).)))))))))))))))))))))((((...........))))... ( -38.40)
>DroYak_CAF1 15942 118 + 1
GGCCGGAUUGGCAGGUGGCAAGUUGGGCAAAGCUGCUUGAGAUGUGCAUGUGCCUCUUGGCGUUGCCGAGUGUUGCAGCUGCAGCUUGCAACGGAUUUCGUUCGGUGUUUGGCCAACU
((((((((.((((.((((((..(..((((....))))..)..))).))).)))).((((((...))))))(((((((((....)).))))))).............)))))))).... ( -47.50)
>consensus
GUCCGGAUUUGCAGGUUGCUAGUUGGGCAAAGCUGCUUGAGAUGU______UGCUCUUGGCAUUGCUGAGUGUUGCAGCUGCAACUUGCAACGGAUUUCCAUCACUUUUUAGGGAACU
(((((....((((((((((.(((((((((.(((.(((.(((............)))..)))...)))...)))).))))))))))))))).)))))...................... (-29.38 = -30.75 +   1.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,466,395 – 8,466,507
Length 112
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 86.67
Mean single sequence MFE -29.21
Consensus MFE -18.54
Energy contribution -19.22
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.63
SVM decision value 0.14
SVM RNA-class probability 0.605155
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466395 112 - 22224390
AGUUCUCUAAGAACUGAAGGAAAUCCAUUGCAAGUUGCAGCUGCAACACUCAGCAAUGCCAAGAGCA------ACAUCUCAAGCCGCUUUGCCCAACUAGCAACCUGCAAAUCCGGAC
(((((.....)))))...((....)).(((((.(((((.((((.......))))..((...(((((.------............)))))...))....))))).)))))........ ( -26.82)
>DroSec_CAF1 9176 112 - 1
AGUUCCCUAAAAGGUGAUGGAAAUCCGUUGCAAGUUGCAGCUGCAACACUCACCAAUGCCAAGAGCA------ACAUCUCAAGCAGCUUUGCCCAACUAGCAACCUGCAAAUCCGCAC
............(((((.((....))((((((.((....))))))))..)))))..(((...(((..------....)))..((((..((((.......)))).))))......))). ( -29.30)
>DroSim_CAF1 17981 112 - 1
AGUUCCCUAAAAAGUGAUGGAAAUCCGUUGCAAGUUGCAGCUGCAACACUCACCAAUGCCAAGAGCA------ACAUCUCAAGCAGCUUUGCCCAACUAGCAACCUGCAAAUCCGGAC
.((((........(..((((....))))..)..(((((....)))))...............)))).------.........((((..((((.......)))).)))).......... ( -26.90)
>DroYak_CAF1 15942 118 - 1
AGUUGGCCAAACACCGAACGAAAUCCGUUGCAAGCUGCAGCUGCAACACUCGGCAACGCCAAGAGGCACAUGCACAUCUCAAGCAGCUUUGCCCAACUUGCCACCUGCCAAUCCGGCC
....((((..................((((((.((....))))))))....((((..(.((((.((((..(((.........)))....))))...)))).)...)))).....)))) ( -33.80)
>consensus
AGUUCCCUAAAAACUGAAGGAAAUCCGUUGCAAGUUGCAGCUGCAACACUCACCAAUGCCAAGAGCA______ACAUCUCAAGCAGCUUUGCCCAACUAGCAACCUGCAAAUCCGGAC
.............(((..((....)).(((((.(((((((((((......((....))....(((............)))..))))))...........))))).)))))...))).. (-18.54 = -19.22 +   0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,466,433 – 8,466,545
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.56
Mean single sequence MFE -27.18
Consensus MFE -12.84
Energy contribution -12.78
Covariance contribution -0.06
Combinations/Pair 1.17
Mean z-score -2.47
Structure conservation index 0.47
SVM decision value 0.62
SVM RNA-class probability 0.803237
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8466433 112 - 22224390
CAAGCAA-ACUGAU-AUUAUAACAGUAUUGUAUUGCGCAAAGUUCUCUAAGAACUGAAGGAAAUCCAUUGCAAGUUGCAGCUGCAACACUCAGCAAUGCCAAGAGCA------ACAUCUC
...((..-((((..-.......))))...((((((((((((((((.....)))))...((....)).))))..(((((....))))).....))))))).....)).------....... ( -30.30)
>DroSec_CAF1 9214 99 - 1
CAAGCAA-ACUGCU-AUUAUAACGG-------------AAAGUUCCCUAAAAGGUGAUGGAAAUCCGUUGCAAGUUGCAGCUGCAACACUCACCAAUGCCAAGAGCA------ACAUCUC
.......-..((((-........((-------------(....)))......(((((.((....))((((((.((....))))))))..))))).........))))------....... ( -23.00)
>DroSim_CAF1 18019 99 - 1
CAAGCAA-ACUGCU-AUUAUAACCG-------------AAAGUUCCCUAAAAAGUGAUGGAAAUCCGUUGCAAGUUGCAGCUGCAACACUCACCAAUGCCAAGAGCA------ACAUCUC
..(((..-...)))-..........-------------...((((........(..((((....))))..)..(((((....)))))...............)))).------....... ( -21.10)
>DroYak_CAF1 15980 107 - 1
CUAUUAAUGCUGCAUUGUAUGGCCG-------------AAAGUUGGCCAAACACCGAACGAAAUCCGUUGCAAGCUGCAGCUGCAACACUCGGCAACGCCAAGAGGCACAUGCACAUCUC
......(((.((((((((.((((((-------------(...))))))).)))((((..(.....)((((((.((....))))))))..))))....(((....)))..))))))))... ( -34.30)
>consensus
CAAGCAA_ACUGCU_AUUAUAACCG_____________AAAGUUCCCUAAAAACUGAAGGAAAUCCGUUGCAAGUUGCAGCUGCAACACUCACCAAUGCCAAGAGCA______ACAUCUC
.........................................((((........((((.((....))((((((.((....))))))))..)))).........)))).............. (-12.84 = -12.78 +  -0.06)

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 10:53:28 2006