Locus 377

Sequence ID 2L_DroMel_CAF1
Location 1,181,878 – 1,182,078
Length 200
Max. P 0.736610
window594 window595 window596

overview

Window 4

Location 1,181,878 – 1,181,998
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.22
Mean single sequence MFE -44.38
Consensus MFE -25.43
Energy contribution -26.72
Covariance contribution 1.28
Combinations/Pair 1.35
Mean z-score -2.16
Structure conservation index 0.57
SVM decision value 0.29
SVM RNA-class probability 0.670327
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1181878 120 + 22407834
CAGGCUGAAGUACGGUGAGAGCGAUCCUCCUCCACCAAAUAGGAGCCGGGAGCGUUUCGAGCAAGAGAUAAAGACUUUGCAGUCGCGCCAGAAGGAUUCUUUUGGCGCCACUGCAGCCAU
..(((((((((..((((.(((.(.....)))))))).....((((((....).)))))...............)))))(((((.((((((((((....)))))))))).))))))))).. ( -50.00)
>DroSim_CAF1 15225 120 + 1
CAGGCUGAAGUACGGUGAGAGCGAUCCUCCUCCACCAAACAGGAGCCGGGAGCGUUUCGAGCAGGAGAUAAAGACUUUGCAGUCGCGCCAGAAGGAUUCUUUUGGCGCUACUCCAGCCAC
..((((...((.(((((.(((.(.....)))))))).....((((((....).)))))).)).((((.....((((....))))((((((((((....))))))))))..)))))))).. ( -48.70)
>DroEre_CAF1 16332 120 + 1
CAGGCUGAAGUACGGAGAAAGCGAUCCUCCUCCCCCAAAUAAGAGUCGGGAGCGUUUCGAGCAGGAGAUAAAGACUUUGCAGUCGCGCCAGAAGGAUUCUUCUGGGGCUACUCCAGCCAU
..((((...((.(((((...((..(((..(((..........)))..))).)).))))).)).((((.....((((....))))((.(((((((....))))))).))..)))))))).. ( -44.60)
>DroYak_CAF1 15995 120 + 1
CAGGCUGAAGUACGGAGAGAGCGAUCCGCCUCCACCGAAUAAAAGCCGGGAGCGUUUCGAGCAGGAGAUAAAGACUUUGCAGUCGCGCCAGAAGGAUUCUUCUGGCGCUACUCCAGCCAU
..(((((.((((((((........)))).((((.(((.........)))..((.......)).)))).....((((....))))((((((((((....)))))))))))))).))))).. ( -49.50)
>DroAna_CAF1 15361 111 + 1
GAGAUUGAAGUAUGGGGAGAGUGAUCCUCCGCCACCAAACCGCAGCCGAGAGCACUUCGAGCAGCAGAUGAAGACUCUCCAGUC-CUCCA--------CAUCUGCGUCCACUCCAUCCGU
(((.(((((((.(((((((.......)))).))).......((........)))))))))...(((((((..((((....))))-.....--------))))))).....)))....... ( -31.60)
>DroPer_CAF1 20075 120 + 1
GAGACUGAAGUACGGGGAGAGCGAUCCACCGCCUCCGAAUCGCAGUCGGGAGCGUUUCGAGCAGGAGAUAAAGACCUUGCAGACGCGUCAGAAGAAUAAUGCCAGCGCGGCUUCAGCUCU
(((.(((((((....((((.(((......)))))))....(((.((.((.(((((((...(((((..........))))))))))).((....))....).)).))))))))))))))). ( -41.90)
>consensus
CAGGCUGAAGUACGGAGAGAGCGAUCCUCCUCCACCAAAUAGGAGCCGGGAGCGUUUCGAGCAGGAGAUAAAGACUUUGCAGUCGCGCCAGAAGGAUUCUUCUGGCGCUACUCCAGCCAU
..(((((.(((.......(((((.(((.....................))).)))))...(((((..........)))))....((((((((((....)))))))))).))).))))).. (-25.43 = -26.72 +   1.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,181,878 – 1,181,998
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.22
Mean single sequence MFE -45.65
Consensus MFE -26.92
Energy contribution -29.12
Covariance contribution 2.20
Combinations/Pair 1.26
Mean z-score -2.21
Structure conservation index 0.59
SVM decision value 0.44
SVM RNA-class probability 0.736610
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1181878 120 - 22407834
AUGGCUGCAGUGGCGCCAAAAGAAUCCUUCUGGCGCGACUGCAAAGUCUUUAUCUCUUGCUCGAAACGCUCCCGGCUCCUAUUUGGUGGAGGAGGAUCGCUCUCACCGUACUUCAGCCUG
..(((((((((.((((((.(((....))).)))))).)))))..))))..........((.......))....((((......(((((((((.....).))).)))))......)))).. ( -42.60)
>DroSim_CAF1 15225 120 - 1
GUGGCUGGAGUAGCGCCAAAAGAAUCCUUCUGGCGCGACUGCAAAGUCUUUAUCUCCUGCUCGAAACGCUCCCGGCUCCUGUUUGGUGGAGGAGGAUCGCUCUCACCGUACUUCAGCCUG
..((((((((((((((((.(((....))).))))))((((....))))....((((((.(.(.((((((.....))....)))).).).)))))).............)))))))))).. ( -48.00)
>DroEre_CAF1 16332 120 - 1
AUGGCUGGAGUAGCCCCAGAAGAAUCCUUCUGGCGCGACUGCAAAGUCUUUAUCUCCUGCUCGAAACGCUCCCGACUCUUAUUUGGGGGAGGAGGAUCGCUUUCUCCGUACUUCAGCCUG
..((((((((((((.(((((((....))))))).))((((....))))....................(((((((.......))))))).((((((.....)))))).)))))))))).. ( -49.70)
>DroYak_CAF1 15995 120 - 1
AUGGCUGGAGUAGCGCCAGAAGAAUCCUUCUGGCGCGACUGCAAAGUCUUUAUCUCCUGCUCGAAACGCUCCCGGCUUUUAUUCGGUGGAGGCGGAUCGCUCUCUCCGUACUUCAGCCUG
..((((((((((((((((((((....))))))))))((((....)))).............(((..(((..(((.(........).)))..)))..))).........)))))))))).. ( -54.00)
>DroAna_CAF1 15361 111 - 1
ACGGAUGGAGUGGACGCAGAUG--------UGGAG-GACUGGAGAGUCUUCAUCUGCUGCUCGAAGUGCUCUCGGCUGCGGUUUGGUGGCGGAGGAUCACUCUCCCCAUACUUCAAUCUC
..((((((((((..(((....)--------))..(-(...(((((((..((.(((((..(.((((.(((........))).)))))..))))).))..))))))))).)))))).)))). ( -44.30)
>DroPer_CAF1 20075 120 - 1
AGAGCUGAAGCCGCGCUGGCAUUAUUCUUCUGACGCGUCUGCAAGGUCUUUAUCUCCUGCUCGAAACGCUCCCGACUGCGAUUCGGAGGCGGUGGAUCGCUCUCCCCGUACUUCAGUCUC
.(((((((((.((((..((..........))..))))...(((.((.........)))))(((((.(((........))).)))))..((((.(((......))))))).)))))).))) ( -35.30)
>consensus
AUGGCUGGAGUAGCGCCAGAAGAAUCCUUCUGGCGCGACUGCAAAGUCUUUAUCUCCUGCUCGAAACGCUCCCGGCUCCUAUUUGGUGGAGGAGGAUCGCUCUCACCGUACUUCAGCCUG
..((((((((((((((((.(((....))).))))))((..((...((((((..((((.((.......))..((((.......)))).)))))))))).))..))....)))))))))).. (-26.92 = -29.12 +   2.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,181,958 – 1,182,078
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -47.85
Consensus MFE -37.44
Energy contribution -38.37
Covariance contribution 0.92
Combinations/Pair 1.36
Mean z-score -1.82
Structure conservation index 0.78
SVM decision value 0.38
SVM RNA-class probability 0.714243
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1181958 120 + 22407834
AGUCGCGCCAGAAGGAUUCUUUUGGCGCCACUGCAGCCAUGCCCAUCAGUUCGACCAACGUGGGCAGCCGCCUGAUGCAGAAGAUGGGCUGGUCGGAGGGCCAGGGACUGGGCAAAAAGA
((((.(((((((((....))))))))(((.((.(.((((.(((((((..(((...((...(((((....))))).))..)))))))))))))).).)))))..).))))........... ( -50.60)
>DroSim_CAF1 15305 120 + 1
AGUCGCGCCAGAAGGAUUCUUUUGGCGCUACUCCAGCCACGCCCAUCAGUUCGAGCAACGUGGGCAGCCGCCUGAUGCAGAAGAUGGGCUGGUCGCAGGGCCAGGGACUGGGCAAAAAAA
(((.((((((((((....)))))))))).)))((((((..(((((((..(((..(((...(((((....))))).))).))))))))))(((((....))))).)).))))......... ( -55.60)
>DroEre_CAF1 16412 120 + 1
AGUCGCGCCAGAAGGAUUCUUCUGGGGCUACUCCAGCCAUGCCCAUCAGUUCGAGCAACGUGGGCAGUCGCCUCAUGCAGAAGAUGGGUUGGUCGGAGGGCCAGGGAUUGGGCAGGAAGA
((((.(.(((((((....)))))))((((.((((.((((.(((((((..(((..(((....((((....))))..))).)))))))))))))).)))))))).).))))........... ( -52.70)
>DroYak_CAF1 16075 120 + 1
AGUCGCGCCAGAAGGAUUCUUCUGGCGCUACUCCAGCCAUGCCCAUCAGUUCGAGCAACGUGGGCAGUCGCCUGAUGCAGAAGAUGGGUUGGUCGGAGGGCCAGGGAUUGGGCAGGAAGA
....((((((((((....))))))))))..((((.((((.(((((((..(((..(((...(((((....))))).))).)))))))))))))).)))).(((........)))....... ( -57.20)
>DroAna_CAF1 15441 111 + 1
AGUC-CUCCA--------CAUCUGCGUCCACUCCAUCCGUGCCCAUCAGCUCUAGCAACGUGGGUAGCCGUCUGAUGCAGAAAAUGGGCUGGUCGGAGGGUCAGGGAUUGGGUAGAAAGA
....-.....--------..(((((..(((.(((.....(((((((..((....))...)))))))(((.((((((.(((........))))))))).)))...))).)))))))).... ( -36.90)
>DroPer_CAF1 20155 120 + 1
AGACGCGUCAGAAGAAUAAUGCCAGCGCGGCUUCAGCUCUGCCAAUCAGCUCGAAUAACGUGGGCAAUCGCUUGAUGCAGAAGAUGGGCUGGACGGAGGGCCAGGGUCUGGGCAGGAAGA
...(((((..(..........)..))))).((((..((((((((..(.(((((.......)))))....((.....))........)..))).)))))(.((((...)))).)..)))). ( -34.10)
>consensus
AGUCGCGCCAGAAGGAUUCUUCUGGCGCUACUCCAGCCAUGCCCAUCAGUUCGAGCAACGUGGGCAGCCGCCUGAUGCAGAAGAUGGGCUGGUCGGAGGGCCAGGGACUGGGCAGAAAGA
....((((((((((....))))))))))..((((..(((.(((((((.(((((.......)))))....((.....))....))))))))))..))))(.((((...)))).)....... (-37.44 = -38.37 +   0.92)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:22 2006