Locus 841

Sequence ID 3R_DroMel_CAF1
Location 2,875,088 – 2,875,242
Length 154
Max. P 0.993617
window1338 window1339 window1340

overview

Window 8

Location 2,875,088 – 2,875,208
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.97
Mean single sequence MFE -34.73
Consensus MFE -28.62
Energy contribution -29.25
Covariance contribution 0.62
Combinations/Pair 1.10
Mean z-score -3.49
Structure conservation index 0.82
SVM decision value 2.41
SVM RNA-class probability 0.993617
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2875088 120 + 27905053
AACGGAGGAUAUUCCAUAGACAACAUCUUUGGAAUAUUUAUUUAUGUAUGUAUAUCCAGUUGUGGGAAUGUACUGCAGAAUCGCGACAACGUAGCCUAUUUUUGGGCUACCCACAAAAAC
...(((((((((((((.(((.....))).))))))))))...((((....)))))))..(((((((..(((...((......)).)))...(((((((....)))))))))))))).... ( -36.60)
>DroSec_CAF1 6212 113 + 1
AACGGAGGAUAUUCCAUAGACAACAUCUUUGGAAUAUUUAUUUAUA-------AUCCAGUUGUGGGAAUGUACUGCGGAAUCGCGACAACGUAGCCUAUUUUCGGGCUACAGACAAAAAC
...(((((((((((((.(((.....))).)))))))))).......-------.))).(((((((...((.....))...)))))))...(((((((......))))))).......... ( -33.80)
>DroSim_CAF1 8440 111 + 1
AACGGAGGAUAUUCCAUAGACAACAUCUUUGGAAUAUUUAUUUAU---------UCCAGUUGUGGGAAUGUACUGCGGAAUCGCGACAACGUAGCCUAUUUUUGGGCUACAGACAAAAAC
..((.((.(((((((....(((((.....(((((((......)))---------))))))))).))))))).)).)).............((((((((....)))))))).......... ( -36.00)
>DroEre_CAF1 7183 112 + 1
AACGGAGGAUAUUCCGAAGACAACAUCUUUGGAAUAUUUAUUGAU--------CUCGAGUUGUGGGAUUGUACAGCAGAAUAGCAAAAACAUAGCCUAUUUUUCGGCUACCGACGAAAAU
..(((.((((((((((((((.....))))))))))))))......--------.(((((..(((((..(((...((......))....)))...)))))..)))))...)))........ ( -32.50)
>consensus
AACGGAGGAUAUUCCAUAGACAACAUCUUUGGAAUAUUUAUUUAU________AUCCAGUUGUGGGAAUGUACUGCAGAAUCGCGACAACGUAGCCUAUUUUUGGGCUACAGACAAAAAC
......((((((((((.(((.....))).))))))))))...................(((((((...((.....))...)))))))...((((((((....)))))))).......... (-28.62 = -29.25 +   0.62)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,875,088 – 2,875,208
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.97
Mean single sequence MFE -26.85
Consensus MFE -20.69
Energy contribution -21.12
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -1.67
Structure conservation index 0.77
SVM decision value 0.35
SVM RNA-class probability 0.698703
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2875088 120 - 27905053
GUUUUUGUGGGUAGCCCAAAAAUAGGCUACGUUGUCGCGAUUCUGCAGUACAUUCCCACAACUGGAUAUACAUACAUAAAUAAAUAUUCCAAAGAUGUUGUCUAUGGAAUAUCCUCCGUU
....((((((((((((........))))))......(((....))).........))))))..((((((......))).....((((((((.((((...)))).))))))))..)))... ( -29.90)
>DroSec_CAF1 6212 113 - 1
GUUUUUGUCUGUAGCCCGAAAAUAGGCUACGUUGUCGCGAUUCCGCAGUACAUUCCCACAACUGGAU-------UAUAAAUAAAUAUUCCAAAGAUGUUGUCUAUGGAAUAUCCUCCGUU
((((..((((((((((........))))))(((((.(((....))).(........)))))).))))-------...))))..((((((((.((((...)))).))))))))........ ( -27.50)
>DroSim_CAF1 8440 111 - 1
GUUUUUGUCUGUAGCCCAAAAAUAGGCUACGUUGUCGCGAUUCCGCAGUACAUUCCCACAACUGGA---------AUAAAUAAAUAUUCCAAAGAUGUUGUCUAUGGAAUAUCCUCCGUU
......((((((((((........))))))......(((....))))).))(((((.......)))---------))......((((((((.((((...)))).))))))))........ ( -26.80)
>DroEre_CAF1 7183 112 - 1
AUUUUCGUCGGUAGCCGAAAAAUAGGCUAUGUUUUUGCUAUUCUGCUGUACAAUCCCACAACUCGAG--------AUCAAUAAAUAUUCCAAAGAUGUUGUCUUCGGAAUAUCCUCCGUU
..(((((...((((((........))))))((....((......))...))............))))--------).......(((((((.(((((...))))).)))))))........ ( -23.20)
>consensus
GUUUUUGUCGGUAGCCCAAAAAUAGGCUACGUUGUCGCGAUUCCGCAGUACAUUCCCACAACUGGAU________AUAAAUAAAUAUUCCAAAGAUGUUGUCUAUGGAAUAUCCUCCGUU
..........((((((........))))))(((((.(((....))).(........)))))).....................((((((((.((((...)))).))))))))........ (-20.69 = -21.12 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,875,128 – 2,875,242
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.62
Mean single sequence MFE -25.58
Consensus MFE -20.60
Energy contribution -21.60
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.81
SVM decision value 0.10
SVM RNA-class probability 0.582470
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2875128 114 + 27905053
UUUAUGUAUGUAUAUCCAGUUGUGGGAAUGUACUGCAGAAUCGCGACAACGUAGCCUAUUUUUGGGCUACCCACAAAAACAACCUCUA----AGAUCACAUUCCUGUCUA--CAAAAGAU
..................((.(..(((((((..(((......))).....((((((((....))))))))..................----.....)))))))..)..)--)....... ( -25.60)
>DroSec_CAF1 6252 109 + 1
UUUAUA-------AUCCAGUUGUGGGAAUGUACUGCGGAAUCGCGACAACGUAGCCUAUUUUCGGGCUACAGACAAAAACAACCUCUG----AGAUCACAUUCCUGUCUUUACAAAAGAU
......-------..........((((((((..((((....)))).....(((((((......)))))))..................----.....))))))))(((((.....))))) ( -26.10)
>DroSim_CAF1 8480 109 + 1
UUUAU---------UCCAGUUGUGGGAAUGUACUGCGGAAUCGCGACAACGUAGCCUAUUUUUGGGCUACAGACAAAAACAACCUAUGUAUAAGAUCACAUUCCUGACUU--CAAAAGAU
.....---------...((((..((((((((..((((....)))).....((((((((....))))))))...........................)))))))))))).--........ ( -27.80)
>DroEre_CAF1 7223 106 + 1
UUGAU--------CUCGAGUUGUGGGAUUGUACAGCAGAAUAGCAAAAACAUAGCCUAUUUUUCGGCUACCGACGAAAAUAAGCCCAA----AGAUCACAUUCCUGUCUA--CAACAGAG
.((((--------((.(((..(((((..(((...((......))....)))...)))))..)))((((.............))))...----)))))).....((((...--..)))).. ( -22.82)
>consensus
UUUAU________AUCCAGUUGUGGGAAUGUACUGCAGAAUCGCGACAACGUAGCCUAUUUUUGGGCUACAGACAAAAACAACCUCUA____AGAUCACAUUCCUGUCUA__CAAAAGAU
.......................((((((((...((......))......((((((((....))))))))...........................))))))))............... (-20.60 = -21.60 +   1.00)

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 09:53:30 2006