Locus 6401

Sequence ID 3R_DroMel_CAF1
Location 16,778,012 – 16,778,146
Length 134
Max. P 0.998960
window10437 window10438 window10439 window10440

overview

Window 7

Location 16,778,012 – 16,778,114
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.13
Mean single sequence MFE -28.94
Consensus MFE -14.42
Energy contribution -14.58
Covariance contribution 0.16
Combinations/Pair 1.33
Mean z-score -2.74
Structure conservation index 0.50
SVM decision value 3.30
SVM RNA-class probability 0.998960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16778012 102 + 27905053
GGAAAAUGUUUUCCAAAUGAUGCAAACAAUUGAAAGAUUGUUCGAAUUCUCGCAGAAGAUACAUACAGUUGU-------------AUAUGUAGCUCAAUUGUGUGUG-----AAUCUGUG
(((((....)))))....((..(.(((((((....))))))).)...)).((((((...((((((((((((.-------------..........))))))))))))-----..)))))) ( -29.70)
>DroSec_CAF1 10381 106 + 1
GGAAAAUGUUUUCCAAAUGAUGCAGACAAUUGAAAGAUUGUUCGAAUUCUCGCAGAAGAUACACACAGUUGUACGU---------AUAUGUAGCUCAAUUGUGUGUG-----AAUCUGUG
(((((....)))))....((..(..((((((....))))))..)...)).((((((...((((((((((((((((.---------...))))...))))))))))))-----..)))))) ( -33.20)
>DroSim_CAF1 12065 110 + 1
GGAAAAUGUUUUCCAAAUGAUGCAGACAAUUGAAAGAUUGUUCGAAUUCUCGCAGAAGAUACACACAGUUGUACGUAU-----GUAUAUGUAGCUCAAUUGUGUUUG-----AAUCUGUG
(((((....)))))....((..(..((((((....))))))..)...)).((((((...((.(((((((((((((((.-----...))))))...))))))))).))-----..)))))) ( -29.90)
>DroEre_CAF1 6218 101 + 1
GGAAAAUGUUUUCCAAACGAUGCAGACAGUUGAAAGAUUGUUCGAAUUCUUGCAGGAGAUACACACAGUUGU-------------AUA-GUAGCUCAAUUGUGUGUG-----AAUCUGUG
(((((....)))))....((..(..((((((....))))))..)...))..(((((...((((((((((((.-------------...-......))))))))))))-----..))))). ( -30.60)
>DroWil_CAF1 4152 109 + 1
AUAAAAUGUAUCUU--AUAGCUCGGGAAACUAGACGAUGGUAUGCAU---------AGGUAUAUAUGUAUGCACAUAUAUUGUUUAAAUGUAACUCAAUUGUGCAUGGAGUCAAUUCGUG
..............--...((((((....))((((((((((((((((---------(......))))))))).....))))))))..(((((.(......)))))).))))......... ( -21.30)
>consensus
GGAAAAUGUUUUCCAAAUGAUGCAGACAAUUGAAAGAUUGUUCGAAUUCUCGCAGAAGAUACACACAGUUGUAC_U_________AUAUGUAGCUCAAUUGUGUGUG_____AAUCUGUG
(((((....))))).......(((((...(((((......)))))..............((((((((((((........................)))))))))))).......))))). (-14.42 = -14.58 +   0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,778,012 – 16,778,114
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.13
Mean single sequence MFE -18.88
Consensus MFE -6.32
Energy contribution -7.08
Covariance contribution 0.76
Combinations/Pair 1.30
Mean z-score -1.72
Structure conservation index 0.33
SVM decision value 0.09
SVM RNA-class probability 0.580185
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16778012 102 - 27905053
CACAGAUU-----CACACACAAUUGAGCUACAUAU-------------ACAACUGUAUGUAUCUUCUGCGAGAAUUCGAACAAUCUUUCAAUUGUUUGCAUCAUUUGGAAAACAUUUUCC
....(((.-----..((.(((((((((.(((((((-------------(....))))))))((((....)))).............))))))))).)).)))....(((((....))))) ( -18.60)
>DroSec_CAF1 10381 106 - 1
CACAGAUU-----CACACACAAUUGAGCUACAUAU---------ACGUACAACUGUGUGUAUCUUCUGCGAGAAUUCGAACAAUCUUUCAAUUGUCUGCAUCAUUUGGAAAACAUUUUCC
...((((.-----.(((((((.(((.((.......---------..)).))).)))))))))))..(((((.((((.(((......))))))).)).)))......(((((....))))) ( -20.90)
>DroSim_CAF1 12065 110 - 1
CACAGAUU-----CAAACACAAUUGAGCUACAUAUAC-----AUACGUACAACUGUGUGUAUCUUCUGCGAGAAUUCGAACAAUCUUUCAAUUGUCUGCAUCAUUUGGAAAACAUUUUCC
....(((.-----((...((((((((((.....((((-----(((((......))))))))).....))((((..........)))))))))))).)).)))....(((((....))))) ( -22.00)
>DroEre_CAF1 6218 101 - 1
CACAGAUU-----CACACACAAUUGAGCUAC-UAU-------------ACAACUGUGUGUAUCUCCUGCAAGAAUUCGAACAAUCUUUCAACUGUCUGCAUCGUUUGGAAAACAUUUUCC
...((((.-----.(((((((.(((......-...-------------.))).)))))))))))..((((.((....(((......))).....))))))......(((((....))))) ( -16.80)
>DroWil_CAF1 4152 109 - 1
CACGAAUUGACUCCAUGCACAAUUGAGUUACAUUUAAACAAUAUAUGUGCAUACAUAUAUACCU---------AUGCAUACCAUCGUCUAGUUUCCCGAGCUAU--AAGAUACAUUUUAU
.((((..((((((.((.....)).))))))...............((((((((..........)---------)))))))...)))).((((((...)))))).--.............. ( -16.10)
>consensus
CACAGAUU_____CACACACAAUUGAGCUACAUAU_________A_GUACAACUGUGUGUAUCUUCUGCGAGAAUUCGAACAAUCUUUCAAUUGUCUGCAUCAUUUGGAAAACAUUUUCC
..(((((.......(((((((.(((........................))).))))))).................(((......)))....)))))........(((((....))))) ( -6.32 =  -7.08 +   0.76)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,778,052 – 16,778,146
Length 94
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 92.79
Mean single sequence MFE -25.43
Consensus MFE -23.33
Energy contribution -23.21
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.09
Structure conservation index 0.92
SVM decision value 1.55
SVM RNA-class probability 0.963282
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16778052 94 + 27905053
UUCGAAUUCUCGCAGAAGAUACAUACAGUUGU--------AUAUGUAGCUCAAUUGUGUGUGAAUCUGUGCCUGUAUCUUUUGAUUCGCACUUUGCUUGUUG
...........((((((((((((((((((((.--------..........)))))))))))..))))((((....(((....)))..)))))))))...... ( -23.70)
>DroSec_CAF1 10421 98 + 1
UUCGAAUUCUCGCAGAAGAUACACACAGUUGUACGU----AUAUGUAGCUCAAUUGUGUGUGAAUCUGUGCCUGUAUCUUUUGAUUCGCACUUUGCUUGUUG
...........((((((((((((((((((((((((.----...))))...)))))))))))..))))((((....(((....)))..)))))))))...... ( -26.60)
>DroSim_CAF1 12105 102 + 1
UUCGAAUUCUCGCAGAAGAUACACACAGUUGUACGUAUGUAUAUGUAGCUCAAUUGUGUUUGAAUCUGUGCCUGUAUCUUUUGAUUCGCACUUUGCUUGUUG
...((((.....((((((((((((((((...((((((....))))))..((((......))))..)))))..)))))))))))))))((.....))...... ( -24.70)
>DroEre_CAF1 6258 93 + 1
UUCGAAUUCUUGCAGGAGAUACACACAGUUGU--------AUA-GUAGCUCAAUUGUGUGUGAAUCUGUGCCUGUAUCUUUUGAUUCGCACUUUGCUUGUUG
.(((((....(((((((((((((((((((((.--------...-......)))))))))))..))))...))))))...)))))...((.....))...... ( -26.70)
>consensus
UUCGAAUUCUCGCAGAAGAUACACACAGUUGU________AUAUGUAGCUCAAUUGUGUGUGAAUCUGUGCCUGUAUCUUUUGAUUCGCACUUUGCUUGUUG
...........((((((((((((((((((((...................)))))))))))..))))((((....(((....)))..)))))))))...... (-23.33 = -23.21 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,778,052 – 16,778,146
Length 94
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 92.79
Mean single sequence MFE -19.40
Consensus MFE -15.66
Energy contribution -16.16
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.81
SVM decision value 0.34
SVM RNA-class probability 0.695240
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16778052 94 - 27905053
CAACAAGCAAAGUGCGAAUCAAAAGAUACAGGCACAGAUUCACACACAAUUGAGCUACAUAU--------ACAACUGUAUGUAUCUUCUGCGAGAAUUCGAA
......(((..(((.(((((................))))).)))......(((.(((((((--------(....)))))))).))).)))........... ( -18.19)
>DroSec_CAF1 10421 98 - 1
CAACAAGCAAAGUGCGAAUCAAAAGAUACAGGCACAGAUUCACACACAAUUGAGCUACAUAU----ACGUACAACUGUGUGUAUCUUCUGCGAGAAUUCGAA
......(((..((((..(((....)))....))))((((..(((((((.(((.((.......----..)).))).)))))))))))..)))........... ( -20.80)
>DroSim_CAF1 12105 102 - 1
CAACAAGCAAAGUGCGAAUCAAAAGAUACAGGCACAGAUUCAAACACAAUUGAGCUACAUAUACAUACGUACAACUGUGUGUAUCUUCUGCGAGAAUUCGAA
..............(((((((.(((((((..((((((.(((((......))))).......(((....)))...))))))))))))).)).....))))).. ( -19.60)
>DroEre_CAF1 6258 93 - 1
CAACAAGCAAAGUGCGAAUCAAAAGAUACAGGCACAGAUUCACACACAAUUGAGCUAC-UAU--------ACAACUGUGUGUAUCUCCUGCAAGAAUUCGAA
......(((..((((..(((....)))....))))((((..(((((((.(((......-...--------.))).)))))))))))..)))........... ( -19.00)
>consensus
CAACAAGCAAAGUGCGAAUCAAAAGAUACAGGCACAGAUUCACACACAAUUGAGCUACAUAU________ACAACUGUGUGUAUCUUCUGCGAGAAUUCGAA
......(((..((((..(((....)))....))))((((..(((((((.(((...................))).)))))))))))..)))........... (-15.66 = -16.16 +   0.50)

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 12:20:41 2006