Locus 1844

Sequence ID 2L_DroMel_CAF1
Location 5,084,328 – 5,084,557
Length 229
Max. P 0.914002
window2965 window2966 window2967 window2968

overview

Window 5

Location 5,084,328 – 5,084,437
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.15
Mean single sequence MFE -45.95
Consensus MFE -33.45
Energy contribution -34.33
Covariance contribution 0.87
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.73
SVM decision value 0.61
SVM RNA-class probability 0.798576
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5084328 109 + 22407834
CUGCAC--UCGGCACUUUAAUGAUCUGUGGCCGAGUGCCAGAAAUGCUGGGGAAUUUGGG---------GAGCUCUGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUG
..((((--(((((((...........)).)))))))))(((....(((((((...((..(---------((((((..((((.....)).))..)))))))..)))))))))...)))... ( -48.80)
>DroSec_CAF1 13815 111 + 1
CUGCACUCUCGGCACUUUAAUGAUCUGUGGCCGAGUGCCAGAAAUGCUGUGGAAUUUGGG---------UAGCUCUGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUG
..((((((..(.(((...........))).).))))))(((....(((..(((.(((.((---------.(((((..((((.....)).))..))))))).))).))))))...)))... ( -39.20)
>DroSim_CAF1 16394 111 + 1
CUGCACUCUCGGCACUUUAAUGAUCUGUGGCCGAGUGCCAGAAAUGCUGGGGAAUUUGGG---------UAGCUCCGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUG
..((((((..(.(((...........))).).))))))(((....(((((((..(((.((---------.(((((((((((.....)).))))))))))).))))))))))...)))... ( -46.10)
>DroYak_CAF1 15228 118 + 1
CUGCAC--UCGGCACUUUAAUGAUCUGUGGCCAACUGCCAGAAAUGCUCGGUAGUUUGGGGGAGCUCUGGAGCUCUGGACUUCUGCAGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUG
.(((..--...)))........(((.(..((((((((((((.....)).)))))))....((((.((..((((((..((((.....)).))..))))))..)).)))))))..)..))). ( -49.70)
>consensus
CUGCAC__UCGGCACUUUAAUGAUCUGUGGCCGAGUGCCAGAAAUGCUGGGGAAUUUGGG_________GAGCUCUGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUG
..((((..(((((((...........)).)))))))))(((....(((((((..(((.((..........(((((((((((.....)).))))))))))).))))))))))...)))... (-33.45 = -34.33 +   0.87)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,084,328 – 5,084,437
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.15
Mean single sequence MFE -35.34
Consensus MFE -28.24
Energy contribution -28.18
Covariance contribution -0.06
Combinations/Pair 1.08
Mean z-score -1.49
Structure conservation index 0.80
SVM decision value 0.13
SVM RNA-class probability 0.597906
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5084328 109 - 22407834
CAUCAGGCAGCCGGAGUUCCAGAGCUCCAGAACCCUACGAGUCCAGAGCUC---------CCCAAAUUCCCCAGCAUUUCUGGCACUCGGCCACAGAUCAUUAAAGUGCCGA--GUGCAG
...((((..((.((((((...((((((..((..(....)..))..))))))---------....))))))...))...))))(((((((((.((...........)))))))--)))).. ( -36.80)
>DroSec_CAF1 13815 111 - 1
CAUCAGGCAGCCGGAGUUCCAGAGCUCCAGAACCCUACGAGUCCAGAGCUA---------CCCAAAUUCCACAGCAUUUCUGGCACUCGGCCACAGAUCAUUAAAGUGCCGAGAGUGCAG
.....(((....((((((....)))))).........(((((((((((((.---------............)))...))))).))))))))..............((((....).))). ( -33.02)
>DroSim_CAF1 16394 111 - 1
CAUCAGGCAGCCGGAGUUCCAGAGCUCCAGAACCCUACGAGUCCGGAGCUA---------CCCAAAUUCCCCAGCAUUUCUGGCACUCGGCCACAGAUCAUUAAAGUGCCGAGAGUGCAG
.....((.....((((((....((((((.((..(....)..)).)))))).---------....)))))))).(((((..(((((((.................)))))))..))))).. ( -33.83)
>DroYak_CAF1 15228 118 - 1
CAUCAGGCAGCCGGAGUUCCAGAGCUCCAGAACUGCAGAAGUCCAGAGCUCCAGAGCUCCCCCAAACUACCGAGCAUUUCUGGCAGUUGGCCACAGAUCAUUAAAGUGCCGA--GUGCAG
(((..((((...(((((((..((((((..((.((.....))))..))))))..))))))).............(.((((.((((.....)))).))))).......))))..--)))... ( -37.70)
>consensus
CAUCAGGCAGCCGGAGUUCCAGAGCUCCAGAACCCUACGAGUCCAGAGCUA_________CCCAAAUUCCCCAGCAUUUCUGGCACUCGGCCACAGAUCAUUAAAGUGCCGA__GUGCAG
.....(((....((((((....)))))).........(((((((((((((......................)))...))))).))))))))..............((((....).))). (-28.24 = -28.18 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,084,366 – 5,084,477
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.20
Mean single sequence MFE -38.80
Consensus MFE -30.23
Energy contribution -30.60
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -2.59
Structure conservation index 0.78
SVM decision value 1.09
SVM RNA-class probability 0.914002
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5084366 111 + 22407834
GAAAUGCUGGGGAAUUUGGG---------GAGCUCUGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUGUGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUA
.....(((((((...((..(---------((((((..((((.....)).))..)))))))..))))))))).((((........))))(.(((((....))))).).............. ( -37.80)
>DroSec_CAF1 13855 111 + 1
GAAAUGCUGUGGAAUUUGGG---------UAGCUCUGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUGUGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUA
....((.((((((.(((.((---------.(((((..((((.....)).))..))))))).))).))).((.((((........))))))(((((....))))))))))........... ( -34.10)
>DroSim_CAF1 16434 111 + 1
GAAAUGCUGGGGAAUUUGGG---------UAGCUCCGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUGUGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUA
.....(((((((..(((.((---------.(((((((((((.....)).))))))))))).)))))))))).((((........))))(.(((((....))))).).............. ( -40.20)
>DroYak_CAF1 15266 120 + 1
GAAAUGCUCGGUAGUUUGGGGGAGCUCUGGAGCUCUGGACUUCUGCAGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUGUGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUA
.....((.(((.(((((...(((((((..(((((.(((....))).)))))..))))))).)))))))))).((((........))))(.(((((....))))).).............. ( -43.10)
>consensus
GAAAUGCUGGGGAAUUUGGG_________GAGCUCUGGACUCGUAGGGUUCUGGAGCUCUGGAACUCCGGCUGCCUGAUGUGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUA
.....(((((((..(((.((..........(((((((((((.....)).))))))))))).)))))))))).((((........))))(.(((((....))))).).............. (-30.23 = -30.60 +   0.37)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,084,437 – 5,084,557
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.81
Mean single sequence MFE -29.45
Consensus MFE -26.79
Energy contribution -26.23
Covariance contribution -0.56
Combinations/Pair 1.09
Mean z-score -1.79
Structure conservation index 0.91
SVM decision value 0.38
SVM RNA-class probability 0.712313
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5084437 120 + 22407834
UGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUAUUUCGGUUUCAUGCUGGCAUGCGGAGAGAAAUCCAGUAAAUUCAGAUAAAUGAUACAAAUUAGCGCUAUAAAUACGCCCC
.....((.(((((.((((((.(((...((((((.....))))).)((.((((.((((..((((((......))).)))...))))....)))).))......))).))))))))))))). ( -27.00)
>DroSec_CAF1 13926 120 + 1
UGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUAUUUCGGUUUCAUGCUGGCAUGCGGGGAGAAAUCCAGUAAAUUCAGGGAAAUGAUACAAAUUAGCGCUAUAAAUACGCCCC
.....((.(((((.((((((.(((...((((((.....))))).)((.((((.((((..(((..(((....))).)))...))))....)))).))......))).))))))))))))). ( -28.70)
>DroSim_CAF1 16505 120 + 1
UGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUAUUUCGGUUUCAUGCUGGCAUGCGGGGAGAAAUCCAGUAAAUUCAGGGAAAUGAUACAAAUUAGCGCUAUAAAUACGCCCC
.....((.(((((.((((((.(((...((((((.....))))).)((.((((.((((..(((..(((....))).)))...))))....)))).))......))).))))))))))))). ( -28.70)
>DroYak_CAF1 15346 120 + 1
UGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUAUUUCGGUUUCAUGCUGGCAUGCGGCGAGAAGCCCAGUAAAUUCGGGGGAAUGAUACAAAUUAGCGCUAUAAAUACGCCCC
.....((.(((((.((((((.(((....................((((((.(((((.....))))).))))))..(((.((((....))))..)))......))).))))))))))))). ( -33.40)
>consensus
UGAAAGGCGCGUAAUUUAUAUUGCACACAAAUAAAAUUUAUUUCGGUUUCAUGCUGGCAUGCGGGGAGAAAUCCAGUAAAUUCAGGGAAAUGAUACAAAUUAGCGCUAUAAAUACGCCCC
.....((.(((((.((((((.(((...........(((((((..((((((.(((......)))....)))))).)))))))(((......))).........))).))))))))))))). (-26.79 = -26.23 +  -0.56)

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 10:12:43 2006