Locus 7784

Sequence ID 2L_DroMel_CAF1
Location 21,941,159 – 21,941,421
Length 262
Max. P 0.989731
window12480 window12481 window12482 window12483

overview

Window 0

Location 21,941,159 – 21,941,268
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.51
Mean single sequence MFE -33.98
Consensus MFE -21.24
Energy contribution -22.52
Covariance contribution 1.28
Combinations/Pair 1.30
Mean z-score -2.46
Structure conservation index 0.63
SVM decision value 2.18
SVM RNA-class probability 0.989731
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21941159 109 + 22407834
AUUUCUCACGAGAGAACCGUUUCCCGUACUCAGGCUAGUGAGCCUCAGAGUCAGAUGCAUCUGUAUCUGCCAGUUGUCAGGC------AUCACCAUCUCUAUUCUGAAUGCGAAC-----
..(((((....)))))........((((.((((..(((((((((((((...(((((((....)))))))....)))..))))------.))))......))..)))).))))...----- ( -30.70)
>DroSec_CAF1 229384 109 + 1
AUUUCUCACGGGAGAACCGUUUCCCGUACUCAGGCUUGUCAGCCUCAGAGUCAGAUGCAUCCGUAUCUGCCAGUCGUCUGGC------AUCACCAUCUCUAUUCCGAAUGCGAAC-----
..(((....((((((....))))))(((.(((((((....))))).((((..((((((....))))))(((((....)))))------........)))).....)).)))))).----- ( -34.10)
>DroSim_CAF1 174304 109 + 1
AUUUCUCACGGGAGAACCGUUUCCCGUACUCAGGCUUGUCGGCCUCAGAGUCAGAUGCAUCUGUAUCUGCCAGUCGUCUGGC------AUCACCAUCUCUAUUCCGAGUGCGAAC-----
..(((....((((((....))))))(((((((((((....))))).((((..((((((....))))))(((((....)))))------........)))).....))))))))).----- ( -40.40)
>DroEre_CAF1 201841 94 + 1
AUUUCUCC--------------------UUCGGGCUUGUCAGCCUCAGAGGCAGUUGCAUCUGUAUCUGCCUGUCGUCAGGC------AUCACAAUCUUCAUUCUGAGUGCGAACGCGAA
......((--------------------....))...((..(((((((((((((.(((....))).)))))((((....)))------).............)))))).))..))..... ( -30.10)
>DroYak_CAF1 193158 115 + 1
AUUUCUCACGAAAAACGCGUUUCACGUACUCAGGCUUGUCAGUCUCACAGGCAGUUGCAUUUGUAUCUGCCUGUCGUUAGGCGUCUUCAUCUCCAUUUUCAUUCUGAGUGGGAAC-----
..(((((((((..((.((((((.(((.....(((((....))))).((((((((.(((....))).))))))))))).)))))).))..)).......((.....))))))))).----- ( -34.60)
>consensus
AUUUCUCACGAGAGAACCGUUUCCCGUACUCAGGCUUGUCAGCCUCAGAGUCAGAUGCAUCUGUAUCUGCCAGUCGUCAGGC______AUCACCAUCUCUAUUCUGAGUGCGAAC_____
........................((((((((((((....))))).((((..((((((....))))))(((((....)))))..............)))).....)))))))........ (-21.24 = -22.52 +   1.28)

alignment

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secondary structure

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Window 1

Location 21,941,199 – 21,941,301
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.09
Mean single sequence MFE -29.38
Consensus MFE -16.80
Energy contribution -18.16
Covariance contribution 1.36
Combinations/Pair 1.13
Mean z-score -1.89
Structure conservation index 0.57
SVM decision value 0.86
SVM RNA-class probability 0.869586
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21941199 102 + 22407834
AGCCUCAGAGUCAGAUGCAUCUGUAUCUGCCAGUUGUCAGGC------AUCACCAUCUCUAUUCUGAAUGCGAAC------------GCGAAUCUACGCCAUCUCGCGUCACCCACUUAA
.((.(((((((.((((((....))))))(((........)))------............)))))))..))((.(------------((((............))))))).......... ( -25.80)
>DroSec_CAF1 229424 81 + 1
AGCCUCAGAGUCAGAUGCAUCCGUAUCUGCCAGUCGUCUGGC------AUCACCAUCUCUAUUCCGAAUGCGAAC------------GCGAAUCCCCGG---------------------
..((..((((..((((((....))))))(((((....)))))------........))))........(((....------------))).......))--------------------- ( -19.40)
>DroSim_CAF1 174344 102 + 1
GGCCUCAGAGUCAGAUGCAUCUGUAUCUGCCAGUCGUCUGGC------AUCACCAUCUCUAUUCCGAGUGCGAAC------------GCGAAUCCCCGCCAUCUCGCGUCACCCACUUAA
((....((((..((((((....))))))(((((....)))))------........))))...))(((((.(.((------------((((............))))))..).))))).. ( -30.00)
>DroEre_CAF1 201861 114 + 1
AGCCUCAGAGGCAGUUGCAUCUGUAUCUGCCUGUCGUCAGGC------AUCACAAUCUUCAUUCUGAGUGCGAACGCGAACGCGAACGCGAAUCCCCGCCAUCUCGCGUCACCCACUUAA
.(((((((((((((.(((....))).)))))((((....)))------).............)))))).))......((.(((((..(((......)))....))))))).......... ( -37.30)
>DroYak_CAF1 193198 108 + 1
AGUCUCACAGGCAGUUGCAUUUGUAUCUGCCUGUCGUUAGGCGUCUUCAUCUCCAUUUUCAUUCUGAGUGGGAAC------------GCGAAACUCCGCCAUCUCGCGUCAGCCACUAAA
......((((((((.(((....))).)))))))).....(((.......((.((((((.......))))))))((------------((((............))))))..)))...... ( -34.40)
>consensus
AGCCUCAGAGUCAGAUGCAUCUGUAUCUGCCAGUCGUCAGGC______AUCACCAUCUCUAUUCUGAGUGCGAAC____________GCGAAUCCCCGCCAUCUCGCGUCACCCACUUAA
.(((((((((..((((((....))))))(((((....)))))...................))))))).))................(((......)))..................... (-16.80 = -18.16 +   1.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,941,268 – 21,941,381
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.56
Mean single sequence MFE -43.31
Consensus MFE -40.29
Energy contribution -40.92
Covariance contribution 0.63
Combinations/Pair 1.06
Mean z-score -1.40
Structure conservation index 0.93
SVM decision value 0.28
SVM RNA-class probability 0.666502
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21941268 113 - 22407834
GGACAGGUCUCCGCCGUAUCUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAGGAGCUACUGGCAAAUUAAGUGGGUGACGCGAGAUGGCGUAGAUUCGC-------
...(..((((.((((((.....(((((.((((((.......((((((....(((.(((.......))))))..))))))......)))))).))))).)))))).))))..).------- ( -39.52)
>DroSim_CAF1 174413 113 - 1
GGACAGGUCUUCGCCGUAUCUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAGGAGCUACUGGCAAAUUAAGUGGGUGACGCGAGAUGGCGGGGAUUCGC-------
...(..(((((((((((.....(((((.((((((.......((((((....(((.(((.......))))))..))))))......)))))).))))).)))))))))))..).------- ( -42.62)
>DroEre_CAF1 201935 119 - 1
GGACAGGUCUCCGCCGUAUUCGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAG-AGCUACUGGCAAAUUAAGUGGGUGACGCGAGAUGGCGGGGAUUCGCGUUCGCG
((((.((((((((((((.....(((((.((((((.......((((((....(((.((........)-))))..))))))......)))))).))))).)))))))))).))..))))... ( -43.72)
>DroYak_CAF1 193273 113 - 1
GGACAGGUCUCCGCCGUAUUUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGUUGUAGGAGCUACUGGCAAGUUUAGUGGCUGACGCGAGAUGGCGGAGUUUCGC-------
.....((.(((((((((...(((((.((((.((((((....((((((....(((.(((.......))))))..)))))))))))))))))))))....)))))))))..))..------- ( -47.40)
>consensus
GGACAGGUCUCCGCCGUAUCUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAGGAGCUACUGGCAAAUUAAGUGGGUGACGCGAGAUGGCGGAGAUUCGC_______
...(..(((((((((((.....(((((.((((((.......((((((....(((.(((.......))))))..))))))......)))))).))))).)))))))))))..)........ (-40.29 = -40.92 +   0.63)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,941,301 – 21,941,421
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.31
Mean single sequence MFE -40.77
Consensus MFE -39.97
Energy contribution -40.10
Covariance contribution 0.13
Combinations/Pair 1.07
Mean z-score -1.42
Structure conservation index 0.98
SVM decision value 0.34
SVM RNA-class probability 0.697910
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21941301 120 - 22407834
UUUGUCAGAAUGUAAACUGAAUGGGAAUAGGAAGACGGCGGGACAGGUCUCCGCCGUAUCUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAGGAGCUACUGGCAAA
.(((((((..........((((((.(((..(((((.((((.((((((((......).))))))).)))).)))...))..))).)))))).(((.(((.......)))))).))))))). ( -44.90)
>DroSim_CAF1 174446 120 - 1
UUUGUCAGGAUGUAAACUGAAUGGGAAUAGGAAGACGGCGGGACAGGUCUUCGCCGUAUCUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAGGAGCUACUGGCAAA
.(((((((..........((((((.(((..(((((.((((.((((((((......).))))))).)))).)))...))..))).)))))).(((.(((.......)))))).))))))). ( -45.10)
>DroEre_CAF1 201975 119 - 1
UUUGUCAGGACGUAAACUGAAUGGGAAUAGGAAGACGGCGGGACAGGUCUCCGCCGUAUUCGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAG-AGCUACUGGCAAA
....((((........))))((((.(..(.(((.(((((((((....)).))))))).))).)..).))))..........((((((....(((.((........)-))))..)))))). ( -37.20)
>DroYak_CAF1 193306 119 - 1
UUUGUCGGAAUGUGAGCUGAAUGGGAAUAGGAAGACGG-GGGACAGGUCUCCGCCGUAUUUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGUUGUAGGAGCUACUGGCAAG
.(((((((((((.((..(..((((.(..(.(((.((((-.(((......))).)))).))).)..).))))..)..)).))))........(((.(((.......)))))).))))))). ( -35.90)
>consensus
UUUGUCAGAAUGUAAACUGAAUGGGAAUAGGAAGACGGCGGGACAGGUCUCCGCCGUAUCUGUCGUGCCAUCUGAAUCUCAUUGCCAUUUGAGCAUCCGGCCGUAGGAGCUACUGGCAAA
((((((((..........((((((.(((..(((((.((((.((((((((......).))))))).)))).)))...))..))).)))))).(((.(((.......)))))).)))))))) (-39.97 = -40.10 +   0.13)

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 12:44:51 2006