Locus 10049

Sequence ID 3R_DroMel_CAF1
Location 26,929,108 – 26,929,265
Length 157
Max. P 0.925921
window16005 window16006 window16007 window16008

overview

Window 5

Location 26,929,108 – 26,929,207
Length 99
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 81.95
Mean single sequence MFE -35.08
Consensus MFE -22.76
Energy contribution -24.93
Covariance contribution 2.17
Combinations/Pair 1.07
Mean z-score -3.29
Structure conservation index 0.65
SVM decision value 1.17
SVM RNA-class probability 0.925921
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26929108 99 + 27905053
CUUCG-------------CGGCCAGUUGGCAGUUGGCUGCCAUAAAACUAGUAACCAUAGUUUUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGGCCGGUCA-GCGCCGUU
.....-------------.((((((((((.....((((((((.(((((((((..((((.(.....).)))).)))))))))))))))))))))))))))(((..-..)))... ( -38.40)
>DroSec_CAF1 3871 92 + 1
CUUCG-------------CGGCCAGU-------UGGCUGCCAUAAAACUAGCAACCGUAGUUUUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGGCCGGUCA-GCGCCGUU
.....-------------.(((((((-------(((((((((.(((((((((.((((((....)))))).))..))))))))))))))..)))))))))(((..-..)))... ( -42.00)
>DroSim_CAF1 3923 92 + 1
CUUCG-------------CGGCCAGU-------UGGCUGCCAUAAAACUAGCAACCGUAGUUUUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGGCCGGUCA-GCGCCGUU
.....-------------.(((((((-------(((((((((.(((((((((.((((((....)))))).))..))))))))))))))..)))))))))(((..-..)))... ( -42.00)
>DroEre_CAF1 4063 92 + 1
UUUCG-------------CGGGCAGU-------UCGCUGCCAUAAAACUGGAAACCGUAGUUUUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGGCCGGCCA-GUGCCGUU
.....-------------.((.((((-------(.(((((((.((((((((..((((((....))))))....)))))))))))))))...))))).))(((..-..)))... ( -35.60)
>DroYak_CAF1 4181 81 + 1
UUUCG-------------CG------------------GCCAUAAAACUAGCAACCAUAGUUUUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGGCUGGUCA-UUGCUGUU
....(-------------(.------------------(((.((((((((.......)))))))).))).))..((((...((((((((......)))).))))-..)))).. ( -24.10)
>DroAna_CAF1 4262 105 + 1
UUUCGAAUCUAGAGGGGAUGGCCAGU-------UGGCAGCCAUAAAACUGGAAACCGUAGU-UUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGCCUGGUCAAGUGUUUUU
......((((.....))))(((((..-------.((((((((.((((((((..(((((...-..)))))....)))))))))))).........))))))))).......... ( -28.40)
>consensus
CUUCG_____________CGGCCAGU_______UGGCUGCCAUAAAACUAGCAACCGUAGUUUUGCGGUGGCAUUAGUUUUUGGCAGUUUUAAUUGGCCGGUCA_GCGCCGUU
...................((((.((........((((((((.((((((((..((((((....))))))....)))))))))))))))).......)).)))).......... (-22.76 = -24.93 +   2.17)

alignment

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secondary structure

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Window 6

Location 26,929,108 – 26,929,207
Length 99
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 81.95
Mean single sequence MFE -26.16
Consensus MFE -15.58
Energy contribution -16.92
Covariance contribution 1.33
Combinations/Pair 1.09
Mean z-score -2.77
Structure conservation index 0.60
SVM decision value 0.71
SVM RNA-class probability 0.830059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26929108 99 - 27905053
AACGGCGC-UGACCGGCCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAAAACUAUGGUUACUAGUUUUAUGGCAGCCAACUGCCAACUGGCCG-------------CGAAG
........-...(((((((..(((((((((((........(((....)))......))))....)))))))((((((....))))))..))))))-------------.)... ( -27.94)
>DroSec_CAF1 3871 92 - 1
AACGGCGC-UGACCGGCCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAAAACUACGGUUGCUAGUUUUAUGGCAGCCA-------ACUGGCCG-------------CGAAG
........-...(((((((.......(((((((((((((..((.((((........)))).))))))))).))))))...-------..))))))-------------.)... ( -32.00)
>DroSim_CAF1 3923 92 - 1
AACGGCGC-UGACCGGCCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAAAACUACGGUUGCUAGUUUUAUGGCAGCCA-------ACUGGCCG-------------CGAAG
........-...(((((((.......(((((((((((((..((.((((........)))).))))))))).))))))...-------..))))))-------------.)... ( -32.00)
>DroEre_CAF1 4063 92 - 1
AACGGCAC-UGGCCGGCCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAAAACUACGGUUUCCAGUUUUAUGGCAGCGA-------ACUGCCCG-------------CGAAA
..((((..-..))))((((..((((((((...........(((....)))((((....)))).)))))))))))).(((.-------......))-------------).... ( -27.20)
>DroYak_CAF1 4181 81 - 1
AACAGCAA-UGACCAGCCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAAAACUAUGGUUGCUAGUUUUAUGGC------------------CG-------------CGAAA
....((..-((......)).........(((((((((((..((.((((........)))).))))))))).))))------------------.)-------------).... ( -16.90)
>DroAna_CAF1 4262 105 - 1
AAAAACACUUGACCAGGCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAA-ACUACGGUUUCCAGUUUUAUGGCUGCCA-------ACUGGCCAUCCCCUCUAGAUUCGAAA
.(((((....((((.((((........)))).........(((....))).-.....))))....)))))((((((....-------...))))))................. ( -20.90)
>consensus
AACGGCAC_UGACCGGCCAAUUAAAACUGCCAAAAACUAAUGCCACCGCAAAACUACGGUUGCUAGUUUUAUGGCAGCCA_______ACUGGCCG_____________CGAAA
..........(.((((..........(((((((((((((.....((((........))))...))))))).))))))...........)))).)................... (-15.58 = -16.92 +   1.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 26,929,174 – 26,929,265
Length 91
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 82.04
Mean single sequence MFE -31.17
Consensus MFE -21.11
Energy contribution -21.03
Covariance contribution -0.08
Combinations/Pair 1.25
Mean z-score -2.09
Structure conservation index 0.68
SVM decision value 0.49
SVM RNA-class probability 0.758109
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26929174 91 + 27905053
UUUGGCAGUUUUAAUUGGCCGGUCA-GCGCCGUUGGCCAA-GUUUUCAGCUGC---CCAGCGCUUCAGCUGAAAUGACAUUUCGUUAUUGUGCUGG-------------
...(((((((....(((((((((..-..)))...))))))-......))))))---)((((((...(((.(((((...))))))))...)))))).------------- ( -33.00)
>DroSec_CAF1 3930 91 + 1
UUUGGCAGUUUUAAUUGGCCGGUCA-GCGCCGUUGGCCAC-GUUUUCAGCUGC---CCAGCGCUUCAGCUGAAAUGACAUUUCGUUAUUGUGCUGG-------------
...(((((((..(((((((((((..-..)))...))))).-)))...))))))---)((((((...(((.(((((...))))))))...)))))).------------- ( -32.00)
>DroSim_CAF1 3982 91 + 1
UUUGGCAGUUUUAAUUGGCCGGUCA-GCGCCGUUGGCCAU-GUUUCCAGCUGC---CCAGCGCUUCAGCUGAAAUGACAUUUCGUUAUUGUGCUGG-------------
...(((((((..(((((((((((..-..)))...))))).-)))...))))))---)((((((...(((.(((((...))))))))...)))))).------------- ( -32.00)
>DroEre_CAF1 4122 91 + 1
UUUGGCAGUUUUAAUUGGCCGGCCA-GUGCCGUUGGCCAC-GUUUUCAGCUGC---CCAGCGCUGCAACUGAAAUGACAUUUCGUUAUUGUGCUGG-------------
...(((((((..(((((((((((..-.....)))))))).-)))...))))))---)((((((...(((.(((((...))))))))...)))))).------------- ( -34.30)
>DroYak_CAF1 4229 94 + 1
UUUGGCAGUUUUAAUUGGCUGGUCA-UUGCUGUUGGCCAC-GUUUUCAGCUGCUGGCCAAAGCUGCAACUGAAAUGACAUUUCGUUAUUGUGCUGG-------------
....(((((((....((((..((..-..((((..(((...-)))..)))).))..)))))))))))......((((((.....)))))).......------------- ( -28.40)
>DroAna_CAF1 4333 107 + 1
UUUGGCAGUUUUAAUUGCCUGGUCAAGUGUUUUUGGCCAUAGUUUCUAGCCUU--GGAAUUGCAGCAGCUAAAAUAACAUUUUGUUAUUGGAUUGGUGGUGGAUGCCCA
...((((......((..((((((((((....))))))))(((((.((.((...--......)))).))))).((((((.....)))))).....))..))...)))).. ( -27.30)
>consensus
UUUGGCAGUUUUAAUUGGCCGGUCA_GCGCCGUUGGCCAC_GUUUUCAGCUGC___CCAGCGCUGCAGCUGAAAUGACAUUUCGUUAUUGUGCUGG_____________
....((((((..(((((((((((.....)))...)))))..)))...))))))...(((((((...(((.(((((...))))))))...)))))))............. (-21.11 = -21.03 +  -0.08)

alignment

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secondary structure

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Window 8

Location 26,929,174 – 26,929,265
Length 91
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 82.04
Mean single sequence MFE -25.65
Consensus MFE -14.96
Energy contribution -14.96
Covariance contribution 0.00
Combinations/Pair 1.29
Mean z-score -2.29
Structure conservation index 0.58
SVM decision value 0.24
SVM RNA-class probability 0.649121
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26929174 91 - 27905053
-------------CCAGCACAAUAACGAAAUGUCAUUUCAGCUGAAGCGCUGG---GCAGCUGAAAAC-UUGGCCAACGGCGC-UGACCGGCCAAUUAAAACUGCCAAA
-------------.((((........(((((...))))).((....))))))(---((((........-((((((...((...-...))))))))......)))))... ( -25.94)
>DroSec_CAF1 3930 91 - 1
-------------CCAGCACAAUAACGAAAUGUCAUUUCAGCUGAAGCGCUGG---GCAGCUGAAAAC-GUGGCCAACGGCGC-UGACCGGCCAAUUAAAACUGCCAAA
-------------.((((........(((((...))))).((....))))))(---((((........-.(((((...((...-...))))))).......)))))... ( -25.99)
>DroSim_CAF1 3982 91 - 1
-------------CCAGCACAAUAACGAAAUGUCAUUUCAGCUGAAGCGCUGG---GCAGCUGGAAAC-AUGGCCAACGGCGC-UGACCGGCCAAUUAAAACUGCCAAA
-------------.((((........(((((...))))).((....))))))(---((((.((....)-)(((((...((...-...))))))).......)))))... ( -28.60)
>DroEre_CAF1 4122 91 - 1
-------------CCAGCACAAUAACGAAAUGUCAUUUCAGUUGCAGCGCUGG---GCAGCUGAAAAC-GUGGCCAACGGCAC-UGGCCGGCCAAUUAAAACUGCCAAA
-------------.((((.(..(((((((((...))))).))))..).))))(---((((........-.(((((...(((..-..)))))))).......)))))... ( -29.99)
>DroYak_CAF1 4229 94 - 1
-------------CCAGCACAAUAACGAAAUGUCAUUUCAGUUGCAGCUUUGGCCAGCAGCUGAAAAC-GUGGCCAACAGCAA-UGACCAGCCAAUUAAAACUGCCAAA
-------------...(((..........((((..((((((((((.((....))..))))))))))))-))(((...((....-))....))).........))).... ( -23.00)
>DroAna_CAF1 4333 107 - 1
UGGGCAUCCACCACCAAUCCAAUAACAAAAUGUUAUUUUAGCUGCUGCAAUUCC--AAGGCUAGAAACUAUGGCCAAAAACACUUGACCAGGCAAUUAAAACUGCCAAA
(((.(((...............((((.....))))((((((((..((......)--).))))))))...))).)))..............((((........))))... ( -20.40)
>consensus
_____________CCAGCACAAUAACGAAAUGUCAUUUCAGCUGAAGCGCUGG___GCAGCUGAAAAC_GUGGCCAACGGCAC_UGACCGGCCAAUUAAAACUGCCAAA
................(((................(((((((((.............)))))))))....(((((..............)))))........))).... (-14.96 = -14.96 +   0.00)

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 13:47:46 2006