Locus 7861

Sequence ID X_DroMel_CAF1
Location 19,582,560 – 19,582,779
Length 219
Max. P 0.991342
window12894 window12895 window12896 window12897 window12898 window12899

overview

Window 4

Location 19,582,560 – 19,582,680
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.67
Mean single sequence MFE -44.70
Consensus MFE -38.28
Energy contribution -38.36
Covariance contribution 0.08
Combinations/Pair 1.22
Mean z-score -1.77
Structure conservation index 0.86
SVM decision value 1.19
SVM RNA-class probability 0.927974
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19582560 120 + 22224390
UUGUCGCGGUUGCGCGCGCAACUCGCAACGGUCUGGUAUCGAUCACAGCUGCGAGCAGGCUGCCAGAUCGCUUCCCGUUCGGGAACGAUUUCGCAUCGAUUUUCGAUUGCUGGCCGGUAU
.....((((((((....))))).)))..(((.(..(((((((.....(.(((((((.....))..(((((.(((((....))))))))))))))).).....)))).)))..)))).... ( -47.70)
>DroSec_CAF1 2481 120 + 1
UUGUCGCGGUUGCGCGCGCAAUUCGCAACGGUCUGUUAUCGAUCACAGCCGCGAGCAGGCUGCCAGAUCGCUUCCCGUAUGGGAACGAUUUCGCAUCAAUUUUCGAUUGCUGACCGGUAU
.....((((((((....)))).))))..(((((.((.(((((....((((.......))))((.((((((.(((((....))))))))))).))........))))).)).))))).... ( -47.40)
>DroSim_CAF1 2487 120 + 1
UUGUCGCGGUUGCGCGCGCAAUUCGCAACGGUCUGUUAUCGAUCACAGCCGCGAGCAGGCUGCCAGAUCGCUUCCCGUAUGGGAACGAUUUCGCAUCAAUUUUCGAUUGCUGGCCGGUAU
.....((((((((....)))).))))..(((((.((.(((((....((((.......))))((.((((((.(((((....))))))))))).))........))))).)).))))).... ( -46.80)
>DroEre_CAF1 2438 120 + 1
UUGUGGCGGUUGCGCGCGCAACUCGCAACGGUCUGUUAUCGAUCACAGCUGCGAACAUGCUGCCAGAUCACCUCUUCUAUGAAAAUGAUACUGUAUCGAUUUCCGAUUGCUGGCCGGUAU
.....((((((((....))))).)))..(((((.((.(((((((.((((((....)).))))...))))...........((((.(((((...))))).)))).))).)).))))).... ( -36.80)
>DroYak_CAF1 2326 120 + 1
UUGUUGCGGUUGCGCGCGCAACUCGCAACGGUCUGUUAUCGAUCACAGCUGCGAGCAGGCUGCCAGACUGCUCCCCUUAUGGGAACAAUUCUGUUUCGAUUUCCGAUUGCUGGCCAGUAU
..(((((((((((....))))).))))))((((.((.(((((((((((....((((((.........))))))(((....))).......))))...)))...)))).)).))))..... ( -44.80)
>consensus
UUGUCGCGGUUGCGCGCGCAACUCGCAACGGUCUGUUAUCGAUCACAGCUGCGAGCAGGCUGCCAGAUCGCUUCCCGUAUGGGAACGAUUUCGCAUCGAUUUUCGAUUGCUGGCCGGUAU
.....((((((((....))))).)))..(((((.((.((((.....((((.......))))((.((((((.(((((....))))))))))).)).........)))).)).))))).... (-38.28 = -38.36 +   0.08)

alignment

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secondary structure

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Window 5

Location 19,582,560 – 19,582,680
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.67
Mean single sequence MFE -44.46
Consensus MFE -36.90
Energy contribution -35.50
Covariance contribution -1.40
Combinations/Pair 1.29
Mean z-score -2.40
Structure conservation index 0.83
SVM decision value 2.26
SVM RNA-class probability 0.991342
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19582560 120 - 22224390
AUACCGGCCAGCAAUCGAAAAUCGAUGCGAAAUCGUUCCCGAACGGGAAGCGAUCUGGCAGCCUGCUCGCAGCUGUGAUCGAUACCAGACCGUUGCGAGUUGCGCGCGCAACCGCGACAA
....((((((((.((((.....))))((((.(((((((((....))).))))))...((.....)))))).)))).).)))..........((((((.(((((....))))))))))).. ( -45.50)
>DroSec_CAF1 2481 120 - 1
AUACCGGUCAGCAAUCGAAAAUUGAUGCGAAAUCGUUCCCAUACGGGAAGCGAUCUGGCAGCCUGCUCGCGGCUGUGAUCGAUAACAGACCGUUGCGAAUUGCGCGCGCAACCGCGACAA
.....((((.(((.((((...)))))))...(((.(((((....)))))..((((..((((((.......)))))))))))))....))))((((((..((((....)))).)))))).. ( -44.40)
>DroSim_CAF1 2487 120 - 1
AUACCGGCCAGCAAUCGAAAAUUGAUGCGAAAUCGUUCCCAUACGGGAAGCGAUCUGGCAGCCUGCUCGCGGCUGUGAUCGAUAACAGACCGUUGCGAAUUGCGCGCGCAACCGCGACAA
......((.(((((((((...)))))((.(.(((((((((....))).)))))).).))....)))).))((((((........)))).))((((((..((((....)))).)))))).. ( -41.90)
>DroEre_CAF1 2438 120 - 1
AUACCGGCCAGCAAUCGGAAAUCGAUACAGUAUCAUUUUCAUAGAAGAGGUGAUCUGGCAGCAUGUUCGCAGCUGUGAUCGAUAACAGACCGUUGCGAGUUGCGCGCGCAACCGCCACAA
.....(((..((((.(((..((((((.(((.((((((((.......)))))))))))(((((.((....))))))).))))))......)))))))(.(((((....))))))))).... ( -40.50)
>DroYak_CAF1 2326 120 - 1
AUACUGGCCAGCAAUCGGAAAUCGAAACAGAAUUGUUCCCAUAAGGGGAGCAGUCUGGCAGCCUGCUCGCAGCUGUGAUCGAUAACAGACCGUUGCGAGUUGCGCGCGCAACCGCAACAA
...(((.((.......))..(((((..((((.((((((((.....))))))))))))(((((.((....)))))))..)))))..)))...((((((.(((((....))))))))))).. ( -50.00)
>consensus
AUACCGGCCAGCAAUCGAAAAUCGAUGCGAAAUCGUUCCCAUACGGGAAGCGAUCUGGCAGCCUGCUCGCAGCUGUGAUCGAUAACAGACCGUUGCGAGUUGCGCGCGCAACCGCGACAA
.....((.(....(((((.............(((((((((....))))).))))...(((((.((....)))))))..)))))....).))((((((.(((((....))))))))))).. (-36.90 = -35.50 +  -1.40)

alignment

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secondary structure

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Window 6

Location 19,582,640 – 19,582,754
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.73
Mean single sequence MFE -33.54
Consensus MFE -19.90
Energy contribution -20.42
Covariance contribution 0.52
Combinations/Pair 1.40
Mean z-score -1.74
Structure conservation index 0.59
SVM decision value 0.04
SVM RNA-class probability 0.554490
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19582640 114 + 22224390
GGGAACGAUUUCGCAUCGAUUUUCGAUUGCUGGCCGGUAUAAUUUGAAAAUGUUACUUU-----GCUGACCGGAUUUUGGUCCU-UGGCCAGAUGUUGGCCAUGAAUCUAAAAGCCAGUA
(..((((((.....)))).))..)...(((((((((((.(((..(((.....)))..))-----)...))))..((((((....-(((((((...))))))).....))))))))))))) ( -32.20)
>DroSec_CAF1 2561 118 + 1
GGGAACGAUUUCGCAUCAAUUUUCGAUUGCUGACCGGUAUAAUUUGAA-AAGUAACUUUUUCAAACUGACCGAAUUUUGGUUCU-UGGCCAGAUGUUGGCCAUGAUUCUAAAAGCUAGUA
(.(((....))).).............(((((..((((....((((((-(((....)))))))))...))))..((((((.((.-(((((((...))))))).))..))))))..))))) ( -28.30)
>DroSim_CAF1 2567 114 + 1
GGGAACGAUUUCGCAUCAAUUUUCGAUUGCUGGCCGGUAUAAUUUGAAAAAGUUACUUU-----GCUGACCGAAUUUUGGUUCU-UGGCCAGAUGUUGGCCAUGAUUCUAAAAGCCAGUA
(.(((....))).).............((((((((((((((((((....))))))...)-----))))......((((((.((.-(((((((...))))))).))..))))))))))))) ( -32.70)
>DroEre_CAF1 2518 115 + 1
GAAAAUGAUACUGUAUCGAUUUCCGAUUGCUGGCCGGUAUAAUUUGAAAAAAUUACUGC-----GCCACUCGGACUUUGAUCCUUUGGUCAGGUCCUGGUUGGGAUUCUUAAAGCCAGCA
((((.(((((...))))).))))....(((((((..(((((((((....)))))).)))-----.(((((.((((((.((((....)))))))))).)).)))..........))))))) ( -36.40)
>DroYak_CAF1 2406 114 + 1
GGGAACAAUUCUGUUUCGAUUUCCGAUUGCUGGCCAGUAUAAUUUGAAAAAGUUACUGA-----GCUGCCCGGACUUUUGUCCU-UGGCCAGGUCCUGGCCAGGAUUUUUAAGGCCUGAA
.((((((....))))))....((((...((.((((((((..((((....))))))))).-----))))).))))(((..(((((-.((((((...)))))))))))....)))....... ( -38.10)
>consensus
GGGAACGAUUUCGCAUCGAUUUUCGAUUGCUGGCCGGUAUAAUUUGAAAAAGUUACUUU_____GCUGACCGGAUUUUGGUCCU_UGGCCAGAUGUUGGCCAUGAUUCUAAAAGCCAGUA
(((((((((.....)))).)))))...(((((((.....((((((....))))))...........((.((((..(((((((....)))))))..)))).))...........))))))) (-19.90 = -20.42 +   0.52)

alignment

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secondary structure

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Window 7

Location 19,582,640 – 19,582,754
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.73
Mean single sequence MFE -27.86
Consensus MFE -16.78
Energy contribution -16.70
Covariance contribution -0.08
Combinations/Pair 1.26
Mean z-score -1.73
Structure conservation index 0.60
SVM decision value 0.05
SVM RNA-class probability 0.560587
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19582640 114 - 22224390
UACUGGCUUUUAGAUUCAUGGCCAACAUCUGGCCA-AGGACCAAAAUCCGGUCAGC-----AAAGUAACAUUUUCAAAUUAUACCGGCCAGCAAUCGAAAAUCGAUGCGAAAUCGUUCCC
..((((((..........((((((.....))))))-..((((.......))))...-----........................))))))..((((.....))))(((....))).... ( -28.20)
>DroSec_CAF1 2561 118 - 1
UACUAGCUUUUAGAAUCAUGGCCAACAUCUGGCCA-AGAACCAAAAUUCGGUCAGUUUGAAAAAGUUACUU-UUCAAAUUAUACCGGUCAGCAAUCGAAAAUUGAUGCGAAAUCGUUCCC
..................((((((.....))))))-.((((......(((((.((((((((((......))-))))))))..)))))...(((.((((...)))))))......)))).. ( -28.40)
>DroSim_CAF1 2567 114 - 1
UACUGGCUUUUAGAAUCAUGGCCAACAUCUGGCCA-AGAACCAAAAUUCGGUCAGC-----AAAGUAACUUUUUCAAAUUAUACCGGCCAGCAAUCGAAAAUUGAUGCGAAAUCGUUCCC
..(((((........((.((((((.....))))))-.)).........((((....-----.....................)))))))))..(((((...)))))(((....))).... ( -22.91)
>DroEre_CAF1 2518 115 - 1
UGCUGGCUUUAAGAAUCCCAACCAGGACCUGACCAAAGGAUCAAAGUCCGAGUGGC-----GCAGUAAUUUUUUCAAAUUAUACCGGCCAGCAAUCGGAAAUCGAUACAGUAUCAUUUUC
(((((((..........(((....((((.(((((...)).)))..))))...)))(-----(..(((((((....)))))))..)))))))))...((((((.((((...)))))))))) ( -28.80)
>DroYak_CAF1 2406 114 - 1
UUCAGGCCUUAAAAAUCCUGGCCAGGACCUGGCCA-AGGACAAAAGUCCGGGCAGC-----UCAGUAACUUUUUCAAAUUAUACUGGCCAGCAAUCGGAAAUCGAAACAGAAUUGUUCCC
.................((((((((((.(((.((.-.((((....)))))).))).-----)).((((.((....)).)))).)))))))).....((((.((......))....)))). ( -31.00)
>consensus
UACUGGCUUUUAGAAUCAUGGCCAACAUCUGGCCA_AGGACCAAAAUCCGGUCAGC_____AAAGUAACUUUUUCAAAUUAUACCGGCCAGCAAUCGAAAAUCGAUGCGAAAUCGUUCCC
..((((((...........(((((.....)))))...(((......)))....................................))))))..(((((...))))).............. (-16.78 = -16.70 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,582,680 – 19,582,779
Length 99
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 78.30
Mean single sequence MFE -29.44
Consensus MFE -19.52
Energy contribution -17.12
Covariance contribution -2.40
Combinations/Pair 1.55
Mean z-score -2.32
Structure conservation index 0.66
SVM decision value 1.84
SVM RNA-class probability 0.979415
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19582680 99 + 22224390
AAUUUGAAAAUGUUACUUU-----GCUGACCGGAUUUUGGUCCU-UGGCCAGAUGUUGGCCAUGAAUCUAAAAGCCAGUAUUUAGUAACUUGCGUUGAUUGCAGC
...........((((((.(-----((((...((((....)))).-(((((((...))))))).............)))))...))))))(((((.....))))). ( -27.30)
>DroSec_CAF1 2601 103 + 1
AAUUUGAA-AAGUAACUUUUUCAAACUGACCGAAUUUUGGUUCU-UGGCCAGAUGUUGGCCAUGAUUCUAAAAGCUAGUAAUUAGCAACUUGCGUUGAUUGCAGC
..((((((-(((....))))))))).........((((((.((.-(((((((...))))))).))..))))))(((.(((((((((.......)))))))))))) ( -29.40)
>DroSim_CAF1 2607 99 + 1
AAUUUGAAAAAGUUACUUU-----GCUGACCGAAUUUUGGUUCU-UGGCCAGAUGUUGGCCAUGAUUCUAAAAGCCAGUAAUUAGCAACUUGCGUUGAUUGCAGC
(((((....))))).....-----(((....(..((((((.((.-(((((((...))))))).))..))))))..).(((((((((.......)))))))))))) ( -26.20)
>DroEre_CAF1 2558 100 + 1
AAUUUGAAAAAAUUACUGC-----GCCACUCGGACUUUGAUCCUUUGGUCAGGUCCUGGUUGGGAUUCUUAAAGCCAGCAUUUAGCAACUUCUGCUGAGUGCAAC
(((((....))))).....-----.(((((.((((((.((((....)))))))))).)).)))..............((((((((((.....))))))))))... ( -31.20)
>DroYak_CAF1 2446 99 + 1
AAUUUGAAAAAGUUACUGA-----GCUGCCCGGACUUUUGUCCU-UGGCCAGGUCCUGGCCAGGAUUUUUAAGGCCUGAAUUUAGUAGCUUCUGCUGAGUGCAAC
.........((((((((((-----.(.(((.((((....))))(-(((((((...)))))))).........)))..)...)))))))))).(((.....))).. ( -33.10)
>consensus
AAUUUGAAAAAGUUACUUU_____GCUGACCGGAUUUUGGUCCU_UGGCCAGAUGUUGGCCAUGAUUCUAAAAGCCAGUAUUUAGCAACUUGCGUUGAUUGCAGC
..........................((.((((..(((((((....)))))))..)))).))...............(((((((((.......)))))))))... (-19.52 = -17.12 +  -2.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,582,680 – 19,582,779
Length 99
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 78.30
Mean single sequence MFE -25.50
Consensus MFE -15.14
Energy contribution -13.50
Covariance contribution -1.64
Combinations/Pair 1.50
Mean z-score -2.35
Structure conservation index 0.59
SVM decision value 1.66
SVM RNA-class probability 0.970560
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19582680 99 - 22224390
GCUGCAAUCAACGCAAGUUACUAAAUACUGGCUUUUAGAUUCAUGGCCAACAUCUGGCCA-AGGACCAAAAUCCGGUCAGC-----AAAGUAACAUUUUCAAAUU
((((.....(((....))).......(((((.((((.(.(((.((((((.....))))))-.)))).)))).)))))))))-----................... ( -26.90)
>DroSec_CAF1 2601 103 - 1
GCUGCAAUCAACGCAAGUUGCUAAUUACUAGCUUUUAGAAUCAUGGCCAACAUCUGGCCA-AGAACCAAAAUUCGGUCAGUUUGAAAAAGUUACUU-UUCAAAUU
((((.(((((((....))))...)))..))))........((.((((((.....))))))-.))(((.......))).((((((((((......))-)))))))) ( -25.00)
>DroSim_CAF1 2607 99 - 1
GCUGCAAUCAACGCAAGUUGCUAAUUACUGGCUUUUAGAAUCAUGGCCAACAUCUGGCCA-AGAACCAAAAUUCGGUCAGC-----AAAGUAACUUUUUCAAAUU
((((....((((....))))......((((..((((.(..((.((((((.....))))))-.))..)))))..))))))))-----................... ( -25.50)
>DroEre_CAF1 2558 100 - 1
GUUGCACUCAGCAGAAGUUGCUAAAUGCUGGCUUUAAGAAUCCCAACCAGGACCUGACCAAAGGAUCAAAGUCCGAGUGGC-----GCAGUAAUUUUUUCAAAUU
.((((..((((..((((((((.....)).)))))).....(((......))).))))(((..((((....))))...))).-----))))............... ( -20.60)
>DroYak_CAF1 2446 99 - 1
GUUGCACUCAGCAGAAGCUACUAAAUUCAGGCCUUAAAAAUCCUGGCCAGGACCUGGCCA-AGGACAAAAGUCCGGGCAGC-----UCAGUAACUUUUUCAAAUU
(((((....(((....)))...........((((.........(((((((...)))))))-.((((....))))))))...-----...)))))........... ( -29.50)
>consensus
GCUGCAAUCAACGCAAGUUGCUAAAUACUGGCUUUUAGAAUCAUGGCCAACAUCUGGCCA_AGGACCAAAAUCCGGUCAGC_____AAAGUAACUUUUUCAAAUU
((((..((((((....))).........................(((((.....)))))...(((......))))))))))........................ (-15.14 = -13.50 +  -1.64)

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 12:49:24 2006