Locus 3763

Sequence ID 3R_DroMel_CAF1
Location 10,205,834 – 10,205,965
Length 131
Max. P 0.857654
window6026 window6027 window6028

overview

Window 6

Location 10,205,834 – 10,205,930
Length 96
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 82.64
Mean single sequence MFE -20.88
Consensus MFE -15.66
Energy contribution -15.82
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.75
SVM decision value 0.81
SVM RNA-class probability 0.857654
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10205834 96 + 27905053
AGC----------------C-----GCCUG-CCGCCCACAAUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGCAUUUUGUAUUUAUUUGCUACACUUU
(((----------------.-----.....-..(((.((((......((((....)))).....)))))))......(((((.......)))))..............)))....... ( -19.00)
>DroVir_CAF1 64880 102 + 1
AUC---------CUAUGG-U-----G-GUGCAAGCCCACAAUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGAUACACUUU
...---------....((-(-----(-.(((((..((((((......((((....)))).....))))))......)))))..((((...(((((.....)))))...)))))))).. ( -23.70)
>DroGri_CAF1 68408 102 + 1
AUA---------CUUUGC-U-----G-CCACACGCCCUCAAUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGCUACACUUU
(((---------..(((.-.-----(-(.....))...)))..))).((((....))))......((((((..(((.(((((...((....))...))))).)))...)))))).... ( -19.40)
>DroYak_CAF1 68902 111 + 1
AGCACAACCCCCCCUCCACC-----GCC--GCCACCCACAAUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGCAUUUUGUAUUUAUUUGCUACACUUU
((((................-----...--.....((((((......((((....)))).....)))))).......(((((.......))))).............))))....... ( -20.10)
>DroMoj_CAF1 71425 102 + 1
AUC---------UCUCGA-U-----G-GCACACGCCCACAGUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGCUACACUUU
...---------......-.-----(-((....)))...........((((....))))......((((((..(((.(((((...((....))...))))).)))...)))))).... ( -22.20)
>DroAna_CAF1 57344 109 + 1
CCC--------CACCCUACGGCCUGGCCC-GCCGCCCACAAUUUAUAAGCCCUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGCAUUUUGUAUUUAUUUGCUACACUUU
...--------.......((((.......-)))).((((((......((((....)))).....)))))).......(((((.......)))))....(((......)))........ ( -20.90)
>consensus
AUC_________CCUCGA_U_____G_CC_CACGCCCACAAUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGCUACACUUU
...............................................((((....))))......((((((..(((.(((((..............))))).)))...)))))).... (-15.66 = -15.82 +   0.17)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,205,834 – 10,205,930
Length 96
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 82.64
Mean single sequence MFE -21.96
Consensus MFE -13.58
Energy contribution -13.97
Covariance contribution 0.39
Combinations/Pair 1.06
Mean z-score -2.35
Structure conservation index 0.62
SVM decision value 0.27
SVM RNA-class probability 0.663432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10205834 96 - 27905053
AAAGUGUAGCAAAUAAAUACAAAAUGCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAAGGCUUAUAAAUUGUGGGCGG-CAGGC-----G----------------GCU
....(((.((..............(((((.......))))).......((((((..(((((((....))).))))..)))))))).)-))...-----.----------------... ( -21.90)
>DroVir_CAF1 64880 102 - 1
AAAGUGUAUCAAAUAAAUACAAAAUUCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAAGGCUUAUAAAUUGUGGGCUUGCAC-C-----A-CCAUAG---------GAU
....(((((.......)))))................((((.....((((((((..(((((((....))).))))..)))).))))))))(-(-----.-.....)---------).. ( -19.40)
>DroGri_CAF1 68408 102 - 1
AAAGUGUAGCAAAUAAAUACAAAAUUCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAAGGCUUAUAAAUUGAGGGCGUGUGG-C-----A-GCAAAG---------UAU
....((((.........))))...............((((..(((..(((.(((..(((((((....))).))))..)))..)))...)))-.-----.-))))..---------... ( -19.20)
>DroYak_CAF1 68902 111 - 1
AAAGUGUAGCAAAUAAAUACAAAAUGCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAAGGCUUAUAAAUUGUGGGUGGC--GGC-----GGUGGAGGGGGGGUUGUGCU
..((..((((.......(((....(((((.......)))))......(((((..(((..((((....)))).....)))....)))))--...-----.)))........))))..)) ( -26.16)
>DroMoj_CAF1 71425 102 - 1
AAAGUGUAGCAAAUAAAUACAAAAUUCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAAGGCUUAUAAACUGUGGGCGUGUGC-C-----A-UCGAGA---------GAU
...(..((((.....................(((.......)))....(((((...(((((((....))).))))...))))))).))..)-.-----(-((....---------))) ( -18.60)
>DroAna_CAF1 57344 109 - 1
AAAGUGUAGCAAAUAAAUACAAAAUGCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAGGGCUUAUAAAUUGUGGGCGGC-GGGCCAGGCCGUAGGGUG--------GGG
....((((.........))))...(((((.......)))))(((....((((((..(((((((....))).))))..))))))(((((-.......)))))..))).--------... ( -26.50)
>consensus
AAAGUGUAGCAAAUAAAUACAAAAUGCAAAAGAUAAUUGCAAUCAAAGCCACAAAAUGUAGCCAAAAGGCUUAUAAAUUGUGGGCGGG_GG_C_____A_UCGAGG_________GAU
........((.....................(((.......)))....((((((..(((((((....))).))))..))))))))................................. (-13.58 = -13.97 +   0.39)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,205,852 – 10,205,965
Length 113
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 85.38
Mean single sequence MFE -23.45
Consensus MFE -15.66
Energy contribution -15.82
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.67
SVM decision value -0.03
SVM RNA-class probability 0.518970
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10205852 113 + 27905053
A-UUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGCAUUUUGUAUUUAUUUGCUACACUUU-GGGCAAUUGUCCGCA-UUCGGCCUUUGUCUCUGGUU
.-......((((....)))).......(((((..(((.(((((..............))))).)))...)))))(((..-((((((..(.(((..-..))))..))))))..))). ( -27.24)
>DroVir_CAF1 64904 109 + 1
A-UUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGAUACACUUU-GCCCAAUUGUACGUUCAUCGGCUUUUGUAUU-----
.-.....(((((....((((((.....)))))).(((.(((((((.((....))....((((((.....))))))....-....)))))))...)))..))))).......----- ( -21.80)
>DroGri_CAF1 68432 109 + 1
A-UUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGCUACACUUU-GCCCAGUUGUUCGUUCAACGGCUUUUGUAUU-----
.-.....(((((....(((.......((((((..(((.(((((...((....))...))))).)))...))))))....-)))..((((......))))))))).......----- ( -25.90)
>DroWil_CAF1 73665 96 + 1
AGUUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGCAUUUUGUAUUUAUUUGCUACACUUUUGCCCAAUUGUUCUCG-U-------------------
........((((....))))(((..(((.(((......(((((.......)))))....(((......))).........)))))).))).....-.------------------- ( -17.30)
>DroMoj_CAF1 71449 109 + 1
G-UUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGCUACACUUU-GUCCAAUUGUUCGCUCAUCGGCUUUUGUAUU-----
.-.....(((((..((((..(((...((((((..(((.(((((...((....))...))))).)))...))))))...)-)))))).((......))..))))).......----- ( -22.70)
>DroAna_CAF1 57375 114 + 1
A-UUUAUAAGCCCUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGCAUUUUGUAUUUAUUUGCUACACUUU-GGGCAAUUGUCCGUUUUUCGGCCUUUGUCUCUGCCA
.-.............((((..((...((((((..(((.(((((..............))))).)))...))))))...)-)(((((..(.(((.....))))..)))))...)))) ( -25.74)
>consensus
A_UUUAUAAGCCUUUUGGCUACAUUUUGUGGCUUUGAUUGCAAUUAUCUUUUGAAUUUUGUAUUUAUUUGCUACACUUU_GCCCAAUUGUUCGCUCAUCGGCUUUUGUAUU_____
........((((....))))......((((((..(((.(((((..............))))).)))...))))))......................................... (-15.66 = -15.82 +   0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:25 2006