Locus 5834

Sequence ID 2R_DroMel_CAF1
Location 18,485,645 – 18,485,833
Length 188
Max. P 0.987243
window9344 window9345 window9346 window9347 window9348 window9349

overview

Window 4

Location 18,485,645 – 18,485,737
Length 92
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 76.87
Mean single sequence MFE -21.97
Consensus MFE -16.64
Energy contribution -17.53
Covariance contribution 0.89
Combinations/Pair 1.10
Mean z-score -1.51
Structure conservation index 0.76
SVM decision value 0.79
SVM RNA-class probability 0.852521
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18485645 92 + 20766785
GGAAAUAUAUUUAAUAGCUGUGCGAAAUUGGCGCAGCUUGUAAACACACACACACACACACAGGGCCAGAA-AGCCAAGGCAACUGCGACUGU
.........((((..((((((((.......))))))))..))))...............(((((((.....-.))).((....))....)))) ( -22.90)
>DroSim_CAF1 42930 82 + 1
GGAAAUAUAUUUAAUAGCUGUGCGAAAUUGGCGCAGCUUGUAAACAC----------ACACAGGGCCAGAA-AGCCAAGGCAACUGCGACUGU
.........((((..((((((((.......))))))))..))))...----------..(((((((.....-.))).((....))....)))) ( -22.90)
>DroAna_CAF1 40337 80 + 1
AGGAAUAUAUUUAAUAGCAGCGCGAAAUUGGCGCAGCUUGUAAACAG-------------GAGGGCCGAAGCGGGUGGGGCAGUUGCAACUGU
................(((((......(((((.(..((((....)))-------------)..)))))).((.......)).)))))...... ( -20.10)
>consensus
GGAAAUAUAUUUAAUAGCUGUGCGAAAUUGGCGCAGCUUGUAAACAC__________ACACAGGGCCAGAA_AGCCAAGGCAACUGCGACUGU
.........((((..((((((((.......))))))))..))))...............(((((((.......)))...((....))..)))) (-16.64 = -17.53 +   0.89)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,485,645 – 18,485,737
Length 92
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 76.87
Mean single sequence MFE -22.13
Consensus MFE -12.65
Energy contribution -14.43
Covariance contribution 1.78
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.57
SVM decision value 0.62
SVM RNA-class probability 0.801987
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18485645 92 - 20766785
ACAGUCGCAGUUGCCUUGGCU-UUCUGGCCCUGUGUGUGUGUGUGUGUGUUUACAAGCUGCGCCAAUUUCGCACAGCUAUUAAAUAUAUUUCC
(((..(((((..(((......-....))).)))))..)))....(((((((((..(((((.((.......)).)))))..))))))))).... ( -25.70)
>DroSim_CAF1 42930 82 - 1
ACAGUCGCAGUUGCCUUGGCU-UUCUGGCCCUGUGU----------GUGUUUACAAGCUGCGCCAAUUUCGCACAGCUAUUAAAUAUAUUUCC
((((...(((..((....)).-..)))...))))((----------(((((((..(((((.((.......)).)))))..))))))))).... ( -23.10)
>DroAna_CAF1 40337 80 - 1
ACAGUUGCAACUGCCCCACCCGCUUCGGCCCUC-------------CUGUUUACAAGCUGCGCCAAUUUCGCGCUGCUAUUAAAUAUAUUCCU
.((((....))))........((....))....-------------.((((((..(((.((((.......)))).)))..))))))....... ( -17.60)
>consensus
ACAGUCGCAGUUGCCUUGGCU_UUCUGGCCCUGUGU__________GUGUUUACAAGCUGCGCCAAUUUCGCACAGCUAUUAAAUAUAUUUCC
((((..((....))...((((.....))))))))............(((((((..(((((.((.......)).)))))..)))))))...... (-12.65 = -14.43 +   1.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,485,658 – 18,485,773
Length 115
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 68.11
Mean single sequence MFE -32.30
Consensus MFE -15.64
Energy contribution -15.95
Covariance contribution 0.31
Combinations/Pair 1.18
Mean z-score -1.87
Structure conservation index 0.48
SVM decision value 0.67
SVM RNA-class probability 0.817952
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18485658 115 + 20766785
AUAGCUGUGCGAAAUUGGCGCAGCUUGUAAACACACACACACACACACAGGGCCAGAA-AGCCAAGGCAACUGCGACUGUAACUGCAAUUAAAAGCCAGCCAGAUAGUGCAC-GAGU-
...((((((((...(((((...((((((......))..........(((((((.....-.))).((....))....))))............))))..)))))....)))))-.)))- ( -28.10)
>DroVir_CAF1 56881 91 + 1
AUAGCAGCGCGAAAUUGGCGCAGCUUGUAAACAAG---------GCAAAGGGCGCAGC-AGC-----------------CAACAGCAAUUAAAAGCCUGCAGGGUCACGCGCUCGCUG
.((((((((((....((((((((((((....))))---------((....(((.....-.))-----------------)....))..........))))...)))))))))).)))) ( -31.10)
>DroSim_CAF1 42943 105 + 1
AUAGCUGUGCGAAAUUGGCGCAGCUUGUAAACAC----------ACACAGGGCCAGAA-AGCCAAGGCAACUGCGACUGUAACUGCAAUUAAAAGCCAGCCAGAUAGUGCAC-GGGU-
....(((((((...(((((...((((.(((.((.----------..(((((((.....-.))).((....))....))))...))...))).))))..)))))....)))))-))..- ( -31.00)
>DroAna_CAF1 40350 103 + 1
AUAGCAGCGCGAAAUUGGCGCAGCUUGUAAACAG-------------GAGGGCCGAAGCGGGUGGGGCAGUUGCAACUGUAACAGCAAUUAAAAGCCGGCCAGACAACGCCC-CACC-
.......(((....(((((.(..((((....)))-------------)..)))))).)))((((((((.((((...(((...(.((........)).)..))).))))))))-))))- ( -39.00)
>consensus
AUAGCAGCGCGAAAUUGGCGCAGCUUGUAAACAC__________ACACAGGGCCAAAA_AGCCAAGGCAACUGCGACUGUAACAGCAAUUAAAAGCCAGCCAGAUAACGCAC_CACU_
......(((((...(((((...((((.(((....................(((.......)))...((....))..............))).))))..)))))....)))))...... (-15.64 = -15.95 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,485,698 – 18,485,798
Length 100
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 73.15
Mean single sequence MFE -30.63
Consensus MFE -14.02
Energy contribution -15.47
Covariance contribution 1.45
Combinations/Pair 1.13
Mean z-score -2.64
Structure conservation index 0.46
SVM decision value 0.41
SVM RNA-class probability 0.725697
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18485698 100 - 20766785
CAUACUCACACAGAUACUCACGCACACUCGUGCACUAUCUGGCUGGCUUUUAAUUGCAGUUACAGUCGCAGUUGCCUUGGCU-UUCUGGCCCUGUGUGUGU
...((.(((((((........((((....)))).......((((((((..(((((((..........)))))))....))))-....))))))))))).)) ( -30.70)
>DroSim_CAF1 42977 96 - 1
CACACUCACACAGAUACUCACGCACACCCGUGCACUAUCUGGCUGGCUUUUAAUUGCAGUUACAGUCGCAGUUGCCUUGGCU-UUCUGGCCCUGUGU----
.......((((((........((((....)))).......((((((((..(((((((..........)))))))....))))-....))))))))))---- ( -26.20)
>DroAna_CAF1 40384 88 - 1
CACACACACACACACACUC------GGUGGGGCGUUGUCUGGCCGGCUUUUAAUUGCUGUUACAGUUGCAACUGCCCCACCCGCUUCGGCCCUC-------
...................------((((((((((((((((..((((........))))...)))..))))).)))))))).((....))....------- ( -35.00)
>consensus
CACACUCACACAGAUACUCACGCACACUCGUGCACUAUCUGGCUGGCUUUUAAUUGCAGUUACAGUCGCAGUUGCCUUGGCU_UUCUGGCCCUGUGU____
..........((((((..((((......))))...))))))...(((....((((((..........)))))))))..((((.....)))).......... (-14.02 = -15.47 +   1.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,485,737 – 18,485,833
Length 96
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 77.40
Mean single sequence MFE -30.00
Consensus MFE -19.98
Energy contribution -21.99
Covariance contribution 2.00
Combinations/Pair 1.08
Mean z-score -2.04
Structure conservation index 0.67
SVM decision value 1.47
SVM RNA-class probability 0.956430
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18485737 96 + 20766785
AACUGCAAUUAAAAGCCAGCCAGAUAGUGCACGAGUGUGCGUGAGUAUCUGUGUGAGUAUGCAUUUAUGUUGUGCACACAGCUG--CAUGUGCAAAUG
...((((......(((((..((((((.(.((((......))))).))))))..)).((.(((((.......))))).)).))).--....)))).... ( -27.20)
>DroSim_CAF1 43012 96 + 1
AACUGCAAUUAAAAGCCAGCCAGAUAGUGCACGGGUGUGCGUGAGUAUCUGUGUGAGUGUGCAUUUAUGCUGUGCACACAGCUG--CAUGUGCAAAUG
...((((......(((((..((((((.(.((((......))))).))))))..)).((((((((.......)))))))).))).--....)))).... ( -33.30)
>DroAna_CAF1 40417 88 + 1
AACAGCAAUUAAAAGCCGGCCAGACAACGCCCCACC------GAGUGUGUGUGUGUGUGUGCAUUUAUGUUGUGCACACACUGGGCCAGAUACA----
....((........)).((((.....(((((.(((.------..))).).))))((((((((((.......))))))))))..)))).......---- ( -29.50)
>consensus
AACUGCAAUUAAAAGCCAGCCAGAUAGUGCACGAGUGUGCGUGAGUAUCUGUGUGAGUGUGCAUUUAUGUUGUGCACACAGCUG__CAUGUGCAAAUG
....(((......(((..((((((((...((((......))))..)))))).))..((((((((.......)))))))).))).......)))..... (-19.98 = -21.99 +   2.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,485,737 – 18,485,833
Length 96
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 77.40
Mean single sequence MFE -27.07
Consensus MFE -17.10
Energy contribution -18.77
Covariance contribution 1.67
Combinations/Pair 1.09
Mean z-score -2.43
Structure conservation index 0.63
SVM decision value 2.07
SVM RNA-class probability 0.987243
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18485737 96 - 20766785
CAUUUGCACAUG--CAGCUGUGUGCACAACAUAAAUGCAUACUCACACAGAUACUCACGCACACUCGUGCACUAUCUGGCUGGCUUUUAAUUGCAGUU
...(((((.(((--((..(((((.....)))))..)))))..(((..((((((.....((((....))))..))))))..)))........))))).. ( -25.50)
>DroSim_CAF1 43012 96 - 1
CAUUUGCACAUG--CAGCUGUGUGCACAGCAUAAAUGCACACUCACACAGAUACUCACGCACACCCGUGCACUAUCUGGCUGGCUUUUAAUUGCAGUU
...(((((...(--((((.(((((((.........))))))).....((((((.....((((....))))..))))))))).)).......))))).. ( -26.80)
>DroAna_CAF1 40417 88 - 1
----UGUAUCUGGCCCAGUGUGUGCACAACAUAAAUGCACACACACACACACACUC------GGUGGGGCGUUGUCUGGCCGGCUUUUAAUUGCUGUU
----........((((.(((((((((.........))))))))).....(((....------.)))))))..........((((........)))).. ( -28.90)
>consensus
CAUUUGCACAUG__CAGCUGUGUGCACAACAUAAAUGCACACUCACACAGAUACUCACGCACACUCGUGCACUAUCUGGCUGGCUUUUAAUUGCAGUU
..............((((.(((((((.........))))))).....((((((..((((......))))...))))))))))((........)).... (-17.10 = -18.77 +   1.67)

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 11:55:40 2006