Locus 139

Sequence ID 3R_DroMel_CAF1
Location 740,034 – 740,227
Length 193
Max. P 0.848553
window223 window224 window225 window226

overview

Window 3

Location 740,034 – 740,149
Length 115
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 86.82
Mean single sequence MFE -31.75
Consensus MFE -25.60
Energy contribution -25.83
Covariance contribution 0.23
Combinations/Pair 1.17
Mean z-score -2.22
Structure conservation index 0.81
SVM decision value 0.58
SVM RNA-class probability 0.788918
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 740034 115 - 27905053
UACAUAU----GUAUAUGUUUGUAUAUGCAGAGGGACAUGUGUGUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUCUGCAUUUCUACUAUUCAGCAAGUGAGCAUAUGAUGUUCCU
......(----(((((((....)))))))).(((((((((((((((((((....)))))...............(((..(((..............)))..))))))))).)))))))) ( -30.34)
>DroSec_CAF1 7406 111 - 1
CACAUUUGUAUGUGUAUAUUUGUGUAUAUAGAGGGGCAUGUGUGUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUCUGCAUUUCUACUAGUCA--------GCAUAUGAUGUUCCU
.(((.(..((((((((.(..(((..((..((((((((.((.((..(((((....)))))...))))))))))))..))..)))..).)))......--------)))))..)))).... ( -32.30)
>DroSim_CAF1 7415 109 - 1
CACAUAUGUAUGUAUAUGUUUGUGUAUAUAGAGGGGCAUGU--GUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUCUGCAUUUCUACUAGUCA--------GCAUAUGAUGUUCCU
..(((((((((((((((....))))))))((((((((..((--..(((((....)))))...))..))))))))......................--------)))))))........ ( -32.60)
>consensus
CACAUAUGUAUGUAUAUGUUUGUGUAUAUAGAGGGGCAUGUGUGUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUCUGCAUUUCUACUAGUCA________GCAUAUGAUGUUCCU
..(((((((..(((((((....)))))))((((((((..((....(((((....)))))...))..))))))))..............................)))))))........ (-25.60 = -25.83 +   0.23)

alignment

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secondary structure

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Window 4

Location 740,074 – 740,189
Length 115
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 88.00
Mean single sequence MFE -25.57
Consensus MFE -23.55
Energy contribution -23.33
Covariance contribution -0.22
Combinations/Pair 1.17
Mean z-score -1.79
Structure conservation index 0.92
SVM decision value 0.78
SVM RNA-class probability 0.848553
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 740074 115 + 27905053
GACGAAGAAGGGCUGGCUCAGGCAAAAAUUUGCCACACACAUGUCCCUCUGCAUAUACAAACAUAUAC----AUAUGUAUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCCCCUAUACC
.....((..(((..(((((((((((....)))))................(((((((((.........----...))))))))).............))).)))...)))..))..... ( -25.00)
>DroSec_CAF1 7438 112 + 1
GACGAAGAAGGGCUGGCUCAGGCAAAAAUUUGCCACACACAUGCCCCUCUAUAUACACAAAUAUACACAUACAAAUGUGUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCC--U-----
.....(((.((((((.....(((((....))))).....)).)))).)))...(((((((((((((((((((....)))))))....)))))).......)).))))....--.----- ( -26.91)
>DroSim_CAF1 7447 110 + 1
GACGAAGAAGGGCUGGCUCAGGCAAAAAUUUGCCAC--ACAUGCCCCUCUAUAUACACAAACAUAUACAUACAUAUGUGUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCC--U-----
.....(((.((((((.....(((((....)))))..--.)).)))).))).....((((.((((((......)))))).))))............................--.----- ( -24.80)
>consensus
GACGAAGAAGGGCUGGCUCAGGCAAAAAUUUGCCACACACAUGCCCCUCUAUAUACACAAACAUAUACAUACAUAUGUGUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCC__U_____
.....(((.((((((.....(((((....))))).....)).)))).)))...........(((((((((....))))))))).................................... (-23.55 = -23.33 +  -0.22)

alignment

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secondary structure

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Window 5

Location 740,074 – 740,189
Length 115
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 88.00
Mean single sequence MFE -34.83
Consensus MFE -28.55
Energy contribution -29.23
Covariance contribution 0.68
Combinations/Pair 1.18
Mean z-score -2.23
Structure conservation index 0.82
SVM decision value 0.54
SVM RNA-class probability 0.776114
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 740074 115 - 27905053
GGUAUAGGGGGGUACAGCAUCAGAAUAAUAUAGGAGCACAUACAUAU----GUAUAUGUUUGUAUAUGCAGAGGGACAUGUGUGUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUC
.....((((((((...((.((((...............(((((((((----((...(.(((((....))))).).)))))))))))((((....))))))))))..))))))))..... ( -37.40)
>DroSec_CAF1 7438 112 - 1
-----A--GGGGUACAGCAUCAGAAUAAUAUAGGAGCACACACAUUUGUAUGUGUAUAUUUGUGUAUAUAGAGGGGCAUGUGUGUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUC
-----(--(((((...((.((((.............((((((((..(((.(.(((((((....))))))).)...)))))))))))((((....))))))))))..))))))....... ( -33.90)
>DroSim_CAF1 7447 110 - 1
-----A--GGGGUACAGCAUCAGAAUAAUAUAGGAGCACACACAUAUGUAUGUAUAUGUUUGUGUAUAUAGAGGGGCAUGU--GUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUC
-----.--..............(((...((((...(((((.(((((((....))))))).))))).))))(((((((..((--..(((((....)))))...))..))))))))))... ( -33.20)
>consensus
_____A__GGGGUACAGCAUCAGAAUAAUAUAGGAGCACACACAUAUGUAUGUAUAUGUUUGUGUAUAUAGAGGGGCAUGUGUGUGGCAAAUUUUUGCCUGAGCCAGCCCUUCUUCGUC
........(((((...((.((((...............(((((((((((.((((((((....)))))))).....)))))))))))((((....))))))))))..)))))........ (-28.55 = -29.23 +   0.68)

alignment

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secondary structure

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dotplot

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Window 6

Location 740,113 – 740,227
Length 114
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 84.16
Mean single sequence MFE -20.27
Consensus MFE -17.82
Energy contribution -17.17
Covariance contribution -0.66
Combinations/Pair 1.21
Mean z-score -1.48
Structure conservation index 0.88
SVM decision value 0.41
SVM RNA-class probability 0.727006
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 740113 114 + 27905053
CAUGUCCCUCUGCAUAUACAAACAUAUAC----AUAUGUAUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCCCCUAUACCCUAUACAUACCACCAAGUGUGUGCCAUAAAGAAAGGCU
...(((..((((((((((((.........----...)))))))))......................................(((((((......)))))))......)))..))). ( -19.00)
>DroSec_CAF1 7477 105 + 1
CAUGCCCCUCUAUAUACACAAAUAUACACAUACAAAUGUGUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCC--U-----------AUACCUCGAAGUGUGUGCCAUAAAGAAAGGCU
...(((..(((.(((((((.(((((((((((((....)))))))....)))))).(((.((.(.((((....--)-----------)))).))))))))))))......)))..))). ( -21.50)
>DroSim_CAF1 7484 105 + 1
CAUGCCCCUCUAUAUACACAAACAUAUACAUACAUAUGUGUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCC--U-----------AUACCUCGAAGUGUGUGCCAUAAAGAAAGGCU
...(((..(((.(((((((...(((((((((....)))))))))...........(((.((.(.((((....--)-----------)))).))))))))))))......)))..))). ( -20.30)
>consensus
CAUGCCCCUCUAUAUACACAAACAUAUACAUACAUAUGUGUGUGCUCCUAUAUUAUUCUGAUGCUGUACCCC__U___________AUACCUCGAAGUGUGUGCCAUAAAGAAAGGCU
...(((..(((.(((((((...(((((((((....)))))))))....((((.(((....))).))))............................)))))))......)))..))). (-17.82 = -17.17 +  -0.66)

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 09:34:11 2006