Locus 871

Sequence ID 2R_DroMel_CAF1
Location 4,024,756 – 4,024,914
Length 158
Max. P 0.998586
window1505 window1506 window1507 window1508

overview

Window 5

Location 4,024,756 – 4,024,874
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.64
Mean single sequence MFE -34.64
Consensus MFE -30.86
Energy contribution -31.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.89
SVM decision value 1.75
SVM RNA-class probability 0.975387
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4024756 118 + 20766785
CGGUAAUCCUGUGGAACCGCCGAAAAUGCGCAUGUGGAGGCCACAGGACUAAGCACUUAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUA--UAUCAUUCGCAAGCAUAU
.(((..((((((((..((((((......))...))))...))))))))....((.(.(((....))).)(((((......)))))..)))))(((((...--.....)))))........ ( -34.20)
>DroSec_CAF1 7569 120 + 1
CGGUAAUCCUGCGGAACCGCCGAAAAUGCGCAUGUGGAGGCCACAGGACUAAGCACUAAAUAUUUUACUGCACAUACUGUUGUGCAGGCACCGUGAAAUAUAUAUCAUACGCAAGCAUAU
.((((.(((((.((..((((((......))...))))...)).)))))...........(((((((((((((((......))))))(....)))))))))).))))...(....)..... ( -32.10)
>DroSim_CAF1 9621 120 + 1
CGGUAAUCCUGUGGAACCGCCGAAAAUGCGCAUGUGGAGGCCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUAUAUAUCAUACGCAAGCAUAU
.((((.((((((((..((((((......))...))))...))))))))...........(((((((((.(((((......))))).(....)))))))))).))))...(....)..... ( -35.70)
>DroEre_CAF1 6856 118 + 1
CGGUAAUCCUGUGGCACCGCCGAAAAUGCGCAUGUGGAGGCCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGCUGUGCAGGCACCGUGAAAUA--UAUCGCACGGCAACAUAU
(((((.(((((((((.((((((......))...))))..)))))))))............((((((((((......((((...))))...))))))))))--)))))...(....).... ( -40.60)
>DroYak_CAF1 9374 118 + 1
CGGUAAUCCUGCGGAACCGCCGAAAAUGCGCAUGUGGAGGCCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUA--UAUCAUACUCCAGCAUAU
.((((.(((((.((..((((((......))...))))...)).)))))...........(((((((((.(((((......))))).(....)))))))))--)....))))......... ( -30.60)
>consensus
CGGUAAUCCUGUGGAACCGCCGAAAAUGCGCAUGUGGAGGCCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUA__UAUCAUACGCAAGCAUAU
.((((.((((((((..((((((......))...))))...))))))))............((((((((.(((((......))))).(....)))))))))..)))).............. (-30.86 = -31.26 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,024,756 – 4,024,874
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.64
Mean single sequence MFE -38.65
Consensus MFE -34.50
Energy contribution -34.34
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -2.24
Structure conservation index 0.89
SVM decision value 3.15
SVM RNA-class probability 0.998586
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4024756 118 - 20766785
AUAUGCUUGCGAAUGAUA--UAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUAAGUGCUUAGUCCUGUGGCCUCCACAUGCGCAUUUUCGGCGGUUCCACAGGAUUACCG
........(((..(((((--(.(((.((((..(.(((......))).)..)))))))))))))..))).(((((((((((((.((..............)).))..)))))))))))... ( -37.44)
>DroSec_CAF1 7569 120 - 1
AUAUGCUUGCGUAUGAUAUAUAUUUCACGGUGCCUGCACAACAGUAUGUGCAGUAAAAUAUUUAGUGCUUAGUCCUGUGGCCUCCACAUGCGCAUUUUCGGCGGUUCCGCAGGAUUACCG
(((((....))))).............((((..(((((((......))))))).................((((((((((((.((..............)).))..)))))))))))))) ( -34.14)
>DroSim_CAF1 9621 120 - 1
AUAUGCUUGCGUAUGAUAUAUAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGGCCUCCACAUGCGCAUUUUCGGCGGUUCCACAGGAUUACCG
..........((((.....((((((.((((..(.(((......))).)..)))).))))))...)))).(((((((((((((.((..............)).))..)))))))))))... ( -37.84)
>DroEre_CAF1 6856 118 - 1
AUAUGUUGCCGUGCGAUA--UAUUUCACGGUGCCUGCACAGCAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGGCCUCCACAUGCGCAUUUUCGGCGGUGCCACAGGAUUACCG
..........(..(...(--(((((.((((..(((((...))))...)..)))).))))))...)..).((((((((((((..((....((.(......))))).))))))))))))... ( -42.50)
>DroYak_CAF1 9374 118 - 1
AUAUGCUGGAGUAUGAUA--UAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGGCCUCCACAUGCGCAUUUUCGGCGGUUCCGCAGGAUUACCG
.......(((((((...(--(((((.((((..(.(((......))).)..)))).))))))...)))))(((((((((((((.((..............)).))..))))))))))))). ( -41.34)
>consensus
AUAUGCUUGCGUAUGAUA__UAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGGCCUCCACAUGCGCAUUUUCGGCGGUUCCACAGGAUUACCG
..........((((......(((((.((((..(.(((......))).)..)))).)))))....)))).(((((((((((((.((..............)).))..)))))))))))... (-34.50 = -34.34 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,024,796 – 4,024,914
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.86
Mean single sequence MFE -31.92
Consensus MFE -22.82
Energy contribution -23.66
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.71
SVM decision value 0.37
SVM RNA-class probability 0.707017
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4024796 118 + 20766785
CCACAGGACUAAGCACUUAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUA--UAUCAUUCGCAAGCAUAUGUAUGUACGUACUAGCCGCACGCAGUGUCCUUUGCCAUCG
.((.(((((...((.(.(((....))).)))....(((((.((((.(((...(((((...--.....)))))........((((....))))..))))))))))))))))).))...... ( -31.90)
>DroSec_CAF1 7609 120 + 1
CCACAGGACUAAGCACUAAAUAUUUUACUGCACAUACUGUUGUGCAGGCACCGUGAAAUAUAUAUCAUACGCAAGCAUAUGUACGUAUGUACUAGCCGCACGCAGUGUCCUUUGCCAUCG
.((.(((((...(((.(((.....))).)))....(((((.((((.(((...((((........))))......((((((....))))))....))))))))))))))))).))...... ( -33.10)
>DroSim_CAF1 9661 120 + 1
CCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUAUAUAUCAUACGCAAGCAUAUGUACGUAUGUACUAGCCGCACGCAGUGUCCUUUGCCAUCG
.((.(((((...((..(((.....)))..))....(((((.((((.(((...((((........))))......((((((....))))))....))))))))))))))))).))...... ( -31.00)
>DroEre_CAF1 6896 102 + 1
CCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGCUGUGCAGGCACCGUGAAAUA--UAUCGCACGGCAACAUAUGUAUGUAG-U---------------GGUCCUUUGCCAUCC
.((.(((((((.(((....(((((((((((......((((...))))...))))))))))--).......(....).......)))..-)---------------)))))).))...... ( -27.80)
>DroYak_CAF1 9414 118 + 1
CCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUA--UAUCAUACUCCAGCAUAUGUAUGUAUGUAGGAGCCGCACGCAGUGUCCUUUGCCAUCG
.((.(((((...((.....(((((((((.(((((......))))).(....)))))))))--)......((((.((((((....)))))).))))......))...))))).))...... ( -35.80)
>consensus
CCACAGGACUAAGCACUAAAUAUUUUACGGCACAUACUGUUGUGCAGGCACCGUGAAAUA__UAUCAUACGCAAGCAUAUGUAUGUAUGUACUAGCCGCACGCAGUGUCCUUUGCCAUCG
.((.(((((...((......((((((((.(((((......))))).(....)))))))))..............((((((....))))))...........))...))))).))...... (-22.82 = -23.66 +   0.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,024,796 – 4,024,914
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.86
Mean single sequence MFE -34.84
Consensus MFE -26.15
Energy contribution -27.34
Covariance contribution 1.19
Combinations/Pair 1.03
Mean z-score -1.58
Structure conservation index 0.75
SVM decision value 0.08
SVM RNA-class probability 0.572451
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4024796 118 - 20766785
CGAUGGCAAAGGACACUGCGUGCGGCUAGUACGUACAUACAUAUGCUUGCGAAUGAUA--UAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUAAGUGCUUAGUCCUGUGG
......((.(((((..(((((((.....))))))).............(((..(((((--(.(((.((((..(.(((......))).)..)))))))))))))..)))...))))).)). ( -35.50)
>DroSec_CAF1 7609 120 - 1
CGAUGGCAAAGGACACUGCGUGCGGCUAGUACAUACGUACAUAUGCUUGCGUAUGAUAUAUAUUUCACGGUGCCUGCACAACAGUAUGUGCAGUAAAAUAUUUAGUGCUUAGUCCUGUGG
......((.(((((((((.(((((((..((..(((..((((((((....)))))).))..)))...))...))).))))..))))....(((.(((.....))).)))...))))).)). ( -34.90)
>DroSim_CAF1 9661 120 - 1
CGAUGGCAAAGGACACUGCGUGCGGCUAGUACAUACGUACAUAUGCUUGCGUAUGAUAUAUAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGG
......((.(((((...(((.(((....((((....))))...))).)))((((.....((((((.((((..(.(((......))).)..)))).))))))...))))...))))).)). ( -37.10)
>DroEre_CAF1 6896 102 - 1
GGAUGGCAAAGGACC---------------A-CUACAUACAUAUGUUGCCGUGCGAUA--UAUUUCACGGUGCCUGCACAGCAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGG
(((((((((((....---------------.-)).(((....))))))))(..(...(--(((((.((((..(((((...))))...)..)))).))))))...)..)...))))..... ( -30.70)
>DroYak_CAF1 9414 118 - 1
CGAUGGCAAAGGACACUGCGUGCGGCUCCUACAUACAUACAUAUGCUGGAGUAUGAUA--UAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGG
......((.(((((...((.....(((((..((((......))))..)))))((...(--(((((.((((..(.(((......))).)..)))).))))))...))))...))))).)). ( -36.00)
>consensus
CGAUGGCAAAGGACACUGCGUGCGGCUAGUACAUACAUACAUAUGCUUGCGUAUGAUA__UAUUUCACGGUGCCUGCACAACAGUAUGUGCCGUAAAAUAUUUAGUGCUUAGUCCUGUGG
......((.(((((.....((((.....)))).(((...((((((....)))))).....(((((.((((..(.(((......))).)..)))).)))))....)))....))))).)). (-26.15 = -27.34 +   1.19)

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 09:49:27 2006