Locus 1594

Sequence ID X_DroMel_CAF1
Location 4,586,473 – 4,586,620
Length 147
Max. P 0.999809
window2612 window2613 window2614 window2615

overview

Window 2

Location 4,586,473 – 4,586,580
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.11
Mean single sequence MFE -27.32
Consensus MFE -15.60
Energy contribution -15.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.57
SVM decision value 0.14
SVM RNA-class probability 0.603785
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4586473 107 + 22224390
CUUUAUCCCGACGCUGG-GGUCAUGCAAAUUUUAUGAAUAUCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACGUCACA------------GCACGCAGCUU
.....(((((....)))-))(((((.......)))))....((((......(((((((...(......)...)))))))(((((((.....)))).)------------))..))))... ( -25.40)
>DroSec_CAF1 10602 106 + 1
CUUUACCCCGUCGCUGU-GGACAUGCAAAUUUUAUG-AUAUCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCACA------------GCACGCAGCUU
........(((.(((((-((.((((.......))))-......(((((..((((((((...(......)...)))))))).)))))......)))))------------)))))...... ( -28.00)
>DroSim_CAF1 12049 107 + 1
CUUUACCCCGUCGCUGU-GGCCAUGCAAAUUUUAUGAAUAUCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCACA------------GCACGCAGCUU
........(((.(((((-((.((((.......)))).......(((((..((((((((...(......)...)))))))).)))))......)))))------------)))))...... ( -27.50)
>DroEre_CAF1 13582 98 + 1
CUUC---------------GCCAUGCAAAUUUUAUGAAUGUCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCGCAGCAC-------GGCACGCAACUU
....---------------(((.(((........((.((((..(((((..((((((((...(......)...)))))))).)))))...))))..))))).-------)))......... ( -24.40)
>DroYak_CAF1 10945 120 + 1
CUUUUCGCAGUUGCGCCGAGCCAUGCAAAUUUUAUGAAUAUCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCCUUACAGCACAGCACAGCGCACAGCACGCAACUU
........(((((((((((((...(((.((.........)).)))......(((((((...(......)...))))))))))))))......((...((.....))...))..)))))). ( -31.30)
>consensus
CUUUACCCCGUCGCUGU_GGCCAUGCAAAUUUUAUGAAUAUCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCACA____________GCACGCAGCUU
.......................(((.........(.....).(((((..((((((((...(......)...)))))))).)))))...........................))).... (-15.60 = -15.60 +  -0.00)

alignment

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secondary structure

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Window 3

Location 4,586,473 – 4,586,580
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.11
Mean single sequence MFE -36.30
Consensus MFE -22.39
Energy contribution -22.83
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -3.06
Structure conservation index 0.62
SVM decision value 1.77
SVM RNA-class probability 0.976311
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4586473 107 - 22224390
AAGCUGCGUGC------------UGUGACGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGAUAUUCAUAAAAUUUGCAUGACC-CCAGCGUCGGGAUAAAG
..(((((((((------------(((((......((((((.((((((((..(......)..))))))))..))))))......)))))......)))))...-.))))............ ( -28.80)
>DroSec_CAF1 10602 106 - 1
AAGCUGCGUGC------------UGUGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGAUAU-CAUAAAAUUUGCAUGUCC-ACAGCGACGGGGUAAAG
..(((.(((((------------((((.......((((((.((((((((..(......)..))))))))..)))))).(((((-((.......)).))))))-))))).))).))).... ( -38.40)
>DroSim_CAF1 12049 107 - 1
AAGCUGCGUGC------------UGUGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGAUAUUCAUAAAAUUUGCAUGGCC-ACAGCGACGGGGUAAAG
..(((.(((((------------(((((((((((((((((.((((((((..(......)..))))))))..)))))).(.....)......)))))))...)-))))).))).))).... ( -38.00)
>DroEre_CAF1 13582 98 - 1
AAGUUGCGUGCC-------GUGCUGCGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGACAUUCAUAAAAUUUGCAUGGC---------------GAAG
........((((-------((((((.(((((...((((((.((((((((..(......)..))))))))..))))))..)))))))........)))))))---------------)... ( -32.30)
>DroYak_CAF1 10945 120 - 1
AAGUUGCGUGCUGUGCGCUGUGCUGUGCUGUAAGGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGAUAUUCAUAAAAUUUGCAUGGCUCGGCGCAACUGCGAAAAG
........(((..(((((((.(((((((......((((((.((((((((..(......)..))))))))..)))))).(.....).........))))))).)))))))...)))..... ( -44.00)
>consensus
AAGCUGCGUGC____________UGUGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGAUAUUCAUAAAAUUUGCAUGGCC_ACAGCGACGGGGUAAAG
......(((((............((((((((...((((((.((((((((..(......)..))))))))..))))))..)))).))))......)))))..................... (-22.39 = -22.83 +   0.44)

alignment

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secondary structure

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Window 4

Location 4,586,512 – 4,586,620
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.69
Mean single sequence MFE -29.24
Consensus MFE -28.12
Energy contribution -28.12
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.96
SVM decision value 4.13
SVM RNA-class probability 0.999809
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4586512 108 + 22224390
UCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACGUCACA------------GCACGCAGCUUGUGCAGCUCGCAAAUUCAUAGUGGGCAACUUUAAAUUUAA
...(((((..((((((((...(......)...)))))))).)))))...........------------(((((.....))))).((((((.........)))))).............. ( -28.40)
>DroSec_CAF1 10640 108 + 1
UCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCACA------------GCACGCAGCUUGUGCAGCUCGCAAAUUCAUGGUGGGCAACUUUAAAUUUAA
...(((((..((((((((...(......)...)))))))).)))))...........------------(((((.....))))).((((((.........)))))).............. ( -28.30)
>DroSim_CAF1 12088 108 + 1
UCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCACA------------GCACGCAGCUUGUGCAGCUCGCAAAUUCAUGGUGGGCAACUUUAAAUUUAA
...(((((..((((((((...(......)...)))))))).)))))...........------------(((((.....))))).((((((.........)))))).............. ( -28.30)
>DroEre_CAF1 13607 113 + 1
UCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCGCAGCAC-------GGCACGCAACUUGUGCAGCUCGCAAAUUCAUAGUGGGCAACUUUAAAUUUCA
...(((((..((((((((...(......)...)))))))).)))))...........((((-------((........)))))).((((((.........)))))).............. ( -28.90)
>DroYak_CAF1 10985 120 + 1
UCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCCUUACAGCACAGCACAGCGCACAGCACGCAACUUGUGCAGCUCGCAAAUUCAUAGUGGGCAACUUUAAAUUCAA
...(((((..((((((((...(......)...)))))))).)))))......((((((....(((.......)))...)))))).((((((.........)))))).............. ( -32.30)
>consensus
UCUGCCAAAAUGGGAAAUAAGCAAAUAAGAACAUUUCCCGCUUGGCUUUACAUCACA____________GCACGCAGCUUGUGCAGCUCGCAAAUUCAUAGUGGGCAACUUUAAAUUUAA
...(((((..((((((((...(......)...)))))))).))))).......................(((((.....))))).((((((.........)))))).............. (-28.12 = -28.12 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,586,512 – 4,586,620
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.69
Mean single sequence MFE -31.14
Consensus MFE -27.08
Energy contribution -27.08
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.46
Structure conservation index 0.87
SVM decision value 0.79
SVM RNA-class probability 0.850353
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4586512 108 - 22224390
UUAAAUUUAAAGUUGCCCACUAUGAAUUUGCGAGCUGCACAAGCUGCGUGC------------UGUGACGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGA
.....((((.(((.....))).))))((((((.((.((((.......))))------------.))..))))))((((((.((((((((..(......)..))))))))..))))))... ( -30.50)
>DroSec_CAF1 10640 108 - 1
UUAAAUUUAAAGUUGCCCACCAUGAAUUUGCGAGCUGCACAAGCUGCGUGC------------UGUGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGA
............(((((.....((..((((((.((.((((.......))))------------.))..))))))..))...((((((((..(......)..)))))))).....))))). ( -28.50)
>DroSim_CAF1 12088 108 - 1
UUAAAUUUAAAGUUGCCCACCAUGAAUUUGCGAGCUGCACAAGCUGCGUGC------------UGUGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGA
............(((((.....((..((((((.((.((((.......))))------------.))..))))))..))...((((((((..(......)..)))))))).....))))). ( -28.50)
>DroEre_CAF1 13607 113 - 1
UGAAAUUUAAAGUUGCCCACUAUGAAUUUGCGAGCUGCACAAGUUGCGUGCC-------GUGCUGCGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGA
..(((((((.(((.....))).)))))))((.(((.((((.......)))).-------..)))))........((((((.((((((((..(......)..))))))))..))))))... ( -31.90)
>DroYak_CAF1 10985 120 - 1
UUGAAUUUAAAGUUGCCCACUAUGAAUUUGCGAGCUGCACAAGUUGCGUGCUGUGCGCUGUGCUGUGCUGUAAGGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGA
..(((((((.(((.....))).)))))))....((.(((((.((.((((.....))))...))))))).))...((((((.((((((((..(......)..))))))))..))))))... ( -36.30)
>consensus
UUAAAUUUAAAGUUGCCCACUAUGAAUUUGCGAGCUGCACAAGCUGCGUGC____________UGUGAUGUAAAGCCAAGCGGGAAAUGUUCUUAUUUGCUUAUUUCCCAUUUUGGCAGA
..(((((((.(((.....))).)))))))(((((((.....)))).))).........................((((((.((((((((..(......)..))))))))..))))))... (-27.08 = -27.08 +   0.00)

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 10:14:17 2006