Locus 1352

Sequence ID 3R_DroMel_CAF1
Location 3,995,374 – 3,995,707
Length 333
Max. P 0.873813
window2215 window2216 window2217 window2218 window2219 window2220

overview

Window 5

Location 3,995,374 – 3,995,470
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 99.31
Mean single sequence MFE -31.27
Consensus MFE -31.49
Energy contribution -31.27
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 1.01
SVM decision value 0.86
SVM RNA-class probability 0.868225
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995374 96 - 27905053
AGCGAUUCGAACCGAAUCGAUCCGAUGACGACUUCAUAUAUGGAGGAUCUUUGUGUCGUUGGUGCAAAAGUGUGAACUGGGCACAGCAGAUCGGGA
..(((((((...))))))).(((........(((((....)))))(((((((((((((((.(..(....)..).)))..))))))).)))))))). ( -31.80)
>DroSec_CAF1 1169 96 - 1
AGCGAUUCGAACCGAAUCGAUCCGAUGACGACUUCAUAUAUGGGGGAUCUUUGUGUCGUUGGUGCAAAAGUGUGAACUGGGCACAGCAGAUCGGGA
..(((((((...))))))).(((........(((((....)))))(((((((((((((((.(..(....)..).)))..))))))).)))))))). ( -31.00)
>DroSim_CAF1 1168 96 - 1
AGCGAUUCGAACCGAAUCGAUCCGAUGACGACUUCAUAUAUGGGGGAUCUUUGUGUCGUUGGUGCAAAAGUGUGAACUGGGCACAGCAGAUCGGGA
..(((((((...))))))).(((........(((((....)))))(((((((((((((((.(..(....)..).)))..))))))).)))))))). ( -31.00)
>consensus
AGCGAUUCGAACCGAAUCGAUCCGAUGACGACUUCAUAUAUGGGGGAUCUUUGUGUCGUUGGUGCAAAAGUGUGAACUGGGCACAGCAGAUCGGGA
..(((((((...))))))).(((........(((((....)))))(((((((((((((((.(..(....)..).)))..))))))).)))))))). (-31.49 = -31.27 +  -0.22)

alignment

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secondary structure

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Window 6

Location 3,995,445 – 3,995,547
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 99.35
Mean single sequence MFE -28.83
Consensus MFE -28.17
Energy contribution -28.50
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.98
SVM decision value 0.41
SVM RNA-class probability 0.726256
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995445 102 + 27905053
UCGGAUCGAUUCGGUUCGAAUCGCUUGUAUGUAAUUUGCCAAGAUCGAGUGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCGGAGGAUGGUUGCAUC
((.((((((((((...)))))))....(((((((((((.((.((((.((((.........)))))))).)).)))))))))))))).)).((((....)))) ( -26.90)
>DroSec_CAF1 1240 102 + 1
UCGGAUCGAUUCGGUUCGAAUCGCUUGUAUGUAAUUUGCCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCGGAGGAUGGUUGCAUC
((.((((((((((...)))))))....(((((((((((.((.((((((.((........)).)))))).)).)))))))))))))).)).((((....)))) ( -29.80)
>DroSim_CAF1 1239 102 + 1
UCGGAUCGAUUCGGUUCGAAUCGCUUGUAUGUAAUUUGCCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCGGAGGAUGGUUGCAUC
((.((((((((((...)))))))....(((((((((((.((.((((((.((........)).)))))).)).)))))))))))))).)).((((....)))) ( -29.80)
>consensus
UCGGAUCGAUUCGGUUCGAAUCGCUUGUAUGUAAUUUGCCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCGGAGGAUGGUUGCAUC
((.((((((((((...)))))))....(((((((((((.((.((((((.((........)).)))))).)).)))))))))))))).)).((((....)))) (-28.17 = -28.50 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,995,470 – 3,995,587
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.62
Mean single sequence MFE -33.53
Consensus MFE -27.27
Energy contribution -27.15
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -2.06
Structure conservation index 0.81
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995470 117 + 27905053
UGUAUGUAAUUUGCCAAGAUCGAGUGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCG---GAGGAUGGUUGCAUCUUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUA
..(((((((((((.((.((((.((((.........)))))))).)).)))))))))))...(---(((((((....)))))))).((.(((((.((......))..))))).))...... ( -30.20)
>DroSec_CAF1 1265 117 + 1
UGUAUGUAAUUUGCCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCG---GAGGAUGGUUGCAUCUUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUA
..(((((((((((.((.((((((.((........)).)))))).)).)))))))))))...(---(((((((....)))))))).((.(((((.((......))..))))).))...... ( -33.10)
>DroSim_CAF1 1264 117 + 1
UGUAUGUAAUUUGCCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCG---GAGGAUGGUUGCAUCUUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUA
..(((((((((((.((.((((((.((........)).)))))).)).)))))))))))...(---(((((((....)))))))).((.(((((.((......))..))))).))...... ( -33.10)
>DroYak_CAF1 712 120 + 1
UGUAUGUAAUUUGGCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCUAAAUUAUAUAGUCGAAGGAGGAUGGUUGCAUCUUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGUUCUUUA
..((((((((((((((.((((((.((........)).)))))).))))))))))))))((((..((((((((....))))))))....(((((......)))))..)))).......... ( -37.70)
>consensus
UGUAUGUAAUUUGCCAAGAUCGAGGGAAAUAAUACCAUUGGUCAUGCCAAAUUAUAUAGUCG___GAGGAUGGUUGCAUCUUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUA
..(((((((((((.((.((((((.((........)).)))))).)).))))))))))).......(((((((....)))))))..((.(((((.((......))..))))).))...... (-27.27 = -27.15 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,995,547 – 3,995,667
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.53
Mean single sequence MFE -36.67
Consensus MFE -33.01
Energy contribution -33.58
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.14
Structure conservation index 0.90
SVM decision value 0.88
SVM RNA-class probability 0.873813
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995547 120 + 27905053
UUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUAAUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGUGGGCUGUUAAUGUUAAUCCCAAGUUAU
...(((((((((((((.(((.......)))..(((((...((((((.(((((((........)))))))))))))))))))))))))......))))))..................... ( -38.90)
>DroSec_CAF1 1342 120 + 1
UUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUAAUUGGCAUGACGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGUAUGCUGUUAAUGUUAAUCCCAAGUUAU
.....((.(((((.((......))..))))).))((((..((((((.((.((((........)))).))))))))((..((((((.((.(((....))).)).))))))..))))))... ( -26.30)
>DroSim_CAF1 1341 120 + 1
UUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUAAUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGCGGGCUGUUAAUGUUAAUCCCAAGUUAU
...(((((((((((((.(((.......)))..(((((...((((((.(((((((........))))))))))))))))))))))(....))))))))))..................... ( -41.30)
>DroYak_CAF1 792 119 + 1
UUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGUUCUUUAAUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGCGGGCUGUUAAUGUUAAUCC-AAGCUAU
...((((((((((((((((((((((.....))))).....((((((.(((((((........)))))))))))))))).)))))(....)))))))))).............-....... ( -40.20)
>consensus
UUUCAGCCCGUUGCCAAAUCAAUGUCCGAUGCGCACUUUAAUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGCGGGCUGUUAAUGUUAAUCCCAAGUUAU
...(((((((((((((((((.......)))...((((...((((((.(((((((........))))))))))))))))))))))))......)))))))..................... (-33.01 = -33.58 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,995,547 – 3,995,667
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.53
Mean single sequence MFE -32.12
Consensus MFE -30.40
Energy contribution -30.52
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.95
SVM decision value 0.12
SVM RNA-class probability 0.591060
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995547 120 - 27905053
AUAACUUGGGAUUAACAUUAACAGCCCACUGAUAUCGCCAACACCAUCGGCUGGCAAAUUGAAAGUUUCGCCAUGCCAAUUAAAGUGCGCAUCGGACAUUGAUUUGGCAACGGGCUGAAA
.....................((((((...(....)((((........(((((((((((.....)))).)))).)))((((((.((.((...)).)).))))))))))...))))))... ( -34.30)
>DroSec_CAF1 1342 120 - 1
AUAACUUGGGAUUAACAUUAACAGCAUACUGAUAUCGCCAACACCAUCGGCUGGCAAAUUGAAAGUUUCGUCAUGCCAAUUAAAGUGCGCAUCGGACAUUGAUUUGGCAACGGGCUGAAA
.....................((((...........((((.(......)..))))............((((..((((((((((.((.((...)).)).)))).))))))))))))))... ( -25.70)
>DroSim_CAF1 1341 120 - 1
AUAACUUGGGAUUAACAUUAACAGCCCGCUGAUAUCGCCAACACCAUCGGCUGGCAAAUUGAAAGUUUCGCCAUGCCAAUUAAAGUGCGCAUCGGACAUUGAUUUGGCAACGGGCUGAAA
.....................(((((((..(....)((((........(((((((((((.....)))).)))).)))((((((.((.((...)).)).))))))))))..)))))))... ( -35.60)
>DroYak_CAF1 792 119 - 1
AUAGCUU-GGAUUAACAUUAACAGCCCGCUGAUAUCGCCAACACCAUCGGCUGGCAAAUUGAAAGUUUCGCCAUGCCAAUUAAAGAACGCAUCGGACAUUGAUUUGGCAACGGGCUGAAA
.......-.............(((((((..(....)((((........(((((((((((.....)))).)))).)))((((((.(..((...))..).))))))))))..)))))))... ( -32.90)
>consensus
AUAACUUGGGAUUAACAUUAACAGCCCACUGAUAUCGCCAACACCAUCGGCUGGCAAAUUGAAAGUUUCGCCAUGCCAAUUAAAGUGCGCAUCGGACAUUGAUUUGGCAACGGGCUGAAA
.....................((((((...(....)((((........(((((((((((.....)))).)))).)))((((((.((.((...)).)).))))))))))...))))))... (-30.40 = -30.52 +   0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,995,587 – 3,995,707
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.10
Mean single sequence MFE -28.38
Consensus MFE -23.98
Energy contribution -24.48
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.84
SVM decision value 0.83
SVM RNA-class probability 0.861545
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995587 120 + 27905053
AUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGUGGGCUGUUAAUGUUAAUCCCAAGUUAUAUGUGAACGUAUGUAAUGUAUUACACAUAUACGAGUAUAU
.(((((.(((((((........))))))))))))(((..((((((.((.(((....))).)).))))))..))).((.(((((((...((((.....))))..)))))))))........ ( -35.10)
>DroSec_CAF1 1382 94 + 1
AUUGGCAUGACGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGUAUGCUGUUAAUGUUAAUCCCAAGUUAUA--------------------------UAUACGAGUAUAU
.(((((.((.((((........)))).)))))))(((..((((((.((.(((....))).)).))))))..)))....(((--------------------------(((....)))))) ( -21.10)
>DroSim_CAF1 1381 94 + 1
AUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGCGGGCUGUUAAUGUUAAUCCCAAGUUAUA--------------------------UAUGCGAGUAUAU
.(((((.(((((((........))))))))))))(((..((((((.((.(((....))).)).))))))..)))....(((--------------------------(((....)))))) ( -28.70)
>DroYak_CAF1 832 108 + 1
AUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGCGGGCUGUUAAUGUUAAUCC-AAGCUAUAUGGCAACUUAUAU--UG---------UAUUCUCGUAUAU
.(((((.(((((((........))))))))))))(((.(((((((.((.(((....))).)).)))))))))-)...((((((((((......)--))---------).....)))))). ( -28.60)
>consensus
AUUGGCAUGGCGAAACUUUCAAUUUGCCAGCCGAUGGUGUUGGCGAUAUCAGCGGGCUGUUAAUGUUAAUCCCAAGUUAUA__________________________UAUACGAGUAUAU
.(((((.(((((((........))))))))))))(((..((((((.((.(((....))).)).))))))..))).............................................. (-23.98 = -24.48 +   0.50)

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 10:07:41 2006