Locus 5915

Sequence ID 2L_DroMel_CAF1
Location 16,702,178 – 16,702,411
Length 233
Max. P 0.648175
window9396 window9397 window9398 window9399 window9400

overview

Window 6

Location 16,702,178 – 16,702,291
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -35.95
Consensus MFE -25.61
Energy contribution -26.99
Covariance contribution 1.38
Combinations/Pair 1.03
Mean z-score -2.06
Structure conservation index 0.71
SVM decision value 0.24
SVM RNA-class probability 0.648175
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702178 113 + 22407834
UUGUUUGGCAAC------GGCAGUGCGCAGCUCUGAUCGAAAUGCUCCAUUGGGUGCACACACCCAGCCCAACAAGGCAUUG-GUUUAGCCCACCCAUCCAAAGCCGAUGACCUUGCCCA
..(((.(((..(------(((((.((...)).))).)))...........((((((....))))))))).)))(((((((((-((((..............))))))))).))))..... ( -36.34)
>DroSec_CAF1 156898 112 + 1
UUGUUUGGCAACA----CG---GUGCGCAGCUCUGAUCGAAAUGCUCCAUUGGGUGCACACACCCAGCCCAACAAGGCAUUGGGUUCAGCCCACCCAUCCA-AGCCGAUGACCUUGCCCA
(((((.(((....----.(---(...(((..((.....))..))).))..((((((....))))))))).)))))((((.((((.....))))..((((..-....))))....)))).. ( -37.40)
>DroSim_CAF1 156842 114 + 1
UUGUUUGGCAACA----CGGCAGUGCGCAGCUCUGAUCGAAAUGCUCCAUUGGUUGCACACACCCAGCCCAACAAGGCAUUG-GUUCAGCCCACCCAUCCA-AGCCGAUGACCUUGCCCA
......(((((((----((((.(((.((((((..(((.((.....)).))))))))).)))(((..(((......)))...)-))................-.)))).))...))))).. ( -31.20)
>DroEre_CAF1 158297 119 + 1
UUGCUUAGCAGCAAAAAAGGCAGUGCGCAGCUCUAAUCGAAAUGCUCCAAUGGGUGCACACACCCAGCCCAAAAAGGCAUUG-GUUCAAACCACCCAUCCAGAGCCGAUGACCUUGCCCA
(((((....)))))....(((.(.(((((..((.....))..))).....((((((....)))))))).)...(((((((((-((((..............))))))))).))))))).. ( -38.84)
>consensus
UUGUUUGGCAACA____CGGCAGUGCGCAGCUCUGAUCGAAAUGCUCCAUUGGGUGCACACACCCAGCCCAACAAGGCAUUG_GUUCAGCCCACCCAUCCA_AGCCGAUGACCUUGCCCA
......(((.........(((.....(((..((.....))..))).....((((((....)))))))))....(((((((((.((((..............))))))))).))))))).. (-25.61 = -26.99 +   1.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,702,178 – 16,702,291
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.48
Mean single sequence MFE -43.57
Consensus MFE -33.31
Energy contribution -34.25
Covariance contribution 0.94
Combinations/Pair 1.11
Mean z-score -1.55
Structure conservation index 0.76
SVM decision value 0.03
SVM RNA-class probability 0.550986
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702178 113 - 22407834
UGGGCAAGGUCAUCGGCUUUGGAUGGGUGGGCUAAAC-CAAUGCCUUGUUGGGCUGGGUGUGUGCACCCAAUGGAGCAUUUCGAUCAGAGCUGCGCACUGCC------GUUGCCAAACAA
..((((((((...(((((((((.((((((.((...((-(...((((....))))..)))..)).)))))).((((....)))).)))))))))......)))------.)))))...... ( -45.30)
>DroSec_CAF1 156898 112 - 1
UGGGCAAGGUCAUCGGCU-UGGAUGGGUGGGCUGAACCCAAUGCCUUGUUGGGCUGGGUGUGUGCACCCAAUGGAGCAUUUCGAUCAGAGCUGCGCAC---CG----UGUUGCCAAACAA
.((((.((.(((((((((-(.(.((((((.((...(((((..((((....)))))))))..)).)))))).).))))....))))..)).))..)).)---).----((((....)))). ( -44.90)
>DroSim_CAF1 156842 114 - 1
UGGGCAAGGUCAUCGGCU-UGGAUGGGUGGGCUGAAC-CAAUGCCUUGUUGGGCUGGGUGUGUGCAACCAAUGGAGCAUUUCGAUCAGAGCUGCGCACUGCCG----UGUUGCCAAACAA
..(((((.(.(..(((((-..(..((.(((......)-))...))...)..)))))((((.((((..((...)).(((.(((.....))).))))))))))))----).)))))...... ( -38.50)
>DroEre_CAF1 158297 119 - 1
UGGGCAAGGUCAUCGGCUCUGGAUGGGUGGUUUGAAC-CAAUGCCUUUUUGGGCUGGGUGUGUGCACCCAUUGGAGCAUUUCGAUUAGAGCUGCGCACUGCCUUUUUUGCUGCUAAGCAA
.(((((..((...(((((((((.....(((..((..(-((((((((....)))).(((((....))))))))))..))..))).))))))))).))..)))))...(((((....))))) ( -45.60)
>consensus
UGGGCAAGGUCAUCGGCU_UGGAUGGGUGGGCUGAAC_CAAUGCCUUGUUGGGCUGGGUGUGUGCACCCAAUGGAGCAUUUCGAUCAGAGCUGCGCACUGCCG____UGUUGCCAAACAA
..((((..((...(((((((((.((((...(((.........((((....))))((((((....))))))....)))..)))).))))))))).))..))))......(((....))).. (-33.31 = -34.25 +   0.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,702,212 – 16,702,331
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.85
Mean single sequence MFE -34.64
Consensus MFE -25.92
Energy contribution -27.04
Covariance contribution 1.12
Combinations/Pair 1.03
Mean z-score -2.51
Structure conservation index 0.75
SVM decision value 0.17
SVM RNA-class probability 0.614758
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702212 119 + 22407834
AAUGCUCCAUUGGGUGCACACACCCAGCCCAACAAGGCAUUG-GUUUAGCCCACCCAUCCAAAGCCGAUGACCUUGCCCAUAUCCACUGAAGUAUAUACACGGGUGGUAUGCCCAAAAAG
.........((((((..((.(((((.......((((((((((-((((..............))))))))).)))))...((((.(......).))))....)))))))..)))))).... ( -36.24)
>DroSec_CAF1 156931 119 + 1
AAUGCUCCAUUGGGUGCACACACCCAGCCCAACAAGGCAUUGGGUUCAGCCCACCCAUCCA-AGCCGAUGACCUUGCCCAUAUUCACUGAAGUAUACACACGGGUGGUAUGCCCAAAAAG
..........((((((....))))))(((......))).((((((.....((((((...((-((........))))...(((((......)))))......))))))...)))))).... ( -34.80)
>DroSim_CAF1 156878 118 + 1
AAUGCUCCAUUGGUUGCACACACCCAGCCCAACAAGGCAUUG-GUUCAGCCCACCCAUCCA-AGCCGAUGACCUUGCCCAUAUCCACUGAAGUAUACACACGGGUGGUAUGCCCAAAAAG
.........((((..(((..(((((.......((((((((((-(((...............-)))))))).)))))...............((......)))))))...))))))).... ( -29.46)
>DroEre_CAF1 158337 119 + 1
AAUGCUCCAAUGGGUGCACACACCCAGCCCAAAAAGGCAUUG-GUUCAAACCACCCAUCCAGAGCCGAUGACCUUGCCCAUAUGCACUGGAGUAUAUACACGAGUGGCAUGCCCAAAAAG
.((((((((.((((((....))))))((.....(((((((((-((((..............))))))))).))))........))..))))))))........(.((....)))...... ( -38.06)
>consensus
AAUGCUCCAUUGGGUGCACACACCCAGCCCAACAAGGCAUUG_GUUCAGCCCACCCAUCCA_AGCCGAUGACCUUGCCCAUAUCCACUGAAGUAUACACACGGGUGGUAUGCCCAAAAAG
.(((((.((.((((((....))))))......((((((((((.((((..............))))))))).)))))...........)).)))))......((((.....))))...... (-25.92 = -27.04 +   1.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,702,212 – 16,702,331
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.85
Mean single sequence MFE -43.90
Consensus MFE -34.16
Energy contribution -33.98
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -1.93
Structure conservation index 0.78
SVM decision value 0.07
SVM RNA-class probability 0.570636
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702212 119 - 22407834
CUUUUUGGGCAUACCACCCGUGUAUAUACUUCAGUGGAUAUGGGCAAGGUCAUCGGCUUUGGAUGGGUGGGCUAAAC-CAAUGCCUUGUUGGGCUGGGUGUGUGCACCCAAUGGAGCAUU
........((...((((((((((...(((....))).)))))))((((((.....))))))..((((((.((...((-(...((((....))))..)))..)).)))))).))).))... ( -43.90)
>DroSec_CAF1 156931 119 - 1
CUUUUUGGGCAUACCACCCGUGUGUAUACUUCAGUGAAUAUGGGCAAGGUCAUCGGCU-UGGAUGGGUGGGCUGAACCCAAUGCCUUGUUGGGCUGGGUGUGUGCACCCAAUGGAGCAUU
.....(((.....)))(((((((...(((....))).)))))))...........(((-(.(.((((((.((...(((((..((((....)))))))))..)).)))))).).))))... ( -45.50)
>DroSim_CAF1 156878 118 - 1
CUUUUUGGGCAUACCACCCGUGUGUAUACUUCAGUGGAUAUGGGCAAGGUCAUCGGCU-UGGAUGGGUGGGCUGAAC-CAAUGCCUUGUUGGGCUGGGUGUGUGCAACCAAUGGAGCAUU
....(((.(((((((.(((((((.(((......))).))))))).........(((((-..(..((.(((......)-))...))...)..)))))))))))).)))............. ( -39.90)
>DroEre_CAF1 158337 119 - 1
CUUUUUGGGCAUGCCACUCGUGUAUAUACUCCAGUGCAUAUGGGCAAGGUCAUCGGCUCUGGAUGGGUGGUUUGAAC-CAAUGCCUUUUUGGGCUGGGUGUGUGCACCCAUUGGAGCAUU
........((...(((...((((((((((.(((((.((...(((((.(((((.(.((((.....)))).)..)).))-)..)))))...)).)))))))))))))))....))).))... ( -46.30)
>consensus
CUUUUUGGGCAUACCACCCGUGUAUAUACUUCAGUGGAUAUGGGCAAGGUCAUCGGCU_UGGAUGGGUGGGCUGAAC_CAAUGCCUUGUUGGGCUGGGUGUGUGCACCCAAUGGAGCAUU
........((...((((((((((((.(((....))).))))...((.(((.....))).)).))))))))............((((....))))((((((....)))))).....))... (-34.16 = -33.98 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,702,291 – 16,702,411
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.39
Mean single sequence MFE -35.35
Consensus MFE -21.45
Energy contribution -22.20
Covariance contribution 0.75
Combinations/Pair 1.17
Mean z-score -2.10
Structure conservation index 0.61
SVM decision value 0.14
SVM RNA-class probability 0.604688
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16702291 120 - 22407834
UUGUCAUUGAAAUGCUCAGAUAUGUCUGGCUUCAGCCAGAUCUGGAAAAACUGGAGCAUGCUACGUUUCGGUUUGGGCCUCUUUUUGGGCAUACCACCCGUGUAUAUACUUCAGUGGAUA
...(((((((((((((((((...(((((((....)))))))..((..((((((((((.......))))))))))...))....))))))))).......(((....)))))))))))... ( -40.40)
>DroSec_CAF1 157010 105 - 1
UUGUCAUUGAAAUGC---------------UUCAGCCAGAUCUGGAAAAACUGGAGCAUGCUACGUUUCGAUUGGGGCCUCUUUUUGGGCAUACCACCCGUGUGUAUACUUCAGUGAAUA
...((((((((((((---------------((((((((....))).....)))))))))..((((...((..(((.((((......))))...)))..))..))))...))))))))... ( -33.40)
>DroSim_CAF1 156956 105 - 1
UUGUCAUUGAAAUGC---------------UUCAGCCAGAUCUGGAAAAACUGGAGCAUGCUACGUUUCGAUUGGGGCCUCUUUUUGGGCAUACCACCCGUGUGUAUACUUCAGUGGAUA
...((((((((((((---------------((((((((....))).....)))))))))..((((...((..(((.((((......))))...)))..))..))))...))))))))... ( -32.50)
>DroEre_CAF1 158416 117 - 1
UUGUCAUUGAAAUGCUCUCUGAUGUCUGGCUGUAGCCAGAUCUGGAAAAACUGG---AUGCUACGUUUCGAUUGGGGCCUCUUUUUGGGCAUGCCACUCGUGUAUAUACUCCAGUGCAUA
...........((((..(((...(((((((....)))))))..)))...(((((---(...((((...(((.(((.((((......))))...))).))))))).....)))))))))). ( -35.10)
>consensus
UUGUCAUUGAAAUGC_______________UUCAGCCAGAUCUGGAAAAACUGGAGCAUGCUACGUUUCGAUUGGGGCCUCUUUUUGGGCAUACCACCCGUGUAUAUACUUCAGUGGAUA
..............................(((..(((....)))....(((((((.((((.(((...(((.(((.((((......))))...))).)))))))))).)))))))))).. (-21.45 = -22.20 +   0.75)

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 11:56:24 2006