Locus 3560

Sequence ID 2R_DroMel_CAF1
Location 11,876,072 – 11,876,232
Length 160
Max. P 0.884100
window5797 window5798 window5799 window5800

overview

Window 7

Location 11,876,072 – 11,876,192
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.06
Mean single sequence MFE -49.13
Consensus MFE -36.10
Energy contribution -36.42
Covariance contribution 0.31
Combinations/Pair 1.25
Mean z-score -2.22
Structure conservation index 0.73
SVM decision value 0.09
SVM RNA-class probability 0.576481
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11876072 120 + 20766785
GCACCAACUUUGCUCCGCUGUGGGCCAGGGCCUUUCCCUUGGUGGACACUGAGAAGGUGUCCAAGGGGGUGAUGCAGUACAUCAAGACCAAUGAUUUGGAUGCGCAGUAUGGUGGUGUGC
((((((.((.((((.(((...((((....))))..(((((..((((((((.....)))))))).)))))(((((.....)))))...((((....))))..))).)))).)))))))).. ( -49.90)
>DroPse_CAF1 14606 120 + 1
CCUCCAACUUCUCGCCGCUGUGGGCCCGCGCCUAUCCCCUGGUGGACACUGAAAAGAUCGCCCGGGGCGUGAUGAAAUACAUCAAGACGCACAAACUGGACGACUACCCCGGCGGAGUGC
..............((((((.(((....((((....(((.(((((...((....)).))))).)))((((((((.....))))...)))).......)).))....)))))))))..... ( -40.30)
>DroSec_CAF1 16515 120 + 1
GCACAAACUUUGCUCCGCUGUGGGCCAGAGCCUUUCCCUUGGUGGACACCGAGAAGGUGUCCAAGGGAGUGAUGGAGUACAUCAAGACCAACGACUUAGAUGCGCAAUACGGUGGGGUGC
...........(((((((((((..(((..((...(((((...((((((((.....)))))))))))))))..))).(..(((((((........))).))))..)..))))))))))).. ( -48.70)
>DroSim_CAF1 16102 120 + 1
GCACCAACUUUGCUCCGCUGUGGGCCAGAGCCUUUCCCUUGGUGGACACCGAGAAGGUGUCCAAGGGAGUGAUGGAGUACAUCAAGACCAACGAUUUGGAUGCGCAAUACGGUGGGGUGC
...........(((((((((((.((((...((.((((((...((((((((.....))))))))))))))(((((.....))))).............)).)).))..))))))))))).. ( -48.60)
>DroEre_CAF1 18604 120 + 1
GCACCAACUUUGCCCCACUGUGGGCCAGGGCCUUUCCCUUGGUGGACACCGAUAAGGUGUCCAAGGGGGUGAUGCAGUACAUCAAGGCCAACGAGUUGGAUGCGCAGUACGGUGGUGUGC
((((((((((.((((......))))...((((((.(((((..((((((((.....)))))))).))))).((((.....))))))))))...))))))).)))(((.(((....)))))) ( -56.60)
>DroYak_CAF1 16621 120 + 1
GCACCAACUUUGCCCCACUAUGGGCCCGGGCCUUUCCCUUGGUGGACACCGAAAAGGUGUCCAAGGGUGUGAUGCAGUAUAUCAAGACCAACGAGUUGGAUGCCCAGUACGGUGGGGUGC
(((((.(((.((((((.....)))...((((...(((((((.((((((((.....))))))))..(((.(((((.....)))))..)))..))))..))).)))).))).)))..))))) ( -50.70)
>consensus
GCACCAACUUUGCUCCGCUGUGGGCCAGGGCCUUUCCCUUGGUGGACACCGAGAAGGUGUCCAAGGGAGUGAUGCAGUACAUCAAGACCAACGAGUUGGAUGCGCAGUACGGUGGGGUGC
...........((.(((((((((((....))).((((((...((((((((.....))))))))))))))(((((.....))))).......................)))))))).)).. (-36.10 = -36.42 +   0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,876,072 – 11,876,192
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.06
Mean single sequence MFE -45.75
Consensus MFE -35.89
Energy contribution -35.48
Covariance contribution -0.41
Combinations/Pair 1.32
Mean z-score -2.33
Structure conservation index 0.78
SVM decision value 0.50
SVM RNA-class probability 0.759063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11876072 120 - 20766785
GCACACCACCAUACUGCGCAUCCAAAUCAUUGGUCUUGAUGUACUGCAUCACCCCCUUGGACACCUUCUCAGUGUCCACCAAGGGAAAGGCCCUGGCCCACAGCGGAGCAAAGUUGGUGC
......(((((.(((..((.(((........((((((((((.....))))...(((((((((((.......)))))))...)))).))))))(((.....))).)))))..)))))))). ( -43.20)
>DroPse_CAF1 14606 120 - 1
GCACUCCGCCGGGGUAGUCGUCCAGUUUGUGCGUCUUGAUGUAUUUCAUCACGCCCCGGGCGAUCUUUUCAGUGUCCACCAGGGGAUAGGCGCGGGCCCACAGCGGCGAGAAGUUGGAGG
...((((((((((((((.((..(.....)..)).))(((((.....))))).))))).)))...((((((..(((((......)))))(.(((.(.....).))).)))))))..)))). ( -45.40)
>DroSec_CAF1 16515 120 - 1
GCACCCCACCGUAUUGCGCAUCUAAGUCGUUGGUCUUGAUGUACUCCAUCACUCCCUUGGACACCUUCUCGGUGUCCACCAAGGGAAAGGCUCUGGCCCACAGCGGAGCAAAGUUUGUGC
((((...((....(((((((((.(((.(....).))))))))..(((.....(((((((((((((.....))))))))...)))))..(((....)))......))))))).))..)))) ( -41.30)
>DroSim_CAF1 16102 120 - 1
GCACCCCACCGUAUUGCGCAUCCAAAUCGUUGGUCUUGAUGUACUCCAUCACUCCCUUGGACACCUUCUCGGUGUCCACCAAGGGAAAGGCUCUGGCCCACAGCGGAGCAAAGUUGGUGC
((((((((.((..(((......)))..)).))).(((((((.....))))..(((((((((((((.....))))))))...))))))))((((((........))))))......))))) ( -43.20)
>DroEre_CAF1 18604 120 - 1
GCACACCACCGUACUGCGCAUCCAACUCGUUGGCCUUGAUGUACUGCAUCACCCCCUUGGACACCUUAUCGGUGUCCACCAAGGGAAAGGCCCUGGCCCACAGUGGGGCAAAGUUGGUGC
(((.((....))..)))(((.((((((....((((((((((.....))))...((((((((((((.....))))))))...)))).))))))...((((......))))..))))))))) ( -51.70)
>DroYak_CAF1 16621 120 - 1
GCACCCCACCGUACUGGGCAUCCAACUCGUUGGUCUUGAUAUACUGCAUCACACCCUUGGACACCUUUUCGGUGUCCACCAAGGGAAAGGCCCGGGCCCAUAGUGGGGCAAAGUUGGUGC
(((((........((((((..((((....))))....................((((((((((((.....))))))))...))))....))))))((((......))))......))))) ( -49.70)
>consensus
GCACCCCACCGUACUGCGCAUCCAAAUCGUUGGUCUUGAUGUACUGCAUCACCCCCUUGGACACCUUCUCGGUGUCCACCAAGGGAAAGGCCCUGGCCCACAGCGGAGCAAAGUUGGUGC
......(((((.(((..((.(((........((((((((((.....))))...((((((((((((.....))))))))...)))).))))))...((.....)))))))..)))))))). (-35.89 = -35.48 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,876,112 – 11,876,232
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.44
Mean single sequence MFE -37.75
Consensus MFE -26.95
Energy contribution -27.10
Covariance contribution 0.15
Combinations/Pair 1.41
Mean z-score -1.80
Structure conservation index 0.71
SVM decision value 0.93
SVM RNA-class probability 0.884100
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11876112 120 + 20766785
GGUGGACACUGAGAAGGUGUCCAAGGGGGUGAUGCAGUACAUCAAGACCAAUGAUUUGGAUGCGCAGUAUGGUGGUGUGCCGUACACGAUGAAUAAGGAGUCGGGCCAGAAUUGGGAUCA
..((((((((.....)))))))).((...(((((.....)))))...))..((((((.(((..((.(((((((.....))))))).((((.........)))).))....))).)))))) ( -39.40)
>DroSec_CAF1 16555 120 + 1
GGUGGACACCGAGAAGGUGUCCAAGGGAGUGAUGGAGUACAUCAAGACCAACGACUUAGAUGCGCAAUACGGUGGGGUGCCGUACACGAUGAAUAAGGAGUCGGGCCAGAACUGGGAUCA
..((((((((.....)))))))).((...(((((.....)))))...))..((((((..((.((...((((((.....))))))..))....))...))))))..(((....)))..... ( -42.60)
>DroSim_CAF1 16142 120 + 1
GGUGGACACCGAGAAGGUGUCCAAGGGAGUGAUGGAGUACAUCAAGACCAACGAUUUGGAUGCGCAAUACGGUGGGGUGCCGUACACGAUGAAUAAGGAGUCGGGCCAGAACUGGGAUCA
..((((((((.....)))))))).((...(((((.....)))))...))...((((..(.((.((..((((((.....))))))..((((.........)))).))))...)..).))). ( -39.70)
>DroEre_CAF1 18644 120 + 1
GGUGGACACCGAUAAGGUGUCCAAGGGGGUGAUGCAGUACAUCAAGGCCAACGAGUUGGAUGCGCAGUACGGUGGUGUGCCGUACACGAUGAACAAGGAGUCGGGCCAGGACUGGGACCA
((((((((((.....)))))))..((...(((((.....)))))...))..(.((((...((.((.(((((((.....))))))).((((.........)))).)))).)))).).))). ( -44.20)
>DroWil_CAF1 19207 117 + 1
UAUGGAGAGAAAAAAAAUAUCGAAAUCUGUAAUGGAUUAUAUCGAAUUCAAUAUGUUAGAUGACUAUCCCGGUGGAGUACCCGUAACUUUGCUCAAC---ACAAAUCAGCAAUGGGAUUA
...................(((((((((.....)))))...))))....................(((((((.(.....)))......(((((....---.......))))).))))).. ( -16.10)
>DroYak_CAF1 16661 120 + 1
GGUGGACACCGAAAAGGUGUCCAAGGGUGUGAUGCAGUAUAUCAAGACCAACGAGUUGGAUGCCCAGUACGGUGGGGUGCCGUACACGAUGAACAAGGAGUCGGGCCAGGAGUGGGACCA
((((((((((.....)))))))...(((.((((.(.((.((((....((((....)))).......(((((((.....)))))))..)))).))...).)))).))).........))). ( -44.50)
>consensus
GGUGGACACCGAGAAGGUGUCCAAGGGAGUGAUGCAGUACAUCAAGACCAACGAGUUGGAUGCGCAGUACGGUGGGGUGCCGUACACGAUGAACAAGGAGUCGGGCCAGAACUGGGAUCA
..((((((((.....)))))))).((...(((((.....)))))...)).................(((((((.....))))))).................((.(((....)))..)). (-26.95 = -27.10 +   0.15)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,876,112 – 11,876,232
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -30.22
Consensus MFE -19.87
Energy contribution -20.66
Covariance contribution 0.78
Combinations/Pair 1.27
Mean z-score -1.97
Structure conservation index 0.66
SVM decision value 0.92
SVM RNA-class probability 0.882366
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11876112 120 - 20766785
UGAUCCCAAUUCUGGCCCGACUCCUUAUUCAUCGUGUACGGCACACCACCAUACUGCGCAUCCAAAUCAUUGGUCUUGAUGUACUGCAUCACCCCCUUGGACACCUUCUCAGUGUCCACC
.....(((((..(((...((........))..((((((.((.......)).))).)))...)))....)))))...(((((.....)))))......(((((((.......))))))).. ( -22.20)
>DroSec_CAF1 16555 120 - 1
UGAUCCCAGUUCUGGCCCGACUCCUUAUUCAUCGUGUACGGCACCCCACCGUAUUGCGCAUCUAAGUCGUUGGUCUUGAUGUACUCCAUCACUCCCUUGGACACCUUCUCGGUGUCCACC
.....(((....))).(((((..((((.....(((((((((.......))))).))))....))))..)))))...(((((.....)))))......((((((((.....)))))))).. ( -34.80)
>DroSim_CAF1 16142 120 - 1
UGAUCCCAGUUCUGGCCCGACUCCUUAUUCAUCGUGUACGGCACCCCACCGUAUUGCGCAUCCAAAUCGUUGGUCUUGAUGUACUCCAUCACUCCCUUGGACACCUUCUCGGUGUCCACC
.....(((....))).(((((...........(((((((((.......))))).))))..........)))))...(((((.....)))))......((((((((.....)))))))).. ( -30.50)
>DroEre_CAF1 18644 120 - 1
UGGUCCCAGUCCUGGCCCGACUCCUUGUUCAUCGUGUACGGCACACCACCGUACUGCGCAUCCAACUCGUUGGCCUUGAUGUACUGCAUCACCCCCUUGGACACCUUAUCGGUGUCCACC
.(((.........((((.(((...(((.....(((((((((.......)))))).)))....)))...)))))))..((((.....)))))))....((((((((.....)))))))).. ( -37.90)
>DroWil_CAF1 19207 117 - 1
UAAUCCCAUUGCUGAUUUGU---GUUGAGCAAAGUUACGGGUACUCCACCGGGAUAGUCAUCUAACAUAUUGAAUUCGAUAUAAUCCAUUACAGAUUUCGAUAUUUUUUUUCUCUCCAUA
..(((((.(((((.(.....---..).)))))......((........)))))))...........((((((((.((..((........))..)).))))))))................ ( -21.40)
>DroYak_CAF1 16661 120 - 1
UGGUCCCACUCCUGGCCCGACUCCUUGUUCAUCGUGUACGGCACCCCACCGUACUGGGCAUCCAACUCGUUGGUCUUGAUAUACUGCAUCACACCCUUGGACACCUUUUCGGUGUCCACC
.(((..........(((((((.....)))......((((((.......)))))).))))..((((....))))...................)))..((((((((.....)))))))).. ( -34.50)
>consensus
UGAUCCCAGUUCUGGCCCGACUCCUUAUUCAUCGUGUACGGCACCCCACCGUACUGCGCAUCCAACUCGUUGGUCUUGAUGUACUCCAUCACACCCUUGGACACCUUCUCGGUGUCCACC
.............((.(((((..............((((((.......))))))..............))))).))(((((.....)))))......((((((((.....)))))))).. (-19.87 = -20.66 +   0.78)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:33 2006