Locus 1014

Sequence ID 2R_DroMel_CAF1
Location 4,216,003 – 4,216,241
Length 238
Max. P 0.985196
window1796 window1797 window1798 window1799 window1800

overview

Window 6

Location 4,216,003 – 4,216,123
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.36
Mean single sequence MFE -31.60
Consensus MFE -26.77
Energy contribution -27.02
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.70
Structure conservation index 0.85
SVM decision value 1.69
SVM RNA-class probability 0.972374
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4216003 120 + 20766785
UUAAAUGCAUUCAUUUUUCUAAACCUGGGUGUGUUUUCCACUCUUCUAUGGUCCACGACGCUGGGAUUUUUCGCCAGGCGCUCCGUGGGCAUAUUUUCUAUCGUGUUUUACUGCAUUUAC
.((((((((.................(((((.(....)))))).......(((((((.((((((((....)).))).)))...))))))).....................)))))))). ( -32.00)
>DroSec_CAF1 27560 120 + 1
UUAAAUGCAUUCAUUUUUUUAAACCUGGGUCUGUUUUCCACUCUUCUAUGGUCCACGACGCUUGGAUUUUUCGCCAGGCGCUCCGUGGGCAUAUUUUCCAUCGUGUUUUACUGCAUUUAC
.((((((((................((((.......))))..........(((((((.(((((((........)))))))...))))))).....................)))))))). ( -32.40)
>DroEre_CAF1 29337 120 + 1
UUAAAUGCAUUCAUUUUUCUGAAUCUGGGCCUGUUUUCCACACUCCUCUGGUCCACGACGCUGGGAUUUUUCGCCAGACGCUCCGUGGGCAUAUUUUGUAUCGUGUUUUACUGCAUUUAC
.((((((((((((......))))...(((..(((.....)))..)))...(((((((.((((((((....)).)))).))...))))))).....................)))))))). ( -30.20)
>DroYak_CAF1 30206 120 + 1
UUAAAUGCAUUCGUUUUUCUAAAUAUCGGACUGUUUUCCACACUCCUCUGGUCCACGACGCUGGGAUUUUUCGCCAGACGCUCCGUGGGCAUAUUUUCUAUCGUCUUUUACUGCAUUUAC
.((((((((..................(((.(((.....))).)))....(((((((.((((((((....)).)))).))...))))))).....................)))))))). ( -31.80)
>consensus
UUAAAUGCAUUCAUUUUUCUAAACCUGGGUCUGUUUUCCACACUCCUAUGGUCCACGACGCUGGGAUUUUUCGCCAGACGCUCCGUGGGCAUAUUUUCUAUCGUGUUUUACUGCAUUUAC
.((((((((..................((........))...........(((((((.((((((((....)).)))).))...))))))).....................)))))))). (-26.77 = -27.02 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,216,003 – 4,216,123
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.36
Mean single sequence MFE -31.60
Consensus MFE -25.45
Energy contribution -26.20
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.81
SVM decision value 1.16
SVM RNA-class probability 0.923608
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4216003 120 - 20766785
GUAAAUGCAGUAAAACACGAUAGAAAAUAUGCCCACGGAGCGCCUGGCGAAAAAUCCCAGCGUCGUGGACCAUAGAAGAGUGGAAAACACACCCAGGUUUAGAAAAAUGAAUGCAUUUAA
.((((((((...........((((...((((.(((((..((((.(((.((....))))))))))))))..)))).....(((.....))).......))))..........)))))))). ( -29.60)
>DroSec_CAF1 27560 120 - 1
GUAAAUGCAGUAAAACACGAUGGAAAAUAUGCCCACGGAGCGCCUGGCGAAAAAUCCAAGCGUCGUGGACCAUAGAAGAGUGGAAAACAGACCCAGGUUUAAAAAAAUGAAUGCAUUUAA
.((((((((((....(((..(......((((.(((((..((((.(((........))).)))))))))..))))..)..)))....))((((....))))...........)))))))). ( -29.90)
>DroEre_CAF1 29337 120 - 1
GUAAAUGCAGUAAAACACGAUACAAAAUAUGCCCACGGAGCGUCUGGCGAAAAAUCCCAGCGUCGUGGACCAGAGGAGUGUGGAAAACAGGCCCAGAUUCAGAAAAAUGAAUGCAUUUAA
.(((((((........................(((((..(((.((((.((....))))))))))))))......((.((.((.....)).))))..(((((......)))))))))))). ( -32.90)
>DroYak_CAF1 30206 120 - 1
GUAAAUGCAGUAAAAGACGAUAGAAAAUAUGCCCACGGAGCGUCUGGCGAAAAAUCCCAGCGUCGUGGACCAGAGGAGUGUGGAAAACAGUCCGAUAUUUAGAAAAACGAAUGCAUUUAA
.((((((((((.....))......((((((..(((((..(((.((((.((....))))))))))))))......(((.(((.....))).))).))))))...........)))))))). ( -34.00)
>consensus
GUAAAUGCAGUAAAACACGAUAGAAAAUAUGCCCACGGAGCGCCUGGCGAAAAAUCCCAGCGUCGUGGACCAGAGAAGAGUGGAAAACAGACCCAGAUUUAGAAAAAUGAAUGCAUUUAA
.((((((((.......................(((((..(((.((((.((....)))))))))))))).((((......))))............................)))))))). (-25.45 = -26.20 +   0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,216,043 – 4,216,163
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -29.45
Consensus MFE -27.40
Energy contribution -27.65
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -2.38
Structure conservation index 0.93
SVM decision value 2.00
SVM RNA-class probability 0.985196
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4216043 120 + 20766785
CUCUUCUAUGGUCCACGACGCUGGGAUUUUUCGCCAGGCGCUCCGUGGGCAUAUUUUCUAUCGUGUUUUACUGCAUUUACUUGCUUUUUGCUAUCCUAAUUCAUAGAAAAGUCAUACAUU
((.((((((((((((((.((((((((....)).))).)))...)))))))..............((......(((......))).....))..........))))))).))......... ( -30.10)
>DroSec_CAF1 27600 120 + 1
CUCUUCUAUGGUCCACGACGCUUGGAUUUUUCGCCAGGCGCUCCGUGGGCAUAUUUUCCAUCGUGUUUUACUGCAUUUACCUGCUUUUUGCUAUCCUAAUUCAUAGAAAAAUCAUACAUU
...((((((((((((((.(((((((........)))))))...)))))))............((((......))))......((.....))..........)))))))............ ( -31.60)
>DroEre_CAF1 29377 120 + 1
CACUCCUCUGGUCCACGACGCUGGGAUUUUUCGCCAGACGCUCCGUGGGCAUAUUUUGUAUCGUGUUUUACUGCAUUUACCUGCUUUUUGCUAUCUUAAUUCAUAGGAAAAUCAUACACU
...((((.(((((((((.((((((((....)).)))).))...))))))).......(((..((((......)))).)))..((.....))..........)).))))............ ( -28.40)
>DroYak_CAF1 30246 120 + 1
CACUCCUCUGGUCCACGACGCUGGGAUUUUUCGCCAGACGCUCCGUGGGCAUAUUUUCUAUCGUCUUUUACUGCAUUUACUUGCUUUUUGCUAUCUUAAUUCAUAGGAAAGUCAUACAUU
...((((.(((((((((.((((((((....)).)))).))...)))))))......................(((......))).................)).))))............ ( -27.70)
>consensus
CACUCCUAUGGUCCACGACGCUGGGAUUUUUCGCCAGACGCUCCGUGGGCAUAUUUUCUAUCGUGUUUUACUGCAUUUACCUGCUUUUUGCUAUCCUAAUUCAUAGAAAAAUCAUACAUU
...((((((((((((((.((((((((....)).)))).))...)))))))......................(((......))).................)))))))............ (-27.40 = -27.65 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,216,043 – 4,216,163
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -28.85
Consensus MFE -27.70
Energy contribution -28.20
Covariance contribution 0.50
Combinations/Pair 1.06
Mean z-score -1.61
Structure conservation index 0.96
SVM decision value 0.79
SVM RNA-class probability 0.852522
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4216043 120 - 20766785
AAUGUAUGACUUUUCUAUGAAUUAGGAUAGCAAAAAGCAAGUAAAUGCAGUAAAACACGAUAGAAAAUAUGCCCACGGAGCGCCUGGCGAAAAAUCCCAGCGUCGUGGACCAUAGAAGAG
.........((((((((((..........(((....(((......))).((.....))...........)))(((((..((((.(((.((....))))))))))))))..)))))))))) ( -31.50)
>DroSec_CAF1 27600 120 - 1
AAUGUAUGAUUUUUCUAUGAAUUAGGAUAGCAAAAAGCAGGUAAAUGCAGUAAAACACGAUGGAAAAUAUGCCCACGGAGCGCCUGGCGAAAAAUCCAAGCGUCGUGGACCAUAGAAGAG
..........(((((((((..........(((....(((......))).((.....))...........)))(((((..((((.(((........))).)))))))))..))))))))). ( -29.10)
>DroEre_CAF1 29377 120 - 1
AGUGUAUGAUUUUCCUAUGAAUUAAGAUAGCAAAAAGCAGGUAAAUGCAGUAAAACACGAUACAAAAUAUGCCCACGGAGCGUCUGGCGAAAAAUCCCAGCGUCGUGGACCAGAGGAGUG
...........(((((.((..........(((....(((......))).(((........)))......)))(((((..(((.((((.((....))))))))))))))..)).))))).. ( -28.30)
>DroYak_CAF1 30246 120 - 1
AAUGUAUGACUUUCCUAUGAAUUAAGAUAGCAAAAAGCAAGUAAAUGCAGUAAAAGACGAUAGAAAAUAUGCCCACGGAGCGUCUGGCGAAAAAUCCCAGCGUCGUGGACCAGAGGAGUG
...........(((((.((..........(((....(((......))).((.....))...........)))(((((..(((.((((.((....))))))))))))))..)).))))).. ( -26.50)
>consensus
AAUGUAUGACUUUCCUAUGAAUUAAGAUAGCAAAAAGCAAGUAAAUGCAGUAAAACACGAUAGAAAAUAUGCCCACGGAGCGCCUGGCGAAAAAUCCCAGCGUCGUGGACCAGAGAAGAG
.........((((((((((..........(((....(((......))).((.....))...........)))(((((..(((.((((.((....))))))))))))))..)))))))))) (-27.70 = -28.20 +   0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,216,123 – 4,216,241
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.27
Mean single sequence MFE -26.90
Consensus MFE -19.99
Energy contribution -20.86
Covariance contribution 0.87
Combinations/Pair 1.13
Mean z-score -1.60
Structure conservation index 0.74
SVM decision value 0.23
SVM RNA-class probability 0.643574
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4216123 118 + 20766785
UUGCUUUUUGCUAUCCUAAUUCAUAGAAAAGUCAUACAUUCGUUUUCUGUGGACUUGCCAGUCAAGGCAGCAUUCGGUGAUAUCUAGGGAAAAA-G-GUUUUCUAUGGAAAUAUACAAAA
(..((...((((.......(((((((((((............)))))))))))...(((......)))))))...))..)..((((.(((((..-.-..))))).))))........... ( -25.10)
>DroSec_CAF1 27680 118 + 1
CUGCUUUUUGCUAUCCUAAUUCAUAGAAAAAUCAUACAUUCGUUUUCUUCGGACCUGCCAGUCACGGCAGCUUUUGGCGAUAUCUAGGGAAAAA-GGGUUUUCUAUGGAAAUAUACAA-A
..((.....))........((((((((((........((((.((((((..(((..((((......))))((.....))....)))..)))))).-)))))))))))))).........-. ( -26.00)
>DroEre_CAF1 29457 118 + 1
CUGCUUUUUGCUAUCUUAAUUCAUAGGAAAAUCAUACACUCCUUUUCUAUGGACUUGCCCAUCAAGGCAGCCUUUGGAGACAUCUAGGGAAAAG-GGCUUUUCUAUUUAUAUAUGCAA-A
.(((.((((.((((........)))).))))........(((((((((.((((.(((((......)))))....((....)))))).)))))))-)).................))).-. ( -26.50)
>DroYak_CAF1 30326 119 + 1
UUGCUUUUUGCUAUCUUAAUUCAUAGGAAAGUCAUACAUUCGUUUUCUAUGGACAUGCCAAUCAAGGCAGCUUUUGGCGAUAUCUAGGGAAAACAUACUUUUCUAUGAAAAUAUACAA-A
..((.....))........(((((((((((((.((......(((((((.((((..((((......))))((.....))....)))).)))))))))))))))))))))).........-. ( -30.00)
>consensus
CUGCUUUUUGCUAUCCUAAUUCAUAGAAAAAUCAUACAUUCGUUUUCUAUGGACUUGCCAAUCAAGGCAGCUUUUGGCGAUAUCUAGGGAAAAA_GGCUUUUCUAUGGAAAUAUACAA_A
..((.....))........(((((((((((...........(((((((.((((..((((......))))((.....))....)))).)))))))....)))))))))))........... (-19.99 = -20.86 +   0.87)

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 09:54:13 2006