Locus 9459

Sequence ID 3R_DroMel_CAF1
Location 25,042,898 – 25,043,016
Length 118
Max. P 0.999729
window15148 window15149 window15150 window15151

overview

Window 8

Location 25,042,898 – 25,042,998
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.33
Mean single sequence MFE -30.20
Consensus MFE -28.53
Energy contribution -28.53
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.94
SVM decision value 2.09
SVM RNA-class probability 0.987765
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25042898 100 + 27905053
---GCU----------------CUUUUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGU-GGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
---...----------------(((..(((((........)))(((((.((((((((((((.(((((.-...............))))))))))).)))))).))))).....))..))) ( -28.69)
>DroPse_CAF1 63871 100 + 1
---GCU----------------CUUCUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGU-UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
---.((----------------(..((..(((........)))(((((.((((((((((((.(((((.-...............))))))))))).)))))).))))).....))..))) ( -28.89)
>DroWil_CAF1 71374 120 + 1
GGAGUCCUUUCUAUGUGGCAGCGUCUCUUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUUUGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
((((((......((((....)))).....))))))........(((((.((((((((((((.(((((.................))))))))))).)))))).)))))............ ( -33.63)
>DroMoj_CAF1 121730 100 + 1
---GCU----------------CUUCUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGU-UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
---.((----------------(..((..(((........)))(((((.((((((((((((.(((((.-...............))))))))))).)))))).))))).....))..))) ( -28.89)
>DroAna_CAF1 70357 103 + 1
GGGGUC----------------UUUUUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGU-GUUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
((((((----------------.......))))))........(((((.((((((((((((.(((((.-.((........))..))))))))))).)))))).)))))............ ( -32.20)
>DroPer_CAF1 73472 100 + 1
---GCU----------------CUUCUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGU-UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
---.((----------------(..((..(((........)))(((((.((((((((((((.(((((.-...............))))))))))).)))))).))))).....))..))) ( -28.89)
>consensus
___GCU________________CUUCUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGU_UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGG
...............................(((.((((.((.(((((.((((((((((((.(((((.................))))))))))).)))))).))))).)).)))).))) (-28.53 = -28.53 +  -0.00)

alignment

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secondary structure

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Window 9

Location 25,042,898 – 25,042,998
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.33
Mean single sequence MFE -26.16
Consensus MFE -24.91
Energy contribution -24.91
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.03
Structure conservation index 0.95
SVM decision value 3.96
SVM RNA-class probability 0.999729
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25042898 100 - 27905053
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACC-ACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAAAAG----------------AGC---
.....(((....(.((((((((..(((((((((((................-..)))).))))))).)))))))).)(((........)))....)))----------------...--- ( -25.47)
>DroPse_CAF1 63871 100 - 1
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA-ACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAGAAG----------------AGC---
.....(((....(.((((((((..(((((((((((................-..)))).))))))).)))))))).)(((........))).)))...----------------...--- ( -25.87)
>DroWil_CAF1 71374 120 - 1
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACAAACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAAGAGACGCUGCCACAUAGAAAGGACUCC
.((.........(.((((((((..(((((((((((...................)))).))))))).)))))))).).......(((.(((....))).)))...........))..... ( -28.41)
>DroMoj_CAF1 121730 100 - 1
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA-ACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAGAAG----------------AGC---
.....(((....(.((((((((..(((((((((((................-..)))).))))))).)))))))).)(((........))).)))...----------------...--- ( -25.87)
>DroAna_CAF1 70357 103 - 1
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAAC-ACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAAAAA----------------GACCCC
.....(((....(.((((((((..(((((((((((................-..)))).))))))).)))))))).)(((........))).....))----------------)..... ( -25.47)
>DroPer_CAF1 73472 100 - 1
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA-ACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAGAAG----------------AGC---
.....(((....(.((((((((..(((((((((((................-..)))).))))))).)))))))).)(((........))).)))...----------------...--- ( -25.87)
>consensus
CCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA_ACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAAAAG________________AGC___
............(.((((((((..(((((((((((...................)))).))))))).)))))))).)(((........)))............................. (-24.91 = -24.91 +   0.00)

alignment

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secondary structure

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Window 0

Location 25,042,919 – 25,043,016
Length 97
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 86.92
Mean single sequence MFE -28.98
Consensus MFE -26.95
Energy contribution -26.56
Covariance contribution -0.39
Combinations/Pair 1.08
Mean z-score -1.89
Structure conservation index 0.93
SVM decision value 1.49
SVM RNA-class probability 0.958168
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25042919 97 + 27905053
GUCGGCGAACAUGGAUCUAGUGCACGGU-GGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA------------------ACGAAGAGAG
.(((((((.((((((((((((.(((((.-...............))))))))))).)))))).)))))......((((........))------------------))))...... ( -29.79)
>DroVir_CAF1 89414 114 + 1
GUCGGCGAACAUGGAUCUAGUGCACGGU-UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACACACACACACACACAUAAAAGAAAAACA-
.(((((((.((((((((((((.(((((.-...............))))))))))).)))))).)))))......((((...))))......................))......- ( -27.19)
>DroGri_CAF1 73634 98 + 1
GUCGGCGAACAUGGAUCUAGUGCACGGU-UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACACAAC--------------ACAAAAA---
...(((((.((((((((((((.(((((.-...............))))))))))).)))))).)))))......((((.((....)).))))--------------.......--- ( -28.99)
>DroWil_CAF1 71414 95 + 1
GUCGGCGAACAUGGAUCUAGUGCACGGUUUGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA------------------ACAA-GAG--
.(((((((.((((((((((((.(((((.................))))))))))).)))))).)))))......((((........))------------------))..-)).-- ( -29.63)
>DroMoj_CAF1 121751 100 + 1
GUCGGCGAACAUGGAUCUAGUGCACGGU-UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAAUACACACA--------------GCGAAAACA-
.(((((((.((((((((((((.(((((.-...............))))))))))).)))))).)))))......((((.((......)).))--------------)))).....- ( -29.49)
>DroAna_CAF1 70381 96 + 1
GUCGGCGAACAUGGAUCUAGUGCACGGU-GUUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA------------------CCAAAGAGU-
.(((((((.((((((((((((.(((((.-.((........))..))))))))))).)))))).))))).......((((((....)).------------------)))).))..- ( -28.80)
>consensus
GUCGGCGAACAUGGAUCUAGUGCACGGU_UGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACA__________________ACAAAAAGA_
...(((((.((((((((((((.(((((.................))))))))))).)))))).)))))......((((...))))............................... (-26.95 = -26.56 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 25,042,919 – 25,043,016
Length 97
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 86.92
Mean single sequence MFE -25.43
Consensus MFE -22.41
Energy contribution -22.41
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.88
SVM decision value 1.06
SVM RNA-class probability 0.908733
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25042919 97 - 27905053
CUCUCUUCGU------------------UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACC-ACCGUGCACUAGAUCCAUGUUCGCCGAC
........((------------------((........))))......(.((((((((..(((((((((((................-..)))).))))))).)))))))).)... ( -24.57)
>DroVir_CAF1 89414 114 - 1
-UGUUUUUCUUUUAUGUGUGUGUGUGUGUGUGUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA-ACCGUGCACUAGAUCCAUGUUCGCCGAC
-......................((.(((..((((...))))...))).))(((((((..(((((((((((................-..)))).))))))).)))))))...... ( -25.57)
>DroGri_CAF1 73634 98 - 1
---UUUUUGU--------------GUUGUGUGUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA-ACCGUGCACUAGAUCCAUGUUCGCCGAC
---.......--------------((((.((....)).))))......(.((((((((..(((((((((((................-..)))).))))))).)))))))).)... ( -25.67)
>DroWil_CAF1 71414 95 - 1
--CUC-UUGU------------------UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACAAACCGUGCACUAGAUCCAUGUUCGCCGAC
--...-..((------------------((........))))......(.((((((((..(((((((((((...................)))).))))))).)))))))).)... ( -24.21)
>DroMoj_CAF1 121751 100 - 1
-UGUUUUCGC--------------UGUGUGUAUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA-ACCGUGCACUAGAUCCAUGUUCGCCGAC
-.....((((--------------...((.((((((......)))))).))(((((((..(((((((((((................-..)))).))))))).)))))))).))). ( -26.77)
>DroAna_CAF1 70381 96 - 1
-ACUCUUUGG------------------UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAAC-ACCGUGCACUAGAUCCAUGUUCGCCGAC
-.....((((------------------.((....)))))).......(.((((((((..(((((((((((................-..)))).))))))).)))))))).)... ( -25.77)
>consensus
_UCUCUUUGU__________________UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACA_ACCGUGCACUAGAUCCAUGUUCGCCGAC
................................................(.((((((((..(((((((((((...................)))).))))))).)))))))).)... (-22.41 = -22.41 +   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 13:35:09 2006