Locus 1822

Sequence ID 3R_DroMel_CAF1
Location 5,212,569 – 5,212,661
Length 92
Max. P 0.803678
window2997 window2998

overview

Window 7

Location 5,212,569 – 5,212,661
Length 92
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 82.89
Mean single sequence MFE -28.57
Consensus MFE -19.90
Energy contribution -19.68
Covariance contribution -0.22
Combinations/Pair 1.22
Mean z-score -2.36
Structure conservation index 0.70
SVM decision value 0.51
SVM RNA-class probability 0.765212
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5212569 92 + 27905053
UACA-GGCCGGACAACUUAUGGCAGUGACUAGCGAAUAAACAGAUACAAAAGUAUCUACAAGUUGUCCCUGUCAA-----GAGACAACGGCAUGUGUG------
((((-.((((((((((((...((........))........((((((....))))))..))))))))).((((..-----..))))..))).))))..------ ( -31.00)
>DroPse_CAF1 19774 100 + 1
UACAUGGCCGGGCAACUUAUGGCAGUGACUAGCAGAUAAACAGAUACAAAAGUAUCUACAAGUUGUCUUUGUGU-UCGCUGGAGCAACAGCAUGUGUGUGU---
((((((...(((((((((...((........))........((((((....))))))..)))))))))((((((-((....)))).)))))))))).....--- ( -27.00)
>DroSec_CAF1 18433 92 + 1
UACA-GGCCGGACAACUUAUGGCACUGACUAGCGAAUAAACAGAUACAAAAGUAUCUACAAGUUGUCCCUGUCAA-----GAGACAACGGCAUGUGUG------
((((-.((((((((((((...((........))........((((((....))))))..))))))))).((((..-----..))))..))).))))..------ ( -31.00)
>DroYak_CAF1 19633 92 + 1
UACA-GGCCGGACAACUUAUGGCAGUGACUAGCGAAUAAACAGAUACAAAAGUAUCUACAAGUUGUCGCUGUCAG-----GAGACAACAGCAUGUGUG------
((((-.((.(.....(((.((((((((((.(((........((((((....))))))....))))))))))))).-----)))....).)).))))..------ ( -28.10)
>DroAna_CAF1 18926 103 + 1
UACA-UGUCAGGCGACUUAUGGCAGUGACUAGCAGAUAAACAGAUACCAAAGUAUCUACAAGUUGUCCCCGUUCGCCGCUAAAGCAAUAGCAUGUGUGUGCGCC
((((-(((..(((((...((((..(..(((.(.(((((....(....)....))))).).)))..)..)))))))))((....))....)))))))........ ( -27.30)
>DroPer_CAF1 19618 99 + 1
UACAUGGCCGGGCAACUUAUGGCAGUGACUAGCAGAUAAACAGAUACAAAAGUAUCUACAAGUUGUCUUUGUGU-UCGCUGGAGCAACAGCAUGUGUGUG----
((((((...(((((((((...((........))........((((((....))))))..)))))))))((((((-((....)))).))))))))))....---- ( -27.00)
>consensus
UACA_GGCCGGACAACUUAUGGCAGUGACUAGCAAAUAAACAGAUACAAAAGUAUCUACAAGUUGUCCCUGUCA______GAAACAACAGCAUGUGUG______
((((..((.(((((((((...((........))........((((((....))))))..))))))))).((((.........))))...))...))))...... (-19.90 = -19.68 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,212,569 – 5,212,661
Length 92
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 82.89
Mean single sequence MFE -29.63
Consensus MFE -17.09
Energy contribution -16.57
Covariance contribution -0.52
Combinations/Pair 1.15
Mean z-score -3.19
Structure conservation index 0.58
SVM decision value 0.63
SVM RNA-class probability 0.803678
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5212569 92 - 27905053
------CACACAUGCCGUUGUCUC-----UUGACAGGGACAACUUGUAGAUACUUUUGUAUCUGUUUAUUCGCUAGUCACUGCCAUAAGUUGUCCGGCC-UGUA
------...(((.(((.(((((..-----..)))))(((((((((((((((((....))))))........((........)).)))))))))))))).-))). ( -34.90)
>DroPse_CAF1 19774 100 - 1
---ACACACACAUGCUGUUGCUCCAGCGA-ACACAAAGACAACUUGUAGAUACUUUUGUAUCUGUUUAUCUGCUAGUCACUGCCAUAAGUUGCCCGGCCAUGUA
---......((((((((((((....))))-.........((((((((((((((....))))))........((........)).))))))))..))).))))). ( -24.00)
>DroSec_CAF1 18433 92 - 1
------CACACAUGCCGUUGUCUC-----UUGACAGGGACAACUUGUAGAUACUUUUGUAUCUGUUUAUUCGCUAGUCAGUGCCAUAAGUUGUCCGGCC-UGUA
------...(((.(((.(((((..-----..)))))(((((((((((((((((....)))))).......((((....))))..)))))))))))))).-))). ( -35.20)
>DroYak_CAF1 19633 92 - 1
------CACACAUGCUGUUGUCUC-----CUGACAGCGACAACUUGUAGAUACUUUUGUAUCUGUUUAUUCGCUAGUCACUGCCAUAAGUUGUCCGGCC-UGUA
------...(((.(((((((((..-----..))))))((((((((((((((((....))))))........((........)).)))))))))).))).-))). ( -32.00)
>DroAna_CAF1 18926 103 - 1
GGCGCACACACAUGCUAUUGCUUUAGCGGCGAACGGGGACAACUUGUAGAUACUUUGGUAUCUGUUUAUCUGCUAGUCACUGCCAUAAGUCGCCUGACA-UGUA
((((.((......((((......))))((((.(((((.....)))))((((((....)))))).................))))....)))))).....-.... ( -27.70)
>DroPer_CAF1 19618 99 - 1
----CACACACAUGCUGUUGCUCCAGCGA-ACACAAAGACAACUUGUAGAUACUUUUGUAUCUGUUUAUCUGCUAGUCACUGCCAUAAGUUGCCCGGCCAUGUA
----.....((((((((((((....))))-.........((((((((((((((....))))))........((........)).))))))))..))).))))). ( -24.00)
>consensus
______CACACAUGCUGUUGCCUC______UGACAGGGACAACUUGUAGAUACUUUUGUAUCUGUUUAUCCGCUAGUCACUGCCAUAAGUUGCCCGGCC_UGUA
.......(((...(((((((.............)))...((((((((((((((....))))))........((........)).))))))))..))))..))). (-17.09 = -16.57 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:21 2006