Locus 1846

Sequence ID 3R_DroMel_CAF1
Location 5,298,912 – 5,299,139
Length 227
Max. P 0.940168
window3037 window3038 window3039

overview

Window 7

Location 5,298,912 – 5,299,023
Length 111
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 82.40
Mean single sequence MFE -33.54
Consensus MFE -20.45
Energy contribution -20.97
Covariance contribution 0.52
Combinations/Pair 1.11
Mean z-score -2.33
Structure conservation index 0.61
SVM decision value 0.86
SVM RNA-class probability 0.868085
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5298912 111 + 27905053
--GUUCAGUGGCUCAGUGGAUUUGUUGGUCAAGAGAUCAACAGAUCAACAGAUCAACAGAUCAAUAGAGCACUAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCU
--....((((((...((.((((((((((((....)))))))))))).)).((((....))))...((((((((....)))))...((((((......))))))))).)))))) ( -38.70)
>DroSec_CAF1 3552 103 + 1
--GUUCAGUGGCUCAGCGGAUUUGUUGGUCAAGAAAUCAACAGA--------UCAACAGAUCAAUAGAGCACCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCU
--....((((((...((.((((((((((((............))--------))))))))))......((((......)))))).((((((......))))))....)))))) ( -33.10)
>DroSim_CAF1 3146 103 + 1
--GUUCAGUGGCUCAGUGGAUUUGUUGGUCAAGAGAUCAACGGA--------UCAACAGAUCAAUAGAGCACCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCU
--....((((((...((.((((((((((((....))))))))))--------)).))(((((......((((......)))).........(((....)))))))).)))))) ( -34.80)
>DroEre_CAF1 3414 97 + 1
UCGCUCGGUGGCUCGGUGGUUUUGUGGGU----------------CAAGGGAUCAAGAGAUCAAUGGAGCACUAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCU
......((((((..(((...(((((((((----------------.((..((((....))))...((.(((((....))))).))...)).)))))))))..)))..)))))) ( -31.50)
>DroYak_CAF1 3156 111 + 1
--GUUAAGUGGCUCAGUGGUUUUGUGGAUCAUGAGAUCAUGAGAUCAAGAGAUCAAGAGAUCAAUAGACCCCCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCU
--....((((((...(((((((..((...))..)))))))(((((((...((((....))))...........(((.((((.....)))).)))......))))))))))))) ( -29.60)
>consensus
__GUUCAGUGGCUCAGUGGAUUUGUUGGUCAAGAGAUCAACAGA_CAA__GAUCAACAGAUCAAUAGAGCACCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCU
......((((((.....((.((((((((((............................))))))))))((((......)))).))((((((......))))))....)))))) (-20.45 = -20.97 +   0.52)

alignment

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secondary structure

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Window 8

Location 5,298,946 – 5,299,063
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 89.57
Mean single sequence MFE -31.52
Consensus MFE -27.24
Energy contribution -28.24
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.86
SVM decision value 1.28
SVM RNA-class probability 0.940168
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5298946 117 + 27905053
UCAACAGAUCAACAGAUCAACAGAUCAAUAGAGCACUAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCUUGAAUGCCUUCGAGCAGAGCGCACAGAUGUAUUUCCGCUC
......((((....))))............((((........((((((.((.........((((....))))..(((((((....))))))).)))))))).((......)).)))) ( -31.80)
>DroSec_CAF1 3586 109 + 1
UCAACAGA--------UCAACAGAUCAAUAGAGCACCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCUUGAAUGCCUUCGAGCAGAGCGCACAGAUGUAUUUCCGCUC
......((--------((....))))....((((........((((((.((.........((((....))))..(((((((....))))))).)))))))).((......)).)))) ( -31.80)
>DroSim_CAF1 3180 109 + 1
UCAACGGA--------UCAACAGAUCAAUAGAGCACCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCUUGAAUGCUUUCGAGCAGAGCGCACAGAUGUAUUUCCGCUC
......((--------((....))))....((((........((((((.((.........((((....))))..(((((((....))))))).)))))))).((......)).)))) ( -32.40)
>DroEre_CAF1 3443 108 + 1
---------CAAGGGAUCAAGAGAUCAAUGGAGCACUAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCUUGAAUGCCUUCGAGCAGAGCGCACAGAUGUAUUUCCGCUC
---------.....((((....))))...((((.....(((.((((((.((.........((((....))))..(((((((....))))))).)))))))).)))....)))).... ( -31.50)
>DroYak_CAF1 3190 117 + 1
UCAUGAGAUCAAGAGAUCAAGAGAUCAAUAGACCCCCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCUUGAAUGCCUUCGAGCAGAGCGCACAGAUGUAUUUCCGCUC
....(((((((...((((....))))................((((((.((.........((((....))))..(((((((....))))))).))))))))...)).)))))..... ( -30.10)
>consensus
UCAACAGA_CAA__GAUCAACAGAUCAAUAGAGCACCAGUUAGUGCGCCUCAUUUACUUACAAGUGAUCUUGCCGCUUGAAUGCCUUCGAGCAGAGCGCACAGAUGUAUUUCCGCUC
..............((((....))))....((((........((((((.((.........((((....))))..(((((((....))))))).)))))))).((......)).)))) (-27.24 = -28.24 +   1.00)

alignment

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secondary structure

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Window 9

Location 5,299,023 – 5,299,139
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.70
Mean single sequence MFE -33.20
Consensus MFE -29.44
Energy contribution -29.22
Covariance contribution -0.22
Combinations/Pair 1.15
Mean z-score -1.26
Structure conservation index 0.89
SVM decision value -0.06
SVM RNA-class probability 0.505348
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5299023 116 - 27905053
----GGACUUUUUAUAGAUUUGUUGCAAGAUCUUUGGAAAUGCCUCGGCGCUGGCCAAGCACAAACUGACGCACAGCGACGAGCGGAAAUACAUCUGUGCGCUCUGCUCGAAGGCAUUCA
----(((.((((((.((((((......)))))).))))))(((((...(((((((..((......))...)).))))).((((((((..(((....)))...)))))))).)))))))). ( -37.20)
>DroVir_CAF1 3453 116 - 1
----GUACUUUUUAUAGAUUUGUAGCAAGAUCUUUGGAAAUGCUUCGGCACUGGCCAAGCACAAACUGACGCACAGCGACGAGCGGAAAUAUAUUUGUGCGCUCUGCUCGAAGGCAUUCA
----....((((((.((((((......)))))).))))))(((....)))...(((.............(((...))).((((((((.(((....)))....))))))))..)))..... ( -31.30)
>DroGri_CAF1 4384 116 - 1
----AUACUUUUUAUAGAUUUGUAGCAAGAUAUUCGGAAAUGCCUCGGCGUUGGCCAAGCACAAAUUGACGCACAGCGACGAACGGAAAUAUAUUUGUGCGCUCUGCUCGAAGGCAUUCA
----...((((.....(((((((.((..(.....)((.(((((....)))))..))..)))))))))((.(((.((((....(((((......))))).)))).)))))))))....... ( -28.90)
>DroWil_CAF1 3183 114 - 1
------CCUUUUUGUAGAUUUGCUGCAAAAUCUUUGGAAAUGCUUCGGCGUUGGCCAAGCACAAACUGACGCACAGCGACGAACGGAAAUACAUUUGCGCGCUUUGCUCUAAGGCAUUCA
------...((((((((.....)))))))).(((((((..(((((.(((....)))))))).........(((.((((.((((.(......).))))..)))).))))))))))...... ( -32.70)
>DroMoj_CAF1 3530 111 - 1
---------UUUAAUAGAUUUGCAGCAAGAUCUUUGGAAAUGCCUCGGCACUAGCCAAGCACAAACUGACGCACAGCGACGAACGGAAAUACAUCUGUGCGCUCUGCUCGAAGGCAUUCA
---------(((((.((((((......)))))))))))(((((((((((....)))...........((.(((.((((....(((((......))))).)))).)))))).))))))).. ( -33.30)
>DroAna_CAF1 3723 120 - 1
UUCUGGCCUUUUUAUAGAUUUGUUGCAAGAUCUUUGGAAAUGCCUCGGCACUGGCCAAGCACAAACUGACGCACAGCGACGAACGGAAAUACAUCUGUGCGCUCUGCUCGAAGGCAUUCA
...(((((((((((.((((((......)))))).))))))(((....)))..))))).((......(((.(((.((((....(((((......))))).)))).))))))...))..... ( -35.80)
>consensus
____G_ACUUUUUAUAGAUUUGUAGCAAGAUCUUUGGAAAUGCCUCGGCACUGGCCAAGCACAAACUGACGCACAGCGACGAACGGAAAUACAUCUGUGCGCUCUGCUCGAAGGCAUUCA
..........((((.((((((......)))))).))))(((((((.(((....)))...........((.(((.((((....(((((......))))).)))).)))))..))))))).. (-29.44 = -29.22 +  -0.22)

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 10:21:00 2006