Locus 3590

Sequence ID 2R_DroMel_CAF1
Location 11,959,196 – 11,959,295
Length 99
Max. P 0.550895
window5852 window5853

overview

Window 2

Location 11,959,196 – 11,959,295
Length 99
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 92.13
Mean single sequence MFE -20.37
Consensus MFE -17.44
Energy contribution -17.50
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -1.48
Structure conservation index 0.86
SVM decision value 0.03
SVM RNA-class probability 0.550895
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11959196 99 + 20766785
UAUAGGUUAAAAGUGGGCAACCUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCCUACGAAUUUUCAAGUGCCACCGCCUUU----UUCUUUUU-----
...((((.....((((((........((((((....))))))...((((((....))))))))))))((....))..........))))..----........----- ( -22.60)
>DroSec_CAF1 10526 98 + 1
UAUAGGUUAAAAGUGGGCAACCUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCCUACGAAUUUUCAAGUGCCACCGCCUU-----UUCUUUUU-----
...((((.....((((((........((((((....))))))...((((((....))))))))))))((....))..........)))).-----........----- ( -22.60)
>DroSim_CAF1 13671 98 + 1
UAUAGGUUAAAAGUGGGCAACCUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCCUACGAAUUUUCAAGUGCCACCGCCUU-----UUCUUUUU-----
...((((.....((((((........((((((....))))))...((((((....))))))))))))((....))..........)))).-----........----- ( -22.60)
>DroEre_CAF1 10583 98 + 1
UACAGGUUAAAAGUGGGCAACCUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCCUCAGAAUUUUCAAGUGCCACCGCCUU-----UUCUUUUU-----
........(((((.((((........((((((....))))))...((((((....))))))........................)))).-----..))))).----- ( -18.30)
>DroYak_CAF1 10612 103 + 1
UACAGGUUAAAAAUGGGCAACCUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCCACAGAAUUUUCAAGUGCCACCGCCUU-----UUCUUUUUUUUUU
....(((..(((((.(((........((((((....))))))...((((((....))))))))).....))))).....)))........-----............. ( -17.90)
>DroAna_CAF1 11064 103 + 1
UUCAGGUUAAAAGUGGGCAACUUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCUUCAGAAUUUUCAAGUGCCAUGGCGUUUUUCUUUCUUUUU-----
...(((..(((.((.((((.(((...((((((....))))))...((((((....))))))..............)))))))...)).)))..))).......----- ( -18.20)
>consensus
UACAGGUUAAAAGUGGGCAACCUUUAUAUGCGAUUCCGUAUACAAAUCAACUUCCGUUGAUGCCUAAGAAUUUUCAAGUGCCACCGCCUU_____UUCUUUUU_____
...((((.......((....))....((((((....))))))...((((((....))))))))))..(((.....(((.((....))))).....))).......... (-17.44 = -17.50 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,959,196 – 11,959,295
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 92.13
Mean single sequence MFE -24.97
Consensus MFE -19.72
Energy contribution -20.05
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.79
SVM decision value -0.05
SVM RNA-class probability 0.508797
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11959196 99 - 20766785
-----AAAAAGAA----AAAGGCGGUGGCACUUGAAAAUUCGUAGGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAGGUUGCCCACUUUUAACCUAUA
-----.......(----((((..((..((.((((....((((((.((((((((....)))))..))).))))))....)).....))))..))..)))))........ ( -26.10)
>DroSec_CAF1 10526 98 - 1
-----AAAAAGAA-----AAGGCGGUGGCACUUGAAAAUUCGUAGGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAGGUUGCCCACUUUUAACCUAUA
-----......((-----(((..((..((.((((....((((((.((((((((....)))))..))).))))))....)).....))))..))..)))))........ ( -26.20)
>DroSim_CAF1 13671 98 - 1
-----AAAAAGAA-----AAGGCGGUGGCACUUGAAAAUUCGUAGGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAGGUUGCCCACUUUUAACCUAUA
-----......((-----(((..((..((.((((....((((((.((((((((....)))))..))).))))))....)).....))))..))..)))))........ ( -26.20)
>DroEre_CAF1 10583 98 - 1
-----AAAAAGAA-----AAGGCGGUGGCACUUGAAAAUUCUGAGGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAGGUUGCCCACUUUUAACCUGUA
-----......((-----(((..((..((.(((....((((((..((((((((....)))))..)))...))))))........)))))..))..)))))........ ( -25.90)
>DroYak_CAF1 10612 103 - 1
AAAAAAAAAAGAA-----AAGGCGGUGGCACUUGAAAAUUCUGUGGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAGGUUGCCCAUUUUUAACCUGUA
..........(((-----((.(.((..((.(((....((((((((((((((((....)))))..))).))))))))........)))))..))).)))))........ ( -25.90)
>DroAna_CAF1 11064 103 - 1
-----AAAAAGAAAGAAAAACGCCAUGGCACUUGAAAAUUCUGAAGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAAGUUGCCCACUUUUAACCUGAA
-----................((....))...((...((((((..((((((((....)))))..)))...))))))..))..(((((((.....)))))))....... ( -19.50)
>consensus
_____AAAAAGAA_____AAGGCGGUGGCACUUGAAAAUUCGGAGGCAUCAACGGAAGUUGAUUUGUAUACGGAAUCGCAUAUAAAGGUUGCCCACUUUUAACCUAUA
..........(((.....(((((....)).))).....)))...(((((((((....)))))(((((((.((....)).)))))))...))))............... (-19.72 = -20.05 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:24 2006