Locus 7966

Sequence ID 3L_DroMel_CAF1
Location 21,095,479 – 21,095,754
Length 275
Max. P 0.999921
window12995 window12996 window12997 window12998

overview

Window 5

Location 21,095,479 – 21,095,599
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -27.62
Consensus MFE -24.22
Energy contribution -24.46
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.31
Structure conservation index 0.88
SVM decision value 0.33
SVM RNA-class probability 0.693614
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21095479 120 - 23771897
AAGGCAAAACAUUUGACAUAUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACCGUUUAAAUGGCAAAGUAGGAAUGAAAAACACACACAAACC
........................(((((((((((...(((.((((..((......))...))).).))).)))))(.((((....)))))..............))))))......... ( -23.00)
>DroSec_CAF1 145683 120 - 1
AAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAACGGCGACCGUUUAAAUGGCAAAGUAGGAGUGAAAAACACACACAAACC
((((((((.((((.((....)).)))))))))))).((((...(....((......)).(((((.(.((....)).).((((....))))........))))).....)...)))).... ( -27.80)
>DroSim_CAF1 53187 120 - 1
AAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACCGUUUAAAUGGCAAAGUAGGAGUGAAAAACACACACAAACC
((((((((.((((.((....)).)))))))))))).((((...(....((......)).(((((.(.((....)).).((((....))))........))))).....)...)))).... ( -27.80)
>DroEre_CAF1 68111 120 - 1
ACGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAAGAGCACCGAAAGCGGACACUCACACCAAAAGGCGACAGUUUAAAUGGCAAAGUAGGAGUGAUAAACACGUGCAAACC
...(((..((.((((.(((((..(.((((.(((((...(((..(((..(((....)))...)))...))).))))))))).)..))))).))))))....(((.....))).)))..... ( -29.70)
>DroYak_CAF1 39918 120 - 1
AAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACAGUUUAAAUGGCAAAGCAGGAGUGAAAAACACACACAAGCC
..(((......((((.(((((..(.((((.(((((...(((.((((..((......))...))).).))).))))))))).)..))))).))))......(((.....)))......))) ( -29.80)
>consensus
AAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACCGUUUAAAUGGCAAAGUAGGAGUGAAAAACACACACAAACC
((((((((.((((.((....)).)))))))))))).((((........((......)).(((((.(.((....)).)...(((.....))).......))))).....))))........ (-24.22 = -24.46 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 21,095,519 – 21,095,639
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.83
Mean single sequence MFE -38.22
Consensus MFE -36.88
Energy contribution -37.32
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.68
Structure conservation index 0.96
SVM decision value 4.57
SVM RNA-class probability 0.999921
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21095519 120 - 23771897
UACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUAUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACC
....((((....(((((((((...(((((.....)))))(((((((((.((((.((....)).)))))))))))))...)))))))))((......))................)))).. ( -39.50)
>DroSec_CAF1 145723 120 - 1
UACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAACGGCGACC
....((((....(((((((((...(((((.....)))))(((((((((.((((.((....)).)))))))))))))...)))))))))((......))................)))).. ( -39.60)
>DroSim_CAF1 53227 120 - 1
UACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACC
....((((....(((((((((...(((((.....)))))(((((((((.((((.((....)).)))))))))))))...)))))))))((......))................)))).. ( -39.60)
>DroEre_CAF1 68151 120 - 1
CACUCCGCAUCCUGCUCCAUCUGGGCAUGGCACACAUGUUACGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAAGAGCACCGAAAGCGGACACUCACACCAAAAGGCGACA
.....(((....(((.((....)))))(((..((((((....((((((.((((.((....)).)))))))))).))))))...(((..(((....)))...)))...)))....)))... ( -32.80)
>DroYak_CAF1 39958 120 - 1
UACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACA
....((((....(((((((((...(((((.....)))))(((((((((.((((.((....)).)))))))))))))...)))))))))((......))................)))).. ( -39.60)
>consensus
UACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUGGAGGAGCACCAAAAGCGGACACUCACACCAAAAGGCGACC
...(((((....(((((((((...(((((.....)))))(((((((((.((((.((....)).)))))))))))))...)))))))))......)))))......(.((....)).)... (-36.88 = -37.32 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 21,095,559 – 21,095,674
Length 115
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 87.34
Mean single sequence MFE -30.43
Consensus MFE -26.24
Energy contribution -26.30
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.86
SVM decision value 1.08
SVM RNA-class probability 0.911962
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21095559 115 - 23771897
CCCGUGC----CGUCCUGCCGCUUUCCGCCUGAUCGUCCUACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUAUCUAGUGUUUGCCUUAUGUG
...((((----((...((((.......((..(((((........)).)))..))..(....))))))))))).(((((.((((((((.((((.((....)).))))))))))))))))) ( -32.50)
>DroSec_CAF1 145763 119 - 1
CCCGUCCCGCCCGUCUUGCCCCUCUCCGCCUGAUCGUCCUACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUG
............(((.(((((......((..(((((........)).)))..)).......))))).))).((((...(((((((((.((((.((....)).))))))))))))))))) ( -32.12)
>DroEre_CAF1 68191 107 - 1
-----------UGUCCUGCUCCUCG-CCCCGGAUCGUCCCACUCCGCAUCCUGCUCCAUCUGGGCAUGGCACACAUGUUACGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUG
-----------.............(-((..((((((........)).))))(((.((....))))).))).((((((....((((((.((((.((....)).)))))))))).)))))) ( -29.00)
>DroYak_CAF1 39998 108 - 1
-----------UGUCCUGCCGCUCUUCCCCUGAUCGUCCUACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUG
-----------.....(((((..........(((((........)).))).(((.((....))))))))))((((...(((((((((.((((.((....)).))))))))))))))))) ( -28.10)
>consensus
___________CGUCCUGCCCCUCUCCCCCUGAUCGUCCUACUUCGCAUCCUGCUCCUUCUGGGCAUGGCACACAUGUUAAGGCAAAACAUUUGACAUUUCUAGUGUUUGCCUUAUGUG
................((((...........(((((........)).))).(((.((....))))).))))((((((...(((((((.((((.((....)).))))))))))))))))) (-26.24 = -26.30 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 21,095,639 – 21,095,754
Length 115
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 85.69
Mean single sequence MFE -40.40
Consensus MFE -30.14
Energy contribution -31.08
Covariance contribution 0.94
Combinations/Pair 1.09
Mean z-score -1.64
Structure conservation index 0.75
SVM decision value 0.29
SVM RNA-class probability 0.669682
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21095639 115 + 23771897
GGACGAUCAGGCGGAAAGCGGCAGGACG----GCACGGGAACGGACAGGAGUAGCAGUCAGGGACAUUUGUCGUGCUGUUGGCUGUUUUUUAUGUCCUGCCCAUUUCCAUAGCAAUUGG
...((((...(((((((..(((((((((----...((....))(((((...(((((((..(.(((....))).)))))))).))))).....)))))))))..)))))...)).)))). ( -40.80)
>DroSec_CAF1 145843 119 + 1
GGACGAUCAGGCGGAGAGGGGCAAGACGGGCGGGACGGGAAAGGACAGGAGUAGCAGUCAGGGACAUUUGUCGUGCUGUUGGCUGUUUUUUAUGUCCUGCCCAUUUCCAUAGCAAUUGG
...((((...(((((((..(......)((((((((((..(((((((((...(((((((..(.(((....))).)))))))).))))))))).)))))))))).)))))...)).)))). ( -44.70)
>DroEre_CAF1 68271 104 + 1
GGACGAUCCGGGG-CGAGGAGCAGGACA--------------GGACGGGAGUAGCAGUCAGGGACAUUUGUCGUGCUGUUGGCUGUUUUUUAUGUCCUGCCCAUUUCCAUAGCAAUUGG
((.....))...(-(..((((..((.((--------------(((((.(((.(((((((((.(.(((.....))).).))))))))).))).))))))).))..))))...))...... ( -35.60)
>DroYak_CAF1 40078 105 + 1
GGACGAUCAGGGGAAGAGCGGCAGGACA--------------UGUCGGGAGAAGCAGUCAGGGACAUUUGUCGUGCUGUUGGCUGUUUUUUAUGUCCUGCCCAUUUCCAUAGCAAUUGG
...((((....(((((.(.(((((((((--------------(.....(((((((((((((.(.(((.....))).).)))))))))))))))))))))))).)))))......)))). ( -40.50)
>consensus
GGACGAUCAGGCGGAGAGCGGCAGGACA______________GGACAGGAGUAGCAGUCAGGGACAUUUGUCGUGCUGUUGGCUGUUUUUUAUGUCCUGCCCAUUUCCAUAGCAAUUGG
...((((.....(((((.((((((((((................((....))(((((((((.(.(((.....))).).))))))))).....)))))))))).)))))......)))). (-30.14 = -31.08 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:18 2006