Locus 7693

Sequence ID	3R_DroMel_CAF1
Location	20,656,897 – 20,657,108
Length	211
Max. P	0.762446

overview

Window 1

Location	20,656,897 – 20,656,988
Length	91
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	83.93
Mean single sequence MFE	-24.32
Consensus MFE	-19.26
Energy contribution	-19.22
Covariance contribution	-0.04
Combinations/Pair	1.14
Mean z-score	-1.77
Structure conservation index	0.79
SVM decision value	0.51
SVM RNA-class probability	0.762446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20656897 91 + 27905053
AUU--------------------------CAUUUUGACCAUACACUAGCCGGCUCACUCUAAUUUCUUGCAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCU
...--------------------------...........((((.(((.(((((((((((((((((.(((.....)))....))..)))))))))....))))))..))).)))).. ( -19.30)
>DroSec_CAF1 13382 91 + 1
AUU--------------------------CAUUUUGAACAUACACGAGCCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCU
...--------------------------...........((((..((.(((((((((((((((..(((((((....)))))))..)))))))))....))))))..))..)))).. ( -22.60)
>DroSim_CAF1 4240 91 + 1
AUU--------------------------CAUUUUGAGCAUACACGAGCCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCU
...--------------------------.......((((((....((.(((((((((((((((..(((((((....)))))))..)))))))))....))))))..))..)))))) ( -25.10)
>DroEre_CAF1 4177 91 + 1
AUU--------------------------CAUUUUGGAUAUACACGAGUCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGGCUAGUUCGAGCUCGAGAGUUGACCUAAUGUGCU
...--------------------------((((..((........(((....)))(((((.....((((.(((((((......)))))))))))....)))))...)).)))).... ( -21.50)
>DroYak_CAF1 3714 117 + 1
AUCCAUUGUACAUACAGUGAACGAAGAUCCAUUUUGAAUAUGCACGAGUUGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACAACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCU
...((((((....))))))......................(((((.((..(((((((((((((..(((((((....)))))))..)))))))))....))))..))....))))). ( -33.10)
>consensus
AUU__________________________CAUUUUGAACAUACACGAGCCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCU
........................................((((..((.(((((((((((((((..(((((((....)))))))..)))))))))....))))))..))..)))).. (-19.26 = -19.22 +  -0.04)

alignment

secondary structure

dotplot

Window 2

Location	20,656,908 – 20,657,028
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-32.44
Consensus MFE	-26.44
Energy contribution	-26.44
Covariance contribution	-0.00
Combinations/Pair	1.13
Mean z-score	-1.42
Structure conservation index	0.82
SVM decision value	0.03
SVM RNA-class probability	0.550799
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20656908 120 + 27905053
CCAUACACUAGCCGGCUCACUCUAAUUUCUUGCAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCUCCGCCAUGUAAUUAAUACGUCUGCUGGAGGGAAAAGUAAU
((.((((.(((.(((((((((((((((((.(((.....)))....))..)))))))))....))))))..))).))))((((((.(((((.....)))))..)).))))))......... ( -30.10)
>DroSec_CAF1 13393 120 + 1
ACAUACACGAGCCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCUCCGCCAUGUAAUUAAUACGUCUGCUGGAGGGAAAAGUAAU
...((((..((.(((((((((((((((..(((((((....)))))))..)))))))))....))))))..))..))))((((((.(((((.....)))))..)).))))........... ( -31.90)
>DroSim_CAF1 4251 120 + 1
GCAUACACGAGCCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCUCCGCCAUGUAAUUAAUACGUCUGCUGGAGGGAAAAGUAAU
...((((..((.(((((((((((((((..(((((((....)))))))..)))))))))....))))))..))..))))((((((.(((((.....)))))..)).))))........... ( -31.90)
>DroEre_CAF1 4188 120 + 1
AUAUACACGAGUCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGGCUAGUUCGAGCUCGAGAGUUGACCUAAUGUGCUCCGCAGUGUAAUUAAUACGUCUGCUGGAAGGAAAAGUAAU
.....((((....((.(((((((.....((((.(((((((......)))))))))))....)))).)))))...)))).(((((((((((.....)))).)))).)))............ ( -31.60)
>DroYak_CAF1 3751 120 + 1
AUAUGCACGAGUUGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACAACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCUCCGCAAUGUAAUUAAUACGUCUGCUGGAGGGAAAAGUAAU
....(((((.((..(((((((((((((..(((((((....)))))))..)))))))))....))))..))....)))))(((((((((((.....))))).))).)))............ ( -36.70)
>consensus
ACAUACACGAGCCGGCUCACUCUAAUUUCUUGUAAUUAGCAUUACGACUAGUUGGAGUUCGAGAGUUGACCUAAUGUGCUCCGCCAUGUAAUUAAUACGUCUGCUGGAGGGAAAAGUAAU
...((((..((.(((((((((((((((..(((((((....)))))))..)))))))))....))))))..))..))))((((((.(((((.....)))))..)).))))........... (-26.44 = -26.44 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	20,656,948 – 20,657,068
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-28.96
Consensus MFE	-26.16
Energy contribution	-26.20
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.32
Structure conservation index	0.90
SVM decision value	0.37
SVM RNA-class probability	0.706883
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20656948 120 - 27905053
AAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGGAGCACAUUAGGUCAACUCUCGAACUCCAACUAGUCGUAAU
....((((......((((((((....)))))))).(((.((((((((....((((.((....(((.....)))...))))))......)))).)).)).))).))))............. ( -28.20)
>DroSec_CAF1 13433 120 - 1
AAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGGAGCACAUUAGGUCAACUCUCGAACUCCAACUAGUCGUAAU
....((((......((((((((....)))))))).(((.((((((((....((((.((....(((.....)))...))))))......)))).)).)).))).))))............. ( -28.20)
>DroSim_CAF1 4291 120 - 1
AAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGGAGCACAUUAGGUCAACUCUCGAACUCCAACUAGUCGUAAU
....((((......((((((((....)))))))).(((.((((((((....((((.((....(((.....)))...))))))......)))).)).)).))).))))............. ( -28.20)
>DroEre_CAF1 4228 120 - 1
AAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGAGUCGUGAUUACUUUUCCUUCCAGCAGACGUAUUAAUUACACUGCGGAGCACAUUAGGUCAACUCUCGAGCUCGAACUAGCCGUAAU
.......(((((.(((((((((....))))))((((((.((((((((....((((.((((..(((.....))).))))))))......)))).)).)).))).)))))).)))))..... ( -30.70)
>DroYak_CAF1 3791 120 - 1
AAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUUGCGGAGCACAUUAGGUCAACUCUCGAACUCCAACUAGUUGUAAU
....((((......((((((((....)))))))).(((.((((((((....((((.((((..(((.....))).))))))))......)))).)).)).))).))))............. ( -29.50)
>consensus
AAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGGAGCACAUUAGGUCAACUCUCGAACUCCAACUAGUCGUAAU
....((((......((((((((....)))))))).(((.((((((((....((((.((....(((.....)))...))))))......)))).)).)).))).))))............. (-26.16 = -26.20 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	20,656,988 – 20,657,108
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.99
Mean single sequence MFE	-32.74
Consensus MFE	-26.00
Energy contribution	-26.84
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.48
Structure conservation index	0.79
SVM decision value	-0.02
SVM RNA-class probability	0.524466
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20656988 120 - 27905053
UCGGGGCCCACUUGAACGUGAACGAAAGUCAAUGUACCAUAAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGG
(((((.....)))))((((..((....))..)))).((((....(((((..((.((((((((....))))))))...((....)).))..))))).......(((.....)))))))... ( -30.80)
>DroSec_CAF1 13473 120 - 1
UCGGAGCCCACUUGGACGUGGACGAAAGUCAAUGUACCAUAAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGG
.....(((....(((((((.(((....))).)))).))).....(((((..((.((((((((....))))))))...((....)).))..))))).......(((.....)))..))).. ( -34.80)
>DroSim_CAF1 4331 120 - 1
UCGGAGCCCACUUGGACGUGGACGAAAGUCAAUGUACCAUAAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGG
.....(((....(((((((.(((....))).)))).))).....(((((..((.((((((((....))))))))...((....)).))..))))).......(((.....)))..))).. ( -34.80)
>DroEre_CAF1 4268 119 - 1
UCGAAGC-GACUUAGACGUGGACGAAAGUCAAUGUACCAUAAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGAGUCGUGAUUACUUUUCCUUCCAGCAGACGUAUUAAUUACACUGCGG
..((((.-((.....((((.(((....))).)))).......((((..((((((((((((((....))))))))))..))))..))))))))))..((((..(((.....))).)))).. ( -33.00)
>DroYak_CAF1 3831 113 - 1
UCGGAGC-GACUU------GGACGAAAGUCAAUGUACCAUAAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUUGCGG
..((((.-(((..------.(((....)))...))......(((((..((((..((((((((....))))))))....))))..))))).))))).((((..(((.....))).)))).. ( -30.30)
>consensus
UCGGAGCCCACUUGGACGUGGACGAAAGUCAAUGUACCAUAAAAGGAGGUUAAUUCUAUGCAAUUUUGCAUGGACUCGUGAUUACUUUUCCCUCCAGCAGACGUAUUAAUUACAUGGCGG
...............((((.(((....))).)))).((......(((((..((.((((((((....))))))))...((....)).))..))))).((....(((.....)))...)))) (-26.00 = -26.84 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:18 2006