Locus 797

Sequence ID	X_DroMel_CAF1
Location	2,203,024 – 2,203,156
Length	132
Max. P	0.998936

overview

Window 1

Location	2,203,024 – 2,203,116
Length	92
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	81.37
Mean single sequence MFE	-36.48
Consensus MFE	-23.44
Energy contribution	-23.76
Covariance contribution	0.32
Combinations/Pair	1.19
Mean z-score	-2.81
Structure conservation index	0.64
SVM decision value	2.02
SVM RNA-class probability	0.985770
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2203024 92 + 22224390
CACAGCUGGAGGUAACGAUGGCCUUUCAACUGGAGAAGUUCUCUGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUGCAGGA---------------------GAAGACGGAU
..(((.(((((((.......))).)))).))).....(((((((.(((((((((.(((((((....))))))).))))))))---------------------).))).)))) ( -36.90)
>DroSec_CAF1 1330 92 + 1
CACAGCUGGAGGUAACGAUGGCCUUUCAACUGGAGAAGUCCUUAGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUACAGGA---------------------GAAGACGGAU
..(((.(((((((.......))).)))).))).....((((((..(((((((((.(((((((....))))))).))))))))---------------------)..)).)))) ( -37.00)
>DroSim_CAF1 658 92 + 1
CACAGCUGGAGGUAACGAUGGCCUUUCAACUGGAGAAGUUCUUAGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUACAGGA---------------------GAAGACGGAU
..(((.(((((((.......))).)))).))).....((((((..(((((((((.(((((((....))))))).))))))))---------------------)..)).)))) ( -34.10)
>DroEre_CAF1 1351 92 + 1
CGCAGCAGGAGGUAACGAUGGCCUUUGAACUGGAGAAGUCCGUUGCUCUUGUACAGCAGGAGAUGACUUCUGCAGCACAGGA---------------------GAGGACGGAU
..(((..((((((.......))))))...))).....(((((((.(((((((.(.(((((((....))))))).).))))))---------------------)..))))))) ( -36.70)
>DroYak_CAF1 1405 113 + 1
UACAGCAGGCGGUAACGAUGGCCCUUCAACUGACGAAGAUCGCUGCUCUGGCACUGCAGGCGAUGACUUCUGCAGUACAGGCGAUGACUUCUGCAGUACGGGUGAGGAUGGAU
.......(((.((....)).)))(((((((((..((((.(((.(((.(((..((((((((........)))))))).)))))).)))))))..)))).....)))))...... ( -37.70)
>consensus
CACAGCUGGAGGUAACGAUGGCCUUUCAACUGGAGAAGUUCUUUGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUACAGGA_____________________GAAGACGGAU
...((((((((((.......)))))......(((....))).)))))(((((((.(((((((....))))))).)))))))................................ (-23.44 = -23.76 +   0.32)

alignment

secondary structure

dotplot

Window 2

Location	2,203,057 – 2,203,156
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.58
Mean single sequence MFE	-39.92
Consensus MFE	-23.62
Energy contribution	-25.02
Covariance contribution	1.40
Combinations/Pair	1.14
Mean z-score	-3.25
Structure conservation index	0.59
SVM decision value	3.29
SVM RNA-class probability	0.998936
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2203057 99 + 22224390
AGAAGUUCUCUGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUGCAGGA---------------------GAAGACGGAUAAGGUUCCUGCACAGCUCUGAAAGUCGGAGAUGUAGGUUU
....(((((((.(((((((((.(((((((....))))))).))))))))---------------------).))).))))......((((((...(((((.....))))).))))))... ( -42.90)
>DroSec_CAF1 1363 99 + 1
AGAAGUCCUUAGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUACAGGA---------------------GAAGACGGAUAAGGUUCCUGCACAGCUUCGAAAGCCGGAGAUGUGGGUUU
....((((((..(((((((((.(((((((....))))))).))))))))---------------------)..)).))))......((..((...(((((.....))))).))..))... ( -40.50)
>DroSim_CAF1 691 99 + 1
AGAAGUUCUUAGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUACAGGA---------------------GAAGACGGAUAAGGUUCCUGCACAGCUUCGAAAGCCGGAGAUGUGGGUUU
....((.((...(((((((((.(((((((....))))))).))))))))---------------------).))))(((......)))..((((.(((((.....))))).))))..... ( -38.00)
>DroEre_CAF1 1384 99 + 1
AGAAGUCCGUUGCUCUUGUACAGCAGGAGAUGACUUCUGCAGCACAGGA---------------------GAGGACGGAUAAGGUUCCUGCCUAGCUUUGACAGCAGGAGAUGUUGUUUU
....(((((((.(((((((.(.(((((((....))))))).).))))))---------------------)..))))))).((((....))))......(((((((.....))))))).. ( -38.90)
>DroYak_CAF1 1438 120 + 1
CGAAGAUCGCUGCUCUGGCACUGCAGGCGAUGACUUCUGCAGUACAGGCGAUGACUUCUGCAGUACGGGUGAGGAUGGAUAGGCUUCCUGCACAGGUUUGACAGCCUGCGAUGUGAUUUG
...((((((((((....))).(((((((...(((((((((((...((.......)).)))))).....(((((((.(......).)))).)))))))).....)))))))..))))))). ( -39.30)
>consensus
AGAAGUUCUUUGCUCUUGUACGGCAGGAGAUGACUUCUGCAGUACAGGA_____________________GAAGACGGAUAAGGUUCCUGCACAGCUUUGAAAGCCGGAGAUGUGGGUUU
...........((((((((((.(((((((....))))))).))))))))...........................(((......))).))(((.(((((.....))))).)))...... (-23.62 = -25.02 +   1.40)

alignment

secondary structure

dotplot

Window 3

Location	2,203,057 – 2,203,156
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.58
Mean single sequence MFE	-29.95
Consensus MFE	-15.84
Energy contribution	-17.36
Covariance contribution	1.52
Combinations/Pair	1.09
Mean z-score	-2.65
Structure conservation index	0.53
SVM decision value	2.07
SVM RNA-class probability	0.987276
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2203057 99 - 22224390
AAACCUACAUCUCCGACUUUCAGAGCUGUGCAGGAACCUUAUCCGUCUUC---------------------UCCUGCACUGCAGAAGUCAUCUCCUGCCGUACAAGAGCAGAGAACUUCU
........................((.((((((((...............---------------------)))))))).))((((((..((((.((((......).))))))))))))) ( -28.76)
>DroSec_CAF1 1363 99 - 1
AAACCCACAUCUCCGGCUUUCGAAGCUGUGCAGGAACCUUAUCCGUCUUC---------------------UCCUGUACUGCAGAAGUCAUCUCCUGCCGUACAAGAGCUAAGGACUUCU
.....((((.((.((.....)).)).))))..(((......)))((((((---------------------((.(((((.((((.((....)).)))).))))).)))...))))).... ( -27.90)
>DroSim_CAF1 691 99 - 1
AAACCCACAUCUCCGGCUUUCGAAGCUGUGCAGGAACCUUAUCCGUCUUC---------------------UCCUGUACUGCAGAAGUCAUCUCCUGCCGUACAAGAGCUAAGAACUUCU
.....((((.((.((.....)).)).))))..(((......))).(((((---------------------((.(((((.((((.((....)).)))).))))).)))..))))...... ( -25.40)
>DroEre_CAF1 1384 99 - 1
AAAACAACAUCUCCUGCUGUCAAAGCUAGGCAGGAACCUUAUCCGUCCUC---------------------UCCUGUGCUGCAGAAGUCAUCUCCUGCUGUACAAGAGCAACGGACUUCU
...........(((((((..........)))))))......(((((...(---------------------((.(((((.((((.((....)).)))).))))).)))..)))))..... ( -33.00)
>DroYak_CAF1 1438 120 - 1
CAAAUCACAUCGCAGGCUGUCAAACCUGUGCAGGAAGCCUAUCCAUCCUCACCCGUACUGCAGAAGUCAUCGCCUGUACUGCAGAAGUCAUCGCCUGCAGUGCCAGAGCAGCGAUCUUCG
........(((((...((((...((..(((.((((.(......).)))))))..))...))))........(((((((((((((..(....)..)))))))).))).)).)))))..... ( -34.70)
>consensus
AAACCCACAUCUCCGGCUUUCAAAGCUGUGCAGGAACCUUAUCCGUCUUC_____________________UCCUGUACUGCAGAAGUCAUCUCCUGCCGUACAAGAGCAAAGAACUUCU
.............(((((.....))))).((.(((......)))...........................((.(((((.((((.((....)).)))).))))).))))........... (-15.84 = -17.36 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:03 2006