Locus 312

Sequence ID	2L_DroMel_CAF1
Location	899,274 – 899,468
Length	194
Max. P	0.987381

overview

Window 4

Location	899,274 – 899,394
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-36.72
Consensus MFE	-35.10
Energy contribution	-34.98
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.18
Structure conservation index	0.96
SVM decision value	0.34
SVM RNA-class probability	0.693904
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 899274 120 + 22407834
CGAUCUACGAGAUCUUCCCACAGUUCUUCUUCAACAGCAAGUUUGUGUUCGAAGCGGAGAAGUUCGACUACGAGAUGUGGAUGAAGAUGACGAUGUACGAGAAGGAGUACAUGGAUGUGU
.((((.....))))....((((..((.((((((.(.(((..((((((.(((((.(......)))))).)))))).))).).)))))).))(.((((((........)))))).).)))). ( -33.70)
>DroSec_CAF1 27427 120 + 1
CGAUCUACGAGAUCUUCCCGCAGUUCUUCUUCAACAGCAAGUUUGUGUUCGAGGCGGAGAAGUUCGACUACGAGAUGUGGAUGAAGAUGACCAUGUACGAGAAGGAGUACAUGGAUGUGU
.((((.....))))....((((..((.((((((.(.(((..((((((.(((((.(......)))))).)))))).))).).)))))).))((((((((........)))))))).)))). ( -37.70)
>DroSim_CAF1 23771 120 + 1
CGAUCUACGAGAUCUUCCCGCAGUUCUUCUUCAACAGCAAGUUUGUGUUCGAGGCGGAGAAGUUCGACUACGAGAUGUGGAUGAAGAUGACCAUGUACGAGAAGGAGUACAUGGAUGUGU
.((((.....))))....((((..((.((((((.(.(((..((((((.(((((.(......)))))).)))))).))).).)))))).))((((((((........)))))))).)))). ( -37.70)
>DroEre_CAF1 30938 120 + 1
CGAUCUACGAGAUCUUCCCGCAGUUCUUCUUCAACAGCAAGUUCGUGUACGAGGCGGAGAAGUUCGACUACGAGAUGUGGAUGAAGGUGACCAUGUACGAGAAGGAGUACAUGGACGUGU
.....((((..(((((((((((...(((((((....((....(((....))).)))))))))((((....)))).)))))..))))))..((((((((........)))))))).)))). ( -37.10)
>DroYak_CAF1 27845 120 + 1
CGAUCUACGAGAUCUUCCCGCAGUUCUUCUUCAACAGCAAGUUCGUGUUCGAGGCGGAGAAGUUCGACUACGAGAUGUGGAUGAAGAUGAGCAUGUACGAGAAGGAGUACAUGGACGUGU
.((((.....))))....(((.((((.((((((.(.(((..((((((.(((((.(......)))))).)))))).))).).)))))).))))((((((........))))))....))). ( -37.40)
>consensus
CGAUCUACGAGAUCUUCCCGCAGUUCUUCUUCAACAGCAAGUUUGUGUUCGAGGCGGAGAAGUUCGACUACGAGAUGUGGAUGAAGAUGACCAUGUACGAGAAGGAGUACAUGGAUGUGU
.((((.....))))....(((...((.((((((.(.(((..((((((.(((((.(......)))))).)))))).))).).)))))).))((((((((........))))))))..))). (-35.10 = -34.98 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	899,274 – 899,394
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.00
Mean single sequence MFE	-31.88
Consensus MFE	-27.84
Energy contribution	-28.28
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.87
SVM decision value	2.08
SVM RNA-class probability	0.987381
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 899274 120 - 22407834
ACACAUCCAUGUACUCCUUCUCGUACAUCGUCAUCUUCAUCCACAUCUCGUAGUCGAACUUCUCCGCUUCGAACACAAACUUGCUGUUGAAGAAGAACUGUGGGAAGAUCUCGUAGAUCG
........((((((........))))))((..((((((..(((((..(((....)))..((((...((((.((((((....)).)))))))).)))).)))))))))))..))....... ( -26.40)
>DroSec_CAF1 27427 120 - 1
ACACAUCCAUGUACUCCUUCUCGUACAUGGUCAUCUUCAUCCACAUCUCGUAGUCGAACUUCUCCGCCUCGAACACAAACUUGCUGUUGAAGAAGAACUGCGGGAAGAUCUCGUAGAUCG
......((((((((........))))))))...((((((........(((..((.((.....)).))..)))(((((....)).))))))))).((.(((((((.....))))))).)). ( -31.80)
>DroSim_CAF1 23771 120 - 1
ACACAUCCAUGUACUCCUUCUCGUACAUGGUCAUCUUCAUCCACAUCUCGUAGUCGAACUUCUCCGCCUCGAACACAAACUUGCUGUUGAAGAAGAACUGCGGGAAGAUCUCGUAGAUCG
......((((((((........))))))))...((((((........(((..((.((.....)).))..)))(((((....)).))))))))).((.(((((((.....))))))).)). ( -31.80)
>DroEre_CAF1 30938 120 - 1
ACACGUCCAUGUACUCCUUCUCGUACAUGGUCACCUUCAUCCACAUCUCGUAGUCGAACUUCUCCGCCUCGUACACGAACUUGCUGUUGAAGAAGAACUGCGGGAAGAUCUCGUAGAUCG
....(.((((((((........)))))))).).............((((((((((...((((..(((.(((....)))....)).)..))))..).))))))))).((((.....)))). ( -35.30)
>DroYak_CAF1 27845 120 - 1
ACACGUCCAUGUACUCCUUCUCGUACAUGCUCAUCUUCAUCCACAUCUCGUAGUCGAACUUCUCCGCCUCGAACACGAACUUGCUGUUGAAGAAGAACUGCGGGAAGAUCUCGUAGAUCG
....(..(((((((........)))))))..).((((((..((((..((((..((((...........))))..))))...)).)).)))))).((.(((((((.....))))))).)). ( -34.10)
>consensus
ACACAUCCAUGUACUCCUUCUCGUACAUGGUCAUCUUCAUCCACAUCUCGUAGUCGAACUUCUCCGCCUCGAACACAAACUUGCUGUUGAAGAAGAACUGCGGGAAGAUCUCGUAGAUCG
......((((((((........))))))))...............(((((((((....((((((.((..(((........)))..)).).))))).))))))))).((((.....)))). (-27.84 = -28.28 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	899,354 – 899,468
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.37
Mean single sequence MFE	-31.68
Consensus MFE	-27.88
Energy contribution	-28.76
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.71
Structure conservation index	0.88
SVM decision value	1.57
SVM RNA-class probability	0.964719
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 899354 114 + 22407834
AUGAAGAUGACGAUGUACGAGAAGGAGUACAUGGAUGUGUACUACAAGACC------AACGGAUACGACUACUCAACCAUGUACCGGUCCAGCGACUACACCUACAUGAAGGACUUCAAG
.(((((.......((((...(..(((((((((((.((.((((.....)...------..((....))..))).)).))))))))...)))..)...))))(((......))).))))).. ( -26.20)
>DroSec_CAF1 27507 114 + 1
AUGAAGAUGACCAUGUACGAGAAGGAGUACAUGGAUGUGUACUACAAGACC------CACGGAAACGACUACACAACCAUGUACCGGUCCAGCGACUACACCUACAUGAAGGACUUCAAG
.(((((.....((((((.(.....(.((((((((.(((((((.....)...------..((....))..)))))).)))))))))((((....))))...).)))))).....))))).. ( -34.10)
>DroSim_CAF1 23851 114 + 1
AUGAAGAUGACCAUGUACGAGAAGGAGUACAUGGAUGUGUACUACAAGACC------CACGGAAACGACUACACAACCAUGUACCGGUCCAGCGACUACACCUACAUGAAGGACUUCAAG
.(((((.....((((((.(.....(.((((((((.(((((((.....)...------..((....))..)))))).)))))))))((((....))))...).)))))).....))))).. ( -34.10)
>DroEre_CAF1 31018 120 + 1
AUGAAGGUGACCAUGUACGAGAAGGAGUACAUGGACGUGUACUACAAGAGCAACUCGCACGGAUACGACUACGCCACCAUGUACCAGUCCAGCGACUACACCUACAUGAAGGACUUCAAG
.((((((((.((((((((........)))))))).(((((.((....(((...)))....)))))))..))).((..((((((..((((....)))).....))))))..)).))))).. ( -33.90)
>DroYak_CAF1 27925 120 + 1
AUGAAGAUGAGCAUGUACGAGAAGGAGUACAUGGACGUGUACUACAAGGGCCACUCCUACGGAUACGACUACCCAAGCAUGUACCAGUCCAGCGACUACACCUACAUGAAGGACUUCAAG
.(((((.....(((((((........)))))))..(((((.((...((((....))))..))))))).....((...((((((..((((....)))).....))))))..)).))))).. ( -30.10)
>consensus
AUGAAGAUGACCAUGUACGAGAAGGAGUACAUGGAUGUGUACUACAAGACC______CACGGAUACGACUACACAACCAUGUACCGGUCCAGCGACUACACCUACAUGAAGGACUUCAAG
.(((((.....((((((.(.....(.((((((((.(((((((.....)...........((....))..)))))).)))))))))((((....))))...).)))))).....))))).. (-27.88 = -28.76 +   0.88)

alignment

secondary structure

dotplot

Window 7

Location	899,354 – 899,468
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.37
Mean single sequence MFE	-37.06
Consensus MFE	-29.02
Energy contribution	-29.86
Covariance contribution	0.84
Combinations/Pair	1.05
Mean z-score	-1.98
Structure conservation index	0.78
SVM decision value	0.98
SVM RNA-class probability	0.893390
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 899354 114 - 22407834
CUUGAAGUCCUUCAUGUAGGUGUAGUCGCUGGACCGGUACAUGGUUGAGUAGUCGUAUCCGUU------GGUCUUGUAGUACACAUCCAUGUACUCCUUCUCGUACAUCGUCAUCUUCAU
..(((((......((((((((.(((...))).)))(((((((((.((.(((.(((...((...------))...)).).))).)).)))))))))........)))))......))))). ( -30.10)
>DroSec_CAF1 27507 114 - 1
CUUGAAGUCCUUCAUGUAGGUGUAGUCGCUGGACCGGUACAUGGUUGUGUAGUCGUUUCCGUG------GGUCUUGUAGUACACAUCCAUGUACUCCUUCUCGUACAUGGUCAUCUUCAU
..(((((....((((((((((.(((...))).)))(((((((((.((((((.(((..((....------))...)).).)))))).)))))))))........)))))))....))))). ( -39.70)
>DroSim_CAF1 23851 114 - 1
CUUGAAGUCCUUCAUGUAGGUGUAGUCGCUGGACCGGUACAUGGUUGUGUAGUCGUUUCCGUG------GGUCUUGUAGUACACAUCCAUGUACUCCUUCUCGUACAUGGUCAUCUUCAU
..(((((....((((((((((.(((...))).)))(((((((((.((((((.(((..((....------))...)).).)))))).)))))))))........)))))))....))))). ( -39.70)
>DroEre_CAF1 31018 120 - 1
CUUGAAGUCCUUCAUGUAGGUGUAGUCGCUGGACUGGUACAUGGUGGCGUAGUCGUAUCCGUGCGAGUUGCUCUUGUAGUACACGUCCAUGUACUCCUUCUCGUACAUGGUCACCUUCAU
..((((....))))((.((((((((((....)))))(((((..(.((((.(.(((((....))))).))))).)..).))))....((((((((........)))))))).))))).)). ( -37.70)
>DroYak_CAF1 27925 120 - 1
CUUGAAGUCCUUCAUGUAGGUGUAGUCGCUGGACUGGUACAUGCUUGGGUAGUCGUAUCCGUAGGAGUGGCCCUUGUAGUACACGUCCAUGUACUCCUUCUCGUACAUGCUCAUCUUCAU
..(((((.....((((((.(.(.(((.(((((((..((((.(((..(((((.((.((....)).)).).))))..)))))))..))))).)))))....).).)))))).....))))). ( -38.10)
>consensus
CUUGAAGUCCUUCAUGUAGGUGUAGUCGCUGGACCGGUACAUGGUUGUGUAGUCGUAUCCGUG______GGUCUUGUAGUACACAUCCAUGUACUCCUUCUCGUACAUGGUCAUCUUCAU
..(((((....((((((((((.(((...))).)))(((((((((.((.(((.(((...((.........))...)).).))).)).)))))))))........)))))))....))))). (-29.02 = -29.86 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:44 2006