Locus 8013

Sequence ID	X_DroMel_CAF1
Location	19,923,508 – 19,923,766
Length	258
Max. P	0.981910

overview

Window 2

Location	19,923,508 – 19,923,625
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.14
Mean single sequence MFE	-29.36
Consensus MFE	-20.04
Energy contribution	-21.64
Covariance contribution	1.60
Combinations/Pair	1.16
Mean z-score	-2.13
Structure conservation index	0.68
SVM decision value	0.34
SVM RNA-class probability	0.696530
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19923508 117 + 22224390
CAUGCUGCAAAGUCA-GUUCUGCGAGCUUACUUCCAACUUUUUGCGUAUUUCAUAAUUUGUG--UGUGCUGCAUAUUUCACAUAUUCAUGAAAUUCCGAGAAUAAGCGCAGUACAUGAUG
..((((((.((((.(-((((...))))).)))).....((((((.(.(((((((....((((--((............))))))...))))))).))))))).....))))))....... ( -26.90)
>DroSec_CAF1 37677 117 + 1
CAUGCUGCAAAGUCA-GUUCUGCGAGUUUGCUCGCAACUUUUUUCGUAUUUCAUAAUUUGUG--UGUGUUGCAUAUUUCACAUAUUCAUGAAAUUCCGAGAACAAGCGCAGUACAUGAUG
..((((((.......-....((((((....)))))).(((((((((.(((((((.....(((--((((..........)))))))..)))))))..)))))).))).))))))....... ( -33.60)
>DroSim_CAF1 29118 117 + 1
CAUGCUGCAAAGUCA-GUUCUGCGAGUUUGCUCGCAACUUUUUUCGUAUUUCAUAAUUUGUG--UGUGUUGCAUAUUUCACAUAUUCAUGAAAUUCCGAGAACAAGCGCAGUACAUGAUG
..((((((.......-....((((((....)))))).(((((((((.(((((((.....(((--((((..........)))))))..)))))))..)))))).))).))))))....... ( -33.60)
>DroEre_CAF1 34683 105 + 1
CAUGUUGCAUAGUCA-GUUCGCCGGC------------UUUUUUUGUAUUUCGUAAUUUGUG--UGUGUUGCAUAUUUCACAUAUUCAUGAAAUUCCGAGAAUAAGCUCGCUACAUGAUG
...........((((-....((.(((------------((((((((.(((((((.....(((--((((..........)))))))..)))))))..)))))).))))).))....)))). ( -24.30)
>DroYak_CAF1 36098 120 + 1
CAUGUUGCAAAGUCAUGUUCUCCGACUUUGCUCGCAACUUUUUUUGUAUUUCAUAAUUUGUGUGUGUGUUGCAUAAUUCACAUAUUCAUGAAAUUCUGAGAAUAAGCGCACUAUAUGAUG
(((((.((((((((.........)))))))).(((....(((((...((((((((((.((((..((((...))))...)))).))).)))))))...)))))...)))....)))))... ( -28.40)
>consensus
CAUGCUGCAAAGUCA_GUUCUGCGAGUUUGCUCGCAACUUUUUUCGUAUUUCAUAAUUUGUG__UGUGUUGCAUAUUUCACAUAUUCAUGAAAUUCCGAGAAUAAGCGCAGUACAUGAUG
((((((((............((((((....))))))....((((((.((((((((((.((((..((((...))))...)))).))).)))))))..)))))).....))))..))))... (-20.04 = -21.64 +   1.60)

alignment

secondary structure

dotplot

Window 3

Location	19,923,625 – 19,923,729
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.99
Mean single sequence MFE	-38.68
Consensus MFE	-30.70
Energy contribution	-30.18
Covariance contribution	-0.52
Combinations/Pair	1.14
Mean z-score	-1.71
Structure conservation index	0.79
SVM decision value	0.49
SVM RNA-class probability	0.754766
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19923625 104 + 22224390
UACC----CGGCACUUCCACUCACAUCCCUGUGACAAUGUACGUUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGUUGCCGUCAUAAGC
....----..((........(((((....)))))........(((((.....)))))(((------------((((((((.((((((((....)).)).)))))))))))))))....)) ( -33.80)
>DroSec_CAF1 37794 104 + 1
UACC----CGGCACUGCCACUCGCAUCCCUGUGACAAUGCACGUUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGCUGCCGUCAUAAGC
....----.(((...)))...........((((((...((.((((((.....))))))))------------((((((((.((((((((....)).)).))))))))))))))))))... ( -40.90)
>DroSim_CAF1 29235 104 + 1
UACC----CGGCACUGCCACUCGCAUCCCUGUGACAAUGCACGUUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGCUGCCGUCAUAAGC
....----.(((...)))...........((((((...((.((((((.....))))))))------------((((((((.((((((((....)).)).))))))))))))))))))... ( -40.90)
>DroEre_CAF1 34788 102 + 1
UACCC------CAGUACCACUCACAUCCCUGUGACAAUGCACGCUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUUGAGUCCGCUGUAUUGCCGUCAUAAGC
.....------..(((....(((((....)))))...)))..(((....(((((((..((------------(((((.(((...(((...)))..)))))))))).)))))))....))) ( -30.80)
>DroYak_CAF1 36218 120 + 1
CACCUACCCGGCACUGCCACUCACAUCCCUGUGACAAUGCACGUUGCACGUGGCAACGGCAACGGUGGCGUCGGUGGCAUUAGUGACCUAGUUUGUGUCCGCUGUGUUGCCGCCAUAAGC
.........(((...((((((((((....))))).......((((((.(((....))))))))))))))...((..((((.(((((((......).)).))))))))..)))))...... ( -47.00)
>consensus
UACC____CGGCACUGCCACUCACAUCCCUGUGACAAUGCACGUUGCACACGGCAACGGC____________GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGUUGCCGUCAUAAGC
....................(((((....)))))....((.((((((.....))))))))............(((((((.((((((((......).)).)))))...)))))))...... (-30.70 = -30.18 +  -0.52)

alignment

secondary structure

dotplot

Window 4

Location	19,923,661 – 19,923,766
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.64
Mean single sequence MFE	-38.86
Consensus MFE	-32.24
Energy contribution	-32.32
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.16
Structure conservation index	0.83
SVM decision value	1.90
SVM RNA-class probability	0.981910
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19923661 105 + 22224390
ACGUUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGUUGCCGUCAUAAGCUCGCAAAAUUCCGAGUACAUUCUUUGAAAGCCACUCA---
..(((((.....)))))(((------------(((((((.(((((((((....)).)).)))))...)))))))....(((((........))))).............))).....--- ( -36.20)
>DroSec_CAF1 37830 105 + 1
ACGUUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGCUGCCGUCAUAAGCUCGCAAAAUUCCGAGUGCAUUCUUUGAAAGCCACUCU---
..(((((.....)))))(((------------((((((((.((((((((....)).)).)))))))))))))))..................((((((.(((...))).).))))).--- ( -38.80)
>DroSim_CAF1 29271 105 + 1
ACGUUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGCUGCCGUCAUAAGCUCGCAAAAUUCCGAGUGCAUUCUUUGAAAGCCACUCU---
..(((((.....)))))(((------------((((((((.((((((((....)).)).)))))))))))))))..................((((((.(((...))).).))))).--- ( -38.80)
>DroEre_CAF1 34822 108 + 1
ACGCUGCACACGGCAACGGC------------GGCGGCAUUAGUGACCUAGUUUGAGUCCGCUGUAUUGCCGUCAUAAGCUGGCAAAAUUCCGAGUGCAUUCUUUGAAAGCCACUCCCCA
..(((((...((....))..------------(((((((.(((((..((......))..)))))...)))))))....)).)))........((((((.(((...))).).))))).... ( -34.10)
>DroYak_CAF1 36258 117 + 1
ACGUUGCACGUGGCAACGGCAACGGUGGCGUCGGUGGCAUUAGUGACCUAGUUUGUGUCCGCUGUGUUGCCGCCAUAAGCUCGCAAAAUUCCGAGUGCAUUCUUUGAAAGCCACUCU---
.((((((.(((....)))))))))(((((...(((((((.((((((((......).)).)))))...)))))))....(((((........))))).............)))))...--- ( -46.40)
>consensus
ACGUUGCACACGGCAACGGC____________GGCGGCAUUAGUGACCUAGUUAGAGUCCGCUGUGUUGCCGUCAUAAGCUCGCAAAAUUCCGAGUGCAUUCUUUGAAAGCCACUCU___
..(((((.....)))))(((............(((((((.((((((((......).)).)))))...)))))))....(((((........))))).............)))........ (-32.24 = -32.32 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:16 2006