Locus 3116

Sequence ID	3L_DroMel_CAF1
Location	9,045,759 – 9,045,864
Length	105
Max. P	0.933721

overview

Window 6

Location	9,045,759 – 9,045,864
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.90
Mean single sequence MFE	-31.27
Consensus MFE	-20.23
Energy contribution	-19.98
Covariance contribution	-0.25
Combinations/Pair	1.21
Mean z-score	-2.44
Structure conservation index	0.65
SVM decision value	1.23
SVM RNA-class probability	0.933721
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9045759 105 + 23771897
CCAUGGCCAAGUUGGCCAUGGAGCGAUGGAAGAAGGCCAACUGAUCAUCGCAUCCCACAUCCAAUUGAAAGCGAAAGUUUCUAAAAUAGCUGAGG----GGUG---------AAAAA--U
((((((((.....)))))))).(((((((....((.....))..)))))))(((((.((.(...(((.((((....)))).)))....).)).))----))).---------.....--. ( -37.30)
>DroSec_CAF1 24163 114 + 1
CCCUGGCCAAGUUGGCCAUGGAGCGAUGGAAGAAGGCCAACUGAUCAUCGCAUCCCACAUCCAAUUGAAAGCGAAAGUUUCUAAAAUAGCUGAGG----GGUGAUAGGUAAUAAUAA--U
((.(((((.....))))).)).(((((((....((.....))..)))))))(((((.((.(...(((.((((....)))).)))....).)).))----)))...............--. ( -33.00)
>DroEre_CAF1 24372 107 + 1
CCCUAGCCAAAUUGGCCAUGGAGCGAUGGAAGAAGGCCAACUGAUCAUCGCAUCCCACAUCCAAUUGAAAGCAAAAGUUUCUAAAAUAGCUGAUG----GGUU---------AAAAAAGA
...(((((.((((((....((((((((((....((.....))..))))))).))).....)))))).....((..((((........))))..))----))))---------)....... ( -25.90)
>DroWil_CAF1 37817 105 + 1
CUUUGGCCAAAUUGGCCAUACUACGAUGGAAGAACGCCAAUUGAUCAUCGUGUGCCACAUCAAGUUGAAAGCGAAAGUUCUUAAAGUAACUGAAA----GAUG---------AAAAA--G
...(((((.....)))))(((.(((((((..((.......))..))))))))))...((((.(((((..(((....))).......)))))....----))))---------.....--. ( -24.10)
>DroYak_CAF1 24568 105 + 1
CCCUGGCCAAAUUGGCCAUGGAGCGAUGGAAGAAGGCCAACUGAUCAUCGCAUCCCACAUCCAAUUGAAAGCGAAAGUUUCUAAAAUAGCUGAGG----GGUA---------AAAAA--A
((.(((((.....))))).)).(((((((....((.....))..)))))))(((((.((.(...(((.((((....)))).)))....).)).))----))).---------.....--. ( -33.00)
>DroMoj_CAF1 31404 117 + 1
CCUUGGCCAGAUUGGCCAUGCUGCGAUGGAAGAACGCCAAUUGCUCAUCCUUAGCCACGUCAAUGUGAAAGCGAAAGUUUCUAAAGUACCUGCAGACGUGGCGAAAGUUCA-AAAUA--A
...(((((.....))))).((((((((((.......)).))))).........((((((((.......((((....)))).....((....)).))))))))...)))...-.....--. ( -34.30)
>consensus
CCCUGGCCAAAUUGGCCAUGGAGCGAUGGAAGAAGGCCAACUGAUCAUCGCAUCCCACAUCCAAUUGAAAGCGAAAGUUUCUAAAAUAGCUGAGG____GGUG_________AAAAA__A
...(((((.....))))).((((((((((.((........))..))))))).))).........(((.((((....)))).))).................................... (-20.23 = -19.98 +  -0.25)

alignment

secondary structure

dotplot

Window 7

Location	9,045,759 – 9,045,864
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.90
Mean single sequence MFE	-27.53
Consensus MFE	-19.53
Energy contribution	-19.06
Covariance contribution	-0.47
Combinations/Pair	1.30
Mean z-score	-1.14
Structure conservation index	0.71
SVM decision value	0.04
SVM RNA-class probability	0.551843
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9045759 105 - 23771897
A--UUUUU---------CACC----CCUCAGCUAUUUUAGAAACUUUCGCUUUCAAUUGGAUGUGGGAUGCGAUGAUCAGUUGGCCUUCUUCCAUCGCUCCAUGGCCAACUUGGCCAUGG
.--.....---------...(----((.((.(((.....((((.......))))...))).)).)))..((((((...((........))..)))))).((((((((.....)))))))) ( -30.10)
>DroSec_CAF1 24163 114 - 1
A--UUAUUAUUACCUAUCACC----CCUCAGCUAUUUUAGAAACUUUCGCUUUCAAUUGGAUGUGGGAUGCGAUGAUCAGUUGGCCUUCUUCCAUCGCUCCAUGGCCAACUUGGCCAGGG
.--.................(----((....................(((.(((....))).)))(((.((((((...((........))..))))))))).(((((.....)))))))) ( -27.50)
>DroEre_CAF1 24372 107 - 1
UCUUUUUU---------AACC----CAUCAGCUAUUUUAGAAACUUUUGCUUUCAAUUGGAUGUGGGAUGCGAUGAUCAGUUGGCCUUCUUCCAUCGCUCCAUGGCCAAUUUGGCUAGGG
........---------..((----(...(((((.....(((((....).))))((((((..(((((..((((((...((........))..)))))))))))..))))))))))).))) ( -27.50)
>DroWil_CAF1 37817 105 - 1
C--UUUUU---------CAUC----UUUCAGUUACUUUAAGAACUUUCGCUUUCAACUUGAUGUGGCACACGAUGAUCAAUUGGCGUUCUUCCAUCGUAGUAUGGCCAAUUUGGCCAAAG
.--.....---------....----.....(((((.(((((...............))))).)))))((((((((.................)))))).)).(((((.....)))))... ( -20.99)
>DroYak_CAF1 24568 105 - 1
U--UUUUU---------UACC----CCUCAGCUAUUUUAGAAACUUUCGCUUUCAAUUGGAUGUGGGAUGCGAUGAUCAGUUGGCCUUCUUCCAUCGCUCCAUGGCCAAUUUGGCCAGGG
.--.....---------...(----((....................(((.(((....))).)))(((.((((((...((........))..))))))))).(((((.....)))))))) ( -27.50)
>DroMoj_CAF1 31404 117 - 1
U--UAUUU-UGAACUUUCGCCACGUCUGCAGGUACUUUAGAAACUUUCGCUUUCACAUUGACGUGGCUAAGGAUGAGCAAUUGGCGUUCUUCCAUCGCAGCAUGGCCAAUCUGGCCAAGG
.--.....-.((......((((((((.....((......((.....))......))...))))))))...(((.((((.......)))).))).))......(((((.....)))))... ( -31.60)
>consensus
U__UUUUU_________CACC____CCUCAGCUAUUUUAGAAACUUUCGCUUUCAAUUGGAUGUGGGAUGCGAUGAUCAGUUGGCCUUCUUCCAUCGCUCCAUGGCCAAUUUGGCCAGGG
...............................................(((.(((....))).)))(((.((((((.................))))))))).(((((.....)))))... (-19.53 = -19.06 +  -0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:54 2006