Locus 1181

Sequence ID	2L_DroMel_CAF1
Location	3,222,955 – 3,223,090
Length	135
Max. P	0.999755

overview

Window 4

Location	3,222,955 – 3,223,055
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-28.72
Consensus MFE	-24.86
Energy contribution	-25.06
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.87
SVM decision value	0.95
SVM RNA-class probability	0.887510
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3222955 100 + 22407834
GCUGCUCGAGAAGUUGUGAAUUAUUUGGUGUGAGCAAUUCGGUGGCUAAACUGAUUUUAGCCAUUUGGCGUGCUCUGGGCCAAAAUAGAUGUAGACGAAG
.(((((((........)))....((((((.((((((..((((((((((((.....)))))))).))))..))))).).))))))......))))...... ( -28.10)
>DroSec_CAF1 57039 99 + 1
GCUGCUCGAGAAGUUGUGAAUUAUUUGGUGUGAGCAGUUCGGUGGCUAAACUGAUUUUAGCCAUUUGGCGUGCUCUGGGCCAAAAUAGAUGUAGAC-AAG
.(((((((........)))....((((((.(((((((((..(((((((((.....)))))))))..))).))))).).))))))......))))..-... ( -31.30)
>DroSim_CAF1 55500 99 + 1
GCUGCUCGAGAAGUUGUGAAUUAUUUGGUGUGAGCAAUUCGGUGGCUAAACUGAUUUUAGCCAUUUGGCGUGCUCUGGGCCAAAAUAGAUGUAGAC-AAG
.(((((((........)))....((((((.((((((..((((((((((((.....)))))))).))))..))))).).))))))......))))..-... ( -28.10)
>DroEre_CAF1 53557 95 + 1
GCUGCUCGAGAAGUUGUGAAUUAUUUGGUGAGAGCAACUGGGUGGCUAAACUGAUUUUAGCCAUUUGGCGAGCUCUGGGCCAAAAUA----UAGAC-GCG
((.(((.....))).........((((((.(((((..(..((((((((((.....))))))))))..)...))))).).)))))...----.....-)). ( -29.60)
>DroYak_CAF1 52249 93 + 1
GCUGCUCGAGAAGUUGUGAAUUAUUUGGUGUGAGCAAUUCGGUGGCUAAACUGAUUUUAGCCAUUUGGCGUGCUCUGGGCCAAAAU------GAAC-GUG
((.(((.....))).))......((((((.((((((..((((((((((((.....)))))))).))))..))))).).))))))..------....-... ( -26.50)
>consensus
GCUGCUCGAGAAGUUGUGAAUUAUUUGGUGUGAGCAAUUCGGUGGCUAAACUGAUUUUAGCCAUUUGGCGUGCUCUGGGCCAAAAUAGAUGUAGAC_AAG
((.(((.....))).))......((((((..(((((....((((((((((.....)))))))))).....)))))...))))))................ (-24.86 = -25.06 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	3,222,955 – 3,223,055
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-21.00
Consensus MFE	-19.90
Energy contribution	-19.74
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.26
Structure conservation index	0.95
SVM decision value	4.01
SVM RNA-class probability	0.999755
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3222955 100 - 22407834
CUUCGUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAAUUCACAACUUCUCGAGCAGC
.((((...........((((((.........))))))((((((((.....)))))))).))))((((((........................)))))). ( -21.56)
>DroSec_CAF1 57039 99 - 1
CUU-GUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAACUGCUCACACCAAAUAAUUCACAACUUCUCGAGCAGC
...-............((((((.........))))))((((((((.....)))))))).....((((((........................)))))). ( -21.46)
>DroSim_CAF1 55500 99 - 1
CUU-GUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAAUUCACAACUUCUCGAGCAGC
...-............((((((.........))))))((((((((.....)))))))).....((((((........................)))))). ( -19.36)
>DroEre_CAF1 53557 95 - 1
CGC-GUCUA----UAUUUUGGCCCAGAGCUCGCCAAAUGGCUAAAAUCAGUUUAGCCACCCAGUUGCUCUCACCAAAUAAUUCACAACUUCUCGAGCAGC
...-.....----...((((((.........))))))((((((((.....))))))))....(((((((........................))))))) ( -21.66)
>DroYak_CAF1 52249 93 - 1
CAC-GUUC------AUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAAUUCACAACUUCUCGAGCAGC
...-((((------..((((((.........))))))((((((((.....))))))))..))))(((((........................))))).. ( -20.96)
>consensus
CUU_GUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAAUUCACAACUUCUCGAGCAGC
................((((((.........))))))((((((((.....)))))))).....((((((........................)))))). (-19.90 = -19.74 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	3,222,975 – 3,223,090
Length	115
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	89.52
Mean single sequence MFE	-27.71
Consensus MFE	-21.28
Energy contribution	-21.64
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.28
Structure conservation index	0.77
SVM decision value	1.28
SVM RNA-class probability	0.939358
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3222975 115 - 22407834
CAUAAUCCGUC--GAGUGCACUGAACUCCGGC-AUCUCCUUCGUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAA
........(((--((((.......))).))))-.....................(((((....(((((.......((((((((.....))))))))......)))))...)))))... ( -25.62)
>DroSec_CAF1 57059 114 - 1
CAUAAUCCGUC--GGGUGCACUGAACUCCGGC-AUCUCCUU-GUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAACUGCUCACACCAAAUAA
........(((--((((.......)).)))))-........-............(((((....(((((.......((((((((.....))))))))......)))))...)))))... ( -27.72)
>DroSim_CAF1 55520 114 - 1
CAUAAUCCGUC--GGGUGCACUGAACUCCGGC-ACCUCCUU-GUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAA
........(((--((((.......)).)))))-........-............(((((....(((((.......((((((((.....))))))))......)))))...)))))... ( -27.72)
>DroEre_CAF1 53577 113 - 1
CAUAAUCCUGCAAGAGUGCACUGAACUCCGGCCAUCUUCGC-GUCUA----UAUUUUGGCCCAGAGCUCGCCAAAUGGCUAAAAUCAGUUUAGCCACCCAGUUGCUCUCACCAAAUAA
.............(((.((((((..(((.(((((.......-.....----.....)))))..))).........((((((((.....))))))))..))).))).)))......... ( -29.93)
>DroYak_CAF1 52269 109 - 1
CAUAAUCCUGC--GAGUGCACUGAACUCCGGCCAUCACCAC-GUUC------AUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAA
.........((--((((((.(((......(((((.......-....------....)))))))).))))......((((((((.....)))))))).....))))............. ( -27.56)
>consensus
CAUAAUCCGUC__GAGUGCACUGAACUCCGGC_AUCUCCUU_GUCUACAUCUAUUUUGGCCCAGAGCACGCCAAAUGGCUAAAAUCAGUUUAGCCACCGAAUUGCUCACACCAAAUAA
......(((....((((.......))))))).......................(((((....(((((.......((((((((.....))))))))......)))))...)))))... (-21.28 = -21.64 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:39 2006