Locus 2559

Sequence ID	X_DroMel_CAF1
Location	6,866,007 – 6,866,257
Length	250
Max. P	0.957620

overview

Window 9

Location	6,866,007 – 6,866,121
Length	114
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	91.86
Mean single sequence MFE	-23.60
Consensus MFE	-18.81
Energy contribution	-19.70
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-2.11
Structure conservation index	0.80
SVM decision value	0.02
SVM RNA-class probability	0.542000
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6866007 114 + 22224390
GCCAAGUUUAUAAAACUAAAUUUAAACCAACAAAUCACUGUUCUACUUAAAUAACUUGAAACGAAGUGGUCGUUUCAGCUCCAUGCAGAUUUAAGUGAUUUCGUUCUGUUU-UUU
...(((((((......)))))))((((.(((((((((((..(((............((((((((.....))))))))((.....)))))....)))))))).)))..))))-... ( -23.30)
>DroSec_CAF1 9726 115 + 1
GCCAAGUUAAUAAAACUAACUAUAAGCCAAACAAUCACUGUUUCACUCAAAUAACUUGAAACGAAGUGGUCAUUUCAGCUCCAUGCAGAUUUAAGUGAUUCAGUUCUGUUUUUUU
....(((((.......))))).......(((((...((((..(((((.((((..........(((((....))))).((.....))..)))).)))))..))))..))))).... ( -20.90)
>DroSim_CAF1 10985 114 + 1
GCCAAGUCAAUAAAACUAACUAUAAGCCAAACAAUCACUGUUUUACUUAAAUAACUUGAAACGAAGUGGUCGUUUCAGCUCCAUGCAGAUUUAAGUGAUUCAGUUCUGUUU-UUU
............................(((((...((((..((((((((((....((((((((.....))))))))((.....))..))))))))))..))))..)))))-... ( -26.60)
>consensus
GCCAAGUUAAUAAAACUAACUAUAAGCCAAACAAUCACUGUUUUACUUAAAUAACUUGAAACGAAGUGGUCGUUUCAGCUCCAUGCAGAUUUAAGUGAUUCAGUUCUGUUU_UUU
....................................((((..((((((((((....((((((((.....))))))))((.....))..))))))))))..))))........... (-18.81 = -19.70 +   0.89)

alignment

secondary structure

dotplot

Window 0

Location	6,866,121 – 6,866,226
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.82
Mean single sequence MFE	-28.66
Consensus MFE	-20.58
Energy contribution	-20.50
Covariance contribution	-0.08
Combinations/Pair	1.25
Mean z-score	-1.59
Structure conservation index	0.72
SVM decision value	0.30
SVM RNA-class probability	0.679126
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6866121 105 + 22224390
CGUAAGUGCACU---------------UUCCACUUUUAAAUAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAGAUGGCUAACAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGA
..((((((((((---------------(((((..((.(((......))).))..)))...)))))((((((..(((((((...(((...)))...)))))))....))))))))))))). ( -31.10)
>DroSec_CAF1 9841 103 + 1
UGUAAGUGCACU---------------UUCC--UUUUAAAUAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAAAUGGCUAACAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGA
..(((((((...---------------....--...........(....)....(((((.(((((.(((((..........)))))...))))).)))))............))))))). ( -27.00)
>DroSim_CAF1 11099 103 + 1
UGUAAGUGCACU---------------UUCC--UUUUAAAUAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAAAUGGCUAACAGCACAGCUCUGGGCCUUCAUAAAUAGCCGUACUUGA
..(((((((...---------------....--...........(....).....((((.(((((.(((((..........)))))...))))).)))).............))))))). ( -25.80)
>DroEre_CAF1 6768 100 + 1
---AAGCGCAUU---------------UUUC--GCUUAAGUAGGGGCCUCACUUUGGCCAAGAGCGGCCGGCAAAUGGCCAAAAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGA
---(((((....---------------...)--))))(((((.((.........(((((.(((((.((.(((.....)))....))...))))).)))))..........)).))))).. ( -34.21)
>DroYak_CAF1 6824 111 + 1
-------GCAUUUGCCUUGCUUUUUGAUUUC--CGUUAAAUAAUGCUUUCACUUUGGCCAAGAGUGGCCGUCAAAUGGCUAAAAGCACAGCUCUGAGCCAUCAUAAAUAGCUGUACUUGA
-------((.((((((..((..((((((...--.))))))....)).........(((((....))))).......))).))).))((((((.(((....))).....))))))...... ( -25.20)
>consensus
_GUAAGUGCACU_______________UUCC__UUUUAAAUAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAAAUGGCUAACAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGA
..........................................................((((..(((((((...((((((...(((...)))...)))))).....)))))))..)))). (-20.58 = -20.50 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	6,866,146 – 6,866,257
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.34
Mean single sequence MFE	-38.54
Consensus MFE	-26.95
Energy contribution	-27.76
Covariance contribution	0.81
Combinations/Pair	1.19
Mean z-score	-2.76
Structure conservation index	0.70
SVM decision value	1.48
SVM RNA-class probability	0.957620
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6866146 111 + 22224390
UAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAGAUGGCUAACAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGAACC---------CGAUGGCCGAGAUGGCCAGACAUGAAAU
......(((((.((((((((......((((((...((.....)).))))))(((.(((((((......((.....))......---------.))))))).)))))))))))..))))). ( -39.12)
>DroSec_CAF1 9864 102 + 1
UAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAAAUGGCUAACAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGAACC---------CGAUG---------GCCAGACAUGAAAU
......(((((.((((((((((..(((((((...((((((...(((...)))...)))))).....)))))))..))......---------...))---------))))))..))))). ( -30.80)
>DroSim_CAF1 11122 111 + 1
UAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAAAUGGCUAACAGCACAGCUCUGGGCCUUCAUAAAUAGCCGUACUUGAACC---------CGAUGGCCGAGAUGGCCAGACAUGAAAU
......(((((.((((((((......((((((...((.....)).))))))(((.((((.((......((.....))......---------.)).)))).)))))))))))..))))). ( -34.82)
>DroEre_CAF1 6788 111 + 1
UAGGGGCCUCACUUUGGCCAAGAGCGGCCGGCAAAUGGCCAAAAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGAACC---------CGCUGGCCGAGAUGGCCAGACAUGAAAU
..((((((.......)))((((.(((((......((((((...(((...)))...))))))........))))).))))..))---------)(((((((.....)))))).)....... ( -44.44)
>DroYak_CAF1 6855 120 + 1
UAAUGCUUUCACUUUGGCCAAGAGUGGCCGUCAAAUGGCUAAAAGCACAGCUCUGAGCCAUCAUAAAUAGCUGUACUUGAACCGGAUGGCUGCGAUGGCCGAGAUGGCCAGACAUUGAAU
.......((((.((((((((....((((((((..((((((...(((...)))...))))))......(((((((.((......))))))))).))))))))...))))))))...)))). ( -43.50)
>consensus
UAACGUUUUCAAUUUGGCCAAGAGUGGUUGUGAAAUGGCUAACAGCACAGCUCUGGGCCAUCAUAAAUAGCCGUACUUGAACC_________CGAUGGCCGAGAUGGCCAGACAUGAAAU
......(((((....(..((((..(((((((...((((((...(((...)))...)))))).....)))))))..))))..).............(((((.....)))))....))))). (-26.95 = -27.76 +   0.81)

alignment

secondary structure

dotplot

Window 2

Location	6,866,146 – 6,866,257
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.34
Mean single sequence MFE	-36.41
Consensus MFE	-24.83
Energy contribution	-25.04
Covariance contribution	0.21
Combinations/Pair	1.14
Mean z-score	-2.35
Structure conservation index	0.68
SVM decision value	0.82
SVM RNA-class probability	0.859791
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6866146 111 - 22224390
AUUUCAUGUCUGGCCAUCUCGGCCAUCG---------GGUUCAAGUACGGCUAUUUAUGAUGGCCCAGAGCUGUGCUGUUAGCCAUCUCACAACCACUCUUGGCCAAAUUGAAAACGUUA
.(((((....((((((....((((((((---------......((.....)).....))))))))..(((.((.((.....)))).)))...........))))))...)))))...... ( -33.20)
>DroSec_CAF1 9864 102 - 1
AUUUCAUGUCUGGC---------CAUCG---------GGUUCAAGUACGGCUAUUUAUGAUGGCCCAGAGCUGUGCUGUUAGCCAUUUCACAACCACUCUUGGCCAAAUUGAAAACGUUA
.(((((....((((---------((...---------((((.......(((((((...)))))))..(((.((.((.....)))).)))..)))).....))))))...)))))...... ( -28.60)
>DroSim_CAF1 11122 111 - 1
AUUUCAUGUCUGGCCAUCUCGGCCAUCG---------GGUUCAAGUACGGCUAUUUAUGAAGGCCCAGAGCUGUGCUGUUAGCCAUUUCACAACCACUCUUGGCCAAAUUGAAAACGUUA
.(((((....((((((....((......---------((((..(((((((((.....((......)).)))))))))...)))).........)).....))))))...)))))...... ( -30.36)
>DroEre_CAF1 6788 111 - 1
AUUUCAUGUCUGGCCAUCUCGGCCAGCG---------GGUUCAAGUACGGCUAUUUAUGAUGGCCCAGAGCUGUGCUUUUGGCCAUUUGCCGGCCGCUCUUGGCCAAAGUGAGGCCCCUA
.......(.((((((.....)))))))(---------((..((((..(((((......(((((((.(((((...))))).)))))))....)))))..))))(((.......)))))).. ( -47.30)
>DroYak_CAF1 6855 120 - 1
AUUCAAUGUCUGGCCAUCUCGGCCAUCGCAGCCAUCCGGUUCAAGUACAGCUAUUUAUGAUGGCUCAGAGCUGUGCUUUUAGCCAUUUGACGGCCACUCUUGGCCAAAGUGAAAGCAUUA
....(((((.(((((.....)))))((((........((((.((((((((((.....(((....))).))))))))))..)))).......(((((....)))))...))))..))))). ( -42.60)
>consensus
AUUUCAUGUCUGGCCAUCUCGGCCAUCG_________GGUUCAAGUACGGCUAUUUAUGAUGGCCCAGAGCUGUGCUGUUAGCCAUUUCACAACCACUCUUGGCCAAAUUGAAAACGUUA
.(((((.((((((((.....)))))............((((..(((((((((.....((......)).)))))))))...)))).................))).....)))))...... (-24.83 = -25.04 +   0.21)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:44 2006