Locus 1043

Sequence ID	X_DroMel_CAF1
Location	3,026,748 – 3,027,016
Length	268
Max. P	0.949234

overview

Window 8

Location	3,026,748 – 3,026,856
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.95
Mean single sequence MFE	-33.98
Consensus MFE	-29.08
Energy contribution	-29.36
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.86
SVM decision value	1.02
SVM RNA-class probability	0.902198
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3026748 108 - 22224390
ACGGCGAUGAGCCGGACAUUGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU-GGGAUGGUAGAAUGAUUAGUUAGCUAGU-----------UAGCU
.((((.....))))..((((...(((((...)))))((((((((((((.((....)).)))))))))))).....-..))))......(((((((....)))))-----------))... ( -34.60)
>DroSec_CAF1 7131 108 - 1
ACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU-GGGAUGGUAGAACGAUUAGUCAGCUAGU-----------GAUAG
.((((.....))))(((((((..(((..(..(((..((((((((((((.((....)).))))))))))))...))-)..)..).))..))))..)))..(((..-----------..))) ( -35.00)
>DroSim_CAF1 2102 108 - 1
ACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU-GAGAUGGUAGAACGAUUAGUCAGCUAGU-----------GAUAG
.((((.....))))(((((((..(((..(.((((..((((((((((((.((....)).))))))))))))...))-)).)..).))..))))..)))..(((..-----------..))) ( -35.80)
>DroEre_CAF1 7145 101 - 1
ACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGAGAGUGGGAAAUGUUGAAAUUAUUAGA-------------------GAUCA
.((((.....))))((((((((........))))...(((((((((((.((....)).)))))))))))...........))))............-------------------..... ( -26.60)
>DroYak_CAF1 7102 119 - 1
ACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUG-GAGAUGGUAAAGUUAUUAGUCAGCUUGCAUGGAAAUACGUAGCA
.((((.....))))(((....((((((((.((.(..((((((((((((.((....)).))))))))))))...).-))....))))))))....))).(((((.((....)).)).))). ( -37.90)
>consensus
ACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU_GAGAUGGUAGAAUGAUUAGUCAGCUAGU___________GAUCA
.((((.....))))..((((...(((((...)))))((((((((((((.((....)).))))))))))))........))))...................................... (-29.08 = -29.36 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	3,026,777 – 3,026,896
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.81
Mean single sequence MFE	-43.56
Consensus MFE	-38.94
Energy contribution	-39.62
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-1.43
Structure conservation index	0.89
SVM decision value	0.85
SVM RNA-class probability	0.865216
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3026777 119 - 22224390
UGCUGAUUGUGCUGCGACGACGGCGACAACAUAUUGGUCGACGGCGAUGAGCCGGACAUUGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU-GGGA
.((((.((((......))))))))..((((.......((((((((.....)))).(((........))).))))..((((((((((((.((....)).))))))))))))..)))-)... ( -41.20)
>DroSec_CAF1 7160 119 - 1
UGCUGGUUGUGCUGCGACGACGGCGACAGCAUGUUGGUCGACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU-GGGA
.(((.(((..((((((((((((((....)).)))).)))).))))))).)))(.(((.((((........))))..((((((((((((.((....)).))))))))))))..)))-.).. ( -46.10)
>DroSim_CAF1 2131 119 - 1
UGCUGGUUGUGCUGCGACGACGGCGACAGCAUGUUGGUCGACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU-GAGA
((((((((((((((((((((((((....)).)))).)))).)))).)).)))))).))((((.(((((...)))))((((((((((((.((....)).))))))))))))...))-)).. ( -46.30)
>DroEre_CAF1 7166 120 - 1
UGCUGAUUGUGCUGCGACGACGGCGACAGCAUGUUGGUCGACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGAGAGUGGGAAA
(((((.((((((((((((((((((....)).)))).)))).)))).))))..))).))((((........))))...(((((((((((.((....)).)))))))))))........... ( -38.50)
>DroYak_CAF1 7142 119 - 1
UGCUGGUUGUGCUGCGACGACGGCGACAGCAUGUUGGUCGACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUG-GAGA
((((((((((((((((((((((((....)).)))).)))).)))).)).)))))).))((((........))))..((((((((((((.((....)).)))))))))))).....-.... ( -45.70)
>consensus
UGCUGGUUGUGCUGCGACGACGGCGACAGCAUGUUGGUCGACGGCGACGAGCCGGACAUCGAACUUUGUAUCGAGGGCGGAUUCAUUUGACCCGAGUGAAAUGAGUCUGCAAGUU_GAGA
((((((((((((((((((((((((....)).)))).)))).)))).)).)))))).))((((........))))..((((((((((((.((....)).)))))))))))).......... (-38.94 = -39.62 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	3,026,896 – 3,027,016
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-41.80
Consensus MFE	-40.38
Energy contribution	-40.42
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.97
SVM decision value	1.39
SVM RNA-class probability	0.949234
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3026896 120 + 22224390
GGCCUUCUACCAGUACCUAACGCCUUCGAGCCAACAUUCCGGCGGCCAUACGCCGCAGCAUUUGGUCCAAACGUUGGAUAGCUAUCCGACGCCCUCGCCGGAGUCACCUGGCCACUGGUC
........((((((..(....).....(.((((..(((((((((((((...((....))...)))))....((((((((....)))))))).....))))))))....))))))))))). ( -43.40)
>DroSec_CAF1 7279 120 + 1
GGCCUUCUACCAGUACCUAACGCCUCCGAGCCAGCAUUCCGGCGGCCAUACGCCGCAGCACUUGGUCCAAACGCUGGACAGCUACCCGACGCCCUCGCCGGAGUCACCUGGCCACUGGUC
........((((((......((....)).(((((.(((((((((((.....)))..(((.....(((((.....))))).))).............))))))))...))))).)))))). ( -41.40)
>DroSim_CAF1 2250 120 + 1
GGCCUUCUACCAGUACCUAACGCCUCCGAGCCAGCAUUCCGGCGGCCAUACGCCGCAGCACUUGGUCCAAACGCUGGACAGCUACCCGACGCCCUCGCCGGAGUCACCUGGCCACUGGUC
........((((((......((....)).(((((.(((((((((((.....)))..(((.....(((((.....))))).))).............))))))))...))))).)))))). ( -41.40)
>DroEre_CAF1 7286 120 + 1
GGCCUUCUACCAGUACCUAACGCCUCCGAGCCAGCAUUCCGGCGGCCAUACGCCGCAGCAUUUGGUCCAAACGCUGGACAGCUAUCCAACGCCCUCGCCGGAGUCACCUGGCCACUGGUC
........((((((......((....)).(((((.(((((((((((.....)))..(((.....(((((.....))))).))).............))))))))...))))).)))))). ( -41.40)
>DroYak_CAF1 7261 120 + 1
GGCCUUCUACCAGUACCUAACGCCACCGAGCCAGCAUUCCGGCGGCCAUACGCCGCAGCAUUUGGUCCAAACGCUGGACAGCUACCCAACGCCCUCGCCGGAGUCACCUGGCCACUGGUC
........((((((......((....)).(((((.(((((((((((.....)))..(((.....(((((.....))))).))).............))))))))...))))).)))))). ( -41.40)
>consensus
GGCCUUCUACCAGUACCUAACGCCUCCGAGCCAGCAUUCCGGCGGCCAUACGCCGCAGCAUUUGGUCCAAACGCUGGACAGCUACCCGACGCCCUCGCCGGAGUCACCUGGCCACUGGUC
........((((((......((....)).(((((.(((((((((((.....)))..(((.....(((((.....))))).))).............))))))))...))))).)))))). (-40.38 = -40.42 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:17 2006