Locus 4153

Sequence ID	X_DroMel_CAF1
Location	10,893,541 – 10,893,664
Length	123
Max. P	0.999901

overview

Window 1

Location	10,893,541 – 10,893,644
Length	103
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	74.55
Mean single sequence MFE	-29.10
Consensus MFE	-16.51
Energy contribution	-16.51
Covariance contribution	-0.00
Combinations/Pair	1.13
Mean z-score	-2.86
Structure conservation index	0.57
SVM decision value	3.46
SVM RNA-class probability	0.999250
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10893541 103 + 22224390
GGUGGGCAGUGAUGGGCGGGUCAACGUAAUCUGCCAUAAUCUUAUGGCAUCUUAUCCUUUCACAAAAUUUUGACCCAC-CCCACCCCACUCACUGAGCGAUGUC
((((((..(((..(((.(((((((.((((..(((((((....)))))))..))))..............))))))).)-))))))))))).............. ( -34.56)
>DroSec_CAF1 47516 81 + 1
GGUGGGCAGUGAUGGGCGGG-------------CCAUAAUCCGA------AUUAUCCUUUCACAAAAA-UUGACCCAC-CCCACCC--AUCACUGAGCGACAUC
.((.(.((((((((((.(((-------------.........((------(.......))).((....-.))......-))).)))--)))))))..).))... ( -26.80)
>DroSim_CAF1 50673 81 + 1
GGUGGGCAGUGAUGGGCGGG-------------CCAUAAUCCGA------AUUAUCCUUUCACAAAAU-UUGACCCAU-CCCACCC--AUCACUGAGCGACAUC
.((.(.((((((((((.(((-------------........(((------(((............)))-)))......-))).)))--)))))))..).))... ( -27.34)
>DroEre_CAF1 24420 87 + 1
GGCGGGCAGUGAUGGGCGGG-CACU-----AUGCCAUGAUUAGA------AUUAUACUUUCG-AAAAC-CUGACCCAG-CCCACCC--AUCACUGAGCGAUAUC
.((...((((((((((.(((-(.((-----(.........))).------.........(((-.....-.)))....)-))).)))--))))))).))...... ( -31.80)
>DroYak_CAF1 48074 87 + 1
AGCGGGCAGUGAUGGGCGGGUCACC-------GUAAUAAUUGGA------AUUAAACUUUUC-AAAAC-AUGACCCAAUCCCACCC--AUCACUAAGUGAUUUG
.......(((((((((.(((.....-------((.....(((((------(.......))))-))...-...)).....))).)))--)))))).......... ( -25.00)
>consensus
GGUGGGCAGUGAUGGGCGGG_CA_________GCCAUAAUCCGA______AUUAUCCUUUCACAAAAC_UUGACCCAC_CCCACCC__AUCACUGAGCGAUAUC
.((...((((((((((.(((...........................................................))).)))..))))))).))...... (-16.51 = -16.51 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	10,893,541 – 10,893,644
Length	103
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	74.55
Mean single sequence MFE	-34.88
Consensus MFE	-17.57
Energy contribution	-17.61
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-3.51
Structure conservation index	0.50
SVM decision value	4.45
SVM RNA-class probability	0.999901
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10893541 103 - 22224390
GACAUCGCUCAGUGAGUGGGGUGGG-GUGGGUCAAAAUUUUGUGAAAGGAUAAGAUGCCAUAAGAUUAUGGCAGAUUACGUUGACCCGCCCAUCACUGCCCACC
....((((...))))((((((((((-(((((((((.(((((((......)))))))((((((....))))))........)))))))))))..)))..))))). ( -42.10)
>DroSec_CAF1 47516 81 - 1
GAUGUCGCUCAGUGAU--GGGUGGG-GUGGGUCAA-UUUUUGUGAAAGGAUAAU------UCGGAUUAUGG-------------CCCGCCCAUCACUGCCCACC
......(..(((((((--(((((((-...((((..-...((((......)))).------...))))....-------------))))))))))))))..)... ( -31.00)
>DroSim_CAF1 50673 81 - 1
GAUGUCGCUCAGUGAU--GGGUGGG-AUGGGUCAA-AUUUUGUGAAAGGAUAAU------UCGGAUUAUGG-------------CCCGCCCAUCACUGCCCACC
......(..(((((((--(((((((-...((((..-...((((......)))).------...))))....-------------))))))))))))))..)... ( -32.10)
>DroEre_CAF1 24420 87 - 1
GAUAUCGCUCAGUGAU--GGGUGGG-CUGGGUCAG-GUUUU-CGAAAGUAUAAU------UCUAAUCAUGGCAU-----AGUG-CCCGCCCAUCACUGCCCGCC
.....((..(((((((--(((((((-(...(((((-(((..-.(((.......)------)).)))).))))..-----...)-))))))))))))))..)).. ( -38.20)
>DroYak_CAF1 48074 87 - 1
CAAAUCACUUAGUGAU--GGGUGGGAUUGGGUCAU-GUUUU-GAAAAGUUUAAU------UCCAAUUAUUAC-------GGUGACCCGCCCAUCACUGCCCGCU
.........(((((((--(((((((((((((...(-(..((-....))..))..------))))))).....-------(....))))))))))))))...... ( -31.00)
>consensus
GAUAUCGCUCAGUGAU__GGGUGGG_GUGGGUCAA_AUUUUGUGAAAGGAUAAU______UCGGAUUAUGGC_________UG_CCCGCCCAUCACUGCCCACC
.........(((((((..(((((((...........................................................))))))))))))))...... (-17.57 = -17.61 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	10,893,565 – 10,893,664
Length	99
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	74.14
Mean single sequence MFE	-24.92
Consensus MFE	-15.46
Energy contribution	-15.14
Covariance contribution	-0.32
Combinations/Pair	1.15
Mean z-score	-1.77
Structure conservation index	0.62
SVM decision value	0.93
SVM RNA-class probability	0.884299
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10893565 99 - 22224390
UACAGCCCAUCUGGCCCAAGGACAUCGCUCAGUGAGUGGGGUGGG-GUGGGUCAAAAUUUUGUGAAAGGAUAAGAUGCCAUAAGAUUAUGGCAGAUUACG
....((((((((.((((....((.((((...)))))).)))).))-))))))..................(((..(((((((....)))))))..))).. ( -34.00)
>DroSec_CAF1 47536 81 - 1
UACAGCCCAAUUGGCCCAAGGAUGUCGCUCAGUGAU--GGGUGGG-GUGGGUCAA-UUUUUGUGAAAGGAUAAU------UCGGAUUAUGG---------
(((((...((((((((((....(.(((((((....)--)))))).-)))))))))-)).)))))..........------...........--------- ( -23.70)
>DroSim_CAF1 50693 81 - 1
UACAGCCCAAUUGGCCCAAGGAUGUCGCUCAGUGAU--GGGUGGG-AUGGGUCAA-AUUUUGUGAAAGGAUAAU------UCGGAUUAUGG---------
......((..((((((((....(.(((((((....)--)))))).-)))))))))-(((((.....)))))...------..)).......--------- ( -22.10)
>DroEre_CAF1 24443 83 - 1
CACAGCC-UUUUGGCCCAAGGAUAUCGCUCAGUGAU--GGGUGGG-CUGGGUCAG-GUUUU-CGAAAGUAUAAU------UCUAAUCAUGGCAU-----A
....(((-.(((((((((..(...(((((((....)--)))))).-)))))))))-)....-(....)......------.........)))..-----. ( -25.30)
>DroYak_CAF1 48098 83 - 1
UACAUCCAUUUUGGCCCAAGCAAAUCACUUAGUGAU--GGGUGGGAUUGGGUCAU-GUUUU-GAAAAGUUUAAU------UCCAAUUAUUAC-------G
...........((((((((.....(((((((....)--))))))..)))))))).-.....-............------............-------. ( -19.50)
>consensus
UACAGCCCAUUUGGCCCAAGGAUAUCGCUCAGUGAU__GGGUGGG_GUGGGUCAA_AUUUUGUGAAAGGAUAAU______UCGGAUUAUGGC________
...........(((((((......((((((........))))))...))))))).............................................. (-15.46 = -15.14 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:42 2006