Locus 5003

Sequence ID	3L_DroMel_CAF1
Location	13,759,088 – 13,759,367
Length	279
Max. P	0.997459

overview

Window 7

Location	13,759,088 – 13,759,207
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.30
Mean single sequence MFE	-27.62
Consensus MFE	-23.52
Energy contribution	-23.76
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.48
Structure conservation index	0.85
SVM decision value	2.86
SVM RNA-class probability	0.997459
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13759088 119 + 23771897
CCACUUCGCCGUU-GCCCCACAACUCGCUAAAUUUAUUAACCCACAUUAACCACUUCCAUCGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCU
.......((.(((-(.....))))..)).................................(((((((((((((..((((((((.......))))).))).))))))))).....)))). ( -27.50)
>DroSec_CAF1 5677 119 + 1
CCACUCCAACGUU-GCCACACAACUCGCUAAAUUUAUUAACCCACAUUAACCACUUCCAUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCU
......((((.((-((((.........................................))))))(((((((((..((((((((.......))))).))).)))))))))....)))).. ( -28.98)
>DroSim_CAF1 1815 119 + 1
CCACUCGGACGUU-GCCACACAACUCGCUAAAUUUAUUAACCCACAUUAACCACUUCCAUGGCAAAAUGUUGAUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCU
......(((.(((-(.....))))..................(((((((.....(((((((((((....))).))))))))......)))))))..)))..((((((.......)))))) ( -25.20)
>DroEre_CAF1 4905 119 + 1
CCACUCCGCGGUU-GCCACACAACUCCCUAAAUUUAUUAACCCACAUUAACCACUUUCCUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCU
.......((((((-(.....))))).....(((((((.............(((......)))...(((((((((..((((((((.......))))).))).)))))))))))))))))). ( -29.10)
>DroYak_CAF1 1933 120 + 1
CCACUCCGCGGUUCACCCCACAGCUCCCUAAAUUUAUUAACCCACAUUAACCACUUUCCUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCU
.......((((......))...........(((((((.............(((......)))...(((((((((..((((((((.......))))).))).)))))))))))))))))). ( -27.30)
>consensus
CCACUCCGCCGUU_GCCACACAACUCGCUAAAUUUAUUAACCCACAUUAACCACUUCCAUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCU
....................(((((.........................(((......)))...(((((((((..((((((((.......))))).))).)))))))))...))))).. (-23.52 = -23.76 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	13,759,127 – 13,759,247
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-32.65
Consensus MFE	-29.48
Energy contribution	-30.24
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-2.15
Structure conservation index	0.90
SVM decision value	2.48
SVM RNA-class probability	0.994413
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13759127 120 + 23771897
CCCACAUUAACCACUUCCAUCGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCUGUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCG
................((((.(((((((((((((..((((((((.......))))).))).))))))))).....)))).)).))..............(((((((.....))))))).. ( -31.60)
>DroSec_CAF1 5716 120 + 1
CCCACAUUAACCACUUCCAUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCUGUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCG
................((((((((((((((((((..((((((((.......))))).))).))))))))).....))))))).))..............(((((((.....))))))).. ( -34.50)
>DroSim_CAF1 1854 120 + 1
CCCACAUUAACCACUUCCAUGGCAAAAUGUUGAUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCUGUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCG
...((((((.....(((((((((((....))).))))))))......))))))((((....((((((.......))))))..)))).............(((((((.....))))))).. ( -31.30)
>DroEre_CAF1 4944 120 + 1
CCCACAUUAACCACUUUCCUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCUGUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAACUGCG
...........((.((((((((((((((((((((..((((((((.......))))).))).))))))))).....))))).....................((....)))))))).)).. ( -29.90)
>DroYak_CAF1 1973 120 + 1
CCCACAUUAACCACUUUCCUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCUGUAGGCUUUUAAAACUUUUCACUUUCCAGAGGAAAGUGCG
...........(((((((((((((((((((((((..((((((((.......))))).))).))))))))).....)))))...((....................))..))))))))).. ( -35.95)
>consensus
CCCACAUUAACCACUUCCAUGGCAAAAUGUUGCUCAUGGGGCGCUCGUAAUGUGCCUCCAAAGCAAUAUUAUAAGUUGCUGUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCG
................((((((((((((((((((..((((((((.......))))).))).))))))))).....))))))).))..............(((((((.....))))))).. (-29.48 = -30.24 +   0.76)

alignment

secondary structure

dotplot

Window 9

Location	13,759,127 – 13,759,247
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-32.34
Consensus MFE	-32.00
Energy contribution	-32.16
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.36
Structure conservation index	0.99
SVM decision value	1.08
SVM RNA-class probability	0.911901
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13759127 120 - 23771897
CGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUACAGCAACUUAUAAUAUUGCUUUGGAGGCACAUUACGAGCGCCCCAUGAGCAACAUUUUGCGAUGGAAGUGGUUAAUGUGGG
..(((((((.....)))))))..............((((((..(((........(((((((((.(((.(.......).)))))).))))))((((((......)))))))))..)))))) ( -33.70)
>DroSec_CAF1 5716 120 - 1
CGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUACAGCAACUUAUAAUAUUGCUUUGGAGGCACAUUACGAGCGCCCCAUGAGCAACAUUUUGCCAUGGAAGUGGUUAAUGUGGG
..(((((((.....)))))))..............((((((..(((........(((((((((.(((.(.......).)))))).))))))((((((......)))))))))..)))))) ( -33.70)
>DroSim_CAF1 1854 120 - 1
CGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUACAGCAACUUAUAAUAUUGCUUUGGAGGCACAUUACGAGCGCCCCAUGAUCAACAUUUUGCCAUGGAAGUGGUUAAUGUGGG
..(((((((.....))))))).............((((..(((((.........)))))....))))((((((...((...(((((..(((....))).)))))..))...))))))... ( -27.80)
>DroEre_CAF1 4944 120 - 1
CGCAGUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUACAGCAACUUAUAAUAUUGCUUUGGAGGCACAUUACGAGCGCCCCAUGAGCAACAUUUUGCCAGGAAAGUGGUUAAUGUGGG
.........((.((((((.(....).)))))).))((((((..(((........(((((((((.(((.(.......).)))))).))))))((((((......)))))))))..)))))) ( -30.40)
>DroYak_CAF1 1973 120 - 1
CGCACUUUCCUCUGGAAAGUGAAAAGUUUUAAAAGCCUACAGCAACUUAUAAUAUUGCUUUGGAGGCACAUUACGAGCGCCCCAUGAGCAACAUUUUGCCAGGAAAGUGGUUAAUGUGGG
..((((((((...))))))))..............((((((..(((........(((((((((.(((.(.......).)))))).))))))((((((......)))))))))..)))))) ( -36.10)
>consensus
CGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUACAGCAACUUAUAAUAUUGCUUUGGAGGCACAUUACGAGCGCCCCAUGAGCAACAUUUUGCCAUGGAAGUGGUUAAUGUGGG
..(((((((.....)))))))..............((((((..(((........(((((((((.(((.(.......).)))))).))))))((((((......)))))))))..)))))) (-32.00 = -32.16 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	13,759,207 – 13,759,327
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-31.22
Consensus MFE	-30.50
Energy contribution	-30.38
Covariance contribution	-0.12
Combinations/Pair	1.03
Mean z-score	-2.02
Structure conservation index	0.98
SVM decision value	2.72
SVM RNA-class probability	0.996623
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13759207 120 + 23771897
GUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCGGUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUC
...((((......(((((((.((....)).)))))))((((((.((((.......)))((((((......(((((((.....)))..)))).....))))))......).)))))))))) ( -31.20)
>DroSec_CAF1 5796 120 + 1
GUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCGGUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUC
...((((......(((((((.((....)).)))))))((((((.((((.......)))((((((......(((((((.....)))..)))).....))))))......).)))))))))) ( -31.20)
>DroSim_CAF1 1934 120 + 1
GUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCGGUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUC
...((((......(((((((.((....)).)))))))((((((.((((.......)))((((((......(((((((.....)))..)))).....))))))......).)))))))))) ( -31.20)
>DroEre_CAF1 5024 120 + 1
GUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAACUGCGGUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUC
.................(((.(((....))))))(((((((((.((((.......)))((((((......(((((((.....)))..)))).....))))))......).))))))))). ( -30.10)
>DroYak_CAF1 2053 120 + 1
GUAGGCUUUUAAAACUUUUCACUUUCCAGAGGAAAGUGCGGUUUCGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCAGUGACCGCAGUC
...((((.............(((((((...)))))))((((((.((((.......)))((((((......(((((((.....)))..)))).....))))))......).)))))))))) ( -32.40)
>consensus
GUAGGCUUUUAAAACUUUUCACUUUCAAGAGGAAAGUGCGGUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUC
...((((......(((((((.((....)).)))))))((((((.((((.......)))((((((......(((((((.....)))..)))).....))))))......).)))))))))) (-30.50 = -30.38 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	13,759,207 – 13,759,327
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-30.66
Consensus MFE	-28.60
Energy contribution	-29.00
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.93
SVM decision value	0.66
SVM RNA-class probability	0.813972
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13759207 120 - 23771897
GACUGCGGUCAGUGGGUUGGCAAAAAUGAUUCAUUAGCAUUCAGCUUGAAAGUUGAUUUGCCGCAAAAGAGAUACCAAACCGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUAC
(((....))).(((((((((((((((((...)))).....((((((....))))))))))))..............((((..(((((((.....)))))))....))))....))))))) ( -30.00)
>DroSec_CAF1 5796 120 - 1
GACUGCGGUCAGUGGGUUGGCAAAAAUGAUUCAUUAGCAUUCAGCUUGAAAGUUGAUUUGCCGCAAAAGAGAUACCAAACCGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUAC
(((....))).(((((((((((((((((...)))).....((((((....))))))))))))..............((((..(((((((.....)))))))....))))....))))))) ( -30.00)
>DroSim_CAF1 1934 120 - 1
GACUGCGGUCAGUGGGUUGGCAAAAAUGAUUCAUUAGCAUUCAGCUUGAAAGUUGAUUUGCCGCAAAAGAGAUACCAAACCGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUAC
(((....))).(((((((((((((((((...)))).....((((((....))))))))))))..............((((..(((((((.....)))))))....))))....))))))) ( -30.00)
>DroEre_CAF1 5024 120 - 1
GACUGCGGUCAGUGGGUUGGCAAAAAUGAUUCAUUAGCAUUCAGCUUGAAAGUUGAUUUGCCGCAAAAGAGAUACCAAACCGCAGUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUAC
(((((((((...(((...((((((((((...)))).....((((((....)))))))))))).(......)...))).)))))))))..((.((((((.(....).)))))).))..... ( -31.30)
>DroYak_CAF1 2053 120 - 1
GACUGCGGUCACUGGGUUGGCAAAAAUGAUUCAUUAGCAUUCAGCUUGAAAGUUGAUUUGCCGCAAAAGAGAUACGAAACCGCACUUUCCUCUGGAAAGUGAAAAGUUUUAAAAGCCUAC
(((....)))..((((((((((((((((...)))).....((((((....)))))))))))).............(((((..((((((((...))))))))....)))))...)))))). ( -32.00)
>consensus
GACUGCGGUCAGUGGGUUGGCAAAAAUGAUUCAUUAGCAUUCAGCUUGAAAGUUGAUUUGCCGCAAAAGAGAUACCAAACCGCACUUUCCUCUUGAAAGUGAAAAGUUUUAAAAGCCUAC
(((....))).(((((((((((((((((...)))).....((((((....))))))))))))..............((((..(((((((.....)))))))....))))....))))))) (-28.60 = -29.00 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	13,759,247 – 13,759,367
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-30.42
Consensus MFE	-28.00
Energy contribution	-28.12
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-1.13
Structure conservation index	0.92
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13759247 120 + 23771897
GUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUCGGUAAAGGUAGCGUUAGUUGGCCCAUACCAUUUAUUAGUG
...((((((.........((((((......(((((((.....)))..)))).....))))))..((.((((((.((..((......))..)))))))).))...)))))).......... ( -30.20)
>DroSec_CAF1 5836 120 + 1
GUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUCGGUAAAGGUAGCGUUAGUUGGCCCAUACCAUUUAUUAGUG
...((((((.........((((((......(((((((.....)))..)))).....))))))..((.((((((.((..((......))..)))))))).))...)))))).......... ( -30.20)
>DroSim_CAF1 1974 120 + 1
GUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUCGGUAAAGGUAGCGUAAGUUGGCCCAUACCAUUUAUUAGUG
...((((((((..(((((((((((......(((((((.....)))..)))).....)))))).(((.((((((....))))))...)))...)))))..))...)))))).......... ( -31.00)
>DroEre_CAF1 5064 120 + 1
GUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUCGGUAAAGGUAGCGUUAGUUGGCCCAUACCAUUUAUUGGUG
....(((....((..(((((((((......(((((((.....)))..)))).....)))))).(((.((((((....))))))...))).)))..))...)))..(((((.....))))) ( -33.60)
>DroYak_CAF1 2093 116 + 1
GUUUCGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCAGUGACCGCAGUCGGUAAAGGUAGCGUUACUUGG----UAUCAUUUAUUAGUG
.....(((.......)))((((((......(((((((.....)))..)))).....)))))).(((.((((((.((..((......))..)))))))).))----).............. ( -27.10)
>consensus
GUUUGGUAUCUCUUUUGCGGCAAAUCAACUUUCAAGCUGAAUGCUAAUGAAUCAUUUUUGCCAACCCACUGACCGCAGUCGGUAAAGGUAGCGUUAGUUGGCCCAUACCAUUUAUUAGUG
...((((((.........((((((......(((((((.....)))..)))).....))))))..((.((((((.((..((......))..)))))))).))...)))))).......... (-28.00 = -28.12 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:17 2006