Locus 2992

Sequence ID	2L_DroMel_CAF1
Location	8,548,240 – 8,548,442
Length	202
Max. P	0.995623

overview

Window 6

Location	8,548,240 – 8,548,346
Length	106
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	94.19
Mean single sequence MFE	-19.84
Consensus MFE	-16.56
Energy contribution	-15.96
Covariance contribution	-0.60
Combinations/Pair	1.17
Mean z-score	-1.69
Structure conservation index	0.83
SVM decision value	0.98
SVM RNA-class probability	0.893405
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8548240 106 + 22407834
UUUUCUUUGUCAGGCCUGCAAAAAUGAAAUGUGAGUAACAAAAUAGUCGAAGAAUUUUUGGGCAAAUAAGAAAGCAAAGUAAACACUUCUAAAUAA-AGGACAGAGA
...((((((((..(((..(((((((......(((.((......)).)))....)))))))))).............((((....))))........-..)))))))) ( -19.80)
>DroSec_CAF1 57766 106 + 1
UUUUCUUUGUCAGCCCUGCAAAAAUGAAAUGUGGGUAACAAAAUAGUCGAGGAAUUUUUGGACAAAUAAGAAAGCAAAGUAAACACUUCUAAAUAA-AGGACAGAGA
...((((((((.((((..((.........))..))..........(((.(((....))).)))..........)).((((....))))........-..)))))))) ( -19.30)
>DroSim_CAF1 57478 106 + 1
UUUUCUUUGUCAGCCCUGCAAAAAUGAAAUGUGGGUAACAAAAUAGUCGAGGAAUUUUUGGACAAAUAAGAAAGCAAAGUAAACACUUCUAAAUAA-AGGACAGAGA
...((((((((.((((..((.........))..))..........(((.(((....))).)))..........)).((((....))))........-..)))))))) ( -19.30)
>DroEre_CAF1 59276 107 + 1
UUUUCUUUGUCAGCCCUGCAAAAAUGAAAUGUGGGUAACAAAAUAGUCGGAGAAUUUUUGGGAAAACAAGAAAGCAAAGUAAACACUUAUAGAUAAAAGGACAGGGA
...((((((((.((((.(((.........))))))).........(((...(..((((((......))))))..).((((....))))...))).....)))))))) ( -20.80)
>DroYak_CAF1 58883 107 + 1
UUUUCUUUGUCAGCCCUGCAAAAAUGAAAUGUGGGUAACAAAAAAGUCGAAGAAUUUUUGGGCAAACAGGAAAGCAAAGUAAACACUUAUAAAUAAAAGGACAGAGA
...((((((((.((((((...........(((.....))).....(((.(((....))).)))...))))...)).((((....))))...........)))))))) ( -20.00)
>consensus
UUUUCUUUGUCAGCCCUGCAAAAAUGAAAUGUGGGUAACAAAAUAGUCGAAGAAUUUUUGGGCAAAUAAGAAAGCAAAGUAAACACUUCUAAAUAA_AGGACAGAGA
...((((((((.....(((..........(((.....))).....(((.(((....))).)))..........)))((((....))))...........)))))))) (-16.56 = -15.96 +  -0.60)

alignment

secondary structure

dotplot

Window 7

Location	8,548,307 – 8,548,402
Length	95
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	92.07
Mean single sequence MFE	-20.29
Consensus MFE	-16.88
Energy contribution	-17.92
Covariance contribution	1.04
Combinations/Pair	1.04
Mean z-score	-2.47
Structure conservation index	0.83
SVM decision value	2.60
SVM RNA-class probability	0.995623
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8548307 95 - 22407834
UAAUUUGGUCAACACGCCA----AGGAAUAU-----UUUCCUACCUUGGCUGCGUUAUUUGUUUUUCUCUGUCCU-UUAUUUAGAAGUGUUUACUUUGCUUUCUU
......(((.(((((((((----(((.....-----.......))))))).................((((....-.....)))).))))).))).......... ( -18.70)
>DroSec_CAF1 57833 104 - 1
UAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUGCGUUAUUUGUUUUUCUCUGUCCU-UUAUUUAGAAGUGUUUACUUUGCUUUCUU
......(((.(((((((((((..(((((.........)))))..)))))).................((((....-.....)))).))))).))).......... ( -22.30)
>DroSim_CAF1 57545 104 - 1
UAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUGCAUUAUUUGUUUUUCUCUGUCCU-UUAUUUAGAAGUGUUUACUUUGCUUUCUU
......(((.(((((((((((..(((((.........)))))..)))))).................((((....-.....)))).))))).))).......... ( -22.30)
>DroEre_CAF1 59343 105 - 1
UAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUUCGCUAUUUGUUUUUCCCUGUCCUUUUAUCUAUAAGUGUUUACUUUGCUUUCUU
......(((.(((((((((((..(((((.........)))))..))))))...((.....))........................))))).))).......... ( -20.50)
>DroYak_CAF1 58950 105 - 1
UAAUUUGGUCAACACGCCAGCCGAGGAAUAUUUUAUUUUCUUACCUUGGCUUCGCUAUUUGUUUUUCUCUGUCCUUUUAUUUAUAAGUGUUUACUUUGCUUUCCU
......(((.(((((((.((((((((.................))))))))..)).....................(((....)))))))).))).......... ( -17.63)
>consensus
UAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUGCGUUAUUUGUUUUUCUCUGUCCU_UUAUUUAGAAGUGUUUACUUUGCUUUCUU
......(((.(((((((((((..(((((.........)))))..)))))).................((((..........)))).))))).))).......... (-16.88 = -17.92 +   1.04)

alignment

secondary structure

dotplot

Window 8

Location	8,548,346 – 8,548,442
Length	96
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	89.58
Mean single sequence MFE	-28.77
Consensus MFE	-21.24
Energy contribution	-22.64
Covariance contribution	1.40
Combinations/Pair	1.06
Mean z-score	-2.58
Structure conservation index	0.74
SVM decision value	1.23
SVM RNA-class probability	0.934130
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8548346 96 + 22407834
AAAACAAAUAACGCAGCCAAGGUAGGAAA-----AUAUUCCU----UGGCGUGUUGACCAAAUUAAGACCGCAAGUGGCUGGCUGGCUGACUGGCCAAAAUGAUU
........((((((.(((((((.......-----.....)))----))))))))))....(((((((.(((....)))))(((..(....)..)))....))))) ( -28.10)
>DroSec_CAF1 57872 105 + 1
AAAACAAAUAACGCAGCCAAGGUAGGAAAAUAAAAUAUUCCUCGCCUGGCGUGUUGACCAAAUUAAGAGCGCAAGUGGCUGGCUGGCUGACUGGCCAAAAUGAUU
........((((((.((((.((((((((.........))))).)))))))))))))....(((((((.((....))..))(((..(....)..)))....))))) ( -31.60)
>DroSim_CAF1 57584 101 + 1
AAAACAAAUAAUGCAGCCAAGGUAGGAAAAUAAAAUAUUCCUCGCCUGGCGUGUUGACCAAAUUAAGACCGCAAGUGGCU----GGCUGACUGGCCAAAAUGAUU
...........(((.((((.((((((((.........))))).)))))))((.((((.....)))).)).)))..((((.----.(....)..))))........ ( -28.50)
>DroEre_CAF1 59383 101 + 1
AAAACAAAUAGCGAAGCCAAGGUAGGAAAAUAAAAUAUUCCUCGCCUGGCGUGUUGACCAAAUUAAGACCGCAAGUGGCUGGCU----GGCUGGCCAAAAUGAUU
..........(((..((((.((((((((.........))))).)))))))((.((((.....)))).)))))...((((..(..----..)..))))........ ( -30.80)
>DroYak_CAF1 58990 101 + 1
AAAACAAAUAGCGAAGCCAAGGUAAGAAAAUAAAAUAUUCCUCGGCUGGCGUGUUGACCAAAUUAAGACCGCAAGUGGCUGGCU----GGCUGGCCAAAAUGAUU
....(((...(((.((((.(((.................))).))))..))).)))....(((((....(....)((((..(..----..)..))))...))))) ( -24.83)
>consensus
AAAACAAAUAACGCAGCCAAGGUAGGAAAAUAAAAUAUUCCUCGCCUGGCGUGUUGACCAAAUUAAGACCGCAAGUGGCUGGCUGGCUGACUGGCCAAAAUGAUU
........((((((.((((.((((((((.........))))).)))))))))))))....(((((....(....)(((((((........)))))))...))))) (-21.24 = -22.64 +   1.40)

alignment

secondary structure

dotplot

Window 9

Location	8,548,346 – 8,548,442
Length	96
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	89.58
Mean single sequence MFE	-25.39
Consensus MFE	-20.39
Energy contribution	-20.83
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.75
Structure conservation index	0.80
SVM decision value	0.76
SVM RNA-class probability	0.843470
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8548346 96 - 22407834
AAUCAUUUUGGCCAGUCAGCCAGCCAGCCACUUGCGGUCUUAAUUUGGUCAACACGCCA----AGGAAUAU-----UUUCCUACCUUGGCUGCGUUAUUUGUUUU
.........(((......)))(((((((((.....(((.......((((......))))----(((((...-----.)))))))).)))))).)))......... ( -23.90)
>DroSec_CAF1 57872 105 - 1
AAUCAUUUUGGCCAGUCAGCCAGCCAGCCACUUGCGCUCUUAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUGCGUUAUUUGUUUU
.......((((((((......((((((....))).)))......))))))))...((((((..(((((.........)))))..))))))............... ( -26.70)
>DroSim_CAF1 57584 101 - 1
AAUCAUUUUGGCCAGUCAGCC----AGCCACUUGCGGUCUUAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUGCAUUAUUUGUUUU
.......((((((((..((((----.((.....)))).))....))))))))...((((((..(((((.........)))))..))))))............... ( -26.30)
>DroEre_CAF1 59383 101 - 1
AAUCAUUUUGGCCAGCC----AGCCAGCCACUUGCGGUCUUAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUUCGCUAUUUGUUUU
...((...((((.((((----((((.(((......))).......((((......))))))).(((((.........)))))....)))))..))))..)).... ( -25.90)
>DroYak_CAF1 58990 101 - 1
AAUCAUUUUGGCCAGCC----AGCCAGCCACUUGCGGUCUUAAUUUGGUCAACACGCCAGCCGAGGAAUAUUUUAUUUUCUUACCUUGGCUUCGCUAUUUGUUUU
.......((((((((..----((((.((.....)))).))....))))))))...((.((((((((.................))))))))..)).......... ( -24.13)
>consensus
AAUCAUUUUGGCCAGUCAGCCAGCCAGCCACUUGCGGUCUUAAUUUGGUCAACACGCCAGGCGAGGAAUAUUUUAUUUUCCUACCUUGGCUGCGUUAUUUGUUUU
.......((((((((...........((.....)).........))))))))...((((((..(((((.........)))))..))))))............... (-20.39 = -20.83 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:36 2006