Locus 1371

Sequence ID	2L_DroMel_CAF1
Location	3,640,448 – 3,640,554
Length	106
Max. P	0.843933

overview

Window 2

Location	3,640,448 – 3,640,554
Length	106
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.47
Mean single sequence MFE	-25.97
Consensus MFE	-19.45
Energy contribution	-19.70
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-1.76
Structure conservation index	0.75
SVM decision value	0.76
SVM RNA-class probability	0.843933
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3640448 106 + 22407834
AACGCAUCCAGGCGGCUUUCCUGAUCAACAGCCGCCACGGAAAACUCAAUCAGCCAGGCGUUGGGAGCCCUACA-AA----AAAAAAAUAAUACAACAAAAAUAGUGCAUA
...((((((.(((((((............)))))))..)))...(((...((((.....)))).))).......-..----........................)))... ( -22.90)
>DroVir_CAF1 141591 101 + 1
AACGCAUCCAGGCGGCUUUCCAGAAGAACCGCCGCCACGUGGAAUUUGCUCAGUUCGUUAAACGCACACCUACACACAGAACGAGAG--------AGAG--AGAGAGCAAA
......((((((((((.(((.....)))..))))))...)))).(((((((.((.((.....)).))..............(....)--------....--...))))))) ( -27.00)
>DroSec_CAF1 108140 98 + 1
AACGCAUCCAGGCGGCUUUCCUGAUCAACAGCCGCCACGGAAAACUCAAUCAGCCAGGCGUUGGGAGCCCUACA-AA----------AUAAUAAACCAA--AGAGUGCAUA
...((.(((.(((((((............)))))))..)))..((((.....((...))((.((....)).)).-..----------............--.))))))... ( -25.70)
>DroSim_CAF1 113863 98 + 1
AACGCAUCCAGGCGGCUUUCCUGAUCAACAGCCGCCACGGAAAACUCAAUCAGCCAGGCGUUGGGAGCCCUACA-AA----------AUAAUAAACCAA--AGAGUGCAUA
...((.(((.(((((((............)))))))..)))..((((.....((...))((.((....)).)).-..----------............--.))))))... ( -25.70)
>DroEre_CAF1 109987 98 + 1
AACGCAUCCAGGCGGCUUUCCUGAUCAACAGCCGCCACGGAAAACUCAAUCAGCCAGGCGUUGGGAGCCCUGCA-AA----------AUAGUAAACCAA--AGAGUGCAUA
...(((..(.(((((((............)))))))..((...(((......((..(((.......)))..)).-..----------..)))...))..--.)..)))... ( -26.90)
>DroYak_CAF1 113362 100 + 1
AACGCAUCCAGGCGGCUUUCCUGAUCAACAGCCGCCACGGAAAACUCAAUCAGCCAGGCGUUGGGAGCCCUGCA-AA----------GUAAUAAACCAAAAAGAGUGCAUA
...((.(((.(((((((............)))))))..)))..((((.....((..(((.......)))..)).-..----------((.....))......))))))... ( -27.60)
>consensus
AACGCAUCCAGGCGGCUUUCCUGAUCAACAGCCGCCACGGAAAACUCAAUCAGCCAGGCGUUGGGAGCCCUACA_AA__________AUAAUAAACCAA__AGAGUGCAUA
...((((((.(((((((............)))))))..)))...............(((.......)))....................................)))... (-19.45 = -19.70 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	3,640,448 – 3,640,554
Length	106
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.47
Mean single sequence MFE	-30.92
Consensus MFE	-24.82
Energy contribution	-25.35
Covariance contribution	0.53
Combinations/Pair	1.12
Mean z-score	-1.09
Structure conservation index	0.80
SVM decision value	0.02
SVM RNA-class probability	0.545623
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3640448 106 - 22407834
UAUGCACUAUUUUUGUUGUAUUAUUUUUUU----UU-UGUAGGGCUCCCAACGCCUGGCUGAUUGAGUUUUCCGUGGCGGCUGUUGAUCAGGAAAGCCGCCUGGAUGCGUU
.(((((...................(((..----((-.((.((((.......)))).)).))..)))...((((.(((((((............)))))))))))))))). ( -28.80)
>DroVir_CAF1 141591 101 - 1
UUUGCUCUCU--CUCU--------CUCUCGUUCUGUGUGUAGGUGUGCGUUUAACGAACUGAGCAAAUUCCACGUGGCGGCGGUUCUUCUGGAAAGCCGCCUGGAUGCGUU
(((((((...--....--------...(((((..(((..(....)..)))..)))))...))))))).((((...((((((..(((....)))..))))))))))...... ( -30.52)
>DroSec_CAF1 108140 98 - 1
UAUGCACUCU--UUGGUUUAUUAU----------UU-UGUAGGGCUCCCAACGCCUGGCUGAUUGAGUUUUCCGUGGCGGCUGUUGAUCAGGAAAGCCGCCUGGAUGCGUU
.((((((((.--(..((((((...----------..-.)))((((.......)))))))..)..))))..((((.(((((((............))))))))))).)))). ( -31.10)
>DroSim_CAF1 113863 98 - 1
UAUGCACUCU--UUGGUUUAUUAU----------UU-UGUAGGGCUCCCAACGCCUGGCUGAUUGAGUUUUCCGUGGCGGCUGUUGAUCAGGAAAGCCGCCUGGAUGCGUU
.((((((((.--(..((((((...----------..-.)))((((.......)))))))..)..))))..((((.(((((((............))))))))))).)))). ( -31.10)
>DroEre_CAF1 109987 98 - 1
UAUGCACUCU--UUGGUUUACUAU----------UU-UGCAGGGCUCCCAACGCCUGGCUGAUUGAGUUUUCCGUGGCGGCUGUUGAUCAGGAAAGCCGCCUGGAUGCGUU
.(((((..(.--..((...(((..----------((-.((.((((.......)))).)).))...)))...))..(((((((............))))))).)..))))). ( -32.30)
>DroYak_CAF1 113362 100 - 1
UAUGCACUCUUUUUGGUUUAUUAC----------UU-UGCAGGGCUCCCAACGCCUGGCUGAUUGAGUUUUCCGUGGCGGCUGUUGAUCAGGAAAGCCGCCUGGAUGCGUU
.((((((((.....(((.....))----------).-.((.((((.......)))).)).....))))..((((.(((((((............))))))))))).)))). ( -31.70)
>consensus
UAUGCACUCU__UUGGUUUAUUAU__________UU_UGUAGGGCUCCCAACGCCUGGCUGAUUGAGUUUUCCGUGGCGGCUGUUGAUCAGGAAAGCCGCCUGGAUGCGUU
.(((((................................((.((((.......)))).))...........((((.(((((((.((......)).)))))))))))))))). (-24.82 = -25.35 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:55 2006