Locus 5459

Sequence ID	2R_DroMel_CAF1
Location	17,569,435 – 17,569,532
Length	97
Max. P	0.972481

overview

Window 3

Location	17,569,435 – 17,569,532
Length	97
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-27.62
Consensus MFE	-20.22
Energy contribution	-21.20
Covariance contribution	0.98
Combinations/Pair	1.31
Mean z-score	-2.25
Structure conservation index	0.73
SVM decision value	1.69
SVM RNA-class probability	0.972481
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17569435 97 + 20766785
AGCCUGAAAAAUCCGGCCCUGGCCUUUUUUU-----UUUAUUGUUGCCUCUUGGUCAACAGCAAAGCGCUUGAGGCCGUGUAAUAACUUUCGGGCAAAUAUU
.((((((((......((..(((((((....(-----(((.((((((((....)).)))))).)))).....))))))).))......))))))))....... ( -31.90)
>DroSec_CAF1 75912 102 + 1
AGCCUGGAAAAUCCGGCCCUGGCCUUUUUUUUUUUUUUUUUUGUUGCCUCUUGGUCAACAGCAAAGCGCUUGAGGCCGUGUAAUAACUUUCGGGCAAAUAUU
.((((((((.....(((((.(((((((.............((((((((....)).)))))).)))).))).).))))((......))))))))))....... ( -30.54)
>DroSim_CAF1 65444 97 + 1
AGCCUGGAAAAUCCGGCCCUGGCCUUUUUUU-----UCUUUUGUUGCCACUUGGUCAACAGCAAAGCGCUUGAGGCCGUGUAAUAACUUUCGGGCAAAUAUU
.((((((((.....(((((.(((((((....-----....((((((((....)).)))))).)))).))).).))))((......))))))))))....... ( -30.80)
>DroEre_CAF1 86790 89 + 1
AGCCUGGAAAAUCCGGCCCUGGCCUUU-------------UUGUUGCCUCUUGGUCAACAGCAAAGCGCUUGAGGCCGUGUAAUAAGUUUCGGGCAAAUAUU
.((((((((...(((((((.(((((((-------------((((((((....)).)))))).)))).))).).))))).).......))))))))....... ( -36.30)
>DroYak_CAF1 79566 85 + 1
AGCCUGAAAAAUCCGGCCCUGGCCUUU-------------UUGUUGCCUCUUGGCCAACAGCAAAGCGCUUGAGGCCGUGUAAUAAGUU----GCAAAUAUU
.............((((((.(((((((-------------((((((((....)).)))))).)))).))).).)))))(((((....))----)))...... ( -27.30)
>DroPer_CAF1 95113 93 + 1
---AU-GGAAGUCCGCCCCUGUUUUUC-AGUUCUCUGGUUCUGUUGUUCCUUAGUCAAA---CAAUUACUUAAAG-CAUGUAAUAACUUUAGCUUAAAUAUU
---..-((....))((....(((.(((-((((....(((...((((((.........))---)))).)))...))-).)).)).)))....))......... (  -8.90)
>consensus
AGCCUGGAAAAUCCGGCCCUGGCCUUU_UUU_____U_UUUUGUUGCCUCUUGGUCAACAGCAAAGCGCUUGAGGCCGUGUAAUAACUUUCGGGCAAAUAUU
.((((((((......((..(((((((...............(((((((....)).)))))((.....))..))))))).))......))))))))....... (-20.22 = -21.20 +   0.98)

alignment

secondary structure

dotplot

Window 4

Location	17,569,435 – 17,569,532
Length	97
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-24.35
Consensus MFE	-14.61
Energy contribution	-16.33
Covariance contribution	1.72
Combinations/Pair	1.20
Mean z-score	-1.56
Structure conservation index	0.60
SVM decision value	0.26
SVM RNA-class probability	0.658051
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17569435 97 - 20766785
AAUAUUUGCCCGAAAGUUAUUACACGGCCUCAAGCGCUUUGCUGUUGACCAAGAGGCAACAAUAAA-----AAAAAAAGGCCAGGGCCGGAUUUUUCAGGCU
.......(((.((((((....)).((((((...((.((((..(((((.((....))))))).....-----....))))))..))))))....)))).))). ( -27.20)
>DroSec_CAF1 75912 102 - 1
AAUAUUUGCCCGAAAGUUAUUACACGGCCUCAAGCGCUUUGCUGUUGACCAAGAGGCAACAAAAAAAAAAAAAAAAAAGGCCAGGGCCGGAUUUUCCAGGCU
.......(((.(((((((....(..(((((..(((.....)))((((.((....)))))).................)))))..)....)))))))..))). ( -26.40)
>DroSim_CAF1 65444 97 - 1
AAUAUUUGCCCGAAAGUUAUUACACGGCCUCAAGCGCUUUGCUGUUGACCAAGUGGCAACAAAAGA-----AAAAAAAGGCCAGGGCCGGAUUUUCCAGGCU
.......(((.(((((((....(..(((((......((((..(((((.((....))))))))))).-----......)))))..)....)))))))..))). ( -27.52)
>DroEre_CAF1 86790 89 - 1
AAUAUUUGCCCGAAACUUAUUACACGGCCUCAAGCGCUUUGCUGUUGACCAAGAGGCAACAA-------------AAAGGCCAGGGCCGGAUUUUCCAGGCU
.......(((...............(((((...((.((((..(((((.((....))))))).-------------))))))..)))))((.....)).))). ( -28.00)
>DroYak_CAF1 79566 85 - 1
AAUAUUUGC----AACUUAUUACACGGCCUCAAGCGCUUUGCUGUUGGCCAAGAGGCAACAA-------------AAAGGCCAGGGCCGGAUUUUUCAGGCU
.......((----...........((((((...((.((((..(((((.((....))))))).-------------))))))..))))))((....))..)). ( -25.40)
>DroPer_CAF1 95113 93 - 1
AAUAUUUAAGCUAAAGUUAUUACAUG-CUUUAAGUAAUUG---UUUGACUAAGGAACAACAGAACCAGAGAACU-GAAAAACAGGGGCGGACUUCC-AU---
...........((((((........)-))))).((..(((---(((......(......).....(((....))-)..))))))..))((....))-..--- ( -11.60)
>consensus
AAUAUUUGCCCGAAAGUUAUUACACGGCCUCAAGCGCUUUGCUGUUGACCAAGAGGCAACAAAA_A_____AAA_AAAGGCCAGGGCCGGAUUUUCCAGGCU
.......(((.(((((((....(..(((((..(((.....)))((((.((....)))))).................)))))..)....)))))))..))). (-14.61 = -16.33 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:27 2006