Locus 4438

Sequence ID	3L_DroMel_CAF1
Location	12,944,807 – 12,944,927
Length	120
Max. P	0.979891

overview

Window 0

Location	12,944,807 – 12,944,927
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.58
Mean single sequence MFE	-32.52
Consensus MFE	-25.88
Energy contribution	-26.16
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.63
Structure conservation index	0.80
SVM decision value	1.62
SVM RNA-class probability	0.967938
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12944807 120 + 23771897
GCAGAGAUGGUCUCAGUGCAAAUGUAAUUUACUGCCAGACGAUAUACGCUGGCCCACAGAAAUAUUUUGGCCGCAAUUUAUUUGCGGCCAUUUAAACAGAAAUAAAAGCAAAUGAAUUUA
...(((.....)))..(((((((((........(((((.((.....)))))))........))))))(((((((((.....))))))))).................))).......... ( -32.79)
>DroSec_CAF1 62049 120 + 1
GCUGAGCUGGUCUCAGUGCAAAUGUAAUUUACUGCCAGACGAUAUACGCUGGCCCACAGAAAUAUUUUGGCCGCAAUUUAUUUGCGGCCAUUUAAACAGAAAUAAAAGCAAAUGAAUUUA
((((((.....))))))((((((((........(((((.((.....)))))))........))))))(((((((((.....))))))))).................))........... ( -35.29)
>DroSim_CAF1 66395 120 + 1
GCUGAGCUGGUCUCAGUGCAAAUGUAAUUUACUGCCAGACGAUAUACGCUGGCCCACAGAAAUAUUUUGGCCGCAAUUUAUUUGCGGCCAUUUAAACAGAAAUAAAAGCAAAUGAAUUUA
((((((.....))))))((((((((........(((((.((.....)))))))........))))))(((((((((.....))))))))).................))........... ( -35.29)
>DroEre_CAF1 68273 120 + 1
GCAGAGACCGUCUCAGUGCAAAUGUAAUUUACGGCCAGACGAUAUACGCUGGCCCACAGAAAUAUUUUGGCCGGAAUUUAUUUGCGGCCAUUUAAACAGAAAUAAAACCAAAUGAAUUUA
((((((.....)))..)))...(((.......((((((.((.....)))))))).............((((((.((.....)).)))))).....)))...................... ( -30.70)
>DroYak_CAF1 65870 120 + 1
GCAGAGAGCGUCUCAGUGCAAAUGUAAUUUACUGCCGCACGAUAUACGCUGGCCCACAGAAAUAUUUUGGCCGGAAUUUAUUUGCGGCCAUUUAAACGGAAAUAAAACCAAAUGAAUUUA
((((((.....)))..)))......((((((..((((((.((((....((((((..............))))))....)))))))))).........((........))...)))))).. ( -28.54)
>consensus
GCAGAGAUGGUCUCAGUGCAAAUGUAAUUUACUGCCAGACGAUAUACGCUGGCCCACAGAAAUAUUUUGGCCGCAAUUUAUUUGCGGCCAUUUAAACAGAAAUAAAAGCAAAUGAAUUUA
((.(((.....)))...))...(((........(((((.((.....)))))))..............(((((((((.....))))))))).....)))...................... (-25.88 = -26.16 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	12,944,807 – 12,944,927
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.58
Mean single sequence MFE	-32.48
Consensus MFE	-26.62
Energy contribution	-27.42
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.82
SVM decision value	1.85
SVM RNA-class probability	0.979891
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12944807 120 - 23771897
UAAAUUCAUUUGCUUUUAUUUCUGUUUAAAUGGCCGCAAAUAAAUUGCGGCCAAAAUAUUUCUGUGGGCCAGCGUAUAUCGUCUGGCAGUAAAUUACAUUUGCACUGAGACCAUCUCUGC
.......(((((((................(((((((((.....)))))))))..............(((((((.....)).)))))))))))).......(((..(((.....)))))) ( -33.60)
>DroSec_CAF1 62049 120 - 1
UAAAUUCAUUUGCUUUUAUUUCUGUUUAAAUGGCCGCAAAUAAAUUGCGGCCAAAAUAUUUCUGUGGGCCAGCGUAUAUCGUCUGGCAGUAAAUUACAUUUGCACUGAGACCAGCUCAGC
(((((..(((((((................(((((((((.....)))))))))..............(((((((.....)).))))))))))))...)))))..(((((.....))))). ( -36.00)
>DroSim_CAF1 66395 120 - 1
UAAAUUCAUUUGCUUUUAUUUCUGUUUAAAUGGCCGCAAAUAAAUUGCGGCCAAAAUAUUUCUGUGGGCCAGCGUAUAUCGUCUGGCAGUAAAUUACAUUUGCACUGAGACCAGCUCAGC
(((((..(((((((................(((((((((.....)))))))))..............(((((((.....)).))))))))))))...)))))..(((((.....))))). ( -36.00)
>DroEre_CAF1 68273 120 - 1
UAAAUUCAUUUGGUUUUAUUUCUGUUUAAAUGGCCGCAAAUAAAUUCCGGCCAAAAUAUUUCUGUGGGCCAGCGUAUAUCGUCUGGCCGUAAAUUACAUUUGCACUGAGACGGUCUCUGC
.....................((((((...((((((.((.....)).)))))).............((((((((.....)).))))))((((((...))))))....))))))....... ( -29.50)
>DroYak_CAF1 65870 120 - 1
UAAAUUCAUUUGGUUUUAUUUCCGUUUAAAUGGCCGCAAAUAAAUUCCGGCCAAAAUAUUUCUGUGGGCCAGCGUAUAUCGUGCGGCAGUAAAUUACAUUUGCACUGAGACGCUCUCUGC
...........((.(((((((((((....))))....)))))))..))((((...(((....))).))))(((((...((((((((..(((...)))..)))))).)).)))))...... ( -27.30)
>consensus
UAAAUUCAUUUGCUUUUAUUUCUGUUUAAAUGGCCGCAAAUAAAUUGCGGCCAAAAUAUUUCUGUGGGCCAGCGUAUAUCGUCUGGCAGUAAAUUACAUUUGCACUGAGACCAUCUCUGC
..............................(((((((((.....))))))))).....((((.(((.(((((((.....)).))))).(((...))).....))).)))).......... (-26.62 = -27.42 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:48 2006