Locus 10307

Sequence ID	3R_DroMel_CAF1
Location	27,640,943 – 27,641,053
Length	110
Max. P	0.811038

overview

Window 8

Location	27,640,943 – 27,641,053
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.53
Mean single sequence MFE	-34.72
Consensus MFE	-26.48
Energy contribution	-25.48
Covariance contribution	-1.00
Combinations/Pair	1.23
Mean z-score	-1.85
Structure conservation index	0.76
SVM decision value	0.65
SVM RNA-class probability	0.811038
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27640943 110 + 27905053
UAAA------UAUAACUUCUAAAAGAAAGAGUAUCCUUUUUUUGCCUCAGUGGGUGUGCAGUCGCAUGAGCGUGCGGCAAAGCCCAGUGGGUGUGGGUGGGAUGGUGGGUUUGCGG----
((((------(...((((((.......))))((((((...((..(((((.(((((.....(((((((....)))))))...))))).)))).)..)).))))))))..)))))...---- ( -36.30)
>DroSim_CAF1 20413 102 + 1
UAAA------UAUAGCUUCUAAAAGAAA--GUAUCCUUUUUUUGCCUCAGUGGGUGUGCAGUCGCAUGAGCGUGCGGCAAAGCCCAGUGGGUGU------GAUGGUGGGUUUGUGG----
((((------(...(((((..(((((((--(....))))))))((((((.(((((.....(((((((....)))))))...))))).)))).))------)).)))..)))))...---- ( -32.40)
>DroEre_CAF1 21035 102 + 1
UUAA------UAUAGCUUCGGGAAGGCA--GUGUCCUUUUUUUGUCUCAGUGGGUGUGCAGUCGCAUGAGCGUGCGGCAAAGCCCAGUGGGUGU------GAUGGUGGGUACGUGG----
....------....((((.....)))).--((..((....((...((((.(((((.....(((((((....)))))))...))))).))))...------))....))..))....---- ( -33.90)
>DroYak_CAF1 20970 112 + 1
UAAAAAUUAUGAUAACUUCUAGAGAGAA--GUAUCCUUUUUUUGCCUCAGUGGGUGUGCAGUCGCAUGAGCGUGCGGCAAAGCCCAGUGGGUGU------GAUGGUGGGUAUGUGGAUAU
..............((((((....))))--))((((.....(..(((((.(((((.....(((((((....)))))))...))))).)))).).------.)....)))).......... ( -36.30)
>consensus
UAAA______UAUAACUUCUAAAAGAAA__GUAUCCUUUUUUUGCCUCAGUGGGUGUGCAGUCGCAUGAGCGUGCGGCAAAGCCCAGUGGGUGU______GAUGGUGGGUAUGUGG____
..............((((((((((((((........)))))))(((.((.(((((.....(((((((....)))))))...))))).)))))..........))).)))).......... (-26.48 = -25.48 +  -1.00)

alignment

secondary structure

dotplot

Window 9

Location	27,640,943 – 27,641,053
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.53
Mean single sequence MFE	-20.55
Consensus MFE	-15.41
Energy contribution	-15.66
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.75
SVM decision value	0.45
SVM RNA-class probability	0.742147
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27640943 110 - 27905053
----CCGCAAACCCACCAUCCCACCCACACCCACUGGGCUUUGCCGCACGCUCAUGCGACUGCACACCCACUGAGGCAAAAAAAGGAUACUCUUUCUUUUAGAAGUUAUA------UUUA
----.............((((..((((.......)))).((((((((((((....)))..))).((.....)).))))))....))))....((((.....)))).....------.... ( -20.80)
>DroSim_CAF1 20413 102 - 1
----CCACAAACCCACCAUC------ACACCCACUGGGCUUUGCCGCACGCUCAUGCGACUGCACACCCACUGAGGCAAAAAAAGGAUAC--UUUCUUUUAGAAGCUAUA------UUUA
----................------..........(((((((((((((((....)))..))).((.....)).)))...(((((((...--.))))))).))))))...------.... ( -20.30)
>DroEre_CAF1 21035 102 - 1
----CCACGUACCCACCAUC------ACACCCACUGGGCUUUGCCGCACGCUCAUGCGACUGCACACCCACUGAGACAAAAAAAGGACAC--UGCCUUCCCGAAGCUAUA------UUAA
----................------..........(((((((..((((((....)))..)))...................((((....--..))))..)))))))...------.... ( -16.40)
>DroYak_CAF1 20970 112 - 1
AUAUCCACAUACCCACCAUC------ACACCCACUGGGCUUUGCCGCACGCUCAUGCGACUGCACACCCACUGAGGCAAAAAAAGGAUAC--UUCUCUCUAGAAGUUAUCAUAAUUUUUA
.(((((.....((((.....------........)))).((((((((((((....)))..))).((.....)).))))))....)))))(--((((....)))))............... ( -24.72)
>consensus
____CCACAAACCCACCAUC______ACACCCACUGGGCUUUGCCGCACGCUCAUGCGACUGCACACCCACUGAGGCAAAAAAAGGAUAC__UUCCUUCUAGAAGCUAUA______UUUA
....((.....((((...................)))).((((((((((((....)))..))).((.....)).))))))....)).................................. (-15.41 = -15.66 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:43 2006