Locus 7277

Sequence ID	3R_DroMel_CAF1
Location	19,218,004 – 19,218,107
Length	103
Max. P	0.776536

overview

Window 3

Location	19,218,004 – 19,218,107
Length	103
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	81.70
Mean single sequence MFE	-38.55
Consensus MFE	-27.20
Energy contribution	-28.40
Covariance contribution	1.20
Combinations/Pair	1.19
Mean z-score	-1.93
Structure conservation index	0.71
SVM decision value	0.54
SVM RNA-class probability	0.776536
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19218004 103 + 27905053
GUUGCCACAUGACUCCGGGCAAUUUGCACGGCCGCCGCAUCGAUGGCGGUGCUCC----AUCUACAAGGAGAACCGGAGACAAGUGGCUGUGCACUGAGAGAAACGC-------
((.(((((.((.((((((((.....))...(((((((......))))))).((((----........))))..)))))).)).)))))...))..............------- ( -41.60)
>DroSec_CAF1 14229 104 + 1
GUUGCCACAUGACUCCGGGCAAUUUGCACGGCCGCCGCAUCGAUGGCGGUGCUCC----AUCUACAAGGAGAACCGGAGACAAGUGGCU--GCACUGAGAGAAAUCUGUA----
((.(((((.((.((((((((.....))...(((((((......))))))).((((----........))))..)))))).)).))))).--))....(((....)))...---- ( -45.10)
>DroSim_CAF1 14359 104 + 1
CUUGCCACAUGACUCCGGGCAAUUUGCACGGCCACCGCAUCGAUGGCGGUGCUCC----AUCUACAAGGAGAACCGGAGACAAGUGGCU--GCACUGAGAGAAAUCUGUA----
...(((((.((.((((((.......((((.((((.((...)).)))).))))(((----........)))...)))))).)).))))).--......(((....)))...---- ( -42.40)
>DroEre_CAF1 14787 98 + 1
GUCGCCACAUGACUCCGGGCAAUUUGCACGGCCGCCGCAUCGAUGGCGGUGCUCC----AUCUACAAGGAGAAGCGGAGACAAGUGGCU--GCACUGAGCGAAA----------
((.(((((.((.(((((.((.....))...(((((((......))))))).((((----........))))...))))).)).))))).--))...........---------- ( -38.90)
>DroYak_CAF1 14938 108 + 1
GUCGCCACAUGACUGCGGGCAAUUUGCACGGCCGCCGCAUCGAUGGCGGUGCUCC----GACUACAAGGAGAACCGGAGACAAGUGGCU--GCACUGAGAGAAACGUAUAUUAA
((.(((((.((.((.(((((.....))...(((((((......))))))).((((----........))))..))).)).)).))))).--))..................... ( -38.50)
>DroAna_CAF1 14578 105 + 1
GUCUUCACAUGACUCCGGGCAAUUUGCACUGCUGAGGCAUCGAUGGUGGUUCUUGGAUCCCCAAAAAGAGGAAAGGGAAACAGGCAGUU--CCACAGGAAAAAAUGC-------
(((.......)))(((..((.....))(((((((((.(((.....))).))).((..((((.............))))..)))))))).--.....)))........------- ( -24.82)
>consensus
GUCGCCACAUGACUCCGGGCAAUUUGCACGGCCGCCGCAUCGAUGGCGGUGCUCC____AUCUACAAGGAGAACCGGAGACAAGUGGCU__GCACUGAGAGAAAUGU_______
...(((((.((.((((((((.....))...(((((((......))))))).((((............))))..)))))).)).))))).......................... (-27.20 = -28.40 +   1.20)

alignment

secondary structure

dotplot

Window 4

Location	19,218,004 – 19,218,107
Length	103
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	81.70
Mean single sequence MFE	-36.65
Consensus MFE	-26.74
Energy contribution	-28.22
Covariance contribution	1.47
Combinations/Pair	1.15
Mean z-score	-1.45
Structure conservation index	0.73
SVM decision value	0.19
SVM RNA-class probability	0.626328
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19218004 103 - 27905053
-------GCGUUUCUCUCAGUGCACAGCCACUUGUCUCCGGUUCUCCUUGUAGAU----GGAGCACCGCCAUCGAUGCGGCGGCCGUGCAAAUUGCCCGGAGUCAUGUGGCAAC
-------(((((......)))))...(((((.((.((((((...(((........----)))((((.(((..((...))..))).)))).......)))))).)).)))))... ( -40.60)
>DroSec_CAF1 14229 104 - 1
----UACAGAUUUCUCUCAGUGC--AGCCACUUGUCUCCGGUUCUCCUUGUAGAU----GGAGCACCGCCAUCGAUGCGGCGGCCGUGCAAAUUGCCCGGAGUCAUGUGGCAAC
----...................--.(((((.((.((((((...(((........----)))((((.(((..((...))..))).)))).......)))))).)).)))))... ( -40.10)
>DroSim_CAF1 14359 104 - 1
----UACAGAUUUCUCUCAGUGC--AGCCACUUGUCUCCGGUUCUCCUUGUAGAU----GGAGCACCGCCAUCGAUGCGGUGGCCGUGCAAAUUGCCCGGAGUCAUGUGGCAAG
----...................--.(((((.((.((((((...(((........----)))((((.(((((((...))))))).)))).......)))))).)).)))))... ( -44.50)
>DroEre_CAF1 14787 98 - 1
----------UUUCGCUCAGUGC--AGCCACUUGUCUCCGCUUCUCCUUGUAGAU----GGAGCACCGCCAUCGAUGCGGCGGCCGUGCAAAUUGCCCGGAGUCAUGUGGCGAC
----------....((.....))--.(((((.((.(((((....(((........----)))((((.(((..((...))..))).))))........))))).)).)))))... ( -38.40)
>DroYak_CAF1 14938 108 - 1
UUAAUAUACGUUUCUCUCAGUGC--AGCCACUUGUCUCCGGUUCUCCUUGUAGUC----GGAGCACCGCCAUCGAUGCGGCGGCCGUGCAAAUUGCCCGCAGUCAUGUGGCGAC
.......................--.(((((.((.((.(((...(((........----)))((((.(((..((...))..))).)))).......))).)).)).)))))... ( -32.70)
>DroAna_CAF1 14578 105 - 1
-------GCAUUUUUUCCUGUGG--AACUGCCUGUUUCCCUUUCCUCUUUUUGGGGAUCCAAGAACCACCAUCGAUGCCUCAGCAGUGCAAAUUGCCCGGAGUCAUGUGAAGAC
-------.....(((((..((((--..((...((..(((((...........)))))..))))..)))).....(((.(((.(((((....)))))...))).)))..))))). ( -23.60)
>consensus
_______ACAUUUCUCUCAGUGC__AGCCACUUGUCUCCGGUUCUCCUUGUAGAU____GGAGCACCGCCAUCGAUGCGGCGGCCGUGCAAAUUGCCCGGAGUCAUGUGGCAAC
..........................(((((.((.((((((...(((............)))((((.(((.(((...))).))).)))).......)))))).)).)))))... (-26.74 = -28.22 +   1.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:55 2006