Locus 5675

Sequence ID	2L_DroMel_CAF1
Location	16,124,730 – 16,124,822
Length	92
Max. P	0.992157

overview

Window 4

Location	16,124,730 – 16,124,822
Length	92
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	77.38
Mean single sequence MFE	-19.02
Consensus MFE	-10.79
Energy contribution	-11.02
Covariance contribution	0.22
Combinations/Pair	1.20
Mean z-score	-3.06
Structure conservation index	0.57
SVM decision value	2.31
SVM RNA-class probability	0.992157
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16124730 92 + 22407834
GGGGGCGGAUGAAGAAAAAAAAAAAAAACUAUGAAAACAUCAUAAAUUUUCCACAGUCAGAAAAGUUUUAGAGAGCUG--CUGACUCACCC--------ACA
(((((..(((...................(((((.....))))).)))..))..((((((...(((((....))))).--))))))..)))--------... ( -18.95)
>DroPse_CAF1 86413 79 + 1
-------AACAAAAA---AAAAGGAAAACUAUGAAAACAUCAUAAAUUUCCCACAGUCGGAAAGGUUCUAGAGAGC-----UGACUCACCC--------GCA
-------........---....(((((..(((((.....)))))..)))))....((.((...(((((....))))-----)......)).--------)). ( -14.30)
>DroEre_CAF1 54689 82 + 1
--GGGCGGAUAAAGAA--------AAAACUAUGAAAACAUCAUAAAUUUUCCGCAGUCAGAAAAGUUUUAGAGAGCUG--CUGACUCGCCC--------ACA
--(((((......(((--------((...(((((.....)))))..)))))...((((((...(((((....))))).--)))))))))))--------... ( -26.00)
>DroYak_CAF1 61933 82 + 1
--GGGCGGAUAAAGAA--------AAAACUAUGAAAACAUCAUAAAUUUUCCACAGUCAGAAAAGUUUUAGAGAGCUG--CUGACUCACCC--------ACA
--(((.(......(((--------((...(((((.....)))))..)))))...((((((...(((((....))))).--))))))).)))--------... ( -20.60)
>DroAna_CAF1 51213 89 + 1
--GGGCG----AAAAA-------GAAAACUAUGAAAACAUCAUAAAUUUCCCGCAGUUGGAAAAGUUUAAGAGAGCUGAGCUGACUCACUCGCUAUCCAACA
--..(((----.....-------((((..(((((.....)))))..)))).))).((((((..(((......(((.((((....)))))))))).)))))). ( -20.30)
>DroPer_CAF1 76442 80 + 1
-------AACAAAAAA--AAAAGGAAAACUAUGAAAACAUCAUAAAUUUCCCACAGUCGGAAAGGUUCUAGAGAGC-----UGACUCACCC--------ACA
-------.........--....(((((..(((((.....)))))..)))))....((.((...(((((....))))-----)......)).--------)). ( -14.00)
>consensus
__GGGCGGAUAAAAAA_______GAAAACUAUGAAAACAUCAUAAAUUUCCCACAGUCAGAAAAGUUUUAGAGAGCUG__CUGACUCACCC________ACA
.......................((((..(((((.....)))))..))))....((((((...(((((....)))))...))))))................ (-10.79 = -11.02 +   0.22)

alignment

secondary structure

dotplot

Window 5

Location	16,124,730 – 16,124,822
Length	92
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	77.38
Mean single sequence MFE	-20.01
Consensus MFE	-11.61
Energy contribution	-10.92
Covariance contribution	-0.69
Combinations/Pair	1.19
Mean z-score	-2.22
Structure conservation index	0.58
SVM decision value	1.35
SVM RNA-class probability	0.944897
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16124730 92 - 22407834
UGU--------GGGUGAGUCAG--CAGCUCUCUAAAACUUUUCUGACUGUGGAAAAUUUAUGAUGUUUUCAUAGUUUUUUUUUUUUUUCUUCAUCCGCCCCC
.((--------(((((((((((--..................)))))...((((((.((((((.....)))))).)))))).........)))))))).... ( -20.47)
>DroPse_CAF1 86413 79 - 1
UGC--------GGGUGAGUCA-----GCUCUCUAGAACCUUUCCGACUGUGGGAAAUUUAUGAUGUUUUCAUAGUUUUCCUUUU---UUUUUGUU-------
..(--------(((.(((...-----.)))...........)))).....((((((.((((((.....)))))).))))))...---........------- ( -15.30)
>DroEre_CAF1 54689 82 - 1
UGU--------GGGCGAGUCAG--CAGCUCUCUAAAACUUUUCUGACUGCGGAAAAUUUAUGAUGUUUUCAUAGUUUU--------UUCUUUAUCCGCCC--
...--------(((((.....(--(((.((..............))))))((((((.((((((.....)))))).)))--------)))......)))))-- ( -22.94)
>DroYak_CAF1 61933 82 - 1
UGU--------GGGUGAGUCAG--CAGCUCUCUAAAACUUUUCUGACUGUGGAAAAUUUAUGAUGUUUUCAUAGUUUU--------UUCUUUAUCCGCCC--
.((--------(((((((((((--..................)))))...((((((.((((((.....)))))).)))--------))).))))))))..-- ( -20.67)
>DroAna_CAF1 51213 89 - 1
UGUUGGAUAGCGAGUGAGUCAGCUCAGCUCUCUUAAACUUUUCCAACUGCGGGAAAUUUAUGAUGUUUUCAUAGUUUUC-------UUUUU----CGCCC--
.((((((.((.(((((((....)))).))).))........)))))).(((..(((.((((((.....)))))).....-------)))..----)))..-- ( -25.10)
>DroPer_CAF1 76442 80 - 1
UGU--------GGGUGAGUCA-----GCUCUCUAGAACCUUUCCGACUGUGGGAAAUUUAUGAUGUUUUCAUAGUUUUCCUUUU--UUUUUUGUU-------
.((--------.((.(((...-----.((....))...))).)).))...((((((.((((((.....)))))).))))))...--.........------- ( -15.60)
>consensus
UGU________GGGUGAGUCAG__CAGCUCUCUAAAACUUUUCCGACUGUGGAAAAUUUAUGAUGUUUUCAUAGUUUUC_______UUCUUUAUCCGCCC__
............((.((((.......)))).))(((((.(((((......)))))...(((((.....))))))))))........................ (-11.61 = -10.92 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:57 2006