Locus 3850

Sequence ID	2L_DroMel_CAF1
Location	11,275,750 – 11,275,980
Length	230
Max. P	0.995639

overview

Window 2

Location	11,275,750 – 11,275,868
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.87
Mean single sequence MFE	-26.72
Consensus MFE	-10.09
Energy contribution	-10.82
Covariance contribution	0.73
Combinations/Pair	1.41
Mean z-score	-2.07
Structure conservation index	0.38
SVM decision value	0.51
SVM RNA-class probability	0.762962
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11275750 118 - 22407834
UUUAAGCUCUUCAUUUCUAGACUCUAGAUGGUCUCU--UACUUCUUGCAGAGAUUUUAGUUUAAUCUGAAGCUCGUCUACUGAACCCUUAAUAUCAGCAAUCUUUUGUUUAAACUGACCU
(((((((...........(((((......)))))..--......((((.(((.((((((......))))))))).((....)).............))))......)))))))....... ( -17.20)
>DroVir_CAF1 91362 118 - 1
UGUGAGCUUGUGGUUUGUUUCUUCCAGCUCCACUUUUUGAGA--CAGCAAUGAGUCCAGUUUUAACUGUAGCUCGUUCUUUGAGCCUUGUAACUCAUUCAAAUUCUGUUCAAAUUGGUGC
...(((((.(.((.......)).).)))))((((.((((((.--(((.(((((((.((((....))))..(((((.....)))))......)))))))......)))))))))..)))). ( -29.00)
>DroSec_CAF1 107841 118 - 1
UUUAAGCUUUUCAUUUUCAGACUCUAGAUUGUCUUU--UACUUCUUGGAGAGAUUUCAGUUUAAGCUGAAGCUCGUCCACUGAUCCCUUAAGAUUGGCAAUCUUUCGUUUAACCUCACCU
..................((((...((((((((...--.......(((((((.(((((((....)))))))))).))))..((((......))))))))))))...)))).......... ( -27.70)
>DroSim_CAF1 115879 118 - 1
UUUAAGCUUUUCAUUUUCAGACUGUAGAUUGUCUUU--UACUUCUUGGAGAGAUUUCAGCUUAAGCUGAAGCUCGUCCACUGAUCCCUUAAGAUUGGCAAUCUUUCGUUUAGAANNNNNN
...............(((((((...((((((((...--.......(((((((.(((((((....)))))))))).))))..((((......))))))))))))...)))).)))...... ( -30.50)
>DroEre_CAF1 110260 118 - 1
UUUAAUCACUUCAUUCGUAGACUCUAGAUUGUCUUU--GACUUCUUGAAGAGAUUUCAGUUUAAGCUGGAGCUCGUCCACUGAACCUUCAAAAUCUGCGAUCUCUCGUCGAAACUGACUU
...((((.(((((.(((.((((........)))).)--)).....))))).))))(((((((..((.((((.((((....(((....)))......)))).)))).))..)))))))... ( -29.80)
>DroYak_CAF1 111925 118 - 1
UUUAAGCUCUGCAUUCCCAGACUCUAGAUUGUCUUU--UACUUCUUGCAGAGAUUUCAGUUUAAGCUGGAGCUCGUCCACUGAACCUUUAAGAUCGGCAAUCUCUCGUUGAAAUUGAACU
......(((((((.....((((........))))..--.......)))))))..((((((((.(((.((((...(((..((.........))...)))...)))).))).)))))))).. ( -26.14)
>consensus
UUUAAGCUCUUCAUUUCCAGACUCUAGAUUGUCUUU__UACUUCUUGCAGAGAUUUCAGUUUAAGCUGAAGCUCGUCCACUGAACCCUUAAGAUCGGCAAUCUUUCGUUUAAACUGACCU
...................(((...(((((((.................(((.(((((((....)))))))))).((....)).............)))))))...)))........... (-10.09 = -10.82 +   0.73)

alignment

secondary structure

dotplot

Window 3

Location	11,275,790 – 11,275,908
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.26
Mean single sequence MFE	-28.20
Consensus MFE	-13.96
Energy contribution	-14.68
Covariance contribution	0.73
Combinations/Pair	1.39
Mean z-score	-2.71
Structure conservation index	0.49
SVM decision value	2.60
SVM RNA-class probability	0.995639
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11275790 118 - 22407834
CCACCAUGUUCUGUAGUUCCUGAGCAUCUUUUAGCUUUCUUUUAAGCUCUUCAUUUCUAGACUCUAGAUGGUCUCU--UACUUCUUGCAGAGAUUUUAGUUUAAUCUGAAGCUCGUCUAC
......(((...(.(((....((.(((((....((((......))))(((........)))....))))).))...--.))).)..)))(((.((((((......)))))))))...... ( -21.60)
>DroGri_CAF1 132043 118 - 1
CCAAAUCACUCUGCAUAUUUAGGACAUUUUUCAGUUUUACUGUCAGCUGCUGAUUCGCUGUCUCCAGCUCCAGUUUAUUAGU--GAGCAAUGAGUCCAGCUGCAACUGCAGUUCAUUCUU
..........(((((....((((((........)))))).((.((((((..(((((((((....))))....(((((....)--))))...)))))))))))))..)))))......... ( -29.80)
>DroSec_CAF1 107881 118 - 1
CCACUUUGUUCUGUAGAUUCUGAGCAUCAUUUAGCUUUAUUUUAAGCUUUUCAUUUUCAGACUCUAGAUUGUCUUU--UACUUCUUGGAGAGAUUUCAGUUUAAGCUGAAGCUCGUCCAC
...........(.((((.((((((........(((((......))))).......)))))).)))).)........--.......(((((((.(((((((....)))))))))).)))). ( -29.16)
>DroSim_CAF1 115919 118 - 1
CCACUUUGUCCUGUAGAUUCUGAGCGUCUUUUAGCUUUAUUUUAAGCUUUUCAUUUUCAGACUGUAGAUUGUCUUU--UACUUCUUGGAGAGAUUUCAGCUUAAGCUGAAGCUCGUCCAC
..........((((((..((((((.((.....(((((......)))))....)).)))))))))))).........--.......(((((((.(((((((....)))))))))).)))). ( -29.70)
>DroEre_CAF1 110300 109 - 1
CCACCAGGU---------CUUGAGCAUCCUUUAGCUUACUUUUAAUCACUUCAUUCGUAGACUCUAGAUUGUCUUU--GACUUCUUGAAGAGAUUUCAGUUUAAGCUGGAGCUCGUCCAC
......((.---------..(((((.(((...((((((.....((((.(((((.(((.((((........)))).)--)).....))))).))))......)))))))))))))).)).. ( -30.80)
>DroYak_CAF1 111965 118 - 1
CCACCAUGUUUUGUAGAUCCUGAGCUUGUUUUAGCUUACCUUUAAGCUCUGCAUUCCCAGACUCUAGAUUGUCUUU--UACUUCUUGCAGAGAUUUCAGUUUAAGCUGGAGCUCGUCCAC
....................((..(..(((((((((((.((..((.(((((((.....((((........))))..--.......))))))).))..))..)))))))))))..)..)). ( -28.14)
>consensus
CCACCAUGUUCUGUAGAUCCUGAGCAUCUUUUAGCUUUAUUUUAAGCUCUUCAUUCCCAGACUCUAGAUUGUCUUU__UACUUCUUGCAGAGAUUUCAGUUUAAGCUGAAGCUCGUCCAC
.....................((((....((((((((.........(((((((.....((((........))))...........)))))))..........))))))))))))...... (-13.96 = -14.68 +   0.73)

alignment

secondary structure

dotplot

Window 4

Location	11,275,830 – 11,275,948
Length	118
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	74.54
Mean single sequence MFE	-27.22
Consensus MFE	-11.69
Energy contribution	-13.42
Covariance contribution	1.73
Combinations/Pair	1.35
Mean z-score	-2.34
Structure conservation index	0.43
SVM decision value	1.29
SVM RNA-class probability	0.940432
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11275830 118 + 22407834
UA-AGAGACCAUCUAGAGUCUAGAAAUGAAGAGCUUAAAAGAAAGCUAAAAGAUGCUCAGGAACUACAGAACAUGGUGGAUAAGGAGCGAAAGCUCAAUUCCUCUCUACGAGAAGAUUU
..-(((((((((((..(((((.((.((....(((((......))))).....))..)).)).)))..)))...))))(((....((((....))))...))).))))............ ( -29.00)
>DroSec_CAF1 107921 118 + 1
UA-AAAGACAAUCUAGAGUCUGAAAAUGAAAAGCUUAAAAUAAAGCUAAAUGAUGCUCAGAAUCUACAGAACAAAGUGGAUAAGGAGCAAAAGCUCAAUUCUUCUCUACGAGAAGAUUU
..-............((((............(((((......)))))......(((((...((((((........))))))...)))))...))))...(((((((...)))))))... ( -28.90)
>DroSim_CAF1 115959 118 + 1
UA-AAAGACAAUCUACAGUCUGAAAAUGAAAAGCUUAAAAUAAAGCUAAAAGACGCUCAGAAUCUACAGGACAAAGUGGAUAAGGAGCAAAAGCUCAAUUCCUCUCUACGAGAAGAUUU
..-..((((........)))).....(((..(((((......))))).......((((...((((((........))))))...))))......)))..((.((((...)))).))... ( -23.90)
>DroEre_CAF1 110340 109 + 1
UC-AAAGACAAUCUAGAGUCUACGAAUGAAGUGAUUAAAAGUAAGCUAAAGGAUGCUCAAG---------ACCUGGUGGAUAAAGAGCGAAAGCUUAAUGCCUCUCUGCAAAAUGAUUU
((-(..((((.(((..((..(((.....((....))....)))..))..))).)).)).((---------(...((((......((((....))))..))))..)))......)))... ( -18.90)
>DroYak_CAF1 112005 118 + 1
UA-AAAGACAAUCUAGAGUCUGGGAAUGCAGAGCUUAAAGGUAAGCUAAAACAAGCUCAGGAUCUACAAAACAUGGUGGAUAAGGAGCGAAAGCUUAAUGCCUCUCUACGAGAUGAUUU
..-.....((.(((((((((((((..((...((((((....))))))....))..))))))((((((........))))))...((((....)))).......))))).))..)).... ( -31.10)
>DroAna_CAF1 103445 119 + 1
CAGAAACAGGAACUGGAGGCCGUAAACGAGGAGAUGAAGUUGAAUUUAAAGGCAUCUCAGCAUCUACAGGCCCAGCUGGAGGAGGAGCGAAAAGUAGUUGCUGAUCUACAAGAAUCCUA
.......((((.(..(.(((((((...(..((((((...(((....)))...))))))..)...))).))))...)..).(((..(((((.......)))))..))).......)))). ( -31.50)
>consensus
UA_AAAGACAAUCUAGAGUCUGAAAAUGAAGAGCUUAAAAGAAAGCUAAAAGAUGCUCAGGAUCUACAGAACAAGGUGGAUAAGGAGCGAAAGCUCAAUGCCUCUCUACGAGAAGAUUU
.............(((((...(((.......(((((......))))).......((((...((((((........))))))...))))..........)))..)))))........... (-11.69 = -13.42 +   1.73)

alignment

secondary structure

dotplot

Window 5

Location	11,275,868 – 11,275,980
Length	112
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	72.83
Mean single sequence MFE	-26.21
Consensus MFE	-10.60
Energy contribution	-13.85
Covariance contribution	3.25
Combinations/Pair	1.20
Mean z-score	-1.82
Structure conservation index	0.40
SVM decision value	-0.04
SVM RNA-class probability	0.513286
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11275868 112 + 22407834
AGAAAGCUAAAAGAUGCUCAGGAACUACAGAACAUGGUGGAUAAGGAGCGAAAGCUCAAUUCCUCUCUACGAGAAGAUUUUGACAAACUGGAACAAACCAAACU---CGAU----CUCG
(((.(((........))).(((((((((........)))).....((((....))))..))))).))).(((((.((.((((................)))).)---)..)----)))) ( -25.59)
>DroSec_CAF1 107959 112 + 1
AUAAAGCUAAAUGAUGCUCAGAAUCUACAGAACAAAGUGGAUAAGGAGCAAAAGCUCAAUUCUUCUCUACGAGAAGAUUUGGGCAAACUGGAACAAACCAAACU---CGGU----CUCG
......(((.....(((((...((((((........))))))...)))))...((((((.(((((((...))))))).))))))....))).....(((.....---.)))----.... ( -32.70)
>DroSim_CAF1 115997 112 + 1
AUAAAGCUAAAAGACGCUCAGAAUCUACAGGACAAAGUGGAUAAGGAGCAAAAGCUCAAUUCCUCUCUACGAGAAGAUUUGGGCAAACUGGAAAAAACCAAACU---CGAU----CUCG
...............((((...((((((........))))))...))))....((((((.((.((((...)))).)).))))))....(((......)))....---....----.... ( -27.70)
>DroEre_CAF1 110378 103 + 1
AGUAAGCUAAAGGAUGCUCAAG---------ACCUGGUGGAUAAAGAGCGAAAGCUUAAUGCCUCUCUGCAAAAUGAUUUGGGCAAACUAGGACAAAUAAAAAC---GGAU----CUCG
.((.(((........)))....---------.((((((.......((((....))))..(((((.((........))...))))).))))))))..........---....----.... ( -23.20)
>DroYak_CAF1 112043 112 + 1
GGUAAGCUAAAACAAGCUCAGGAUCUACAAAACAUGGUGGAUAAGGAGCGAAAGCUUAAUGCCUCUCUACGAGAUGAUUUGGGCAAACUGGAACAAACACAAAC---UGAU----CUCG
((((((((.......((((...((((((........))))))...))))...))))...))))......((((((.(((((..................)))).---).))----)))) ( -27.07)
>DroAna_CAF1 103484 116 + 1
UUGAAUUUAAAGGCAUCUCAGCAUCUACAGGCCCAGCUGGAGGAGGAGCGAAAAGUAGUUGCUGAUCUACAAGAAUCCUACUCCAAUCUGAAA---ACUAAAUUAAAGGAUAUGACUCG
...((((((..(((................)))(((.(((((.((((.......((((........)))).....)))).)))))..)))...---..))))))............... ( -20.99)
>consensus
AGAAAGCUAAAAGAUGCUCAGGAUCUACAGAACAAGGUGGAUAAGGAGCGAAAGCUCAAUGCCUCUCUACGAGAAGAUUUGGGCAAACUGGAACAAACCAAACU___CGAU____CUCG
......(((......((((...((((((........))))))...))))....((((((.((.((((...)))).)).))))))....)))............................ (-10.60 = -13.85 +   3.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:57 2006