Locus 8132

Sequence ID	X_DroMel_CAF1
Location	20,226,223 – 20,226,354
Length	131
Max. P	0.998729

overview

Window 4

Location	20,226,223 – 20,226,315
Length	92
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	78.77
Mean single sequence MFE	-40.42
Consensus MFE	-27.55
Energy contribution	-27.93
Covariance contribution	0.38
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.68
SVM decision value	0.70
SVM RNA-class probability	0.827538
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20226223 92 + 22224390
AGCCCGGCCAGAAAGUAAUCCGCCCCAGGAACACCACCCACCGCCC-----------------GCCCAUUUGGAUAUGGAAAUGGGCAGUGGGGGCGGCGAUUGGCGCU
(((...((((((......))((((((.((....)).(((((.((((-----------------(.((((......))))...))))).))))))).))))..))))))) ( -38.10)
>DroSec_CAF1 13225 85 + 1
-------CCAGAAAGCAGUCCGCCCCAGGAACACCGCCCACUGCCC-----------------GCCCAUUUGGAUAUGGAAAUGGGCAGUGGGGGCGGCGAUUGGCGCU
-------......(((.(((((((((.((....)).((((((((((-----------------(.((((......))))...))))))))))))).))))...)))))) ( -40.90)
>DroSim_CAF1 12532 91 + 1
AGCCCGGCCAGAAAGCAGUCCGCCCCAGGAACACCGCCCACUGCCC-----------------GCCCAUUUGGAUAUGGAAAUGGGCAGUGG-GGCGGCGAUUGGCGCU
(((...(((((.......(((......))).(.(((((((((((((-----------------(.((((......))))...)))))))).)-))))).).)))))))) ( -42.50)
>DroEre_CAF1 13084 108 + 1
AGUCCGGGCAGCAAGUGAUCCGC-CCAGGCGCACCGCCCACCAGCCACCACACACCACACAGCUCCUAUUUCGAUAUGGAAAUGGGCAGUGGGGGCGGGGAUUGGCGCU
.....((((............))-)).(((((.((((((.((.(......)..........(((((((((((......)))))))).)))))))))))......))))) ( -40.20)
>consensus
AGCCCGGCCAGAAAGCAAUCCGCCCCAGGAACACCGCCCACCGCCC_________________GCCCAUUUGGAUAUGGAAAUGGGCAGUGGGGGCGGCGAUUGGCGCU
.....................((.((((...(.((((((.((((...................((((((((........)))))))).)))))))))).).)))).)). (-27.55 = -27.93 +   0.38)

alignment

secondary structure

dotplot

Window 5

Location	20,226,223 – 20,226,315
Length	92
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	78.77
Mean single sequence MFE	-46.97
Consensus MFE	-31.25
Energy contribution	-31.38
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-2.98
Structure conservation index	0.67
SVM decision value	3.20
SVM RNA-class probability	0.998729
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20226223 92 - 22224390
AGCGCCAAUCGCCGCCCCCACUGCCCAUUUCCAUAUCCAAAUGGGC-----------------GGGCGGUGGGUGGUGUUCCUGGGGCGGAUUACUUUCUGGCCGGGCU
(((((((..((((((((.....((((((((........))))))))-----------------))))))))..))))))).((.((.((((......)))).)).)).. ( -48.00)
>DroSec_CAF1 13225 85 - 1
AGCGCCAAUCGCCGCCCCCACUGCCCAUUUCCAUAUCCAAAUGGGC-----------------GGGCAGUGGGCGGUGUUCCUGGGGCGGACUGCUUUCUGG-------
.((.(((..((((((((..(((((((...(((((......))))).-----------------)))))))))))))))....))).))..............------- ( -41.80)
>DroSim_CAF1 12532 91 - 1
AGCGCCAAUCGCCGCC-CCACUGCCCAUUUCCAUAUCCAAAUGGGC-----------------GGGCAGUGGGCGGUGUUCCUGGGGCGGACUGCUUUCUGGCCGGGCU
...(((...(((((((-(.(((((((...(((((......))))).-----------------)))))))))))))))......((.((((......)))).)).))). ( -47.80)
>DroEre_CAF1 13084 108 - 1
AGCGCCAAUCCCCGCCCCCACUGCCCAUUUCCAUAUCGAAAUAGGAGCUGUGUGGUGUGUGGUGGCUGGUGGGCGGUGCGCCUGG-GCGGAUCACUUGCUGCCCGGACU
.((((......((((((((((..(((((..((((((.(.........).)))))).))).))..).))).)))))).))))((((-((((........))))))))... ( -50.30)
>consensus
AGCGCCAAUCGCCGCCCCCACUGCCCAUUUCCAUAUCCAAAUGGGC_________________GGGCAGUGGGCGGUGUUCCUGGGGCGGACUACUUUCUGGCCGGGCU
.((.(((..(((((((..((((((((...(((((......)))))..................)))))))))))))))....))).))..................... (-31.25 = -31.38 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	20,226,255 – 20,226,354
Length	99
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	66.44
Mean single sequence MFE	-37.42
Consensus MFE	-14.68
Energy contribution	-16.32
Covariance contribution	1.64
Combinations/Pair	1.38
Mean z-score	-1.70
Structure conservation index	0.39
SVM decision value	0.27
SVM RNA-class probability	0.660523
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20226255 99 - 22224390
-UUCGAUCGAACCGCUAAGUGGGUGUGGGAAUUAUGGGUUAGCGCCAAUCGCCGCCCCC--ACUGCCCAUUUCCAUAUCCAAAUGGGC-----------------GGGCGGUGGGUGGU
-..(.(((..((((((.((((((.((((((....((((....).))).)).)))).)))--)))((((((((........))))))))-----------------.)))))).))).). ( -42.50)
>DroPse_CAF1 12218 82 - 1
GCUCCAGCAAGUAUGCAAGAGGGUGUGCAAAUUACGGGGCACAGU------------GUAAACCGAUUACUUCCUGAUCU------------------------UUGUUGGUUGGCUG-
((((((((((((((((......))))))......(((((...(((------------(.........)))))))))....------------------------)))))))..)))..- ( -21.50)
>DroSec_CAF1 13250 86 - 1
--------------CUAAGUGGGUGUGGGAAUUAUGGGUUAGCGCCAAUCGCCGCCCCC--ACUGCCCAUUUCCAUAUCCAAAUGGGC-----------------GGGCAGUGGGCGGU
--------------.......((((..((..(((.....)))..))...))))((((((--(((((((...(((((......))))).-----------------)))))))))).))) ( -38.50)
>DroSim_CAF1 12564 98 - 1
-UUCGAUCGAACCGCUAAGUGGGUGUGGGAAUUAUGGGUUAGCGCCAAUCGCCGCC-CC--ACUGCCCAUUUCCAUAUCCAAAUGGGC-----------------GGGCAGUGGGCGGU
-.........((((((....(((((.(.((....((((....).))).)).)))))-)(--(((((((...(((((......))))).-----------------)))))))))))))) ( -40.70)
>DroEre_CAF1 13115 116 - 1
-UUCGAUCGAACCGCUAAGUGGGUGUGGGAAUUAUGGGUUAGCGCCAAUCCCCGCCCCC--ACUGCCCAUUUCCAUAUCGAAAUAGGAGCUGUGUGGUGUGUGGUGGCUGGUGGGCGGU
-.........(((((.....(((((.((((....((((....).))).)))))))))((--(((..(((((..(((((((..((((...)))).))))))).)))))..)))))))))) ( -43.50)
>DroYak_CAF1 12739 103 - 1
-UUCGAUUGAAACCCUAAGAGGGUGCUGGAAUUAUGGGUUAUCGCCAAUCC-UGCCCCCAAACCGCCCAUUUCCAUAUCAAAAUGGGAG--------------GUGGCUGGCGGGCGGU
-...(((((..((((.....))))((...(((.....)))...)))))))(-((((((((.(((.(((((((........))))))).)--------------))...))).)))))). ( -37.80)
>consensus
_UUCGAUCGAACCGCUAAGUGGGUGUGGGAAUUAUGGGUUAGCGCCAAUCGCCGCCCCC__ACUGCCCAUUUCCAUAUCCAAAUGGGC_________________GGGCGGUGGGCGGU
.....................(((((...(((.....))).))))).....((((((....(((((((.....................................))))))))))))). (-14.68 = -16.32 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:35 2006