Locus 2258

Sequence ID	X_DroMel_CAF1
Location	6,109,386 – 6,109,489
Length	103
Max. P	0.881797

overview

Window 3

Location	6,109,386 – 6,109,489
Length	103
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	73.91
Mean single sequence MFE	-30.64
Consensus MFE	-20.90
Energy contribution	-22.70
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.68
SVM decision value	0.92
SVM RNA-class probability	0.881797
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6109386 103 + 22224390
GCGCCGCCAAUCGGGCCAUAAAGUGCGCACAUAUUUGGAAAAACUUUUCGAGUCAAUGACUCACUUGGCG-GGCCAAGUGAGUUUUGGCCAGGCCCGCCAAUGA-
...........((((((..(((((.....((....)).....)))))..(.(((((.(((((((((((..-..))))))))))))))))).)))))).......- ( -38.80)
>DroSec_CAF1 5824 98 + 1
GCG---CCAAUCGGGCCAUAAAGUGCGCACAUAUUUGG-AAAACUUCUCGAGUCAAUGACUCACUCGGCG-AGCCAAGUGA-UUUUGGCCAGGCCCGCCAAGGA-
...---((...((((((........(((.((....)).-..........(((((...))))).....)))-.((((((...-.))))))..))))))....)).- ( -30.70)
>DroSim_CAF1 5576 98 + 1
NNN---NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNAGUCAAUGACUCACUCGGCG-AGCCAAGUGA-UUUUGGCCAGGCCCGCCAAGGA-
...---................................-............(((...)))(((((.((..-..)).)))))-(((((((.......))))))).- ( -14.70)
>DroEre_CAF1 6825 99 + 1
GCG---CCAAUCGGGCCAUAAAGUGCGCACAUAUUUGGAAAAACUUCUCGAGUCAAUGACUCAUU-GUCGGGGCCAAGUGC-UUUUGGCCAGGCCCGCAAAGGG-
...---((...((((((........((.(((.....((((....)))).(((((...)))))..)-)))).(((((((...-.))))))).))))))....)).- ( -33.90)
>DroYak_CAF1 5862 99 + 1
GCG---CCAAUCGGGCCAUAAAGUGCGCACAUAUUUGGAAAAACUUCUCGAGUCAAUGACUCACU-GGCG-GGCCAAGUGC-UUUUGGCCAGGCCCGCAAAAGGA
...---((...((((((........(((.((.....((((....)))).(((((...)))))..)-))))-(((((((...-.))))))).)))))).....)). ( -35.10)
>consensus
GCG___CCAAUCGGGCCAUAAAGUGCGCACAUAUUUGGAAAAACUUCUCGAGUCAAUGACUCACU_GGCG_GGCCAAGUGA_UUUUGGCCAGGCCCGCCAAGGA_
...........((((((................................(((((...))))).........(((((((.....))))))).))))))........ (-20.90 = -22.70 +   1.80)

alignment

secondary structure

dotplot

Window 4

Location	6,109,386 – 6,109,489
Length	103
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	73.91
Mean single sequence MFE	-30.40
Consensus MFE	-19.94
Energy contribution	-21.10
Covariance contribution	1.16
Combinations/Pair	1.06
Mean z-score	-1.34
Structure conservation index	0.66
SVM decision value	0.04
SVM RNA-class probability	0.555976
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6109386 103 - 22224390
-UCAUUGGCGGGCCUGGCCAAAACUCACUUGGCC-CGCCAAGUGAGUCAUUGACUCGAAAAGUUUUUCCAAAUAUGUGCGCACUUUAUGGCCCGAUUGGCGGCGC
-...((((((((((.((..........)).))))-)))))).((((((...))))))....................((((.(.....)(((.....))).)))) ( -35.00)
>DroSec_CAF1 5824 98 - 1
-UCCUUGGCGGGCCUGGCCAAAA-UCACUUGGCU-CGCCGAGUGAGUCAUUGACUCGAGAAGUUUU-CCAAAUAUGUGCGCACUUUAUGGCCCGAUUGG---CGC
-..(((((((((((.((......-...)).))))-)))))))((((((...)))))).(((((...-(((....)).)...)))))...(((.....))---).. ( -30.30)
>DroSim_CAF1 5576 98 - 1
-UCCUUGGCGGGCCUGGCCAAAA-UCACUUGGCU-CGCCGAGUGAGUCAUUGACUNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNN
-(((((((((((((.((......-...)).))))-))))))).))(((...)))............-................................---... ( -22.40)
>DroEre_CAF1 6825 99 - 1
-CCCUUUGCGGGCCUGGCCAAAA-GCACUUGGCCCCGAC-AAUGAGUCAUUGACUCGAGAAGUUUUUCCAAAUAUGUGCGCACUUUAUGGCCCGAUUGG---CGC
-.((....((((((.((((((..-....)))))).((((-(..(((((...)))))((((....))))......))).))........))))))...))---... ( -31.50)
>DroYak_CAF1 5862 99 - 1
UCCUUUUGCGGGCCUGGCCAAAA-GCACUUGGCC-CGCC-AGUGAGUCAUUGACUCGAGAAGUUUUUCCAAAUAUGUGCGCACUUUAUGGCCCGAUUGG---CGC
.((.....((((((.((((((..-....))))))-((((-(..(((((...)))))((((....))))......)).)))........))))))...))---... ( -32.80)
>consensus
_UCCUUGGCGGGCCUGGCCAAAA_UCACUUGGCC_CGCC_AGUGAGUCAUUGACUCGAGAAGUUUUUCCAAAUAUGUGCGCACUUUAUGGCCCGAUUGG___CGC
........((((((.((((((.......)))))).........(((((...)))))................................))))))........... (-19.94 = -21.10 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:54 2006