Locus 276

Sequence ID	2R_DroMel_CAF1
Location	1,675,954 – 1,676,101
Length	147
Max. P	0.885636

overview

Window 5

Location	1,675,954 – 1,676,064
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.74
Mean single sequence MFE	-27.52
Consensus MFE	-24.71
Energy contribution	-25.65
Covariance contribution	0.94
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.90
SVM decision value	0.20
SVM RNA-class probability	0.628697
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1675954 110 + 20766785
GAGCA-GGGGAAACAACAACGACGUCUGCUUGCCCCAAUCUACAUAUGU--------GCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGCCGC-AACAGAAGCAGACGACGAAAACAAA
(((((-((.(............).))))))).........((((((...--------...))))))....((((((((.(((.((((((.....-..)))))).))).)).))))))... ( -28.20)
>DroSec_CAF1 59985 118 + 1
GAGCA-CGGGAAACAACAACGACGUCUGCUUGCCCCAAUCUACAUAUGUAUUGUAUUGCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGUCGC-AACAGAAGCAGACGACGAAAACAAA
.....-..(....).....((.(((((((...........((((((.(((......))).))))))..................(((((.....-..)))))))))))).))........ ( -26.90)
>DroSim_CAF1 56970 110 + 1
GAGCA-GGGGAAACAACAACGACGUCUGCUUGCCCCAAUCUACAUAUGU--------GCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGUCGC-AACAGAAGCACACGACGAAAACAAA
(((((-((.(............).))))))).........((((((...--------...))))))....((((((((.....((((((.....-..)))))).....)).))))))... ( -23.30)
>DroEre_CAF1 67253 112 + 1
GAGCAUGGGGAAACAACAACGACGUCUGCUUGCCCCAAUCUACAUAUGU--------GCUUUUGUAUUACGUUUUCUCUUCUCUUUCUGCUCCCGAGCAGAAGCAGACGAUGAAAACAAA
((((.(((((((.((((......)).)).)).)))))....((....))--------)))).........((((((((.(((.((((((((....)))))))).))).)).))))))... ( -31.70)
>consensus
GAGCA_GGGGAAACAACAACGACGUCUGCUUGCCCCAAUCUACAUAUGU________GCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGUCGC_AACAGAAGCAGACGACGAAAACAAA
......((((((.((((......)).)).)).))))....((((((.(((......))).))))))....((((((((.(((.((((((........)))))).))).)).))))))... (-24.71 = -25.65 +   0.94)

alignment

secondary structure

dotplot

Window 6

Location	1,675,993 – 1,676,101
Length	108
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	88.59
Mean single sequence MFE	-26.70
Consensus MFE	-21.59
Energy contribution	-21.90
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-2.01
Structure conservation index	0.81
SVM decision value	0.94
SVM RNA-class probability	0.885636
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1675993 108 + 20766785
UACAUAUGU--------GCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGCCGC-AACAGAAGCAGACGACGAAAACAAAAAGGCAUGUGAAAAACAGAAUAUACGAAGCACCGAGG
.......((--------((((.(((((...((((((((.(((.((((((.....-..)))))).))).)).)))))).........(((.....)))....)))))))))))..... ( -27.10)
>DroSec_CAF1 60024 116 + 1
UACAUAUGUAUUGUAUUGCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGUCGC-AACAGAAGCAGACGACGAAAACAAAAAAGCAUGUGAAAAACAGAAUAUUCGAAGCACCGAGG
..(((((((....((.(((....))).)).((((((((.(((.((((((.....-..)))))).))).)).))))))......)))))))............((((......)))). ( -26.50)
>DroSim_CAF1 57009 108 + 1
UACAUAUGU--------GCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGUCGC-AACAGAAGCACACGACGAAAACAAAAAAGCAUGUGAAAAACAGAAUAUUCGAAGCACCGAGG
.......((--------((((..(((((..((((((((.....((((((.....-..)))))).....)).)))))).........(((.....))).)))))...))))))..... ( -22.30)
>DroEre_CAF1 67293 108 + 1
UACAUAUGU--------GCUUUUGUAUUACGUUUUCUCUUCUCUUUCUGCUCCCGAGCAGAAGCAGACGAUGAAAACAAAAAAGCAUGUGAGAAACAGAAUAGGCAAGGCACCAAG-
.......((--------((((((.((((..((((((((.(((.((((((((....)))))))).))).)).)))))).........(((.....))).)))).).)))))))....- ( -30.90)
>consensus
UACAUAUGU________GCUUAUGUAUUAAGUUUUCUCUUCUCUUUCUGGUCGC_AACAGAAGCAGACGACGAAAACAAAAAAGCAUGUGAAAAACAGAAUAUUCGAAGCACCGAGG
.................((((..(((((..((((((((.(((.((((((........)))))).))).)).)))))).........(((.....))).)))))...))))....... (-21.59 = -21.90 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:21 2006