Locus 6220

Sequence ID	3R_DroMel_CAF1
Location	16,252,589 – 16,252,720
Length	131
Max. P	0.743943

overview

Window 3

Location	16,252,589 – 16,252,697
Length	108
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.61
Mean single sequence MFE	-28.78
Consensus MFE	-21.17
Energy contribution	-21.20
Covariance contribution	0.03
Combinations/Pair	1.21
Mean z-score	-1.71
Structure conservation index	0.74
SVM decision value	0.46
SVM RNA-class probability	0.743943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16252589 108 + 27905053
AGACCAUUGGAUGUGCUUUGGCCGGUUGCCCAAAAUGCAAUUGGCUUCAUGCAAAAUUCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUU----
.(((..((((((.(((...((((((((((.......))))))))))....)))..))))))((((.......)))))))..(((.(((((.-....)))))..)))...---- ( -33.00)
>DroPse_CAF1 64567 100 + 1
-----------CGUCCUUUGGCUGACUGCCCA-AAUGCAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUUCGUU
-----------........(((.....))).(-(((((((..((((((.(((.....)))))))))................((((((...-..)))))).)))))))).... ( -28.60)
>DroEre_CAF1 54382 108 + 1
AGACCAUUGGAUGUGCUUUGGCCGGCUGCCCAAAAUGCAAUUGGCUUCAUGCAAAAUUCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUU----
........(((((((((.((((((((.(..(((...((((..((((((.((.......))))))))....)))))))..)..)))))))).-.....)))...))))))---- ( -31.00)
>DroWil_CAF1 65681 94 + 1
UGAUUUUUG---GUCCUUUGGCUG------------GCAAUUGGCUUCAUGCAAAAUGCAGCAGCUUAAUUUGUUUGUCCUUGUUGACUGUUUUGUUGGCUUUGCAAUU----
......(((---.......(((..------------((((..((((...(((.....)))..))))....))))..)))...((..((......))..))....)))..---- ( -19.40)
>DroAna_CAF1 71180 105 + 1
---CCACCGAACGUCCUUUGGCCAGUUGCCCAAAAUGCAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUU----
---................((((((((((.......))))))))))..(((((((..(((((..(...........)..)))))..((((.-....)))))))))))..---- ( -32.10)
>DroPer_CAF1 69868 100 + 1
-----------CGUCCUUUGGCUGACUGCCCA-AAUGCAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUUCGUU
-----------........(((.....))).(-(((((((..((((((.(((.....)))))))))................((((((...-..)))))).)))))))).... ( -28.60)
>consensus
___CCAUUG__CGUCCUUUGGCCGGCUGCCCA_AAUGCAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU_UUGUUGGCUUUGCAUUU____
...................((((((.(((.......))).))))))..(((((((....((((((.......))...)))).((((((......)))))))))))))...... (-21.17 = -21.20 +   0.03)

alignment

secondary structure

dotplot

Window 4

Location	16,252,626 – 16,252,720
Length	94
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	80.84
Mean single sequence MFE	-28.12
Consensus MFE	-18.91
Energy contribution	-18.67
Covariance contribution	-0.25
Combinations/Pair	1.25
Mean z-score	-1.29
Structure conservation index	0.67
SVM decision value	-0.03
SVM RNA-class probability	0.519474
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16252626 94 + 27905053
CAAUUGGCUUCAUGCAAAAUUCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUU----CGGGCAUCGCCGGA-----GUUCGAGUU------------
...(((((((((((((((....((((((.......))...)))).((((((...-..)))))))))))))..----..(((...))))))-----).))))...------------ ( -24.30)
>DroPse_CAF1 64592 107 + 1
CAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUUCGUUCGGGCUUUCCCGGAGUGAAGUUCG--UUGCAGUU------
((((..((((((((((((..(((((..(...........)..)))))..((((.-....)))))))))......((((((....)))))))))))))..)--))).....------ ( -35.00)
>DroEre_CAF1 54419 94 + 1
CAAUUGGCUUCAUGCAAAAUUCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUU----CGGGCAUCGCCGGA-----GUUCGAGUU------------
...(((((((((((((((....((((((.......))...)))).((((((...-..)))))))))))))..----..(((...))))))-----).))))...------------ ( -24.30)
>DroWil_CAF1 65703 89 + 1
CAAUUGGCUUCAUGCAAAAUGCAGCAGCUUAAUUUGUUUGUCCUUGUUGACUGUUUUGUUGGCUUUGCAAUU----CAG------UUGCA-----GUUGCAGUU------------
.....((((...(((.....)))(((((((((((...((((....((..((......))..))...))))..----.))------))).)-----)))))))))------------ ( -20.70)
>DroAna_CAF1 71214 106 + 1
CAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUU----GGGGCUUGGCUGGA-----GUUCGAGUUAUAGUUGGAGUU
(((((((((((.(((.....)))))))).(((((((....(((..(((((((..-.(((.......)))...----..))).)))).)))-----...)))))))))))))..... ( -32.20)
>DroPer_CAF1 69893 107 + 1
CAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU-UUGUUGGCUUUGCAUUUCGUUCGGGCUUUCCCGGAGUGAAGUUCGAGUUUCAG--------
...(((((((((((((((..(((((..(...........)..)))))..((((.-....)))))))))......((((((....)))))))))))).)))).......-------- ( -32.20)
>consensus
CAAUUGGCUUCAUGCAAAAUGCAGGAGCUUAAUUUGUUUGUCCUUGCCGGCCAU_UUGUUGGCUUUGCAUUU____CGGGCUUCGCCGGA_____GUUCGAGUU____________
(((..((((((.(((.....)))))))))....)))..(((....((((((......))))))...))).......(((......)))............................ (-18.91 = -18.67 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:54 2006