Locus 2468

Sequence ID	3L_DroMel_CAF1
Location	6,972,090 – 6,972,227
Length	137
Max. P	0.928395

overview

Window 7

Location	6,972,090 – 6,972,187
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.19
Mean single sequence MFE	-33.92
Consensus MFE	-17.08
Energy contribution	-17.76
Covariance contribution	0.68
Combinations/Pair	1.14
Mean z-score	-2.15
Structure conservation index	0.50
SVM decision value	0.47
SVM RNA-class probability	0.750195
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6972090 97 + 23771897
UGGUCGGUGCAAAGAC---GACAGCAGGGAGAAGUCGGAAAAUGCUGAAGCCAUAAGCACCUGCAGUCGCUGCACCUUGCAGCGGAAAAUUGC--------------------CGCUUUG
.....((((((..(.(---(((.(((((......((((......)))).((.....)).))))).)))))))))))....(((((.......)--------------------))))... ( -34.40)
>DroSec_CAF1 42039 97 + 1
UGGUUGGUGCAAAGAC---GACAGCAGGGAAAAGUCGGAAAAUGCUGAAGCCAUAAGCACCUGCAGUCGCUGCACCAAGCAGCGGAAAAUUGC--------------------CGCUUUG
((.((((((((..(.(---(((.(((((......((((......)))).((.....)).))))).))))))))))))).))((((.......)--------------------))).... ( -38.70)
>DroSim_CAF1 41778 97 + 1
UGGUUGGUGCAAAGAC---GACAGCAGGGAAAAGUCGGAAAAUGCUGAAGCCAUAAGCACCUGCAGUCGCAGCACCAUGCAGCGGAAAAUUGC--------------------CGCUUUG
..((((((((...(.(---(((.(((((......((((......)))).((.....)).))))).))))).)))))).))(((((.......)--------------------))))... ( -34.50)
>DroEre_CAF1 42060 91 + 1
UGGUCGCCGCCAAGAC---GACAGCGGGGAAAAGUCGGAAAAUGCAGAAGCCUUAAGCACCUGCAGUCACAACACCAUGCAGCGGAAAAUUGCA--------------------------
(((((.((((......---....)))).))...((.(((...(((((..((.....))..))))).)).).)).)))(((((.......)))))-------------------------- ( -22.80)
>DroYak_CAF1 43211 120 + 1
UGGUCGCCGCAAAGACGACGACAGCUGGGAAAAGUCGGAAAAUGCAGAAGCCCUAAGCACCUGCAGUCACAGUCCCAUGCAGUGGAAAAUUGCGCUGCAACUGGCGAAAUUGCGCCUUUG
..((((.((......)).))))...(((((.......((...(((((..((.....))..))))).))....)))))(((((((........)))))))...((((......)))).... ( -39.20)
>consensus
UGGUCGGUGCAAAGAC___GACAGCAGGGAAAAGUCGGAAAAUGCUGAAGCCAUAAGCACCUGCAGUCGCAGCACCAUGCAGCGGAAAAUUGC____________________CGCUUUG
........((((.......(((.(((((......((((......)))).((.....)).))))).)))((.((.....)).))......))))........................... (-17.08 = -17.76 +   0.68)

alignment

secondary structure

dotplot

Window 8

Location	6,972,090 – 6,972,187
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.19
Mean single sequence MFE	-34.88
Consensus MFE	-16.42
Energy contribution	-17.18
Covariance contribution	0.76
Combinations/Pair	1.13
Mean z-score	-2.54
Structure conservation index	0.47
SVM decision value	1.19
SVM RNA-class probability	0.928395
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6972090 97 - 23771897
CAAAGCG--------------------GCAAUUUUCCGCUGCAAGGUGCAGCGACUGCAGGUGCUUAUGGCUUCAGCAUUUUCCGACUUCUCCCUGCUGUC---GUCUUUGCACCGACCA
....(((--------------------((........)))))..(((((((((((.(((((((((.(.....).))))......((....))))))).)))---))...))))))..... ( -35.00)
>DroSec_CAF1 42039 97 - 1
CAAAGCG--------------------GCAAUUUUCCGCUGCUUGGUGCAGCGACUGCAGGUGCUUAUGGCUUCAGCAUUUUCCGACUUUUCCCUGCUGUC---GUCUUUGCACCAACCA
..(((((--------------------((........)))))))(((((((((((.(((((((((.(.....).))))......((....))))))).)))---))...))))))..... ( -36.40)
>DroSim_CAF1 41778 97 - 1
CAAAGCG--------------------GCAAUUUUCCGCUGCAUGGUGCUGCGACUGCAGGUGCUUAUGGCUUCAGCAUUUUCCGACUUUUCCCUGCUGUC---GUCUUUGCACCAACCA
....(((--------------------((........))))).((((((.(((((.(((((((((.(.....).))))......((....))))))).)))---))....)))))).... ( -34.60)
>DroEre_CAF1 42060 91 - 1
--------------------------UGCAAUUUUCCGCUGCAUGGUGUUGUGACUGCAGGUGCUUAAGGCUUCUGCAUUUUCCGACUUUUCCCCGCUGUC---GUCUUGGCGGCGACCA
--------------------------((((.........))))((((((((.((.((((((.((.....)).))))))...)))))).......(((((((---.....))))))))))) ( -29.00)
>DroYak_CAF1 43211 120 - 1
CAAAGGCGCAAUUUCGCCAGUUGCAGCGCAAUUUUCCACUGCAUGGGACUGUGACUGCAGGUGCUUAGGGCUUCUGCAUUUUCCGACUUUUCCCAGCUGUCGUCGUCUUUGCGGCGACCA
....((((......))))((((((((.(........).)))))(((((..((((.((((((.((.....)).))))))...))..))...))))))))((((((((....)))))))).. ( -39.40)
>consensus
CAAAGCG____________________GCAAUUUUCCGCUGCAUGGUGCUGCGACUGCAGGUGCUUAUGGCUUCAGCAUUUUCCGACUUUUCCCUGCUGUC___GUCUUUGCACCGACCA
...........................(((.........)))..(((((((.((((((.((.((.....)).)).)))......(((...........)))...))).)))))))..... (-16.42 = -17.18 +   0.76)

alignment

secondary structure

dotplot

Window 9

Location	6,972,127 – 6,972,227
Length	100
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.48
Mean single sequence MFE	-31.33
Consensus MFE	-18.47
Energy contribution	-18.71
Covariance contribution	0.25
Combinations/Pair	1.13
Mean z-score	-1.80
Structure conservation index	0.59
SVM decision value	0.02
SVM RNA-class probability	0.541494
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6972127 100 + 23771897
AAUGCUGAAGCCAUAAGCACCUGCAGUCGCUGCACCUUGCAGCGGAAAAUUGC--------------------CGCUUUGAUUUGGCUUGCAGGAAAUUCGCGUUACUGGAAAUAUUGUU
(((((.(((((.....)).((((((((((((((.....)))))))......((--------------------((........)))))))))))...))))))))............... ( -32.20)
>DroSec_CAF1 42076 100 + 1
AAUGCUGAAGCCAUAAGCACCUGCAGUCGCUGCACCAAGCAGCGGAAAAUUGC--------------------CGCUUUGAUUUGACUUGCAGGAAAUUCGCGUUACUGGAAAUAUUGUU
(((((.(((((.....)).((((((((((((......)))(((((.......)--------------------)))).......))).))))))...))))))))............... ( -30.50)
>DroSim_CAF1 41815 100 + 1
AAUGCUGAAGCCAUAAGCACCUGCAGUCGCAGCACCAUGCAGCGGAAAAUUGC--------------------CGCUUUGAUUUGACCUGCAGGAAAUUCGCGUUACUGGAAAUAUUGUU
(((((.(((((.....)).((((((((((((......)))(((((.......)--------------------)))).......)).)))))))...))))))))............... ( -30.20)
>DroYak_CAF1 43251 111 + 1
AAUGCAGAAGCCCUAAGCACCUGCAGUCACAGUCCCAUGCAGUGGAAAAUUGCGCUGCAACUGGCGAAAUUGCGCCUUUGAUUUCACUCGCAGGA---------UACUUGAAGUAUUGCU
...((((..((..((((..((((((((...((((...(((((((........)))))))...((((......))))...))))..))).))))).---------..))))..)).)))). ( -32.40)
>consensus
AAUGCUGAAGCCAUAAGCACCUGCAGUCGCAGCACCAUGCAGCGGAAAAUUGC____________________CGCUUUGAUUUGACUUGCAGGAAAUUCGCGUUACUGGAAAUAUUGUU
..((((.........))))((((((((((((((.....))))))).(((((............................)))))...))))))).......................... (-18.47 = -18.71 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:04 2006