Locus 4007

Sequence ID	X_DroMel_CAF1
Location	10,603,830 – 10,603,933
Length	103
Max. P	0.998578

overview

Window 7

Location	10,603,830 – 10,603,933
Length	103
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	90.87
Mean single sequence MFE	-26.59
Consensus MFE	-22.50
Energy contribution	-22.78
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-2.65
Structure conservation index	0.85
SVM decision value	3.12
SVM RNA-class probability	0.998486
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10603830 103 + 22224390
AAAAA-----AUGGCACCUCUUCAAUGCGAAUUCGGCAACAAAGAGUGCAAAAUUCCAUGCAGCCAAGGAUUCAGCACAACGCUGAGUUUUAGCUUACA--AAAAUGCCA
.....-----.(((((........(((.(((((..(((........)))..))))))))..(((..((((((((((.....)))))))))).)))....--....))))) ( -27.30)
>DroSec_CAF1 1253 108 + 1
AAAAAUAAACAUGGCACCUCUUCAAUGCGAAUUCGGCGACAAAGAGUGCAAAAUUCCAUGCAGCCAAGGAUUUAGAAAAACGCUGAGUUUUAGCUUACA--AAAAUGCCA
...........(((((..........((......(((..((..((((.....))))..))..))).(((((((((.......))))))))).)).....--....))))) ( -21.91)
>DroSim_CAF1 1256 108 + 1
AAAAAUAAACAUGGCACCUCUUCAAUGCGAAUUCGGCGACAAAGAGUGCAAAAUUCCAUGCAGCCAAGGAUUCAGAAAAACGCUGAGUUUUAGCUUACA--AAAAUGCCA
...........(((((..........((......(((..((..((((.....))))..))..))).(((((((((.......))))))))).)).....--....))))) ( -24.11)
>DroEre_CAF1 1268 106 + 1
AAAA--GAUAACGGCAUCUCUUCAAUGCGAAUUCGGCGACAAAGCGUGCUAAAUUCCACGCAGCCAAGGAUUCAGCACAACGCCGAGUUUUAGCUUACA--AAAAUGCCA
....--......(((((.........((((((((((((.....(((((........))))).((..........))....))))))))))..)).....--...))))). ( -30.43)
>DroYak_CAF1 1289 108 + 1
AAAA--AAAAAUGGCACCUCUUCAAUGCGAAUUCGGCGACAAAGAGUGCGAAAUUCCACGCAGCCAAGGAUUCAGCACAACGCUGAGUUUUAGCGUACAGAAAAAUGCCA
....--.....(((((....(((..((((.....(((.((.....))(((........))).))).((((((((((.....))))))))))..))))..)))...))))) ( -29.20)
>consensus
AAAAA_AAAAAUGGCACCUCUUCAAUGCGAAUUCGGCGACAAAGAGUGCAAAAUUCCAUGCAGCCAAGGAUUCAGCACAACGCUGAGUUUUAGCUUACA__AAAAUGCCA
............((((.........((((((((..(((........)))..)))))...)))((..((((((((((.....)))))))))).))...........)))). (-22.50 = -22.78 +   0.28)

alignment

secondary structure

dotplot

Window 8

Location	10,603,830 – 10,603,933
Length	103
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	90.87
Mean single sequence MFE	-30.48
Consensus MFE	-27.90
Energy contribution	-27.78
Covariance contribution	-0.12
Combinations/Pair	1.11
Mean z-score	-2.16
Structure conservation index	0.92
SVM decision value	3.15
SVM RNA-class probability	0.998578
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10603830 103 - 22224390
UGGCAUUUU--UGUAAGCUAAAACUCAGCGUUGUGCUGAAUCCUUGGCUGCAUGGAAUUUUGCACUCUUUGUUGCCGAAUUCGCAUUGAAGAGGUGCCAU-----UUUUU
(((((((((--((((.(((((...(((((.....)))))....))))))))(((((((((.((((.....).))).)))))).)))...)))))))))).-----..... ( -32.00)
>DroSec_CAF1 1253 108 - 1
UGGCAUUUU--UGUAAGCUAAAACUCAGCGUUUUUCUAAAUCCUUGGCUGCAUGGAAUUUUGCACUCUUUGUCGCCGAAUUCGCAUUGAAGAGGUGCCAUGUUUAUUUUU
(((((((((--(.(((((.(((((.....))))).........(((((.(((.(((.........))).))).)))))....)).))).))))))))))........... ( -24.90)
>DroSim_CAF1 1256 108 - 1
UGGCAUUUU--UGUAAGCUAAAACUCAGCGUUUUUCUGAAUCCUUGGCUGCAUGGAAUUUUGCACUCUUUGUCGCCGAAUUCGCAUUGAAGAGGUGCCAUGUUUAUUUUU
(((((((((--((((.(((((...((((.......))))....))))))))(((((((((.((((.....)).)).)))))).)))...))))))))))........... ( -27.70)
>DroEre_CAF1 1268 106 - 1
UGGCAUUUU--UGUAAGCUAAAACUCGGCGUUGUGCUGAAUCCUUGGCUGCGUGGAAUUUAGCACGCUUUGUCGCCGAAUUCGCAUUGAAGAGAUGCCGUUAUC--UUUU
.((((((((--(.(((((...((.((((((.((((((((((((.((....)).)).))))))))))......)))))).)).)).))).)))))))))......--.... ( -35.80)
>DroYak_CAF1 1289 108 - 1
UGGCAUUUUUCUGUACGCUAAAACUCAGCGUUGUGCUGAAUCCUUGGCUGCGUGGAAUUUCGCACUCUUUGUCGCCGAAUUCGCAUUGAAGAGGUGCCAUUUUU--UUUU
(((((((((((.(((.(((((...(((((.....)))))....))))))))(((((((((.((((.....)).)).)))))).))).))))).)))))).....--.... ( -32.00)
>consensus
UGGCAUUUU__UGUAAGCUAAAACUCAGCGUUGUGCUGAAUCCUUGGCUGCAUGGAAUUUUGCACUCUUUGUCGCCGAAUUCGCAUUGAAGAGGUGCCAUGUUU_UUUUU
(((((((((...(((.(((((...(((((.....)))))....))))))))(((((((((.((((.....)).)).)))))).)))....)))))))))........... (-27.90 = -27.78 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:06 2006