Locus 5893

Sequence ID	X_DroMel_CAF1
Location	15,178,546 – 15,178,670
Length	124
Max. P	0.994927

overview

Window 7

Location	15,178,546 – 15,178,643
Length	97
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	81.88
Mean single sequence MFE	-31.70
Consensus MFE	-21.95
Energy contribution	-23.04
Covariance contribution	1.09
Combinations/Pair	1.07
Mean z-score	-3.60
Structure conservation index	0.69
SVM decision value	2.52
SVM RNA-class probability	0.994927
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15178546 97 + 22224390
UUCAAAGUUAGAGGCGGAAAAACAUUUUAGGCCAACAU---------CGAUGUCUUCGAAAUAUCAGAAACAUCGAUGUU-UUCGGUGAAUCAGCGAUGUUUUUUCA
...............(((((((((((....((((((((---------((((((.(((.........))))))))))))))-...)))........))))))))))). ( -26.20)
>DroSec_CAF1 6546 106 + 1
UUCGAAGCUAAAGGCGGAGAAACAUU-GACGCCAACAUCGAUGACAUCGAUGUCUACGAAAAAUCACAGUCAUCGAUGUUAUUCGAGAAAUCAUCGAUGAUUUGCCA
......((....((((..((....))-..))))..(((((((((((((((((.((..((....))..)).))))))))))....((....)))))))))....)).. ( -34.80)
>DroSim_CAF1 6328 106 + 1
UUCGAAGCUAAAGGCGGAGAAACAUU-GACGCCAACAUCGAUGACAUCGAUGUCUACGAAAAAUCACAGUCAUCGAUGUUAUUCGAGGAAUCAUCGAUGAUUUGCCA
((((((......((((..((....))-..))))((((((((((((...(((...........)))...)))))))))))).))))))((((((....)))))).... ( -34.10)
>consensus
UUCGAAGCUAAAGGCGGAGAAACAUU_GACGCCAACAUCGAUGACAUCGAUGUCUACGAAAAAUCACAGUCAUCGAUGUUAUUCGAGGAAUCAUCGAUGAUUUGCCA
((((.((.....((((.............)))).(((((((.....))))))))).)))).......(((((((((((.............)))))))))))..... (-21.95 = -23.04 +   1.09)

alignment

secondary structure

dotplot

Window 8

Location	15,178,546 – 15,178,643
Length	97
Sequences	3
Columns	107
Reading direction	reverse
Mean pairwise identity	81.88
Mean single sequence MFE	-29.83
Consensus MFE	-19.65
Energy contribution	-20.52
Covariance contribution	0.87
Combinations/Pair	1.10
Mean z-score	-3.01
Structure conservation index	0.66
SVM decision value	1.83
SVM RNA-class probability	0.979232
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15178546 97 - 22224390
UGAAAAAACAUCGCUGAUUCACCGAA-AACAUCGAUGUUUCUGAUAUUUCGAAGACAUCG---------AUGUUGGCCUAAAAUGUUUUUCCGCCUCUAACUUUGAA
.(.((((((((((.((...)).))).-(((((((((((((.(((....))).))))))))---------))))).........))))))).)............... ( -23.90)
>DroSec_CAF1 6546 106 - 1
UGGCAAAUCAUCGAUGAUUUCUCGAAUAACAUCGAUGACUGUGAUUUUUCGUAGACAUCGAUGUCAUCGAUGUUGGCGUC-AAUGUUUCUCCGCCUUUAGCUUCGAA
.(((....(((((((((............((((((((.((((((....)))))).)))))))))))))))))..((((..-..........))))....)))..... ( -32.20)
>DroSim_CAF1 6328 106 - 1
UGGCAAAUCAUCGAUGAUUCCUCGAAUAACAUCGAUGACUGUGAUUUUUCGUAGACAUCGAUGUCAUCGAUGUUGGCGUC-AAUGUUUCUCCGCCUUUAGCUUCGAA
.(((....((((((((((((...)))).(((((((((.((((((....)))))).)))))))))))))))))..((((..-..........))))....)))..... ( -33.40)
>consensus
UGGCAAAUCAUCGAUGAUUCCUCGAAUAACAUCGAUGACUGUGAUUUUUCGUAGACAUCGAUGUCAUCGAUGUUGGCGUC_AAUGUUUCUCCGCCUUUAGCUUCGAA
.......(((((((((((((...))))..))))))))).........((((..((((((((.....))))))))((((.............))))........)))) (-19.65 = -20.52 +   0.87)

alignment

secondary structure

dotplot

Window 9

Location	15,178,573 – 15,178,670
Length	97
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	82.55
Mean single sequence MFE	-29.17
Consensus MFE	-18.75
Energy contribution	-18.95
Covariance contribution	0.20
Combinations/Pair	1.12
Mean z-score	-2.63
Structure conservation index	0.64
SVM decision value	1.05
SVM RNA-class probability	0.907223
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15178573 97 + 22224390
UAGGCCAACAU---------CGAUGUCUUCGAAAUAUCAGAAACAUCGAUGUU-UUCGGUGAAUCAGCGAUGUUUUUUCAUCUCUAUUGCUCAUCGGAGAAUAAAAG
......(((((---------((((((.(((.........))))))))))))))-((((((((...((.((((......)))).)).....))))))))......... ( -27.20)
>DroSec_CAF1 6572 107 + 1
GACGCCAACAUCGAUGACAUCGAUGUCUACGAAAAAUCACAGUCAUCGAUGUUAUUCGAGAAAUCAUCGAUGAUUUGCCAUCUCUAUUGCGCAUCGGAGGAAAAAAG
..(.((..(((((((((((((((((.((..((....))..)).))))))))))....((....)))))))))...(((((.......)).)))..)).)........ ( -31.10)
>DroSim_CAF1 6354 106 + 1
GACGCCAACAUCGAUGACAUCGAUGUCUACGAAAAAUCACAGUCAUCGAUGUUAUUCGAGGAAUCAUCGAUGAUUUGCCAUCUCUAUUGCGCAUCGGAGGAA-AAAG
....((((((((((((((...(((...........)))...)))))))))))).(((((.((((((....))))))((((.......)).)).)))))))..-.... ( -29.20)
>consensus
GACGCCAACAUCGAUGACAUCGAUGUCUACGAAAAAUCACAGUCAUCGAUGUUAUUCGAGGAAUCAUCGAUGAUUUGCCAUCUCUAUUGCGCAUCGGAGGAAAAAAG
.......(((((((.....)))))))..............(((((((((((.............))))))))))).....(((((..(....)..)))))....... (-18.75 = -18.95 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	15,178,573 – 15,178,670
Length	97
Sequences	3
Columns	107
Reading direction	reverse
Mean pairwise identity	82.55
Mean single sequence MFE	-32.93
Consensus MFE	-21.30
Energy contribution	-22.83
Covariance contribution	1.53
Combinations/Pair	1.09
Mean z-score	-3.52
Structure conservation index	0.65
SVM decision value	2.00
SVM RNA-class probability	0.985189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15178573 97 - 22224390
CUUUUAUUCUCCGAUGAGCAAUAGAGAUGAAAAAACAUCGCUGAUUCACCGAA-AACAUCGAUGUUUCUGAUAUUUCGAAGACAUCG---------AUGUUGGCCUA
...........((.((((...(((.((((......)))).))).)))).))..-(((((((((((((.(((....))).))))))))---------)))))...... ( -27.10)
>DroSec_CAF1 6572 107 - 1
CUUUUUUCCUCCGAUGCGCAAUAGAGAUGGCAAAUCAUCGAUGAUUUCUCGAAUAACAUCGAUGACUGUGAUUUUUCGUAGACAUCGAUGUCAUCGAUGUUGGCGUC
............(((((.(((((..((((((......((((.(....))))).....(((((((.((((((....)))))).)))))))))))))..)))))))))) ( -35.60)
>DroSim_CAF1 6354 106 - 1
CUUU-UUCCUCCGAUGCGCAAUAGAGAUGGCAAAUCAUCGAUGAUUCCUCGAAUAACAUCGAUGACUGUGAUUUUUCGUAGACAUCGAUGUCAUCGAUGUUGGCGUC
....-.......(((((.(((((..(((((((..(((((((((((((...))))..)))))))))((((((....)))))).......)))))))..)))))))))) ( -36.10)
>consensus
CUUUUUUCCUCCGAUGCGCAAUAGAGAUGGCAAAUCAUCGAUGAUUCCUCGAAUAACAUCGAUGACUGUGAUUUUUCGUAGACAUCGAUGUCAUCGAUGUUGGCGUC
...............((((...((((((.((...(((((((((((((...))))..)))))))))..)).))))))....((((((((.....)))))))).)))). (-21.30 = -22.83 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:02 2006