Locus 3985

Sequence ID	X_DroMel_CAF1
Location	10,546,481 – 10,546,640
Length	159
Max. P	0.788559

overview

Window 2

Location	10,546,481 – 10,546,600
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.82
Mean single sequence MFE	-37.15
Consensus MFE	-28.92
Energy contribution	-28.80
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.78
SVM decision value	0.58
SVM RNA-class probability	0.788559
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10546481 119 + 22224390
UUGCAUUUUGGGGGCACAGUAAUCUC-UAUUUACAUUUGUCGAAACACGAUUUCAAGCUUUGCUUCUUUCGUAGAAGUAGCACCCCUAUGCGGUUGCACGUGCCUGCAGCAAUUUGCGGC
.(((((...((((((...((((....-...))))....((((.....)))).........(((((((.....))))))))).)))).)))))((((((..(((.....)))...)))))) ( -34.10)
>DroSec_CAF1 72810 118 + 1
UUUCAUUUUGGGGGCACAGUAAUCUC-UAUUUACAUUUGUCGAAACACGAUUUGAAGCGUUGCUUCAUUCGUAGAAGCAGCAAC-CUGUGCGGUUGCACGUGCCUGCAGCAAUUUGCGGC
........((.((((((.((((....-...))))............((((..((((((...)))))).)))).......(((((-(.....))))))..)))))).))((.....))... ( -36.30)
>DroSim_CAF1 76830 118 + 1
UUUCAUUUUGGGGGCACAGUAAUCUC-UAUUUACAUUUGUCGAAACACGAUUUGAAGCGUUGCUUCAUUCGUAGAAGCAGCAAC-CUGUGCGGUUGCACGUGCCUGCAGCAAUUUGCGGC
........((.((((((.((((....-...))))............((((..((((((...)))))).)))).......(((((-(.....))))))..)))))).))((.....))... ( -36.30)
>DroYak_CAF1 76290 115 + 1
UGGCAUUCUGGGGGCACAGAAACCUUUUAUUUAUAUG----GAUACACCAUUGGCAGUGUUGCUUCUUUUCGAGAAGCAGCAAC-CUAUGCGGUUGCACGUGCCUGCAGCAAUUUGCGGC
..(((..(((.((((((...((((..........(((----(.....))))..(((.(((((((((((...)))))))))))..-...)))))))....)))))).))).....)))... ( -41.90)
>consensus
UUGCAUUUUGGGGGCACAGUAAUCUC_UAUUUACAUUUGUCGAAACACGAUUUGAAGCGUUGCUUCAUUCGUAGAAGCAGCAAC_CUAUGCGGUUGCACGUGCCUGCAGCAAUUUGCGGC
........((.((((((.((((((....................................((((((.......))))))(((......)))))))))..)))))).))((.....))... (-28.92 = -28.80 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	10,546,481 – 10,546,600
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.82
Mean single sequence MFE	-34.00
Consensus MFE	-24.69
Energy contribution	-25.25
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	0.52
SVM RNA-class probability	0.766575
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10546481 119 - 22224390
GCCGCAAAUUGCUGCAGGCACGUGCAACCGCAUAGGGGUGCUACUUCUACGAAAGAAGCAAAGCUUGAAAUCGUGUUUCGACAAAUGUAAAUA-GAGAUUACUGUGCCCCCAAAAUGCAA
((((((......))).)))..........((((.((((..(....(((.(....)..(((....(((((((...)))))))....))).....-.))).....)..))))....)))).. ( -30.00)
>DroSec_CAF1 72810 118 - 1
GCCGCAAAUUGCUGCAGGCACGUGCAACCGCACAG-GUUGCUGCUUCUACGAAUGAAGCAACGCUUCAAAUCGUGUUUCGACAAAUGUAAAUA-GAGAUUACUGUGCCCCCAAAAUGAAA
((.((.....)).)).(((((((((((((.....)-))))).))....((((.((((((...))))))..))))(((((.((....)).....-)))))....)))))............ ( -33.20)
>DroSim_CAF1 76830 118 - 1
GCCGCAAAUUGCUGCAGGCACGUGCAACCGCACAG-GUUGCUGCUUCUACGAAUGAAGCAACGCUUCAAAUCGUGUUUCGACAAAUGUAAAUA-GAGAUUACUGUGCCCCCAAAAUGAAA
((.((.....)).)).(((((((((((((.....)-))))).))....((((.((((((...))))))..))))(((((.((....)).....-)))))....)))))............ ( -33.20)
>DroYak_CAF1 76290 115 - 1
GCCGCAAAUUGCUGCAGGCACGUGCAACCGCAUAG-GUUGCUGCUUCUCGAAAAGAAGCAACACUGCCAAUGGUGUAUC----CAUAUAAAUAAAAGGUUUCUGUGCCCCCAGAAUGCCA
((.((.....)).)).((((.((((((((.....)-)))))(((((((.....)))))))..)))))).((((.....)----)))..........((((((((......))))).))). ( -39.60)
>consensus
GCCGCAAAUUGCUGCAGGCACGUGCAACCGCACAG_GUUGCUGCUUCUACGAAAGAAGCAACGCUUCAAAUCGUGUUUCGACAAAUGUAAAUA_GAGAUUACUGUGCCCCCAAAAUGAAA
((.((.....)).)).(((((..((((((.....).)))))((((((.......))))))((((........))))...........................)))))............ (-24.69 = -25.25 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	10,546,520 – 10,546,640
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.31
Mean single sequence MFE	-44.18
Consensus MFE	-28.73
Energy contribution	-29.73
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-1.95
Structure conservation index	0.65
SVM decision value	0.15
SVM RNA-class probability	0.609915
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10546520 120 - 22224390
AAGGCUCUACCGAGCGAAGAGGCAGGCGGUGGUCCUUCGAGCCGCAAAUUGCUGCAGGCACGUGCAACCGCAUAGGGGUGCUACUUCUACGAAAGAAGCAAAGCUUGAAAUCGUGUUUCG
...((((....))))...(((((.((.(((((..((((..((((((......))).)))..((((....)))).))))..))))).))((((...((((...))))....))))))))). ( -37.70)
>DroSec_CAF1 72849 119 - 1
AAUGCUCUACCGAGCGAAGAGGCAGGCGGUGGUCCUUCGAGCCGCAAAUUGCUGCAGGCACGUGCAACCGCACAG-GUUGCUGCUUCUACGAAUGAAGCAACGCUUCAAAUCGUGUUUCG
..(((((....)))))..(((((((((((..(.(((....((((((......))).)))..((((....))))))-))..))))))..((((.((((((...))))))..))))))))). ( -45.60)
>DroSim_CAF1 76869 119 - 1
AAGGCUCUACCGAGCGAAGAGGCAGGCGGUGGUCGUUCGAGCCGCAAAUUGCUGCAGGCACGUGCAACCGCACAG-GUUGCUGCUUCUACGAAUGAAGCAACGCUUCAAAUCGUGUUUCG
...((((....))))((((.(((((.(.(((((.((.((.((((((......))).))).)).)).)))))...)-.))))).))))(((((.((((((...))))))..)))))..... ( -47.00)
>DroYak_CAF1 76327 114 - 1
AACGCUCCACCGAGUG----GAGAGCCGUUGGUCCUUCAAGCCGCAAAUUGCUGCAGGCACGUGCAACCGCAUAG-GUUGCUGCUUCUCGAAAAGAAGCAACACUGCCAAUGGUGUAUC-
....((((((...)))----))).(((((((((.......((((((......))).)))..((((((((.....)-)))))(((((((.....)))))))))...))))))))).....- ( -46.40)
>consensus
AAGGCUCUACCGAGCGAAGAGGCAGGCGGUGGUCCUUCGAGCCGCAAAUUGCUGCAGGCACGUGCAACCGCACAG_GUUGCUGCUUCUACGAAAGAAGCAACGCUUCAAAUCGUGUUUCG
...((((....))))...((((((.(..(((((....((.((((((......))).))).))....)))))..........((((((.......))))))...........).)))))). (-28.73 = -29.73 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:36 2006