Locus 4670

Sequence ID	3R_DroMel_CAF1
Location	12,319,550 – 12,319,710
Length	160
Max. P	0.935175

overview

Window 5

Location	12,319,550 – 12,319,670
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-25.77
Consensus MFE	-24.92
Energy contribution	-24.70
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	0.97
SVM decision value	0.08
SVM RNA-class probability	0.573017
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12319550 120 + 27905053
UAUUUGUGGCUUAGUUUUAUUCCAUUUUCGCUGUAACUGCUUCUUGCUAUUGCCGCAGUUGUAAUUUGAGCUGCAAUUUCUAUUAUUUACUUGCAGUUUCUGGCUCACUUCGGUGUGAAU
.....((((..((....))..)))).((((((..((((((.....((....)).((((((........))))))..................))))))...))).(((....))).))). ( -25.90)
>DroSec_CAF1 10805 120 + 1
UAUUUGUGGCUUAGUUUUAUUCCAUUUUCGCUGUAGCUGCUUCUUGCUAUUGCCGCAGUUGUAAUUUGAGCUGCAAUUUCUAUUAUUUACUUGCAGUUUCUGGCUCACUUUGGUGUGAAC
...(((((((..(((..............)))(((((........))))).)))))))..((.....(((((((((..............)))))))))...))((((......)))).. ( -25.08)
>DroSim_CAF1 6900 120 + 1
UAUUUGUGGCUUAGUUUUAUUCCAUUUUCGCUGUAGCUGCUUCUUGCUAUUGCCGCAGUUGUAAUUUGAGCUGCAAUUUCUAUUAUUUACUUGCAGUUUCUGGCUCACUUCGGUGUGAAC
.....((((..((....))..)))).(((((.(((((........))))).((((.(((.((.....(((((((((..............)))))))))...))..))).))))))))). ( -26.34)
>consensus
UAUUUGUGGCUUAGUUUUAUUCCAUUUUCGCUGUAGCUGCUUCUUGCUAUUGCCGCAGUUGUAAUUUGAGCUGCAAUUUCUAUUAUUUACUUGCAGUUUCUGGCUCACUUCGGUGUGAAC
.....((((..((....))..))))....(((..((((((.....((....)).((((((........))))))..................))))))...)))((((......)))).. (-24.92 = -24.70 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	12,319,550 – 12,319,670
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-21.87
Consensus MFE	-20.19
Energy contribution	-20.31
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.93
Structure conservation index	0.92
SVM decision value	0.40
SVM RNA-class probability	0.720247
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12319550 120 - 27905053
AUUCACACCGAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAAGCAGUUACAGCGAAAAUGGAAUAAAACUAAGCCACAAAUA
.(((((......)))))(((((..((((((..............)))))).)).......((((((.((....)).....))))))..........)))..................... ( -21.14)
>DroSec_CAF1 10805 120 - 1
GUUCACACCAAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAAGCAGCUACAGCGAAAAUGGAAUAAAACUAAGCCACAAAUA
((((((......))))))..((..((((((..............)))))).))..........((.(((....((.....)).((....))...................))).)).... ( -22.24)
>DroSim_CAF1 6900 120 - 1
GUUCACACCGAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAAGCAGCUACAGCGAAAAUGGAAUAAAACUAAGCCACAAAUA
((((((......))))))..((..((((((..............)))))).))..........((.(((....((.....)).((....))...................))).)).... ( -22.24)
>consensus
GUUCACACCGAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAAGCAGCUACAGCGAAAAUGGAAUAAAACUAAGCCACAAAUA
((((((......))))))..((..((((((..............)))))).))..........((.(((....((.....)).((....))...................))).)).... (-20.19 = -20.31 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	12,319,590 – 12,319,710
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-28.87
Consensus MFE	-26.01
Energy contribution	-27.01
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.73
Structure conservation index	0.90
SVM decision value	1.24
SVM RNA-class probability	0.935175
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12319590 120 - 27905053
GCUGCACAUAUCUGACAAGUGAAACCCUGCAACACAAACAAUUCACACCGAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAA
((((((....((((....(((...........)))......(((((......))))).))))..((((((..............)))))).............))))))........... ( -23.74)
>DroSec_CAF1 10845 120 - 1
GCUGCACAUAUCUGCCCAGGGAAACCCUGCAACGCAAACCGUUCACACCAAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAA
((((((....((((..(((((...)))))...........((((((......))))))))))..((((((..............)))))).............))))))........... ( -31.44)
>DroSim_CAF1 6940 120 - 1
GCUGCACAUAUCUGCCCAGGGAAACCCUGCAACGCAAACCGUUCACACCGAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAA
((((((....((((..(((((...)))))...........((((((......))))))))))..((((((..............)))))).............))))))........... ( -31.44)
>consensus
GCUGCACAUAUCUGCCCAGGGAAACCCUGCAACGCAAACCGUUCACACCGAAGUGAGCCAGAAACUGCAAGUAAAUAAUAGAAAUUGCAGCUCAAAUUACAACUGCGGCAAUAGCAAGAA
((((((....((((..(((((...)))))...........((((((......))))))))))..((((((..............)))))).............))))))........... (-26.01 = -27.01 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:00 2006