Locus 5847

Sequence ID	2R_DroMel_CAF1
Location	18,499,295 – 18,499,495
Length	200
Max. P	0.968835

overview

Window 5

Location	18,499,295 – 18,499,415
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-34.60
Consensus MFE	-32.83
Energy contribution	-33.83
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.76
Structure conservation index	0.95
SVM decision value	1.63
SVM RNA-class probability	0.968835
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499295 120 + 20766785
GCACCCAGUUGUUGUAUGGUAUGCGAUAGGAUUUUUAUGUAAAACAUAAUUGCAGAUUAGUCGCGGCGGCAAUGUGCAAAUAAAAGCAAAGGCAUCCAGCAGUGGCAAAAACUGAGAAAA
.......((..((((.(((.((((..........(((((.....)))))(((((.(((.((((...))))))).)))))............)))))))))))..)).............. ( -29.10)
>DroSec_CAF1 18098 120 + 1
GCACCCAGUUGUUGUAUGGGAUGCGAUAGGAUUUUUAUGUAAAACAUAAUUGCAGAUUAGUCGCGGCGGCAUUGUGCAAAUAAAAGCAAAGGCAUCCAGCAGUGGCAAAAACUGGGAAAA
...(((((((.((((.((((((((..........(((((.....)))))(((((.(...((((...))))..).)))))............))))))..))...)))).))))))).... ( -36.00)
>DroSim_CAF1 7136 120 + 1
GCACCCAGUUGUUGUAUGGGAUGCGAUAGGAUUUUUAUGUAAAACAUAAUUGCAGAUUAGUCGCGGCGGCAAUGUGCAAAUAAAAGCAAAGGCAUCCUGCAGUGGCAAAAACUGGGAAAA
...(((((((.((((.((((((((..........(((((.....)))))(((((.(((.((((...))))))).)))))............)))))))).....)))).))))))).... ( -38.70)
>consensus
GCACCCAGUUGUUGUAUGGGAUGCGAUAGGAUUUUUAUGUAAAACAUAAUUGCAGAUUAGUCGCGGCGGCAAUGUGCAAAUAAAAGCAAAGGCAUCCAGCAGUGGCAAAAACUGGGAAAA
...(((((((.((((.((((((((..........(((((.....)))))(((((.(((.((((...))))))).)))))............))))))..))...)))).))))))).... (-32.83 = -33.83 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	18,499,295 – 18,499,415
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-27.47
Consensus MFE	-26.19
Energy contribution	-26.30
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.35
Structure conservation index	0.95
SVM decision value	1.24
SVM RNA-class probability	0.934446
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499295 120 - 20766785
UUUUCUCAGUUUUUGCCACUGCUGGAUGCCUUUGCUUUUAUUUGCACAUUGCCGCCGCGACUAAUCUGCAAUUAUGUUUUACAUAAAAAUCCUAUCGCAUACCAUACAACAACUGGGUGC
....(((((((.(((....((.(((((((..((((..(((.((((...........)))).)))...))))(((((.....)))))..........)))).)))))))).)))))))... ( -23.40)
>DroSec_CAF1 18098 120 - 1
UUUUCCCAGUUUUUGCCACUGCUGGAUGCCUUUGCUUUUAUUUGCACAAUGCCGCCGCGACUAAUCUGCAAUUAUGUUUUACAUAAAAAUCCUAUCGCAUCCCAUACAACAACUGGGUGC
....(((((((.(((....((..((((((..((((..(((.((((...........)))).)))...))))(((((.....)))))..........))))))))..))).)))))))... ( -29.20)
>DroSim_CAF1 7136 120 - 1
UUUUCCCAGUUUUUGCCACUGCAGGAUGCCUUUGCUUUUAUUUGCACAUUGCCGCCGCGACUAAUCUGCAAUUAUGUUUUACAUAAAAAUCCUAUCGCAUCCCAUACAACAACUGGGUGC
....(((((((..(((....)))((((((..((((..(((.((((...........)))).)))...))))(((((.....)))))..........))))))........)))))))... ( -29.80)
>consensus
UUUUCCCAGUUUUUGCCACUGCUGGAUGCCUUUGCUUUUAUUUGCACAUUGCCGCCGCGACUAAUCUGCAAUUAUGUUUUACAUAAAAAUCCUAUCGCAUCCCAUACAACAACUGGGUGC
....(((((((.(((....((..((((((..((((..(((.((((...........)))).)))...))))(((((.....)))))..........))))))))..))).)))))))... (-26.19 = -26.30 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	18,499,375 – 18,499,495
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.08
Mean single sequence MFE	-25.20
Consensus MFE	-23.36
Energy contribution	-24.36
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.93
SVM decision value	0.63
SVM RNA-class probability	0.806504
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18499375 120 - 20766785
UUUCGGGAAUCCCGGCAGCUCUUUCACUCAUGUUUAAUCCUCUUCAAGCGGCAACAGAACGAUUACAUUUUGAUUUUUUUUUUUCUCAGUUUUUGCCACUGCUGGAUGCCUUUGCUUUUA
....(((.((((.(((((.............((((.(......).))))(((((..((((............................))))))))).))))))))).)))......... ( -21.19)
>DroSec_CAF1 18178 117 - 1
UUUCGGCAAUCCCGGCAGCUCUUUCACUCAUGUUUAAUCCUCUUUAAGCGGCAACAGAACGAUUACAUUUUGAUUUU---UUUUCCCAGUUUUUGCCACUGCUGGAUGCCUUUGCUUUUA
....((((...(((((((.............((((((......))))))(((((..((((.................---........))))))))).))))))).)))).......... ( -28.21)
>DroSim_CAF1 7216 117 - 1
UUUCGGCAAUCCCGGCAGCUCUUUCACUCAUGUUUAAUCCUCUUUAAGCGGCAACAGAACGAUUACAUUUUGAUUUU---UUUUCCCAGUUUUUGCCACUGCAGGAUGCCUUUGCUUUUA
....((((.(((..((((.............((((((......))))))(((((..((((.................---........))))))))).)))).))))))).......... ( -26.21)
>consensus
UUUCGGCAAUCCCGGCAGCUCUUUCACUCAUGUUUAAUCCUCUUUAAGCGGCAACAGAACGAUUACAUUUUGAUUUU___UUUUCCCAGUUUUUGCCACUGCUGGAUGCCUUUGCUUUUA
....((((...(((((((.............((((((......))))))(((((..((((............................))))))))).))))))).)))).......... (-23.36 = -24.36 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:16 2006