Locus 9445

Sequence ID	3R_DroMel_CAF1
Location	25,012,649 – 25,012,780
Length	131
Max. P	0.976707

overview

Window 5

Location	25,012,649 – 25,012,756
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.98
Mean single sequence MFE	-30.12
Consensus MFE	-16.40
Energy contribution	-18.98
Covariance contribution	2.58
Combinations/Pair	1.08
Mean z-score	-3.38
Structure conservation index	0.54
SVM decision value	1.78
SVM RNA-class probability	0.976707
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25012649 107 + 27905053
GAC-CCACCUUUAAUUUUCAUAAUGAGAAAACGACAUGUGCUCAUUAAUUGGCACAUGGAAAUGUGUCUCACUGAGCCCAUGUAAACA------------UGCACUGAAUAUUUGUGAUU
...-.(((......(((((.....)))))....(((((.(((((......(((((((....)))))))....))))).))))).....------------..............)))... ( -26.80)
>DroSec_CAF1 33792 118 + 1
GACCCCAGCUUUAAUUUUCAUAAUGAGAAUACGACAUGUGCUCAUUAAUUGGCACAUGGAAAUAUGU--CACUGAGCCCAUGUAAACAUGAAAAAGCAAAUGCACUGAAUAUUGGUGAUU
.......(((((.((((((.....))))))...(((((.(((((.....(((((.((....)).)))--)).))))).))))).........))))).....(((..(...)..)))... ( -28.10)
>DroSim_CAF1 27869 117 + 1
GAC-CCAGCUUUAAUUUUCAUAAUGAGAAAAAGACAUGUGCUCAUUAAUUGGCACAUGGAAAUGUGU--CACUGAGCCCAUGUAAACAUGAAAAAGCAAAUGCACUGAAUAUUGGCGAUU
...-...(((((..(((((.....)))))....(((((.(((((.....((((((((....))))))--)).))))).))))).........)))))...(((.(........))))... ( -31.50)
>DroEre_CAF1 36131 109 + 1
-AC-CCAACUUUAAUUUUCAUAAUGAGAAAACGACAGGUGCUCAUUAAUUGGCACAUGAAAAUGUGU--CACUGAGGCCAUGUAAACAUGG----AAAAACAC---AAAUAUUGGAAACC
-..-(((((((((.......(((((((...((.....)).)))))))..((((((((....))))))--)).)))))(((((....)))))----........---.....))))..... ( -29.90)
>DroYak_CAF1 27546 114 + 1
GAC-CCGCCUUUAAUUUUCAUAAUGAGAAAACGACAGGUGCUCAUUAAUUGGCACAUGGAAAUGUGC--CACAGAGGCCAUGUAAACAUGAAGCAAAAAACAC---AAAUAUUGGUAACC
.((-(.((((((........(((((((...((.....)).)))))))..((((((((....))))))--)).))))))((((....)))).............---.......))).... ( -34.30)
>consensus
GAC_CCACCUUUAAUUUUCAUAAUGAGAAAACGACAUGUGCUCAUUAAUUGGCACAUGGAAAUGUGU__CACUGAGCCCAUGUAAACAUGAA__AAAAAAUGCACUGAAUAUUGGUGAUU
....(((.......(((((.....)))))....(((((.(((((.......((((((....)))))).....))))).))))).............................)))..... (-16.40 = -18.98 +   2.58)

alignment

secondary structure

dotplot

Window 6

Location	25,012,688 – 25,012,780
Length	92
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-25.38
Consensus MFE	-12.54
Energy contribution	-14.73
Covariance contribution	2.19
Combinations/Pair	1.09
Mean z-score	-2.41
Structure conservation index	0.49
SVM decision value	-0.01
SVM RNA-class probability	0.528652
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25012688 92 + 27905053
CUCAUUAAUUGGCACAUGGAAAUGUGUCUCACUGAGCCCAUGUAAACA------------UGCACUGAAUAUUUGUGAUUAGU------UGAAAAAGCUCUGAGUAAAUA
((((......(((((((....))))))).....((((.((((....))------------))(((.........)))......------.......))))))))...... ( -21.80)
>DroSec_CAF1 33832 108 + 1
CUCAUUAAUUGGCACAUGGAAAUAUGU--CACUGAGCCCAUGUAAACAUGAAAAAGCAAAUGCACUGAAUAUUGGUGAUUAGUUAGCGUUGAAAAAGCUCUGAGUAAAUA
((((.....(((((.((....)).)))--))..((((.((((....)))).....((.(((.(((..(...)..)))....))).)).........))))))))...... ( -22.70)
>DroSim_CAF1 27908 108 + 1
CUCAUUAAUUGGCACAUGGAAAUGUGU--CACUGAGCCCAUGUAAACAUGAAAAAGCAAAUGCACUGAAUAUUGGCGAUUAGUUAGCGUUGAAAAAGCUCUGAGUAAAUA
((((.....((((((((....))))))--))..((((.((((....))))........((((((((((..........)))))..)))))......))))))))...... ( -27.10)
>DroEre_CAF1 36169 101 + 1
CUCAUUAAUUGGCACAUGAAAAUGUGU--CACUGAGGCCAUGUAAACAUGG----AAAAACAC---AAAUAUUGGAAACCAGCGGGCGUUGGAAAAGCUCUGAGGAAAUA
((((.....((((((((....))))))--))..(((.(((((....)))))----........---............(((((....))))).....)))))))...... ( -29.90)
>consensus
CUCAUUAAUUGGCACAUGGAAAUGUGU__CACUGAGCCCAUGUAAACAUGA____GCAAAUGCACUGAAUAUUGGUGAUUAGUUAGCGUUGAAAAAGCUCUGAGUAAAUA
((((.......((((((....))))))......((((.((((....))))............................((((......))))....))))))))...... (-12.54 = -14.73 +   2.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:48 2006