Locus 4425

Sequence ID	3L_DroMel_CAF1
Location	12,920,462 – 12,920,642
Length	180
Max. P	0.898637

overview

Window 1

Location	12,920,462 – 12,920,575
Length	113
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.80
Mean single sequence MFE	-28.18
Consensus MFE	-14.19
Energy contribution	-14.47
Covariance contribution	0.28
Combinations/Pair	1.36
Mean z-score	-2.10
Structure conservation index	0.50
SVM decision value	0.54
SVM RNA-class probability	0.773837
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12920462 113 + 23771897
AAGAAAAAAUAAAUGUGCGCCUAAAACAUAAAGGUGGACCAACGAAUUUGCCGGAAAAGCCCCUUGCAAAGUGGCUAAAUGAGCCAACGGCCAGAACUGGCUUAGCAAAGUAG-
..............((.(((((.........))))).)).......(((((.....(((((.((.((....(((((.....)))))...)).))....))))).)))))....- ( -26.10)
>DroSec_CAF1 41188 113 + 1
AAGAA-AAAUAAAUGUGCGCCUAAAACAUAAAGGUGGACGAACGAAUUUGCCGGGAAAGCCCCUCGCAAAGUGGCUAAAUGAGCCAACGGCCAGCACUGGCUUAGCAAAGUGGA
.....-.......(((.(((((.........))))).)))..((..(((((.(((.....)))..))))).(((((.....))))).))((((....))))............. ( -30.30)
>DroSim_CAF1 40276 113 + 1
AAGAA-AAAUAAAUGUGCGCCUAAAACAUAAAGGUGGACGAACGAAUUUGCCGGGAAAGCCCCUUGCAAAGUGGCUAAAUGAGCCAACGGCCAGAACUGGCUUAGCAAAGUGGA
.....-.......(((.(((((.........))))).)))..........(((((.....)))((((....(((((.....)))))..(((((....)))))..))))...)). ( -31.20)
>DroEre_CAF1 46609 99 + 1
AAA---AAAUAA------------AACAUAAAGUUAGGCCAACGAAUUUGCCGGGAAUGCCCCGUGCAAAGUGGCCAAAUGAGCCGAAGGCCAGCACUGGCUUAACAAAGUGGA
...---......------------..(((...(((((((((.....(((((((((.....)))).))))).(((((............)))))....)))))))))...))).. ( -34.00)
>DroYak_CAF1 44168 111 + 1
AAA---AAAUAAAAGUGCGCCCAAAACAUAAAGGUAGGCCAAGGAAUUUGCCGGGAAUGCCUCGUGCAAAGUGGCUAAAUGAGCCGACGGCCAGAACUGGCUUAGCAAAGUGGA
...---.........((((((....((......)).((((......(((((((((.....)))).)))))((((((.....)))).))))))......)))...)))....... ( -29.20)
>DroAna_CAF1 66420 97 + 1
AAA---AAU------UCCG-GCAAAAUAUAAAGGUUGACGAGGGAUUUGGGAGGGAAGUGGCAGAGCAAAGUGGCUAAAUGAAGCGACAGCCAUAACUGGCUUAGUU-------
..(---(((------(((.-.(((..(....)..)))....))))))).........((..((.(((......)))...))..))((((((((....)))))..)))------- ( -18.30)
>consensus
AAA___AAAUAAAUGUGCGCCUAAAACAUAAAGGUGGACCAACGAAUUUGCCGGGAAAGCCCCGUGCAAAGUGGCUAAAUGAGCCAACGGCCAGAACUGGCUUAGCAAAGUGGA
................................((((((........))))))(((.....))).(((....(((((.....)))))..(((((....)))))..)))....... (-14.19 = -14.47 +   0.28)

alignment

secondary structure

dotplot

Window 2

Location	12,920,536 – 12,920,642
Length	106
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	78.61
Mean single sequence MFE	-25.07
Consensus MFE	-18.14
Energy contribution	-18.03
Covariance contribution	-0.10
Combinations/Pair	1.22
Mean z-score	-1.83
Structure conservation index	0.72
SVM decision value	1.00
SVM RNA-class probability	0.898637
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12920536 106 - 23771897
AUUUUUCAGCCACUUCUUAAUCUUGUAUAAUAAUAUAGCGCCUUGCUUUUGGUGCUGCCUUACCGAA--------------CUACUUUGCUAAGCCAGUUCUGGCCGUUGGCUCAUUUAG
.......(((((........................((((((........))))))(((.....(((--------------((.(((....)))..))))).)))...)))))....... ( -23.40)
>DroEre_CAF1 46668 120 - 1
AUUUUUCAGUCACUUCCUAAAUGUGCUUAAUAAUAAAGCACCUUUCCGUUGGAGCUCCCUUACCAAACUCCAAACGAAAAUCCACUUUGUUAAGCCAGUGCUGGCCUUCGGCUCAUUUGG
................(((((((.(((...((((((((....((((..((((((.............))))))..)))).....)))))))).((((....))))....))).))))))) ( -27.72)
>DroYak_CAF1 44239 120 - 1
AUUCUUCAGUCACUUCUUAAAUUUGUAUAAUAAUAAAGCACCUUUCCUUUGGUGCUUCCUUGCCGAACUCCAACAGAAAAUCCACUUUGCUAAGCCAGUUCUGGCCGUCGGCUCAUUUAG
...................................(((((((........)))))))....(((((.......((((........))))....((((....))))..)))))........ ( -24.10)
>consensus
AUUUUUCAGUCACUUCUUAAAUUUGUAUAAUAAUAAAGCACCUUUCCUUUGGUGCUCCCUUACCGAACUCCAA__GAAAAUCCACUUUGCUAAGCCAGUUCUGGCCGUCGGCUCAUUUAG
.......((((...................(((..(((((((........)))))))..)))...............................((((....))))....))))....... (-18.14 = -18.03 +  -0.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:20 2006