Locus 3494

Sequence ID	3L_DroMel_CAF1
Location	10,262,017 – 10,262,110
Length	93
Max. P	0.958461

overview

Window 6

Location	10,262,017 – 10,262,110
Length	93
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	84.31
Mean single sequence MFE	-16.45
Consensus MFE	-11.99
Energy contribution	-12.03
Covariance contribution	0.04
Combinations/Pair	1.23
Mean z-score	-1.79
Structure conservation index	0.73
SVM decision value	0.34
SVM RNA-class probability	0.697858
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10262017 93 + 23771897
GUGAAGUUUUCGCAUCGCCCACUUCUUUACUUUACCACCUAAAAAAACAAUCGAUAUCCU--------UGCUCUUCCGCUCACAAUUAAGCGGGAA-AACAA
.....(((((((((..............................................--------)))....(((((........))))))))-))).. ( -13.45)
>DroSec_CAF1 137300 92 + 1
GUGGAGUUUUCACAUCGCCCACUUCUUUACCUUACCACCUAAA-AAACAAUCGAUAUCCU--------UGCUCUCCCGCUCACAAUUAAGCGGGAA-AACAU
((((.((.........)))))).....................-................--------.....(((((((........))))))).-..... ( -16.40)
>DroSim_CAF1 142697 97 + 1
GUGGAGUUUUCACAUCGCCCACUUCUUUACCUUACCACCUAAA-AAACAAUCGAUAUCCUCGA---UAUGCUCUCCCGCUCACAAUUAAGCGGGAA-AACAU
((((.((.........)))))).....................-.....(((((.....))))---)......(((((((........))))))).-..... ( -19.90)
>DroEre_CAF1 147177 99 + 1
GUGGAGUU-UUCCAUCGCCCAGCUCUUCAGUUCACCACCUAAA-AAACAAUCAAUAUCCUUCAGCUUUUGCUCUCCCGCUCACAAUUAAGCGGGAA-AACAA
(.((((((-...........)))))).).(((...........-..................(((....))).(((((((........))))))).-))).. ( -17.80)
>DroYak_CAF1 144615 97 + 1
GUGGAGUUUUUCCAUCGCC----UCUUCAGUUCACUACCUAAA-AAACAAUCGAUAUACUUCAGCUUUUGCUCUCCCACUCACAAUUAAGCGGGAAAAACAU
.....((((((((..(((.----....................-........((......))(((....))).................))))))))))).. ( -14.70)
>consensus
GUGGAGUUUUCACAUCGCCCACUUCUUUACUUUACCACCUAAA_AAACAAUCGAUAUCCU__A___U_UGCUCUCCCGCUCACAAUUAAGCGGGAA_AACAU
((((((..................))))))...........................................(((((((........)))))))....... (-11.99 = -12.03 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	10,262,017 – 10,262,110
Length	93
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	84.31
Mean single sequence MFE	-30.72
Consensus MFE	-18.37
Energy contribution	-18.01
Covariance contribution	-0.36
Combinations/Pair	1.13
Mean z-score	-3.26
Structure conservation index	0.60
SVM decision value	1.49
SVM RNA-class probability	0.958461
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10262017 93 - 23771897
UUGUU-UUCCCGCUUAAUUGUGAGCGGAAGAGCA--------AGGAUAUCGAUUGUUUUUUUAGGUGGUAAAGUAAAGAAGUGGGCGAUGCGAAAACUUCAC
(((((-((.(((((((....))))))).))))))--------).(.(((((.(..((((((((..(....)..))))))))..).))))))........... ( -25.60)
>DroSec_CAF1 137300 92 - 1
AUGUU-UUCCCGCUUAAUUGUGAGCGGGAGAGCA--------AGGAUAUCGAUUGUUU-UUUAGGUGGUAAGGUAAAGAAGUGGGCGAUGUGAAAACUCCAC
.((((-((((((((((....))))))))))))))--------.(((.((((.(..(((-(((.(.(.....).).))))))..).))))((....))))).. ( -31.40)
>DroSim_CAF1 142697 97 - 1
AUGUU-UUCCCGCUUAAUUGUGAGCGGGAGAGCAUA---UCGAGGAUAUCGAUUGUUU-UUUAGGUGGUAAGGUAAAGAAGUGGGCGAUGUGAAAACUCCAC
(((((-((((((((((....))))))))))))))).---..(((.((((((.(..(((-(((.(.(.....).).))))))..).)))))).....)))... ( -32.20)
>DroEre_CAF1 147177 99 - 1
UUGUU-UUCCCGCUUAAUUGUGAGCGGGAGAGCAAAAGCUGAAGGAUAUUGAUUGUUU-UUUAGGUGGUGAACUGAAGAGCUGGGCGAUGGAA-AACUCCAC
(((((-((((((((((....)))))))))))))))........((((((((...((((-(((((........)))))))))....)))))...-...))).. ( -35.40)
>DroYak_CAF1 144615 97 - 1
AUGUUUUUCCCGCUUAAUUGUGAGUGGGAGAGCAAAAGCUGAAGUAUAUCGAUUGUUU-UUUAGGUAGUGAACUGAAGA----GGCGAUGGAAAAACUCCAC
.((((((.((((((((....)))))))))))))).....((.(((.(.((.(((((((-(((.(((.....))).))))----)))))).)).).))).)). ( -29.00)
>consensus
AUGUU_UUCCCGCUUAAUUGUGAGCGGGAGAGCA_A___U__AGGAUAUCGAUUGUUU_UUUAGGUGGUAAAGUAAAGAAGUGGGCGAUGGGAAAACUCCAC
.((((.((((((((((....))))))))))))))............(((((........((((..........))))........)))))............ (-18.37 = -18.01 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:30 2006