Locus 7003

Sequence ID	3R_DroMel_CAF1
Location	18,471,467 – 18,471,660
Length	193
Max. P	0.549459

overview

Window 2

Location	18,471,467 – 18,471,580
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.49
Mean single sequence MFE	-27.87
Consensus MFE	-20.26
Energy contribution	-20.86
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.73
SVM decision value	0.03
SVM RNA-class probability	0.549459
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18471467 113 - 27905053
AUGCUUUAGUUUAGCCCUUCAAGCGAGGCGCUUCACUGCCAAUA-------GAGAAUUGGCAAAGGCAAACACAAACACGAAAUUUCCAUUUUGGCCUGCGUUAGCAUAAUUGUUAAAUU
..(((.......))).......((.((((((((...(((((((.-------....))))))).))))...........((((((....)))))))))))).((((((....))))))... ( -27.80)
>DroSec_CAF1 26706 117 - 1
AUGCUUCACUUGAACCCGUCAAGCGAGGCGCUCCACUGCCAAUG---GAUGGAAAAUUGGCAAAAACAAACACAAACACGAAAUUUCCAUUUUGGCCUGCGUUAGCAUAAUUGUUAAAUU
..(((((.(((((.....))))).)))))((......(((((..---((((((((.((.(..................).)).)))))))))))))..)).((((((....))))))... ( -30.07)
>DroSim_CAF1 26412 117 - 1
AUGCUUCACUUGAACCCUUCAAGCGAGGCGCUCCACUGCCAAUG---GAUGGAGAAUUGGCAAAAACAAACACAAACACGAAAUUUCCAUUUUGGCCUGCGUUAGCAUAAUUGUUAAAUU
..(((((.(((((.....))))).)))))((......(((((..---((((((((.((.(..................).)).)))))))))))))..)).((((((....))))))... ( -30.17)
>DroEre_CAF1 27049 118 - 1
AUGCUUCACUUUAACCCUUCAAGCGAGGCGCUCCACUGCCAAUACUGAAAAGGCA--AGGCAAAGAUAAACACAAACACGAAAUUUCCAUUUUGGCCUGCGUUGGCAUAAUUGCUAAAUU
..(((((.(((.........))).)))))((.....(((((((.((....))(((--.(((...(.....).......((((((....))))))))))))))))))).....))...... ( -28.60)
>DroYak_CAF1 27661 119 - 1
AUGCUUCACUUUAACCCUUCGAGCGAGGCGCUCCACUGCCAAUAAUGAAUGGGCAA-AGGCAAAUACAAACACAAACACGAAAUUUCCAUUUUGGCCUGCGUUGGCAUAAUUGUUAAAUU
..(((((.(((.........))).)))))(((....((((.((.....)).)))).-.))).............((((((((((....))))))(((......))).....))))..... ( -22.70)
>consensus
AUGCUUCACUUUAACCCUUCAAGCGAGGCGCUCCACUGCCAAUA___AAUGGACAAUUGGCAAAAACAAACACAAACACGAAAUUUCCAUUUUGGCCUGCGUUAGCAUAAUUGUUAAAUU
......................((.((((.......(((((((............)))))))................((((((....)))))))))))).((((((....))))))... (-20.26 = -20.86 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	18,471,540 – 18,471,660
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-27.02
Consensus MFE	-23.58
Energy contribution	-23.46
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.30
Structure conservation index	0.87
SVM decision value	-0.04
SVM RNA-class probability	0.512291
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18471540 120 - 27905053
GUCAAAAGUGUUAAUUGACAGACUAAUUGAAACAGCCGCAAAAGGCAAUUUGCAAAUGGAAUUUGAGAUAAACACAAUUAAUGCUUUAGUUUAGCCCUUCAAGCGAGGCGCUUCACUGCC
....(((((((((((((.................(((......))).((((.(((((...))))))))).....)))))))))))))(((..(((((((.....)))).)))..)))... ( -27.50)
>DroSec_CAF1 26783 120 - 1
GUCAAAAGUGUUAAUUGACAGACUAAUUGAAACAGCCGCAAAAGGCAAUUUGCAAAUGGAAUUUGAGAUAAACACAAUUAAUGCUUCACUUGAACCCGUCAAGCGAGGCGCUCCACUGCC
.......(((((.(((..(((((((.((((((..(((......)))..))).))).)))..)))).))).))))).......(((((.(((((.....))))).)))))((......)). ( -29.30)
>DroSim_CAF1 26489 120 - 1
GUCAAAAGUGUUAAUUGACAGACUAAUUGAAACAGCCGCAAAAGGCAAUUUGCAAAUGGAAUUUGAGAUAAACACAAUUAAUGCUUCACUUGAACCCUUCAAGCGAGGCGCUCCACUGCC
.......(((((.(((..(((((((.((((((..(((......)))..))).))).)))..)))).))).))))).......(((((.(((((.....))))).)))))((......)). ( -29.30)
>DroEre_CAF1 27127 120 - 1
GUCAAAAGUGUUAAUUGACAGACUAAUUGAAACAGCCGCAAAAGGCAAUUUGCAAAUGGAAUUUGAGAUAAACACAAUUAAUGCUUCACUUUAACCCUUCAAGCGAGGCGCUCCACUGCC
.......(((((.(((..(((((((.((((((..(((......)))..))).))).)))..)))).))).))))).......(((((.(((.........))).)))))((......)). ( -23.80)
>DroYak_CAF1 27740 120 - 1
GUCAAAAGUGUUAAUUGACAGACUAAUUGAAACGGCCGCAAAAGGCAAUUUGCAAAUGGAAUUUGAGAUAAACACAAUUAAUGCUUCACUUUAACCCUUCGAGCGAGGCGCUCCACUGCC
.......(((((.(((..(((((((.((((((..(((......)))..))).))).)))..)))).))).))))).......(((((.(((.........))).)))))((......)). ( -25.20)
>consensus
GUCAAAAGUGUUAAUUGACAGACUAAUUGAAACAGCCGCAAAAGGCAAUUUGCAAAUGGAAUUUGAGAUAAACACAAUUAAUGCUUCACUUUAACCCUUCAAGCGAGGCGCUCCACUGCC
.......(((((.(((..(((((((.((((((..(((......)))..))).))).)))..)))).))).))))).......(((((.(((.........))).)))))((......)). (-23.58 = -23.46 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:17 2006