Locus 6822

Sequence ID	3R_DroMel_CAF1
Location	18,037,766 – 18,037,929
Length	163
Max. P	0.712406

overview

Window 5

Location	18,037,766 – 18,037,865
Length	99
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-29.60
Consensus MFE	-19.68
Energy contribution	-20.40
Covariance contribution	0.72
Combinations/Pair	1.17
Mean z-score	-2.04
Structure conservation index	0.66
SVM decision value	0.09
SVM RNA-class probability	0.578149
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18037766 99 - 27905053
GGCCAGACAAGGAGCCUCGAAAUU-UCGGGCUCUUAGAUGGGCAAUUGGAAACGAGAGCUCUGGAAAAGCCAGAGACCCACAUGAGGGAAUAUAUAUUAC
.(((...(.(((((((.(((....-)))))))))).)...)))..(((....)))...((((((.....)))))).(((......)))............ ( -35.70)
>DroSec_CAF1 80332 99 - 1
GGCCAGACAAGGAUCCUCGAAAUU-UCGGGCUCUAAGGUGGGCAAUUGGAAACGGGAGCUCUGGGAAAGCCAGAAACCCACAUGAGGGAAUAUAUAUUAC
..((......))...(((((....-)))))((((...((((((..(((....)))..))(((((.....)))))...))))...))))............ ( -27.20)
>DroSim_CAF1 82197 98 - 1
GGCCAGACAAGGAGCCUCGAAAUU-UCGGGC-CUAAGGUGGGCAAUUGGAAACGGGAGCUCUGGAAAAGCCAGAAACCCACAUGAGGGAAUAUAUAUUAC
(((.......(((((((((...((-(((.((-((.....))))...))))).)))).)))))......))).....(((......)))............ ( -28.42)
>DroEre_CAF1 82408 100 - 1
GGCCAGACAAGAAGGCUCGAUUUUACGGGGCACUACGGUGGGUAACUGGAAACGGGAGCUCUGGAAAAGCCAGAGAGCCACAUGAAUGAAUAUAAUUUAC
..((((.........((((......)))).(((....))).....)))).....((..((((((.....))))))..))...(((((.......))))). ( -27.60)
>DroYak_CAF1 84313 99 - 1
GGCCACACAAGGUGUCUCGAUUUU-UGGGGCUCUAUGAUGGGUAACUGGAAACGGGUGCUCUGGAAAAGCCAGAAACCCACAUGAAGGAAUAUAAAUUAC
.(((.((((.((.(((((((...)-)))))).)).)).)))))....(....)((((..(((((.....))))).))))..................... ( -29.10)
>consensus
GGCCAGACAAGGAGCCUCGAAAUU_UCGGGCUCUAAGGUGGGCAAUUGGAAACGGGAGCUCUGGAAAAGCCAGAAACCCACAUGAGGGAAUAUAUAUUAC
...............(((((.....)))))((((...((((((..(((....)))..))(((((.....)))))...))))...))))............ (-19.68 = -20.40 +   0.72)

alignment

secondary structure

dotplot

Window 6

Location	18,037,831 – 18,037,929
Length	98
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.94
Mean single sequence MFE	-30.22
Consensus MFE	-16.70
Energy contribution	-20.37
Covariance contribution	3.67
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.55
SVM decision value	0.38
SVM RNA-class probability	0.712406
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18037831 98 + 27905053
AAGAGCCCGA-AAUUUCGAGGCUCCUUGUCUGGCCUUCAGUUUGCUGUCAACUCUUUGCAUACUAGGAGUGACAGAUUGAGGUACCGGACACACAACAU
..((((((((-....))).)))))..(((((((.(((((((...((((((.(((((........))))))))))))))))))..)))))))........ ( -39.60)
>DroVir_CAF1 92473 86 + 1
CAG-GGCUGA-AGCUUCGGGACUGCUGAAAAGGCGUGUAGAUUGCUGUCAAAUAUUUGCUCAUUUUGAGGCACAU--------AAAGAACACACAA---
(((-..((((-....))))..)))((....))(.((((.(((....)))...(((.(((((.....)).))).))--------)....)))).)..--- ( -16.10)
>DroSec_CAF1 80397 98 + 1
UAGAGCCCGA-AAUUUCGAGGAUCCUUGUCUGGCCUUCAGUUUGCUGUCAACUCUUUGCUUACUAGGAGUGACAGAUUGAGGUACCGGACACACAACAU
..((.(((((-....))).)).))..(((((((.(((((((...((((((.(((((........))))))))))))))))))..)))))))........ ( -33.00)
>DroSim_CAF1 82262 97 + 1
UAG-GCCCGA-AAUUUCGAGGCUCCUUGUCUGGCCUUCAGUUUGCUGUCAACUCUUUGCUUACUAGGAGUGACAGAUUGAGGUACCGGACACACAACAU
..(-((((((-....))).))))...(((((((.(((((((...((((((.(((((........))))))))))))))))))..)))))))........ ( -36.10)
>DroEre_CAF1 82473 99 + 1
UAGUGCCCCGUAAAAUCGAGCCUUCUUGUCUGGCCUUCAGUUUGCUGUCAACUCUUUGCUUACUAGGAGUGACAGAUUGAGGUACCGGACACACACCAU
..(((...((......))........(((((((.(((((((...((((((.(((((........))))))))))))))))))..))))))))))..... ( -30.80)
>DroYak_CAF1 84378 98 + 1
UAGAGCCCCA-AAAAUCGAGACACCUUGUGUGGCCUUCAGUUUGCUGUCAACUCUUUGCUUACUAGGAGUGACAGAUUGAGGUACCGGACACACAACAU
..........-..............(((((((.((.(((((...((((((.(((((........))))))))))))))))(....))).)))))))... ( -25.70)
>consensus
UAGAGCCCGA_AAUUUCGAGGCUCCUUGUCUGGCCUUCAGUUUGCUGUCAACUCUUUGCUUACUAGGAGUGACAGAUUGAGGUACCGGACACACAACAU
..........................(((((((.(((((((...((((((.(((((........))))))))))))))))))..)))))))........ (-16.70 = -20.37 +   3.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:50 2006