Locus 3202

Sequence ID	3R_DroMel_CAF1
Location	8,495,901 – 8,496,061
Length	160
Max. P	0.954491

overview

Window 5

Location	8,495,901 – 8,496,021
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.68
Mean single sequence MFE	-37.43
Consensus MFE	-26.61
Energy contribution	-26.70
Covariance contribution	0.09
Combinations/Pair	1.23
Mean z-score	-0.89
Structure conservation index	0.71
SVM decision value	0.03
SVM RNA-class probability	0.549841
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8495901 120 + 27905053
ACCCGCUCCAUCAUCAUGUAUGGGCGCAGUGAGUUGGCCAGCACCUCGGGCGACACGCCGCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGGAAUGGGUCAGGGUCAGGGGCAG
....(((((.............(((((.(((.((((.((........)).)))).))).)))))((((((.(...(((((((.((....)).)))))))...).))))))...))))).. ( -54.90)
>DroVir_CAF1 14501 96 + 1
ACGCGUUCCAUCAUCAUGUAUGGACGUAGUGAGCUGGCCAGCACCUCGGGCGAUAAGCCGAGAUCGCUCAGCAGCUUUCUGCAGGAG-ACA-----------------------AGCGAA
.(((((.(((((.....).))))))((((.((((((...(((..(((((.(.....))))))...)))...)))))).)))).(...-.).-----------------------.))).. ( -34.50)
>DroGri_CAF1 15479 96 + 1
ACGCGUUCCAUCAUCAUGUAUGGACGUAGUGAGCUGGCCAGCACCACGGGCGAUAAGCCGCCAUCGCUGAGCAGUUUCCUGCAGGAG-ACG-----------------------GGCGAA
.(((((.(((((.....).))))))((((..(((((..((((......((((......))))...))))..)))))..)))).(...-.).-----------------------.))).. ( -34.90)
>DroWil_CAF1 4343 96 + 1
ACGCGCUCCAUCAUAAUGUAUGGGCGUAGUGAGUUGGCCAGCACCGCGGGCGACAACGGACGUUCGCUGAGCAGCUUUCUGCACGAG-UC-----------------------GAGCGAG
.(((((.(((((.....).))))))((((.((((((..((((...(((..((....))..)))..))))..)))))).)))).....-..-----------------------..))).. ( -33.50)
>DroMoj_CAF1 12474 96 + 1
ACACGUUCCAUCAUCAUGUAUGGACGUAGUGAGCUGGCCAGCACCUCAGGCGACAAGCCGCGAUCGCUGAGCAGCUUCCUGCAGGAG-UCA-----------------------AGCGAU
...(((((((((.....).))))).((((..(((((..((((...((.(((.....)))..))..))))..)))))..)))).....-...-----------------------.))).. ( -32.80)
>DroAna_CAF1 4434 99 + 1
ACCCGCUCCAUCAUCAUGUAUGGGCGCAGUGAGUUGGCCAGCACUGGCGGCGAUCCACCCCGUUCCUUGAGCAGCUUCCUGCAGGACAACA---------------------CGGGGCAG
.(((((.(((((.....).))))))((((..(((((((((....))))((((........)))).......)))))..)))).........---------------------.))).... ( -34.00)
>consensus
ACGCGCUCCAUCAUCAUGUAUGGACGUAGUGAGCUGGCCAGCACCUCGGGCGACAAGCCGCGAUCGCUGAGCAGCUUCCUGCAGGAG_ACA_______________________AGCGAG
.(((((.(((((.....).))))))((((..(((((..((((......(((.....)))......))))..)))))..)))).................................))).. (-26.61 = -26.70 +   0.09)

alignment

secondary structure

dotplot

Window 6

Location	8,495,941 – 8,496,061
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.17
Mean single sequence MFE	-44.87
Consensus MFE	-27.43
Energy contribution	-26.85
Covariance contribution	-0.58
Combinations/Pair	1.30
Mean z-score	-1.79
Structure conservation index	0.61
SVM decision value	1.14
SVM RNA-class probability	0.920641
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8495941 120 + 27905053
GCACCUCGGGCGACACGCCGCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGGAAUGGGUCAGGGUCAGGGGCAGACGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGC
((((((.((.((....(((.(...((((((.(...(((((((.((....)).)))))))...).))))))...).)))...)).)).))))))((((((...))))))............ ( -59.70)
>DroVir_CAF1 14541 96 + 1
GCACCUCGGGCGAUAAGCCGAGAUCGCUCAGCAGCUUUCUGCAGGAG-ACA-----------------------AGCGAAUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAACGAUGUGC
((((.(((((((....(((((..(((((..((((....)))).(...-.).-----------------------))))).))))).....))))(((((...))))).....))).)))) ( -42.70)
>DroGri_CAF1 15519 96 + 1
GCACCACGGGCGAUAAGCCGCCAUCGCUGAGCAGUUUCCUGCAGGAG-ACG-----------------------GGCGAAUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAACGAUGUGC
((((..((..(.....((((((.(((((..((((....)))).(...-.).-----------------------))))).(((((((......)))))))))))))...)..))..)))) ( -47.00)
>DroWil_CAF1 4383 96 + 1
GCACCGCGGGCGACAACGGACGUUCGCUGAGCAGCUUUCUGCACGAG-UC-----------------------GAGCGAGUCUGCCAAGGUUCUGGCCGAGGCGGCUAAAAAUGACGUGG
...(((((............(((((((((.((((....)))).).))-.)-----------------------)))))((.(((((..(((....)))..)))))))........))))) ( -34.30)
>DroMoj_CAF1 12514 96 + 1
GCACCUCAGGCGACAAGCCGCGAUCGCUGAGCAGCUUCCUGCAGGAG-UCA-----------------------AGCGAUUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAUGACGUGC
((((.(((..(.....(((((..(((((((((((....)))).....-)).-----------------------)))))((((((((......)))))))))))))...)..))).)))) ( -41.80)
>DroAna_CAF1 4474 99 + 1
GCACUGGCGGCGAUCCACCCCGUUCCUUGAGCAGCUUCCUGCAGGACAACA---------------------CGGGGCAGUCGGCCAAGGUGUUGGCCGAGGCGGCCAAAAAGGAUGUGC
((((((((.((......((((((((((...((((....))))))))....)---------------------)))))...((((((((....)))))))).)).))))........)))) ( -43.70)
>consensus
GCACCUCGGGCGACAAGCCGCGAUCGCUGAGCAGCUUCCUGCAGGAG_ACA_______________________AGCGAGUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAACGACGUGC
(((((...((((((.........(((((..((((....)))).(.....)........................)))))))).)))..)))))((((((...))))))............ (-27.43 = -26.85 +  -0.58)

alignment

secondary structure

dotplot

Window 7

Location	8,495,941 – 8,496,061
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.17
Mean single sequence MFE	-43.57
Consensus MFE	-26.71
Energy contribution	-27.43
Covariance contribution	0.73
Combinations/Pair	1.33
Mean z-score	-1.95
Structure conservation index	0.61
SVM decision value	1.44
SVM RNA-class probability	0.954491
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8495941 120 - 27905053
GCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGUCUGCCCCUGACCCUGACCCAUUCCCUGCUGGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGCGGCGUGUCGCCCGAGGUGC
............((((((...))))))(((((((((.((.((((((((..((((((.(..((.(((((.((....)).))))).))..).)))))))).).)))).).)).))))))))) ( -55.00)
>DroVir_CAF1 14541 96 - 1
GCACAUCGUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGAUUCGCU-----------------------UGU-CUCCUGCAGAAAGCUGCUGAGCGAUCUCGGCUUAUCGCCCGAGGUGC
............((((((...))))))(((((((((.((((..(((-----------------------((.-(((..((((....)))).))))).....)))..)))).))))))))) ( -40.90)
>DroGri_CAF1 15519 96 - 1
GCACAUCGUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGAUUCGCC-----------------------CGU-CUCCUGCAGGAAACUGCUCAGCGAUGGCGGCUUAUCGCCCGUGGUGC
............((((((...))))))(((((.(((.((((..(((-----------------------.((-(((((((((....))))..)).)).))))))..)))).))).))))) ( -44.10)
>DroWil_CAF1 4383 96 - 1
CCACGUCAUUUUUAGCCGCCUCGGCCAGAACCUUGGCAGACUCGCUC-----------------------GA-CUCGUGCAGAAAGCUGCUCAGCGAACGUCCGUUGUCGCCCGCGGUGC
..............(((((....(((((....))))).(((.((..(-----------------------(.-.((((((((....))))...)))).))..))..)))....))))).. ( -28.40)
>DroMoj_CAF1 12514 96 - 1
GCACGUCAUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGAAUCGCU-----------------------UGA-CUCCUGCAGGAAGCUGCUCAGCGAUCGCGGCUUGUCGCCUGAGGUGC
((((.(((.....((((((.((((((((....))))))))((((((-----------------------.((-.....((((....)))))))))))).)))))).......))).)))) ( -44.80)
>DroAna_CAF1 4474 99 - 1
GCACAUCCUUUUUGGCCGCCUCGGCCAACACCUUGGCCGACUGCCCCG---------------------UGUUGUCCUGCAGGAAGCUGCUCAAGGAACGGGGUGGAUCGCCGCCAGUGC
((((........((((.((.((((((((....))))))))(..(((((---------------------(....((((((((....))))...))))))))))..)...)).)))))))) ( -48.20)
>consensus
GCACAUCAUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGACUCGCC_______________________UGU_CUCCUGCAGGAAGCUGCUCAGCGAUCGCGGCUUAUCGCCCGAGGUGC
((((.(((((...(((....((((((((....))))))))...)))................................((((....))))..))))).((((((.....))).))))))) (-26.71 = -27.43 +   0.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:35 2006