When I use Biostring pairwiseAlignment, I can't get the same result with EMBOSS needle using the same parameters.

library(readr)
library(dplyr)
library(Biostrings)

EDNAFULL<-read_tsv("/run/media/panxiaoguang/myLinux/Zebrafish/EDNAFULL",col_names = T)%>%
  tibble::column_to_rownames(var="index")%>%
  as.matrix()

EDNAFULL

   A  T  G  C  S  W  R  Y  K  M  B  V  H  D  N  U
A  5 -4 -4 -4 -4  1  1 -4 -4  1 -4 -1 -1 -1 -2 -4
T -4  5 -4 -4 -4  1 -4  1  1 -4 -1 -4 -1 -1 -2  5
G -4 -4  5 -4  1 -4  1 -4  1 -4 -1 -1 -4 -1 -2 -4
C -4 -4 -4  5  1 -4 -4  1 -4  1 -1 -1 -1 -4 -2 -4
S -4 -4  1  1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4
W  1  1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1  1
R  1 -4  1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4
Y -4  1 -4  1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1  1
K -4  1  1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1  1
M  1 -4 -4  1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4
B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1
V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4
H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1
D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1
N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2
U -4  5 -4 -4 -4  1 -4  1  1 -4 -1 -4 -1 -1 -2  5

pairwiseAlignment(pattern = "GATGAACAGCAACTTTTATGAATGGGAGGGCTCTATCTTAGGGGGCAACAACACTGTTGATGTTCCCAATTACATTGCTA", 
                  subject = "GGGGAGGGCTCTATCTTAGG",
                  type = "global",
                  substitutionMatrix=EDNAFULL,
                  gapOpening=10,
                  gapExtension=0.5
)

Global PairwiseAlignmentsSingleSubject (1 of 1)
pattern: GATGAACAGCAACTTTTATGAATGGGAGGGCTCTATCTTAGGGGGCAACAACACTGTTGATGTTCCCAATTACATTGCTA
subject: G----------------------GGGAGGGCTCTATCTTAGG--------------------------------------
score: 50 

sessionInfo( )
R version 4.2.2 (2022-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Stream 8

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
 [4] LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biostrings_2.66.0   GenomeInfoDb_1.34.3 XVector_0.38.0      IRanges_2.32.0     
[5] S4Vectors_0.36.0    BiocGenerics_0.44.0 readr_2.1.3         dplyr_1.0.10       

loaded via a namespace (and not attached):
 [1] pillar_1.8.1           compiler_4.2.2         bitops_1.0-7           tools_4.2.2           
 [5] zlibbioc_1.44.0        bit_4.0.5              lifecycle_1.0.3        tibble_3.1.8          
 [9] pkgconfig_2.0.3        rlang_1.0.6            DBI_1.1.3              cli_3.4.1             
[13] rstudioapi_0.14        parallel_4.2.2         GenomeInfoDbData_1.2.9 withr_2.5.0           
[17] generics_0.1.3         vctrs_0.5.1            hms_1.1.2              bit64_4.0.5           
[21] tidyselect_1.2.0       glue_1.6.2             R6_2.5.1               fansi_1.0.3           
[25] vroom_1.6.0            tzdb_0.3.0             magrittr_2.0.3         ellipsis_0.3.2        
[29] assertthat_0.2.1       utf8_1.2.2             RCurl_1.98-1.9         crayon_1.5.2

when I use needle, I get

#=======================================
#
# Aligned_sequences: 2
# 1: 
# 2: 
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 80
# Identity:      19/80 (23.8%)
# Similarity:    19/80 (23.8%)
# Gaps:          60/80 (75.0%)
# Score: 91.0
# 
#
#=======================================

                   1 GATGAACAGCAACTTTTATGAATGGGAGGGCTCTATCTTAGGGGGCAACA     50
                                           .|||||||||||||||||||        
                   1 ----------------------GGGGAGGGCTCTATCTTAGG--------     20

                  51 ACACTGTTGATGTTCCCAATTACATTGCTA     80

                  20 ------------------------------     20


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