AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene031590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031590.t1 MTR_4g080200 93.137 204 13 1 1 203 55 258 2.18e-139 394
MS.gene031590.t1 MTR_1g023400 49.765 213 76 11 14 208 72 271 9.73e-48 160
MS.gene031590.t1 MTR_1g009110 47.664 214 92 10 1 203 82 286 7.06e-45 154
MS.gene031590.t1 MTR_1g022200 47.343 207 82 12 14 203 84 280 1.59e-39 140
MS.gene031590.t1 MTR_1g037540 41.176 204 100 7 13 203 108 304 1.20e-36 132
MS.gene031590.t1 MTR_1g022105 31.746 189 78 5 18 203 108 248 1.38e-17 80.1
MS.gene031590.t1 MTR_5g027370 27.488 211 133 10 12 217 128 323 2.61e-12 65.9
MS.gene031590.t1 MTR_5g010550 27.273 198 108 10 29 207 173 353 3.01e-12 65.5
MS.gene031590.t1 MTR_4g133170 27.136 199 118 7 26 211 85 269 3.05e-12 65.5
MS.gene031590.t1 MTR_8g093280 65.854 41 14 0 2 42 65 105 3.19e-12 61.6
MS.gene031590.t1 MTR_5g010550 27.273 198 108 10 29 207 187 367 3.29e-12 65.5
MS.gene031590.t1 MTR_5g027330 27.488 211 133 10 12 217 139 334 4.98e-12 65.1
MS.gene031590.t1 MTR_5g010560 26.562 192 111 9 29 205 173 349 8.62e-12 64.3
MS.gene031590.t1 MTR_5g010610 26.042 192 112 9 29 205 162 338 7.17e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATACATCATCACAGAAAA+AGG 0.202241 4.2:+44456991 None:intergenic
GTATCGTTTGGTTGGAAATA+TGG 0.217514 4.2:-44456926 MS.gene031590:CDS
GTTGCAAGAATTGAAATTTA+TGG 0.226085 4.2:-44457481 MS.gene031590:CDS
GATGAATCCTTGTATGGTTT+TGG 0.233004 4.2:-44457322 MS.gene031590:CDS
AACAATGATTTGATGGGAAT+TGG 0.286013 4.2:+44457514 None:intergenic
CTTGGTTATGTGTGCAATAT+AGG 0.302638 4.2:-44456953 MS.gene031590:CDS
TAAACATCTCTGATACTAAT+AGG 0.315807 4.2:-44457267 MS.gene031590:CDS
GATGATGTATTTGAGATAAA+AGG 0.355883 4.2:-44456980 MS.gene031590:CDS
GAGCTTCTAGTTTCTGAAAC+TGG 0.364523 4.2:+44457035 None:intergenic
GATGGACATCTTTAGTTGTT+GGG 0.365174 4.2:+44457383 None:intergenic
TTTGAGATAAAAGGTTATCT+TGG 0.370177 4.2:-44456971 MS.gene031590:CDS
TACTCTGATGAATCCTTGTA+TGG 0.371043 4.2:-44457328 MS.gene031590:CDS
CAGCCATCCTCCTATTACTA+TGG 0.376905 4.2:-44457173 MS.gene031590:CDS
TTGTTAACGGTGTTTATCAT+TGG 0.381352 4.2:-44457117 MS.gene031590:CDS
AAACTAGAAGCTCCAAAGTT+AGG 0.388884 4.2:-44457025 MS.gene031590:CDS
AGATATAACACTCTTGTTAA+CGG 0.395015 4.2:-44457130 MS.gene031590:CDS
TTGAGGAAACAATGATTTGA+TGG 0.396928 4.2:+44457507 None:intergenic
ACAAGAGTGTTATATCTTGA+AGG 0.406492 4.2:+44457136 None:intergenic
AGCCGTGTGACCATAGTAAT+AGG 0.454782 4.2:+44457163 None:intergenic
AATATAGGTGTAGTATCGTT+TGG 0.455302 4.2:-44456938 MS.gene031590:CDS
TATGGACTCTGGAACAAAAC+GGG 0.458302 4.2:-44456908 MS.gene031590:CDS
AGATGGACATCTTTAGTTGT+TGG 0.470051 4.2:+44457382 None:intergenic
TCAATTCTTGCAACGTCTTG+AGG 0.481185 4.2:+44457490 None:intergenic
ATATGGACTCTGGAACAAAA+CGG 0.496728 4.2:-44456909 MS.gene031590:CDS
GGGATATAGTGACCTAACTT+TGG 0.499776 4.2:+44457013 None:intergenic
CATTGGATTACAAGCTCTGA+TGG 0.509722 4.2:-44457100 MS.gene031590:CDS
ATGACCTAAGCACAAAATCA+TGG 0.510246 4.2:-44457207 MS.gene031590:CDS
TAGGTGTAGTATCGTTTGGT+TGG 0.513898 4.2:-44456934 MS.gene031590:CDS
TTGGTTGGAAATATGGACTC+TGG 0.520615 4.2:-44456919 MS.gene031590:CDS
ATTCCTCGTGCTCCCTCACT+CGG 0.521887 4.2:-44457358 MS.gene031590:CDS
TGAGGAAACAATGATTTGAT+GGG 0.538403 4.2:+44457508 None:intergenic
AGGGAGCACGAGGAATAAGA+TGG 0.548435 4.2:+44457365 None:intergenic
AACAGCACCAAAACCATACA+AGG 0.549888 4.2:+44457315 None:intergenic
AGGAGGATGGCTGACGAGGA+GGG 0.562111 4.2:+44457183 None:intergenic
AGAGTAATGGTTACCGAGTG+AGG 0.564348 4.2:+44457345 None:intergenic
GAAATTTATGGTAGTTGCGA+CGG 0.568199 4.2:-44457469 MS.gene031590:CDS
ACAAGGATTCATCAGAGTAA+TGG 0.574491 4.2:+44457332 None:intergenic
CATCTCTGATACTAATAGGA+TGG 0.575178 4.2:-44457263 MS.gene031590:CDS
GACTCTGGAACAAAACGGGT+GGG 0.578193 4.2:-44456904 MS.gene031590:CDS
TAGGAGGATGGCTGACGAGG+AGG 0.596364 4.2:+44457182 None:intergenic
GAGTAATGGTTACCGAGTGA+GGG 0.602835 4.2:+44457346 None:intergenic
CTCCTATTACTATGGTCACA+CGG 0.608239 4.2:-44457165 MS.gene031590:CDS
TAATAGGAGGATGGCTGACG+AGG 0.618048 4.2:+44457179 None:intergenic
TGACCATAGTAATAGGAGGA+TGG 0.619998 4.2:+44457170 None:intergenic
GGACTCTGGAACAAAACGGG+TGG 0.624566 4.2:-44456905 MS.gene031590:CDS
CGTGTGACCATAGTAATAGG+AGG 0.626714 4.2:+44457166 None:intergenic
TATCGCGAAAGTCAAAGCAA+AGG 0.669569 4.2:+44457059 None:intergenic
TTACCGAGTGAGGGAGCACG+AGG 0.676218 4.2:+44457355 None:intergenic
ATCGTGATGAGTTATGCATG+AGG 0.771175 4.2:+44457423 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAAATAAATTCTCTTTTGA+AGG - chr4.2:44457208-44457227 MS.gene031590:CDS 20.0%
! AAATACATCATCACAGAAAA+AGG + chr4.2:44457459-44457478 None:intergenic 25.0%
! AATACATCATCACAGAAAAA+GGG + chr4.2:44457458-44457477 None:intergenic 25.0%
! AGATATAACACTCTTGTTAA+CGG - chr4.2:44457317-44457336 MS.gene031590:CDS 25.0%
! GTTGCAAGAATTGAAATTTA+TGG - chr4.2:44456966-44456985 MS.gene031590:CDS 25.0%
! TAAACATCTCTGATACTAAT+AGG - chr4.2:44457180-44457199 MS.gene031590:CDS 25.0%
!! GATGATGTATTTGAGATAAA+AGG - chr4.2:44457467-44457486 MS.gene031590:CDS 25.0%
!! TTTGAGATAAAAGGTTATCT+TGG - chr4.2:44457476-44457495 MS.gene031590:CDS 25.0%
AACAATGATTTGATGGGAAT+TGG + chr4.2:44456936-44456955 None:intergenic 30.0%
AATATAGGTGTAGTATCGTT+TGG - chr4.2:44457509-44457528 MS.gene031590:CDS 30.0%
ATACATCATCACAGAAAAAG+GGG + chr4.2:44457457-44457476 None:intergenic 30.0%
TGAGGAAACAATGATTTGAT+GGG + chr4.2:44456942-44456961 None:intergenic 30.0%
TTGAGGAAACAATGATTTGA+TGG + chr4.2:44456943-44456962 None:intergenic 30.0%
TTGTTAACGGTGTTTATCAT+TGG - chr4.2:44457330-44457349 MS.gene031590:CDS 30.0%
! ATGAAGTTCATCTTTTGTGA+TGG - chr4.2:44456897-44456916 MS.gene031590:CDS 30.0%
!! ACAAGAGTGTTATATCTTGA+AGG + chr4.2:44457314-44457333 None:intergenic 30.0%
!! ATCACGATCAATTGATTTTG+TGG - chr4.2:44457039-44457058 MS.gene031590:CDS 30.0%
AAACTAGAAGCTCCAAAGTT+AGG - chr4.2:44457422-44457441 MS.gene031590:CDS 35.0%
ACAAGGATTCATCAGAGTAA+TGG + chr4.2:44457118-44457137 None:intergenic 35.0%
AGATGGACATCTTTAGTTGT+TGG + chr4.2:44457068-44457087 None:intergenic 35.0%
ATGACCTAAGCACAAAATCA+TGG - chr4.2:44457240-44457259 MS.gene031590:CDS 35.0%
CATCTCTGATACTAATAGGA+TGG - chr4.2:44457184-44457203 MS.gene031590:CDS 35.0%
CTTGGTTATGTGTGCAATAT+AGG - chr4.2:44457494-44457513 MS.gene031590:CDS 35.0%
GAAATTTATGGTAGTTGCGA+CGG - chr4.2:44456978-44456997 MS.gene031590:CDS 35.0%
GATGGACATCTTTAGTTGTT+GGG + chr4.2:44457067-44457086 None:intergenic 35.0%
GTATCGTTTGGTTGGAAATA+TGG - chr4.2:44457521-44457540 MS.gene031590:CDS 35.0%
TACTCTGATGAATCCTTGTA+TGG - chr4.2:44457119-44457138 MS.gene031590:CDS 35.0%
! AAGTTCATCTTTTGTGATGG+AGG - chr4.2:44456900-44456919 MS.gene031590:CDS 35.0%
! GATGAATCCTTGTATGGTTT+TGG - chr4.2:44457125-44457144 MS.gene031590:CDS 35.0%
!! ATATGGACTCTGGAACAAAA+CGG - chr4.2:44457538-44457557 MS.gene031590:CDS 35.0%
AACAGCACCAAAACCATACA+AGG + chr4.2:44457135-44457154 None:intergenic 40.0%
ATCGTGATGAGTTATGCATG+AGG + chr4.2:44457027-44457046 None:intergenic 40.0%
CTCCTATTACTATGGTCACA+CGG - chr4.2:44457282-44457301 MS.gene031590:CDS 40.0%
GGGATATAGTGACCTAACTT+TGG + chr4.2:44457437-44457456 None:intergenic 40.0%
TAGGTGTAGTATCGTTTGGT+TGG - chr4.2:44457513-44457532 MS.gene031590:CDS 40.0%
TATCGCGAAAGTCAAAGCAA+AGG + chr4.2:44457391-44457410 None:intergenic 40.0%
TCAATTCTTGCAACGTCTTG+AGG + chr4.2:44456960-44456979 None:intergenic 40.0%
TGACCATAGTAATAGGAGGA+TGG + chr4.2:44457280-44457299 None:intergenic 40.0%
TTGGTTGGAAATATGGACTC+TGG - chr4.2:44457528-44457547 MS.gene031590:CDS 40.0%
! CATTGGATTACAAGCTCTGA+TGG - chr4.2:44457347-44457366 MS.gene031590:CDS 40.0%
!! GAGCTTCTAGTTTCTGAAAC+TGG + chr4.2:44457415-44457434 None:intergenic 40.0%
!! TATGGACTCTGGAACAAAAC+GGG - chr4.2:44457539-44457558 MS.gene031590:CDS 40.0%
!!! GACGGTGTTTTTTGTCTCAA+AGG - chr4.2:44456996-44457015 MS.gene031590:CDS 40.0%
AGAGTAATGGTTACCGAGTG+AGG + chr4.2:44457105-44457124 None:intergenic 45.0%
AGCCGTGTGACCATAGTAAT+AGG + chr4.2:44457287-44457306 None:intergenic 45.0%
CAGCCATCCTCCTATTACTA+TGG - chr4.2:44457274-44457293 MS.gene031590:CDS 45.0%
CGTGTGACCATAGTAATAGG+AGG + chr4.2:44457284-44457303 None:intergenic 45.0%
GAGTAATGGTTACCGAGTGA+GGG + chr4.2:44457104-44457123 None:intergenic 45.0%
! GGGTCCATGATTTTGTGCTT+AGG + chr4.2:44457247-44457266 None:intergenic 45.0%
TAATAGGAGGATGGCTGACG+AGG + chr4.2:44457271-44457290 None:intergenic 50.0%
! AGGGAGCACGAGGAATAAGA+TGG + chr4.2:44457085-44457104 None:intergenic 50.0%
!! GACTCTGGAACAAAACGGGT+GGG - chr4.2:44457543-44457562 MS.gene031590:CDS 50.0%
ATTCCTCGTGCTCCCTCACT+CGG - chr4.2:44457089-44457108 MS.gene031590:CDS 55.0%
!! GGACTCTGGAACAAAACGGG+TGG - chr4.2:44457542-44457561 MS.gene031590:CDS 55.0%
AGGAGGATGGCTGACGAGGA+GGG + chr4.2:44457267-44457286 None:intergenic 60.0%
TAGGAGGATGGCTGACGAGG+AGG + chr4.2:44457268-44457287 None:intergenic 60.0%
! TTACCGAGTGAGGGAGCACG+AGG + chr4.2:44457095-44457114 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 44456897 44457572 44456897 ID=MS.gene031590
chr4.2 mRNA 44456897 44457572 44456897 ID=MS.gene031590.t1;Parent=MS.gene031590
chr4.2 exon 44456897 44457572 44456897 ID=MS.gene031590.t1.exon1;Parent=MS.gene031590.t1
chr4.2 CDS 44456897 44457572 44456897 ID=cds.MS.gene031590.t1;Parent=MS.gene031590.t1
Gene Sequence

>MS.gene031590

ATGAAGTTCATCTTTTGTGATGGAGGCAATGAGAAACCAATTCCCATCAAATCATTGTTTCCTCAAGACGTTGCAAGAATTGAAATTTATGGTAGTTGCGACGGTGTTTTTTGTCTCAAAGGTATTTCCTCATGCATAACTCATCACGATCAATTGATTTTGTGGAACCCAACAACTAAAGATGTCCATCTTATTCCTCGTGCTCCCTCACTCGGTAACCATTACTCTGATGAATCCTTGTATGGTTTTGGTGCTGTTAACGACGACTTCAAAGTTGTCAAACTAAACATCTCTGATACTAATAGGATGGTGAAAATAAATTCTCTTTTGAAGGCAGACATTTATGACCTAAGCACAAAATCATGGACCCTCCTCGTCAGCCATCCTCCTATTACTATGGTCACACGGCTACAGCCTTCAAGATATAACACTCTTGTTAACGGTGTTTATCATTGGATTACAAGCTCTGATGGCTCTAATGCTGCACAAATCCTTTGCTTTGACTTTCGCGATAACCAGTTTCAGAAACTAGAAGCTCCAAAGTTAGGTCACTATATCCCCTTTTTCTGTGATGATGTATTTGAGATAAAAGGTTATCTTGGTTATGTGTGCAATATAGGTGTAGTATCGTTTGGTTGGAAATATGGACTCTGGAACAAAACGGGTGGGCCAAAAA
Protein sequence

>MS.gene031590.t1

MKFIFCDGGNEKPIPIKSLFPQDVARIEIYGSCDGVFCLKGISSCITHHDQLILWNPTTKDVHLIPRAPSLGNHYSDESLYGFGAVNDDFKVVKLNISDTNRMVKINSLLKADIYDLSTKSWTLLVSHPPITMVTRLQPSRYNTLVNGVYHWITSSDGSNAAQILCFDFRDNQFQKLEAPKLGHYIPFFCDDVFEIKGYLGYVCNIGVVSFGWKYGLWNKTGGPK