AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180002494.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180002494.01.T01 MTR_5g021880 59.091 264 83 6 1 249 1 254 2.00e-96 290
MsG0180002494.01.T01 MTR_5g021880 59.091 264 83 6 1 249 1 254 3.56e-96 290
MsG0180002494.01.T01 MTR_5g021880 59.091 264 83 6 1 249 1 254 6.34e-96 290
MsG0180002494.01.T01 MTR_5g022040 59.245 265 86 6 1 249 1 259 8.14e-96 289
MsG0180002494.01.T01 MTR_0627s0010 59.363 251 85 4 1 250 1 235 7.51e-92 277
MsG0180002494.01.T01 MTR_6g046320 57.769 251 95 3 1 250 1 241 1.97e-90 275
MsG0180002494.01.T01 MTR_4g027370 57.634 262 79 6 1 249 1 243 4.05e-89 273
MsG0180002494.01.T01 MTR_5g021860 57.252 262 80 6 1 249 1 243 5.22e-89 271
MsG0180002494.01.T01 MTR_5g021860 57.252 262 80 6 1 249 1 243 1.23e-88 271
MsG0180002494.01.T01 MTR_5g021920 55.422 249 102 2 1 248 1 241 4.68e-88 263
MsG0180002494.01.T01 MTR_5g022750 58.800 250 53 4 1 246 1 204 3.66e-87 265
MsG0180002494.01.T01 MTR_5g022900 55.682 264 89 8 1 250 1 250 4.59e-82 254
MsG0180002494.01.T01 MTR_5g007940 52.510 259 96 4 1 249 1 242 1.70e-80 249
MsG0180002494.01.T01 MTR_5g010610 53.200 250 102 5 1 249 1 236 1.51e-75 239
MsG0180002494.01.T01 MTR_5g010550 49.286 280 94 7 1 249 1 263 2.93e-73 231
MsG0180002494.01.T01 MTR_5g010550 50.769 260 97 7 3 249 8 249 4.33e-71 225
MsG0180002494.01.T01 MTR_5g010560 49.615 260 98 7 3 249 8 247 1.19e-69 221
MsG0180002494.01.T01 MTR_5g022090 48.770 244 80 5 1 243 1 200 4.02e-63 202
MsG0180002494.01.T01 MTR_5g022045 47.012 251 98 7 1 249 1 218 2.15e-62 202
MsG0180002494.01.T01 MTR_5g010660 47.809 251 88 6 1 250 1 209 9.87e-62 201
MsG0180002494.01.T01 MTR_7g090810 47.348 264 80 6 1 250 1 219 1.88e-61 199
MsG0180002494.01.T01 MTR_7g117100 53.086 162 55 4 101 249 1 154 3.26e-47 158
MsG0180002494.01.T01 MTR_7g117100 53.086 162 55 4 101 249 1 154 3.11e-46 158
MsG0180002494.01.T01 MTR_5g027370 42.623 244 102 7 1 243 1 207 2.76e-44 154
MsG0180002494.01.T01 MTR_5g027330 42.623 244 102 7 1 243 12 218 2.87e-44 155
MsG0180002494.01.T01 MTR_3g463170 45.263 95 52 0 1 95 54 148 6.59e-24 94.7
MsG0180002494.01.T01 MTR_5g074870 46.465 99 53 0 1 99 44 142 2.85e-22 90.1
MsG0180002494.01.T01 MTR_7g090810 64.062 64 23 0 187 250 12 75 9.14e-21 89.4
MsG0180002494.01.T01 MTR_7g407070 26.540 211 121 5 39 249 32 208 5.29e-15 73.9
MsG0180002494.01.T01 MTR_1g017970 34.254 181 62 5 1 181 1 124 6.27e-15 69.7
MsG0180002494.01.T01 MTR_3g436150 26.066 211 121 5 39 249 32 207 5.88e-13 68.2
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 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAAATGAGAAGAGATTTAA+TGG 0.185410 1:+39100377 None:intergenic
AGAATTCACAACTTTAAATT+TGG 0.190607 1:+39100032 None:intergenic
CACCTTTGGCTAGTCCTTGC+AGG 0.217479 1:+39100504 None:intergenic
AAAACGACAAGAACAATAAT+AGG 0.225564 1:-39100092 MsG0180002494.01.T01:CDS
GTCCGAATCATGAGACTAAT+TGG 0.318992 1:+39100282 None:intergenic
ACCTAAAACTAATAATTATA+AGG 0.322891 1:-39099845 MsG0180002494.01.T01:CDS
AAGAGATGCAAAATTAGATT+TGG 0.333412 1:-39100118 MsG0180002494.01.T01:CDS
GATATTCAAGCTTCCGCTTA+AGG 0.335860 1:-39100163 MsG0180002494.01.T01:CDS
AAACGACAAGAACAATAATA+GGG 0.373783 1:-39100091 MsG0180002494.01.T01:CDS
GTAAATGTGTGTGCAAGATT+TGG 0.381865 1:-39100356 MsG0180002494.01.T01:CDS
AAAGGTGCAATAAAGCAAAA+AGG 0.389508 1:-39100488 MsG0180002494.01.T01:CDS
ACAGGATTCTTATTAGCTTC+AGG 0.400161 1:+39099922 None:intergenic
CTTATGAATTCCCCAGTGAC+TGG 0.411466 1:+39099949 None:intergenic
GTGGTTTGCAACCCAGTCAC+TGG 0.413921 1:-39099961 MsG0180002494.01.T01:CDS
ACCTTTGGCTAGTCCTTGCA+GGG 0.428414 1:+39100505 None:intergenic
GATGGAAGATCATCAAAGTA+AGG 0.451107 1:+39100432 None:intergenic
CTGTCGGGTTACACACAAAA+CGG 0.453996 1:-39099903 MsG0180002494.01.T01:CDS
CTGGGTTGCAAACCACTAAA+GGG 0.458935 1:+39099968 None:intergenic
TCACAACTTTAAATTTGGTA+TGG 0.481672 1:+39100037 None:intergenic
CACCAATTAGTCTCATGATT+CGG 0.483573 1:-39100284 MsG0180002494.01.T01:CDS
ACTGGGTTGCAAACCACTAA+AGG 0.487749 1:+39099967 None:intergenic
TGGTTTGCAACCCAGTCACT+GGG 0.506786 1:-39099960 MsG0180002494.01.T01:CDS
ACGCCCAAACACCTAGTCAT+TGG 0.510386 1:+39099789 None:intergenic
TGTCGGGTTACACACAAAAC+GGG 0.510886 1:-39099902 MsG0180002494.01.T01:CDS
TTATGAATTCCCCAGTGACT+GGG 0.546931 1:+39099950 None:intergenic
AGGTACAACATTCTTGCCTC+CGG 0.552747 1:+39100246 None:intergenic
AAAGTTGTGAATTCTTGCAA+TGG 0.560422 1:-39100024 MsG0180002494.01.T01:CDS
AACAGTTTCGCATCCTTAAG+CGG 0.560628 1:+39100150 None:intergenic
ATGTGGGCAGTGAGGTGAGA+TGG 0.560862 1:+39100414 None:intergenic
AGGGTTCAGTTGCCCCTGCA+AGG 0.563344 1:-39100518 MsG0180002494.01.T01:CDS
TGTTAGAGCTGCCAATGACT+AGG 0.565376 1:-39099800 None:intergenic
TCTTAAGCTCGCACTCGAGA+AGG 0.567121 1:+39100226 None:intergenic
GCACTAATCCAACAACATGT+TGG 0.568433 1:-39099880 MsG0180002494.01.T01:CDS
TAAGGATGCGAAACTGTTGA+TGG 0.572101 1:-39100145 MsG0180002494.01.T01:CDS
AAGCTAATAAGAATCCTGTC+GGG 0.574753 1:-39099918 MsG0180002494.01.T01:CDS
TGGAGAGCTGAAGCAAAATG+TGG 0.577499 1:+39100397 None:intergenic
ACAAGAACAATAATAGGGGC+AGG 0.579127 1:-39100086 MsG0180002494.01.T01:CDS
TAGCAACAATCATGTAAAGC+TGG 0.587815 1:-39100190 MsG0180002494.01.T01:CDS
AATTGCAATGTAGTAAAATG+TGG 0.589121 1:+39100315 None:intergenic
ATGGAAGATCATCAAAGTAA+GGG 0.592462 1:+39100433 None:intergenic
TCGGACTGATGACTATAGAC+CGG 0.609316 1:-39100265 MsG0180002494.01.T01:CDS
GAAGCTAATAAGAATCCTGT+CGG 0.629339 1:-39099919 MsG0180002494.01.T01:CDS
CCTTTGGCTAGTCCTTGCAG+GGG 0.631677 1:+39100506 None:intergenic
CCCCTGCAAGGACTAGCCAA+AGG 0.635800 1:-39100506 MsG0180002494.01.T01:CDS
AACGACAAGAACAATAATAG+GGG 0.639710 1:-39100090 MsG0180002494.01.T01:CDS
GGAGAGCTGAAGCAAAATGT+GGG 0.658312 1:+39100398 None:intergenic
GACTGATGACTATAGACCGG+AGG 0.696088 1:-39100262 MsG0180002494.01.T01:CDS
GAAGCAAAATGTGGGCAGTG+AGG 0.740570 1:+39100406 None:intergenic
GGTTTGCAACCCAGTCACTG+GGG 0.755561 1:-39099959 MsG0180002494.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACCTAAAACTAATAATTATA+AGG - Chr1:39100487-39100506 MsG0180002494.01.T01:CDS 15.0%
!!! ACCTTATAATTATTAGTTTT+AGG + Chr1:39100491-39100510 None:intergenic 15.0%
!! AGAATTCACAACTTTAAATT+TGG + Chr1:39100303-39100322 None:intergenic 20.0%
! AAAACGACAAGAACAATAAT+AGG - Chr1:39100240-39100259 MsG0180002494.01.T01:CDS 25.0%
! AAACGACAAGAACAATAATA+GGG - Chr1:39100241-39100260 MsG0180002494.01.T01:CDS 25.0%
! AAGAGATGCAAAATTAGATT+TGG - Chr1:39100214-39100233 MsG0180002494.01.T01:CDS 25.0%
! AATTGCAATGTAGTAAAATG+TGG + Chr1:39100020-39100039 None:intergenic 25.0%
! ACAAATGAGAAGAGATTTAA+TGG + Chr1:39099958-39099977 None:intergenic 25.0%
! TCACAACTTTAAATTTGGTA+TGG + Chr1:39100298-39100317 None:intergenic 25.0%
AAAGTTGTGAATTCTTGCAA+TGG - Chr1:39100308-39100327 MsG0180002494.01.T01:CDS 30.0%
AACAAAAACCAACATGTTGT+TGG + Chr1:39100463-39100482 None:intergenic 30.0%
AACGACAAGAACAATAATAG+GGG - Chr1:39100242-39100261 MsG0180002494.01.T01:CDS 30.0%
ATCTAACAAAAACCCTTTAG+TGG - Chr1:39100352-39100371 MsG0180002494.01.T01:CDS 30.0%
ATGGAAGATCATCAAAGTAA+GGG + Chr1:39099902-39099921 None:intergenic 30.0%
! AAAGGTGCAATAAAGCAAAA+AGG - Chr1:39099844-39099863 MsG0180002494.01.T01:CDS 30.0%
! ACTAAAGGGTTTTTGTTAGA+TGG + Chr1:39100353-39100372 None:intergenic 30.0%
! CTAAAGGGTTTTTGTTAGAT+GGG + Chr1:39100352-39100371 None:intergenic 30.0%
!! TTTTTGCTTTATTGCACCTT+TGG + Chr1:39099845-39099864 None:intergenic 30.0%
AAGCTAATAAGAATCCTGTC+GGG - Chr1:39100414-39100433 MsG0180002494.01.T01:CDS 35.0%
GAAGCTAATAAGAATCCTGT+CGG - Chr1:39100413-39100432 MsG0180002494.01.T01:CDS 35.0%
GATGGAAGATCATCAAAGTA+AGG + Chr1:39099903-39099922 None:intergenic 35.0%
GTAAATGTGTGTGCAAGATT+TGG - Chr1:39099976-39099995 MsG0180002494.01.T01:CDS 35.0%
TAGCAACAATCATGTAAAGC+TGG - Chr1:39100142-39100161 MsG0180002494.01.T01:CDS 35.0%
! ACAGGATTCTTATTAGCTTC+AGG + Chr1:39100413-39100432 None:intergenic 35.0%
! CACCAATTAGTCTCATGATT+CGG - Chr1:39100048-39100067 MsG0180002494.01.T01:CDS 35.0%
!! AGCAAAAAGGAAAGTTGATG+AGG - Chr1:39099857-39099876 MsG0180002494.01.T01:CDS 35.0%
AACAGTTTCGCATCCTTAAG+CGG + Chr1:39100185-39100204 None:intergenic 40.0%
ACAAGAACAATAATAGGGGC+AGG - Chr1:39100246-39100265 MsG0180002494.01.T01:CDS 40.0%
GATATTCAAGCTTCCGCTTA+AGG - Chr1:39100169-39100188 MsG0180002494.01.T01:CDS 40.0%
GCACTAATCCAACAACATGT+TGG - Chr1:39100452-39100471 MsG0180002494.01.T01:CDS 40.0%
GTCCGAATCATGAGACTAAT+TGG + Chr1:39100053-39100072 None:intergenic 40.0%
TAAGGATGCGAAACTGTTGA+TGG - Chr1:39100187-39100206 MsG0180002494.01.T01:CDS 40.0%
TTATGAATTCCCCAGTGACT+GGG + Chr1:39100385-39100404 None:intergenic 40.0%
ACTGGGTTGCAAACCACTAA+AGG + Chr1:39100368-39100387 None:intergenic 45.0%
AGGTACAACATTCTTGCCTC+CGG + Chr1:39100089-39100108 None:intergenic 45.0%
CTGGGTTGCAAACCACTAAA+GGG + Chr1:39100367-39100386 None:intergenic 45.0%
CTGTCGGGTTACACACAAAA+CGG - Chr1:39100429-39100448 MsG0180002494.01.T01:CDS 45.0%
CTTATGAATTCCCCAGTGAC+TGG + Chr1:39100386-39100405 None:intergenic 45.0%
GGAGAGCTGAAGCAAAATGT+GGG + Chr1:39099937-39099956 None:intergenic 45.0%
TCGGACTGATGACTATAGAC+CGG - Chr1:39100067-39100086 MsG0180002494.01.T01:CDS 45.0%
TGGAGAGCTGAAGCAAAATG+TGG + Chr1:39099938-39099957 None:intergenic 45.0%
TGTCGGGTTACACACAAAAC+GGG - Chr1:39100430-39100449 MsG0180002494.01.T01:CDS 45.0%
GAAGCAAAATGTGGGCAGTG+AGG + Chr1:39099929-39099948 None:intergenic 50.0%
GACTGATGACTATAGACCGG+AGG - Chr1:39100070-39100089 MsG0180002494.01.T01:CDS 50.0%
TCTTAAGCTCGCACTCGAGA+AGG + Chr1:39100109-39100128 None:intergenic 50.0%
! ACCTTTGGCTAGTCCTTGCA+GGG + Chr1:39099830-39099849 None:intergenic 50.0%
! CGTTTTGTGTGTAACCCGAC+AGG + Chr1:39100431-39100450 None:intergenic 50.0%
! TGGTTTGCAACCCAGTCACT+GGG - Chr1:39100372-39100391 MsG0180002494.01.T01:CDS 50.0%
ATGTGGGCAGTGAGGTGAGA+TGG + Chr1:39099921-39099940 None:intergenic 55.0%
GGTTTGCAACCCAGTCACTG+GGG - Chr1:39100373-39100392 MsG0180002494.01.T01:CDS 55.0%
! CACCTTTGGCTAGTCCTTGC+AGG + Chr1:39099831-39099850 None:intergenic 55.0%
! CCTTTGGCTAGTCCTTGCAG+GGG + Chr1:39099829-39099848 None:intergenic 55.0%
! GTGGTTTGCAACCCAGTCAC+TGG - Chr1:39100371-39100390 MsG0180002494.01.T01:CDS 55.0%
AGGGTTCAGTTGCCCCTGCA+AGG - Chr1:39099814-39099833 MsG0180002494.01.T01:CDS 60.0%
!! CCCCTGCAAGGACTAGCCAA+AGG - Chr1:39099826-39099845 MsG0180002494.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 39099801 39100553 39099801 ID=MsG0180002494.01;Name=MsG0180002494.01
Chr1 mRNA 39099801 39100553 39099801 ID=MsG0180002494.01.T01;Parent=MsG0180002494.01;Name=MsG0180002494.01.T01;_AED=0.22;_eAED=0.22;_QI=0|-1|0|1|-1|1|1|0|250
Chr1 exon 39099801 39100553 39099801 ID=MsG0180002494.01.T01:exon:12413;Parent=MsG0180002494.01.T01
Chr1 CDS 39099801 39100553 39099801 ID=MsG0180002494.01.T01:cds;Parent=MsG0180002494.01.T01
Gene Sequence

>MsG0180002494.01.T01

ATGAAAAGAAAAAAGGGTTCAGTTGCCCCTGCAAGGACTAGCCAAAGGTGCAATAAAGCAAAAAGGAAAGTTGATGAGGCAGAAAGTCATGAACTTTGCCCTTACTTTGATGATCTTCCATCTCACCTCACTGCCCACATTTTGCTTCAGCTCTCCATTAAATCTCTTCTCATTTGTAAATGTGTGTGCAAGATTTGGAAAATAATGATATCAGAGCCACATTTTACTACATTGCAATTTGAGCGAGCACCAATTAGTCTCATGATTCGGACTGATGACTATAGACCGGAGGCAAGAATGTTGTACCTTCTCGAGTGCGAGCTTAAGAATTTTGAACTTGCTAGCAACAATCATGTAAAGCTGGAGTCGATATTCAAGCTTCCGCTTAAGGATGCGAAACTGTTGATGGTGAAAAGAGATGCAAAATTAGATTTGGCAAAAAACGACAAGAACAATAATAGGGGCAGGCAGAATCTTATTGTTTCTAACATAGACCATACCAAATTTAAAGTTGTGAATTCTTGCAATGGTTTGCTTTGTTTATTTGACCCATCTAACAAAAACCCTTTAGTGGTTTGCAACCCAGTCACTGGGGAATTCATAAGACTTCCTGAAGCTAATAAGAATCCTGTCGGGTTACACACAAAACGGGCACTAATCCAACAACATGTTGGTTTTTGTTATCAACCTAAAACTAATAATTATAAGGTGATAAAAATGTCGACGAGACGTGTTAGAGCTGCCAATGACTAG
Protein sequence

>MsG0180002494.01.T01

MKRKKGSVAPARTSQRCNKAKRKVDEAESHELCPYFDDLPSHLTAHILLQLSIKSLLICKCVCKIWKIMISEPHFTTLQFERAPISLMIRTDDYRPEARMLYLLECELKNFELASNNHVKLESIFKLPLKDAKLLMVKRDAKLDLAKNDKNNNRGRQNLIVSNIDHTKFKVVNSCNGLLCLFDPSNKNPLVVCNPVTGEFIRLPEANKNPVGLHTKRALIQQHVGFCYQPKTNNYKVIKMSTRRVRAAND*