AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene061547

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061547.t1 MTR_3g065020 94.142 239 13 1 1 239 1 238 3.46e-161 446
MS.gene061547.t1 MTR_5g077370 59.514 247 82 9 1 239 1 237 1.98e-86 256
MS.gene061547.t1 MTR_1g033340 43.028 251 125 7 3 239 5 251 1.24e-59 189
MS.gene061547.t1 MTR_2g104900 65.432 81 20 3 81 154 76 155 6.36e-27 104
MS.gene061547.t1 MTR_1g013130 52.000 100 30 3 74 155 80 179 1.53e-25 101
MS.gene061547.t1 MTR_1g107055 40.299 134 74 4 70 202 47 175 1.33e-24 97.1
MS.gene061547.t1 MTR_3g106230 49.541 109 30 6 72 159 60 164 2.85e-20 86.3
MS.gene061547.t1 MTR_4g006575 62.857 70 18 3 87 155 67 129 1.33e-18 81.6
MS.gene061547.t1 MTR_4g006600 62.857 70 18 3 87 155 67 129 1.33e-18 81.6
MS.gene061547.t1 MTR_4g128340 66.071 56 18 1 86 140 44 99 3.46e-17 76.6
MS.gene061547.t1 MTR_8g466760 48.780 82 32 4 87 160 98 177 8.07e-14 69.7
MS.gene061547.t1 MTR_7g083210 75.758 33 8 0 87 119 39 71 2.15e-12 64.3
MS.gene061547.t1 MTR_7g086860 67.568 37 12 0 87 123 30 66 4.82e-12 62.4
MS.gene061547.t1 MTR_5g008280 44.186 86 38 4 87 165 46 128 1.69e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061547.t1 AT1G66140 50.000 184 57 8 86 239 82 260 9.97e-47 156
MS.gene061547.t1 AT1G24625 40.777 206 84 11 46 239 30 209 1.14e-31 115
MS.gene061547.t1 AT1G80730 53.261 92 25 2 82 155 61 152 1.06e-23 95.5
MS.gene061547.t1 AT5G10970 46.721 122 49 5 47 155 56 174 9.97e-23 94.0
MS.gene061547.t1 AT5G25160 56.410 78 28 2 84 155 56 133 6.41e-22 90.9
MS.gene061547.t1 AT5G57520 52.113 71 34 0 87 157 50 120 2.83e-16 73.9
MS.gene061547.t1 AT5G14010 68.421 38 12 0 87 124 36 73 1.15e-13 67.0
MS.gene061547.t1 AT3G58070 55.357 56 21 1 67 122 73 124 8.51e-12 63.5
MS.gene061547.t1 AT5G01860 60.000 40 16 0 87 126 65 104 1.48e-11 62.4

Find 38 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCCTCTTAATGGTTCTTTC+AGG 0.209061 3.2:-60471802 MS.gene061547:CDS
CTTGCATCTCTGCCTCTTAA+TGG 0.234261 3.2:-60471812 MS.gene061547:CDS
CAAAGTTTCAATGTTAATTC+AGG 0.241054 3.2:+60471515 None:intergenic
AATGGTTCTTTCAGGTCATT+AGG 0.297972 3.2:-60471794 MS.gene061547:CDS
AATTGCAAGAGAAAATTCTT+TGG 0.318566 3.2:+60471957 None:intergenic
TTTCTCTCTTGTGCGCGTTT+TGG 0.325608 3.2:+60471891 None:intergenic
AACCTGGAGAGGTTTCAATT+TGG 0.372940 3.2:+60472122 None:intergenic
GCAAAGCGAGCTATGCGAAT+TGG 0.383652 3.2:-60471860 MS.gene061547:CDS
GGACTAGGCCTTATTGTTGA+TGG 0.394683 3.2:+60471734 None:intergenic
TATCGGTCATCCGATATTCT+TGG 0.398517 3.2:-60471675 MS.gene061547:CDS
CTGGAGAGGTTTCAATTTGG+TGG 0.433921 3.2:+60472125 None:intergenic
TCATCGTCCTCCAAGAATAT+CGG 0.434665 3.2:+60471665 None:intergenic
TAATTCAGATTCCATCTCAC+TGG 0.457739 3.2:-60472080 MS.gene061547:CDS
AAGTTCGTTGCTGCTCTCAC+TGG 0.464039 3.2:+60471985 None:intergenic
TTGGTTGCTCGAGATTCAAC+AGG 0.467504 3.2:-60472025 MS.gene061547:CDS
ATTAGAAAGACTGTTACTAT+AGG 0.476036 3.2:+60472099 None:intergenic
GCAAGAGAAAATTCTTTGGA+TGG 0.480537 3.2:+60471961 None:intergenic
AGCAGTGCTAGATTCAAGTT+AGG 0.490778 3.2:-60471701 MS.gene061547:CDS
GACCTGAAAGAACCATTAAG+AGG 0.490795 3.2:+60471800 None:intergenic
TGGAGAGGTTTCAATTTGGT+GGG 0.530109 3.2:+60472126 None:intergenic
CACCAAATTGAAACCTCTCC+AGG 0.534773 3.2:-60472124 MS.gene061547:CDS
TTTCAACAACAACAACGACT+TGG 0.535603 3.2:-60472044 MS.gene061547:CDS
AGATTCAAGTTAGGATCTAT+CGG 0.563874 3.2:-60471692 MS.gene061547:CDS
CGGTCATCCGATATTCTTGG+AGG 0.568620 3.2:-60471672 MS.gene061547:CDS
GAATTCTCTATGTCAACCAA+TGG 0.572984 3.2:+60471542 None:intergenic
AGAGGTTTCAATTTGGTGGG+TGG 0.575688 3.2:+60472129 None:intergenic
GAGTGTTAAGTCCAGTGAGA+TGG 0.580909 3.2:+60472069 None:intergenic
ATCAGATTCATATTCTTCTG+TGG 0.583159 3.2:+60472180 None:intergenic
TTTCATCAGGTTACTGAGGG+AGG 0.597854 3.2:-60471617 MS.gene061547:CDS
TGGATATAGTCGAAGCAACA+TGG 0.599561 3.2:+60472149 None:intergenic
TACAGCTCTCAGGCGCTCGG+TGG 0.607796 3.2:-60471917 MS.gene061547:CDS
TGAGGTGAATGTGAAACCAT+TGG 0.612040 3.2:-60471558 MS.gene061547:CDS
AGACTGTTACTATAGGAACC+TGG 0.640109 3.2:+60472106 None:intergenic
ACGATGAGACAGAACTGATG+TGG 0.646574 3.2:-60471649 MS.gene061547:CDS
GAGACAGAACTGATGTGGCA+AGG 0.647919 3.2:-60471644 MS.gene061547:CDS
GTTACTATAGGAACCTGGAG+AGG 0.687906 3.2:+60472111 None:intergenic
ACACACTCTTCACTACACCA+TGG 0.697590 3.2:-60471764 MS.gene061547:CDS
GAATTGGACTATTCACTGAG+AGG 0.709982 3.2:-60471844 MS.gene061547:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATTGCAAGAGAAAATTCTT+TGG + chr3.2:60471771-60471790 None:intergenic 25.0%
! ATTAGAAAGACTGTTACTAT+AGG + chr3.2:60471629-60471648 None:intergenic 25.0%
! CAAAGTTTCAATGTTAATTC+AGG + chr3.2:60472213-60472232 None:intergenic 25.0%
! TCTACTTCAAGATCAAAAAT+TGG + chr3.2:60471523-60471542 None:intergenic 25.0%
!! AATTTTTGATCTTGAAGTAG+AGG - chr3.2:60471522-60471541 MS.gene061547:CDS 25.0%
!! TTCAAATATGTGTTTTACTG+AGG - chr3.2:60472149-60472168 MS.gene061547:CDS 25.0%
ATCAGATTCATATTCTTCTG+TGG + chr3.2:60471548-60471567 None:intergenic 30.0%
! AGATTCAAGTTAGGATCTAT+CGG - chr3.2:60472033-60472052 MS.gene061547:CDS 30.0%
! TTTTCTCTTGCAATTACTGT+CGG - chr3.2:60471776-60471795 MS.gene061547:CDS 30.0%
GAATTCTCTATGTCAACCAA+TGG + chr3.2:60472186-60472205 None:intergenic 35.0%
GCAAGAGAAAATTCTTTGGA+TGG + chr3.2:60471767-60471786 None:intergenic 35.0%
TAATTCAGATTCCATCTCAC+TGG - chr3.2:60471645-60471664 MS.gene061547:CDS 35.0%
TTTCAACAACAACAACGACT+TGG - chr3.2:60471681-60471700 MS.gene061547:CDS 35.0%
! AATGGTTCTTTCAGGTCATT+AGG - chr3.2:60471931-60471950 MS.gene061547:CDS 35.0%
! AGTTTTCATCAGGTTACTGA+GGG - chr3.2:60472105-60472124 MS.gene061547:CDS 35.0%
! GTTTTTCGCCATCAACAATA+AGG - chr3.2:60471983-60472002 MS.gene061547:CDS 35.0%
! TAGTTTTCATCAGGTTACTG+AGG - chr3.2:60472104-60472123 MS.gene061547:CDS 35.0%
AACCTGGAGAGGTTTCAATT+TGG + chr3.2:60471606-60471625 None:intergenic 40.0%
AGACTGTTACTATAGGAACC+TGG + chr3.2:60471622-60471641 None:intergenic 40.0%
GAATTGGACTATTCACTGAG+AGG - chr3.2:60471881-60471900 MS.gene061547:CDS 40.0%
GACCTGAAAGAACCATTAAG+AGG + chr3.2:60471928-60471947 None:intergenic 40.0%
TATCGGTCATCCGATATTCT+TGG - chr3.2:60472050-60472069 MS.gene061547:CDS 40.0%
TCATCGTCCTCCAAGAATAT+CGG + chr3.2:60472063-60472082 None:intergenic 40.0%
TGAGGTGAATGTGAAACCAT+TGG - chr3.2:60472167-60472186 MS.gene061547:CDS 40.0%
TGCCTCTTAATGGTTCTTTC+AGG - chr3.2:60471923-60471942 MS.gene061547:CDS 40.0%
TGGAGAGGTTTCAATTTGGT+GGG + chr3.2:60471602-60471621 None:intergenic 40.0%
TGGATATAGTCGAAGCAACA+TGG + chr3.2:60471579-60471598 None:intergenic 40.0%
! AGCAGTGCTAGATTCAAGTT+AGG - chr3.2:60472024-60472043 MS.gene061547:CDS 40.0%
!! TTGTTGATGGCGAAAAACCA+TGG + chr3.2:60471981-60472000 None:intergenic 40.0%
!!! CTAGCACTGCTTTTTATCTC+AGG + chr3.2:60472015-60472034 None:intergenic 40.0%
!!! CTGCTTTTTATCTCAGGACT+AGG + chr3.2:60472009-60472028 None:intergenic 40.0%
ACACACTCTTCACTACACCA+TGG - chr3.2:60471961-60471980 MS.gene061547:CDS 45.0%
ACGATGAGACAGAACTGATG+TGG - chr3.2:60472076-60472095 MS.gene061547:CDS 45.0%
CACCAAATTGAAACCTCTCC+AGG - chr3.2:60471601-60471620 MS.gene061547:CDS 45.0%
CTGGAGAGGTTTCAATTTGG+TGG + chr3.2:60471603-60471622 None:intergenic 45.0%
CTTGCATCTCTGCCTCTTAA+TGG - chr3.2:60471913-60471932 MS.gene061547:CDS 45.0%
GAGTGTTAAGTCCAGTGAGA+TGG + chr3.2:60471659-60471678 None:intergenic 45.0%
GTTACTATAGGAACCTGGAG+AGG + chr3.2:60471617-60471636 None:intergenic 45.0%
TTGGTTGCTCGAGATTCAAC+AGG - chr3.2:60471700-60471719 MS.gene061547:CDS 45.0%
TTTCATCAGGTTACTGAGGG+AGG - chr3.2:60472108-60472127 MS.gene061547:CDS 45.0%
! AGAGGTTTCAATTTGGTGGG+TGG + chr3.2:60471599-60471618 None:intergenic 45.0%
! GCGCAAATTTTACAGCTCTC+AGG - chr3.2:60471798-60471817 MS.gene061547:CDS 45.0%
! GTGGCAAGGTAGTTTTCATC+AGG - chr3.2:60472095-60472114 MS.gene061547:CDS 45.0%
! TTTCTCTCTTGTGCGCGTTT+TGG + chr3.2:60471837-60471856 None:intergenic 45.0%
!! GGACTAGGCCTTATTGTTGA+TGG + chr3.2:60471994-60472013 None:intergenic 45.0%
AAGTTCGTTGCTGCTCTCAC+TGG + chr3.2:60471743-60471762 None:intergenic 50.0%
CGGTCATCCGATATTCTTGG+AGG - chr3.2:60472053-60472072 MS.gene061547:CDS 50.0%
GAGACAGAACTGATGTGGCA+AGG - chr3.2:60472081-60472100 MS.gene061547:CDS 50.0%
GCAAAGCGAGCTATGCGAAT+TGG - chr3.2:60471865-60471884 MS.gene061547:CDS 50.0%
! TTTTACAGCTCTCAGGCGCT+CGG - chr3.2:60471805-60471824 MS.gene061547:CDS 50.0%
! CTCTCTTGTGCGCGTTTTGG+TGG + chr3.2:60471834-60471853 None:intergenic 55.0%
TACAGCTCTCAGGCGCTCGG+TGG - chr3.2:60471808-60471827 MS.gene061547:CDS 65.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 60471514 60472233 60471514 ID=MS.gene061547
chr3.2 mRNA 60471514 60472233 60471514 ID=MS.gene061547.t1;Parent=MS.gene061547
chr3.2 exon 60471514 60472233 60471514 ID=MS.gene061547.t1.exon1;Parent=MS.gene061547.t1
chr3.2 CDS 60471514 60472233 60471514 ID=cds.MS.gene061547.t1;Parent=MS.gene061547.t1
Gene Sequence

>MS.gene061547

ATGAAACCAATTTTTGATCTTGAAGTAGAGGCCACAGAAGAATATGAATCTGATGTTAGTAGCCATGTTGCTTCGACTATATCCACCCACCAAATTGAAACCTCTCCAGGTTCCTATAGTAACAGTCTTTCTAATTCAGATTCCATCTCACTGGACTTAACACTCAATTTCAACAACAACAACGACTTGGTTGCTCGAGATTCAACAGGAGTCTCATTCTCAAGCACCAGTGAGAGCAGCAACGAACTTACCATCCAAAGAATTTTCTCTTGCAATTACTGTCGGCGCAAATTTTACAGCTCTCAGGCGCTCGGTGGCCACCAAAACGCGCACAAGAGAGAAAGAACATTAGCAAAGCGAGCTATGCGAATTGGACTATTCACTGAGAGGTATGCAAGTCTTGCATCTCTGCCTCTTAATGGTTCTTTCAGGTCATTAGGTATAAAGACACACTCTTCACTACACCATGGTTTTTCGCCATCAACAATAAGGCCTAGTCCTGAGATAAAAAGCAGTGCTAGATTCAAGTTAGGATCTATCGGTCATCCGATATTCTTGGAGGACGATGAGACAGAACTGATGTGGCAAGGTAGTTTTCATCAGGTTACTGAGGGAGGTAGTAACACTTATCAGAGTTCAAATATGTGTTTTACTGAGGTGAATGTGAAACCATTGGTTGACATAGAGAATTCAGCACCTGAATTAACATTGAAACTTTGA
Protein sequence

>MS.gene061547.t1

MKPIFDLEVEATEEYESDVSSHVASTISTHQIETSPGSYSNSLSNSDSISLDLTLNFNNNNDLVARDSTGVSFSSTSESSNELTIQRIFSCNYCRRKFYSSQALGGHQNAHKRERTLAKRAMRIGLFTERYASLASLPLNGSFRSLGIKTHSSLHHGFSPSTIRPSPEIKSSARFKLGSIGHPIFLEDDETELMWQGSFHQVTEGGSNTYQSSNMCFTEVNVKPLVDIENSAPELTLKL