AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96600

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96600.t1 MTR_5g094740 61.062 113 44 0 8 120 709 821 1.63e-42 148
MS.gene96600.t1 MTR_1g019580 53.571 112 52 0 8 119 19 130 1.78e-40 131
MS.gene96600.t1 MTR_1g105780 53.571 112 52 0 8 119 162 273 1.00e-39 134
MS.gene96600.t1 MTR_1g105765 53.571 112 52 0 8 119 162 273 1.02e-39 134
MS.gene96600.t1 MTR_3g452180 48.739 119 61 0 2 120 71 189 6.91e-37 124
MS.gene96600.t1 MTR_7g110090 48.739 119 61 0 2 120 155 273 1.57e-36 125
MS.gene96600.t1 MTR_4g032560 47.863 117 61 0 3 119 185 301 1.18e-35 124
MS.gene96600.t1 MTR_4g032580 47.863 117 61 0 3 119 185 301 1.27e-35 124
MS.gene96600.t1 MTR_4g062370 61.053 95 37 0 3 97 160 254 2.33e-33 122
MS.gene96600.t1 MTR_1g069260 45.528 123 55 1 8 118 166 288 1.12e-30 110
MS.gene96600.t1 MTR_8g042540 53.488 86 40 0 35 120 3 88 2.12e-29 102
MS.gene96600.t1 MTR_8g042540 53.571 84 39 0 37 120 17 100 8.99e-29 100
MS.gene96600.t1 MTR_1g087870 41.284 109 64 0 11 119 117 225 4.29e-28 103
MS.gene96600.t1 MTR_1g047540 44.444 117 65 0 2 118 140 256 5.54e-28 106
MS.gene96600.t1 MTR_4g121040 44.248 113 63 0 2 114 59 171 1.34e-26 97.8
MS.gene96600.t1 MTR_0152s0060 46.067 89 48 0 24 112 228 316 5.72e-22 89.4
MS.gene96600.t1 MTR_3g048970 39.394 99 60 0 20 118 178 276 1.67e-20 84.0
MS.gene96600.t1 MTR_1g084880 39.394 99 60 0 20 118 178 276 1.77e-20 84.0
MS.gene96600.t1 MTR_3g070250 35.849 106 68 0 13 118 176 281 6.24e-19 79.7
MS.gene96600.t1 MTR_3g085990 43.000 100 39 2 20 119 155 236 4.87e-18 76.6
MS.gene96600.t1 MTR_4g057880 42.254 71 41 0 48 118 2 72 9.89e-17 69.3
MS.gene96600.t1 MTR_2g016390 39.535 86 52 0 11 96 602 687 3.33e-16 73.6
MS.gene96600.t1 MTR_4g081330 50.877 57 28 0 38 94 1085 1141 1.48e-14 68.9
MS.gene96600.t1 MTR_2g100360 37.113 97 55 1 4 94 156 252 1.60e-14 67.8
MS.gene96600.t1 MTR_4g117740 49.123 57 29 0 6 62 141 197 2.19e-13 63.9
MS.gene96600.t1 MTR_6g016445 48.333 60 31 0 42 101 13 72 1.59e-12 59.3
MS.gene96600.t1 MTR_1g037600 37.079 89 56 0 13 101 71 159 1.85e-12 62.4
MS.gene96600.t1 MTR_2g072800 41.791 67 39 0 39 105 202 268 3.04e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTTTGTTGAGATCGATTC+TGG 0.241191 6.3:-57996807 MS.gene96600:CDS
TTGATGAATGTGGTTGTATA+TGG 0.268575 6.3:-57996628 MS.gene96600:CDS
ATGCAGGATTTGGCTCATAT+TGG 0.290632 6.3:-57996698 MS.gene96600:intron
TGAGATCGATTCTGGATTCT+TGG 0.324173 6.3:-57996799 MS.gene96600:intron
TGCAGGATTTGGCTCATATT+GGG 0.361232 6.3:-57996697 MS.gene96600:intron
GGTCAAGGCTAGAAGGTTAA+AGG 0.364042 6.3:-57996537 MS.gene96600:CDS
TTCTCATTGACACCGATATA+TGG 0.377396 6.3:+57996488 None:intergenic
GACGATGACAGTGTCGTTAT+CGG 0.379316 6.3:-57996515 MS.gene96600:CDS
GTTATCGGTGCTCCATATAT+CGG 0.401878 6.3:-57996500 MS.gene96600:CDS
CCTCATGCTCACTTTAAGAT+TGG 0.409855 6.3:-57996578 MS.gene96600:CDS
AGATTGGCGGTGGCTGGAAC+AGG 0.416190 6.3:-57996562 MS.gene96600:CDS
ACTTTAAGATTGGCGGTGGC+TGG 0.418939 6.3:-57996568 MS.gene96600:CDS
TGAAACTGAGAATCTGAGTT+TGG 0.418987 6.3:-57996651 MS.gene96600:CDS
TTAAATTCATTATGCACAAA+TGG 0.431644 6.3:+57996858 None:intergenic
TGCACAAATGGCGCAGGAAA+AGG 0.441091 6.3:+57996870 None:intergenic
CATGAGGGCGTGTAACAAAC+TGG 0.441451 6.3:+57996594 None:intergenic
ACAGGATGGTCAAGGCTAGA+AGG 0.443921 6.3:-57996544 MS.gene96600:CDS
CATGCTCACTTTAAGATTGG+CGG 0.482279 6.3:-57996575 MS.gene96600:CDS
CTGAGTTTGGTTGATGAATG+TGG 0.483514 6.3:-57996638 MS.gene96600:CDS
TGATGAATGTGGTTGTATAT+GGG 0.484155 6.3:-57996627 MS.gene96600:CDS
GCTCACTTTAAGATTGGCGG+TGG 0.568885 6.3:-57996572 MS.gene96600:CDS
TCATTATGCACAAATGGCGC+AGG 0.577394 6.3:+57996864 None:intergenic
CCAATCTTAAAGTGAGCATG+AGG 0.578221 6.3:+57996578 None:intergenic
TGGCGGTGGCTGGAACAGGA+TGG 0.649155 6.3:-57996558 MS.gene96600:CDS
TGGCTGGAACAGGATGGTCA+AGG 0.676417 6.3:-57996552 MS.gene96600:CDS
AGGGCGTGTAACAAACTGGA+GGG 0.676724 6.3:+57996598 None:intergenic
CAATCTTAAAGTGAGCATGA+GGG 0.680650 6.3:+57996579 None:intergenic
GAGGGCGTGTAACAAACTGG+AGG 0.699235 6.3:+57996597 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATTCATTATGCACAAA+TGG + chr6.3:57996490-57996509 None:intergenic 20.0%
!!! TGTTAAAAAAGATATTGACT+TGG - chr6.3:57996580-57996599 MS.gene96600:CDS 20.0%
!!! ATATGATGTTTTGATTATGC+AGG - chr6.3:57996631-57996650 MS.gene96600:CDS 25.0%
TGATGAATGTGGTTGTATAT+GGG - chr6.3:57996718-57996737 MS.gene96600:intron 30.0%
TTGATGAATGTGGTTGTATA+TGG - chr6.3:57996717-57996736 MS.gene96600:intron 30.0%
!!! TGTTTTGATTATGCAGGATT+TGG - chr6.3:57996637-57996656 MS.gene96600:CDS 30.0%
CAATCTTAAAGTGAGCATGA+GGG + chr6.3:57996769-57996788 None:intergenic 35.0%
TGAAACTGAGAATCTGAGTT+TGG - chr6.3:57996694-57996713 MS.gene96600:CDS 35.0%
TTCTCATTGACACCGATATA+TGG + chr6.3:57996860-57996879 None:intergenic 35.0%
CCAATCTTAAAGTGAGCATG+AGG + chr6.3:57996770-57996789 None:intergenic 40.0%
! ATGCAGGATTTGGCTCATAT+TGG - chr6.3:57996647-57996666 MS.gene96600:CDS 40.0%
! GACTTTGTTGAGATCGATTC+TGG - chr6.3:57996538-57996557 MS.gene96600:CDS 40.0%
! GTTATCGGTGCTCCATATAT+CGG - chr6.3:57996845-57996864 MS.gene96600:CDS 40.0%
! TGAGATCGATTCTGGATTCT+TGG - chr6.3:57996546-57996565 MS.gene96600:CDS 40.0%
! TGCAGGATTTGGCTCATATT+GGG - chr6.3:57996648-57996667 MS.gene96600:CDS 40.0%
!! CATGCTCACTTTAAGATTGG+CGG - chr6.3:57996770-57996789 MS.gene96600:intron 40.0%
!! CCTCATGCTCACTTTAAGAT+TGG - chr6.3:57996767-57996786 MS.gene96600:intron 40.0%
!! CTGAGTTTGGTTGATGAATG+TGG - chr6.3:57996707-57996726 MS.gene96600:intron 40.0%
GGTCAAGGCTAGAAGGTTAA+AGG - chr6.3:57996808-57996827 MS.gene96600:CDS 45.0%
TCATTATGCACAAATGGCGC+AGG + chr6.3:57996484-57996503 None:intergenic 45.0%
! GACGATGACAGTGTCGTTAT+CGG - chr6.3:57996830-57996849 MS.gene96600:CDS 45.0%
ACAGGATGGTCAAGGCTAGA+AGG - chr6.3:57996801-57996820 MS.gene96600:CDS 50.0%
AGGGCGTGTAACAAACTGGA+GGG + chr6.3:57996750-57996769 None:intergenic 50.0%
TGCACAAATGGCGCAGGAAA+AGG + chr6.3:57996478-57996497 None:intergenic 50.0%
! CATGAGGGCGTGTAACAAAC+TGG + chr6.3:57996754-57996773 None:intergenic 50.0%
!! ACTTTAAGATTGGCGGTGGC+TGG - chr6.3:57996777-57996796 MS.gene96600:intron 50.0%
!! GCTCACTTTAAGATTGGCGG+TGG - chr6.3:57996773-57996792 MS.gene96600:intron 50.0%
TGGCTGGAACAGGATGGTCA+AGG - chr6.3:57996793-57996812 MS.gene96600:intron 55.0%
! GAGGGCGTGTAACAAACTGG+AGG + chr6.3:57996751-57996770 None:intergenic 55.0%
AGATTGGCGGTGGCTGGAAC+AGG - chr6.3:57996783-57996802 MS.gene96600:intron 60.0%
TGGCGGTGGCTGGAACAGGA+TGG - chr6.3:57996787-57996806 MS.gene96600:intron 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 57996460 57996907 57996460 ID=MS.gene96600
chr6.3 mRNA 57996460 57996907 57996460 ID=MS.gene96600.t1;Parent=MS.gene96600
chr6.3 exon 57996800 57996907 57996800 ID=MS.gene96600.t1.exon1;Parent=MS.gene96600.t1
chr6.3 CDS 57996800 57996907 57996800 ID=cds.MS.gene96600.t1;Parent=MS.gene96600.t1
chr6.3 exon 57996460 57996714 57996460 ID=MS.gene96600.t1.exon2;Parent=MS.gene96600.t1
chr6.3 CDS 57996460 57996714 57996460 ID=cds.MS.gene96600.t1;Parent=MS.gene96600.t1
Gene Sequence

>MS.gene96600

ATGCATTTGTTCAATCCTTTTCCTGCGCCATTTGTGCATAATGAATTTAACTTTCAACTGACATATGAGAAAAAGCTTGACTTTGTTGAGATCGATTCTGGATTCTTGGTATGTTTTATGTGTTAAAAAAGATATTGACTTGGTGTTGCAATTGATTCGACTTCAACTAATATATGATGTTTTGATTATGCAGGATTTGGCTCATATTGGGTTCTGTCAGCTTGCTTTGAACACTGAAACTGAGAATCTGAGTTTGGTTGATGAATGTGGTTGTATATGGGATTGCACCCTCCAGTTTGTTACACGCCCTCATGCTCACTTTAAGATTGGCGGTGGCTGGAACAGGATGGTCAAGGCTAGAAGGTTAAAGGACGATGACAGTGTCGTTATCGGTGCTCCATATATCGGTGTCAATGAGAAGCTCTTTTTTTTTGTTGTTCGTTATTAG
Protein sequence

>MS.gene96600.t1

MHLFNPFPAPFVHNEFNFQLTYEKKLDFVEIDSGFLDLAHIGFCQLALNTETENLSLVDECGCIWDCTLQFVTRPHAHFKIGGGWNRMVKARRLKDDDSVVIGAPYIGVNEKLFFFVVRY