AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060577

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060577.t1 MTR_2g076060 92.174 230 11 4 1 228 1 225 6.89e-142 396
MS.gene060577.t1 MTR_5g014400 85.366 41 6 0 51 91 77 117 3.52e-21 89.0
MS.gene060577.t1 MTR_4g021270 67.857 56 10 2 45 100 51 98 4.97e-20 87.0
MS.gene060577.t1 MTR_3g068095 73.333 45 11 1 44 88 46 89 3.59e-19 83.6
MS.gene060577.t1 MTR_5g080660 66.667 48 15 1 44 91 38 84 5.06e-18 80.1
MS.gene060577.t1 MTR_1g070265 81.579 38 7 0 51 88 32 69 7.00e-18 78.6
MS.gene060577.t1 MTR_4g064873 33.858 127 74 2 53 177 20 138 2.19e-15 71.6
MS.gene060577.t1 MTR_7g063220 65.000 40 14 0 50 89 20 59 5.61e-14 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060577.t1 AT3G23130 33.784 222 76 7 30 222 23 202 1.77e-25 99.4
MS.gene060577.t1 AT2G42410 33.641 217 100 8 30 222 16 212 9.11e-23 92.4
MS.gene060577.t1 AT2G42410 33.641 217 100 8 30 222 16 212 9.11e-23 92.4
MS.gene060577.t1 AT2G42410 33.796 216 99 8 31 222 43 238 1.17e-22 92.8
MS.gene060577.t1 AT5G06070 55.263 76 29 1 38 108 37 112 4.77e-22 90.9
MS.gene060577.t1 AT2G37740 63.077 65 22 1 24 88 9 71 1.79e-20 88.2
MS.gene060577.t1 AT4G17810 86.111 36 5 0 51 86 41 76 9.08e-18 78.2
MS.gene060577.t1 AT4G17810 86.111 36 5 0 51 86 41 76 1.76e-17 78.2
MS.gene060577.t1 AT3G09290 50.847 59 27 1 54 110 33 91 6.86e-14 67.8
MS.gene060577.t1 AT3G53820 53.061 49 20 1 43 88 5 53 1.06e-12 63.9

Find 44 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAATGTGAGAATAAATT+AGG 0.181994 2.2:-17698678 None:intergenic
TTAAGGATGGATTTGGAGAT+AGG 0.323598 2.2:+17698924 MS.gene060577:CDS
TCTCAAAGTGATAATAATAA+TGG 0.324416 2.2:+17698414 MS.gene060577:CDS
AAGGGTAATGTGCAAGTAAT+AGG 0.332503 2.2:-17698750 None:intergenic
TTAGGGTTAGTAGTGATAGT+AGG 0.333789 2.2:-17698660 None:intergenic
CTTGGATCTTGAGCTTCGTT+TGG 0.338483 2.2:+17698968 MS.gene060577:CDS
GTCACATGAATGTTCATAGA+AGG 0.359608 2.2:+17698544 MS.gene060577:CDS
TACTACTACTTACTCTAATT+AGG 0.371898 2.2:+17698992 MS.gene060577:CDS
GAGGTCTTTGTGCTCAAAGT+AGG 0.390132 2.2:-17698834 None:intergenic
TTGGATCTTGAGCTTCGTTT+GGG 0.406516 2.2:+17698969 MS.gene060577:CDS
GAAGAACCTTGATCAATTTG+AGG 0.415797 2.2:-17698612 None:intergenic
ATGAATGTGAGAATAAATTA+GGG 0.439290 2.2:-17698677 None:intergenic
TAGGGTTAGTAGTGATAGTA+GGG 0.449276 2.2:-17698659 None:intergenic
GCCAGGAGATTATGATAACT+TGG 0.465506 2.2:+17698950 MS.gene060577:CDS
AATATGAACACAAGCTTGAA+AGG 0.476718 2.2:+17698342 MS.gene060577:CDS
AGGTCTTTGTGCTCAAAGTA+GGG 0.478191 2.2:-17698833 None:intergenic
TTTAAATCAGCTCAAGCACT+TGG 0.494247 2.2:+17698519 MS.gene060577:CDS
GTGTATGATCTTGGTGGCCA+TGG 0.499774 2.2:-17698474 None:intergenic
AATAGATATGTTGTTGTGGA+TGG 0.501785 2.2:+17698798 MS.gene060577:CDS
CATGAACCTCAAATTGATCA+AGG 0.507634 2.2:+17698606 MS.gene060577:CDS
GACCTCAGAGAAATCAAAGA+TGG 0.508422 2.2:+17698851 MS.gene060577:CDS
AAGCTACATGTGTATGATCT+TGG 0.515500 2.2:-17698483 None:intergenic
CTTGAGAGTTGTTGCTGAAG+AGG 0.522978 2.2:-17698727 None:intergenic
AAATCAGCTCAAGCACTTGG+AGG 0.523713 2.2:+17698522 MS.gene060577:CDS
GATTTGGAGATAGGATTGCC+AGG 0.525003 2.2:+17698933 MS.gene060577:CDS
TGAGGTTCATGAGTTGGTGG+TGG 0.545714 2.2:-17698594 None:intergenic
TCAGAGGATTACATGATGAA+TGG 0.551588 2.2:+17698444 MS.gene060577:CDS
TCCAAGTTATCATAATCTCC+TGG 0.553984 2.2:-17698951 None:intergenic
TCAATTTGAGGTTCATGAGT+TGG 0.558616 2.2:-17698600 None:intergenic
AAGGTGTATATATGATGAAG+AGG 0.562048 2.2:+17698316 None:intergenic
TGATGAATGGTTGTTATCCA+TGG 0.592785 2.2:+17698457 MS.gene060577:CDS
TTCATAGAAGGGATAGAGCA+AGG 0.597565 2.2:+17698556 MS.gene060577:CDS
ATTTGAGGTTCATGAGTTGG+TGG 0.598442 2.2:-17698597 None:intergenic
TCACATGAATGTTCATAGAA+GGG 0.603355 2.2:+17698545 MS.gene060577:CDS
ATCCATCTTTGATTTCTCTG+AGG 0.605445 2.2:-17698853 None:intergenic
TCAGAGAAATCAAAGATGGA+TGG 0.606828 2.2:+17698855 MS.gene060577:CDS
ACATATCTATTAAACTCAGA+AGG 0.608200 2.2:-17698786 None:intergenic
AGAAGGAGGTGAAACAAACA+AGG 0.612191 2.2:-17698769 None:intergenic
GTTTAATAGATATGTTGTTG+TGG 0.616672 2.2:+17698794 MS.gene060577:CDS
CTACATGTGTATGATCTTGG+TGG 0.625534 2.2:-17698480 None:intergenic
TATCTATTAAACTCAGAAGG+AGG 0.651729 2.2:-17698783 None:intergenic
TAATAATGGATCATCATCAG+AGG 0.674019 2.2:+17698428 MS.gene060577:CDS
ATGTGAAGATGATTGTAGCA+TGG 0.675289 2.2:+17698884 MS.gene060577:CDS
GAAGGAGGTGAAACAAACAA+GGG 0.747063 2.2:-17698768 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGAATGTGAGAATAAATTA+GGG - chr2.2:17698680-17698699 None:intergenic 20.0%
!! TCTCAAAGTGATAATAATAA+TGG + chr2.2:17698414-17698433 MS.gene060577:CDS 20.0%
! ACATATCTATTAAACTCAGA+AGG - chr2.2:17698789-17698808 None:intergenic 25.0%
! GATGAATGTGAGAATAAATT+AGG - chr2.2:17698681-17698700 None:intergenic 25.0%
! GTTTAATAGATATGTTGTTG+TGG + chr2.2:17698794-17698813 MS.gene060577:CDS 25.0%
!! TGAAGAAAAGTGAGATTTTA+AGG + chr2.2:17698907-17698926 MS.gene060577:CDS 25.0%
AATAGATATGTTGTTGTGGA+TGG + chr2.2:17698798-17698817 MS.gene060577:CDS 30.0%
AATATGAACACAAGCTTGAA+AGG + chr2.2:17698342-17698361 MS.gene060577:CDS 30.0%
TATCTATTAAACTCAGAAGG+AGG - chr2.2:17698786-17698805 None:intergenic 30.0%
TCACATGAATGTTCATAGAA+GGG + chr2.2:17698545-17698564 MS.gene060577:CDS 30.0%
!! ACTTTGAGAATGACTTTTGT+TGG - chr2.2:17698403-17698422 None:intergenic 30.0%
!! GAAAAGTGAGATTTTAAGGA+TGG + chr2.2:17698911-17698930 MS.gene060577:CDS 30.0%
!! TAATAATGGATCATCATCAG+AGG + chr2.2:17698428-17698447 MS.gene060577:CDS 30.0%
!! TGAGATTTTAAGGATGGATT+TGG + chr2.2:17698917-17698936 MS.gene060577:CDS 30.0%
AAGCTACATGTGTATGATCT+TGG - chr2.2:17698486-17698505 None:intergenic 35.0%
AAGGGTAATGTGCAAGTAAT+AGG - chr2.2:17698753-17698772 None:intergenic 35.0%
ATGTGAAGATGATTGTAGCA+TGG + chr2.2:17698884-17698903 MS.gene060577:CDS 35.0%
CATGAACCTCAAATTGATCA+AGG + chr2.2:17698606-17698625 MS.gene060577:CDS 35.0%
GAAGAACCTTGATCAATTTG+AGG - chr2.2:17698615-17698634 None:intergenic 35.0%
GTCACATGAATGTTCATAGA+AGG + chr2.2:17698544-17698563 MS.gene060577:CDS 35.0%
TCAGAGAAATCAAAGATGGA+TGG + chr2.2:17698855-17698874 MS.gene060577:CDS 35.0%
TCAGAGGATTACATGATGAA+TGG + chr2.2:17698444-17698463 MS.gene060577:CDS 35.0%
TCCAAGTTATCATAATCTCC+TGG - chr2.2:17698954-17698973 None:intergenic 35.0%
TGATGAATGGTTGTTATCCA+TGG + chr2.2:17698457-17698476 MS.gene060577:CDS 35.0%
TTTAAATCAGCTCAAGCACT+TGG + chr2.2:17698519-17698538 MS.gene060577:CDS 35.0%
! ATCCATCTTTGATTTCTCTG+AGG - chr2.2:17698856-17698875 None:intergenic 35.0%
! TAGGGTTAGTAGTGATAGTA+GGG - chr2.2:17698662-17698681 None:intergenic 35.0%
! TCAATTTGAGGTTCATGAGT+TGG - chr2.2:17698603-17698622 None:intergenic 35.0%
! TTAAGGATGGATTTGGAGAT+AGG + chr2.2:17698924-17698943 MS.gene060577:CDS 35.0%
! TTAGGGTTAGTAGTGATAGT+AGG - chr2.2:17698663-17698682 None:intergenic 35.0%
!!! TGACTTTTGTTGGTGATGAT+TGG - chr2.2:17698393-17698412 None:intergenic 35.0%
AGAAGGAGGTGAAACAAACA+AGG - chr2.2:17698772-17698791 None:intergenic 40.0%
AGGTCTTTGTGCTCAAAGTA+GGG - chr2.2:17698836-17698855 None:intergenic 40.0%
CTACATGTGTATGATCTTGG+TGG - chr2.2:17698483-17698502 None:intergenic 40.0%
GAAGGAGGTGAAACAAACAA+GGG - chr2.2:17698771-17698790 None:intergenic 40.0%
GACCTCAGAGAAATCAAAGA+TGG + chr2.2:17698851-17698870 MS.gene060577:CDS 40.0%
GCCAGGAGATTATGATAACT+TGG + chr2.2:17698950-17698969 MS.gene060577:CDS 40.0%
TTCATAGAAGGGATAGAGCA+AGG + chr2.2:17698556-17698575 MS.gene060577:CDS 40.0%
TTGGATCTTGAGCTTCGTTT+GGG + chr2.2:17698969-17698988 MS.gene060577:CDS 40.0%
! ATTTGAGGTTCATGAGTTGG+TGG - chr2.2:17698600-17698619 None:intergenic 40.0%
AAATCAGCTCAAGCACTTGG+AGG + chr2.2:17698522-17698541 MS.gene060577:CDS 45.0%
CTTGAGAGTTGTTGCTGAAG+AGG - chr2.2:17698730-17698749 None:intergenic 45.0%
CTTGGATCTTGAGCTTCGTT+TGG + chr2.2:17698968-17698987 MS.gene060577:CDS 45.0%
GAGGTCTTTGTGCTCAAAGT+AGG - chr2.2:17698837-17698856 None:intergenic 45.0%
GATTTGGAGATAGGATTGCC+AGG + chr2.2:17698933-17698952 MS.gene060577:CDS 45.0%
! GTGTATGATCTTGGTGGCCA+TGG - chr2.2:17698477-17698496 None:intergenic 50.0%
!! TGAGGTTCATGAGTTGGTGG+TGG - chr2.2:17698597-17698616 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 17698327 17699013 17698327 ID=MS.gene060577
chr2.2 mRNA 17698327 17699013 17698327 ID=MS.gene060577.t1;Parent=MS.gene060577
chr2.2 exon 17698327 17699013 17698327 ID=MS.gene060577.t1.exon1;Parent=MS.gene060577.t1
chr2.2 CDS 17698327 17699013 17698327 ID=cds.MS.gene060577.t1;Parent=MS.gene060577.t1
Gene Sequence

>MS.gene060577

ATGATGAAGAGGAACAATATGAACACAAGCTTGAAAGGCTATAATCACACTTATTACAACAGTCCAATCATCACCAACAAAAGTCATTCTCAAAGTGATAATAATAATGGATCATCATCAGAGGATTACATGATGAATGGTTGTTATCCATGGCCACCAAGATCATACACATGTAGCTTTTGCAGAAAAGAGTTTAAATCAGCTCAAGCACTTGGAGGTCACATGAATGTTCATAGAAGGGATAGAGCAAGGCTTAGACAATCATCACCACCACCAACTCATGAACCTCAAATTGATCAAGGTTCTTCTATGCTTAATCTTAATCTTAATAACCCTACTATCACTACTAACCCTAATTTATTCTCACATTCATCTTCATCTTCTTCATCATTATCATCAACCTCTTCAGCAACAACTCTCAAGCCTATTACTTGCACATTACCCTTGTTTGTTTCACCTCCTTCTGAGTTTAATAGATATGTTGTTGTGGATGGTATTTTGTTGAACCCTACTTTGAGCACAAAGACCTCAGAGAAATCAAAGATGGATGGTTTTGAATGTGAAGATGATTGTAGCATGGTGAAGAAAAGTGAGATTTTAAGGATGGATTTGGAGATAGGATTGCCAGGAGATTATGATAACTTGGATCTTGAGCTTCGTTTGGGTACTACTACTTACTCTAATTAG
Protein sequence

>MS.gene060577.t1

MMKRNNMNTSLKGYNHTYYNSPIITNKSHSQSDNNNGSSSEDYMMNGCYPWPPRSYTCSFCRKEFKSAQALGGHMNVHRRDRARLRQSSPPPTHEPQIDQGSSMLNLNLNNPTITTNPNLFSHSSSSSSSLSSTSSATTLKPITCTLPLFVSPPSEFNRYVVVDGILLNPTLSTKTSEKSKMDGFECEDDCSMVKKSEILRMDLEIGLPGDYDNLDLELRLGTTTYSN