AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40419

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40419.t1 MTR_4g051538 67.917 240 37 5 1 206 1 234 3.54e-96 280
MS.gene40419.t1 MTR_3g104630 39.062 128 36 4 106 192 16 142 3.43e-17 75.5
MS.gene40419.t1 MTR_3g052920 43.590 78 44 0 5 82 5 82 1.07e-15 73.2
MS.gene40419.t1 MTR_8g043650 41.463 82 48 0 1 82 1 82 1.35e-15 73.2
MS.gene40419.t1 MTR_1g012570 45.588 68 37 0 5 72 5 72 1.54e-15 72.8
MS.gene40419.t1 MTR_1g106070 44.444 72 40 0 1 72 1 72 1.91e-15 71.6
MS.gene40419.t1 MTR_3g052870 42.308 78 45 0 5 82 5 82 2.44e-15 72.0
MS.gene40419.t1 MTR_1g105910 42.308 78 45 0 5 82 5 82 2.49e-15 72.4
MS.gene40419.t1 MTR_1g105920 42.308 78 45 0 5 82 5 82 2.78e-15 72.0
MS.gene40419.t1 MTR_1g077360 40.244 82 49 0 1 82 1 82 3.90e-15 71.6
MS.gene40419.t1 MTR_2g085250 40.260 77 46 0 1 77 1 77 4.27e-15 71.6
MS.gene40419.t1 MTR_2g085280 40.260 77 46 0 1 77 1 77 4.59e-15 71.6
MS.gene40419.t1 MTR_3g080940 31.852 135 83 2 1 126 1 135 5.51e-15 70.9
MS.gene40419.t1 MTR_2g030740 42.308 78 45 0 5 82 5 82 5.62e-15 71.2
MS.gene40419.t1 MTR_5g053390 37.500 88 55 0 1 88 1 88 1.09e-14 70.5
MS.gene40419.t1 MTR_5g055100 30.935 139 79 4 1 126 1 135 1.19e-14 70.5
MS.gene40419.t1 MTR_1g108580 41.667 72 42 0 1 72 1 72 5.20e-14 68.6
MS.gene40419.t1 MTR_1g108510 29.927 137 86 2 1 127 1 137 5.64e-14 68.6
MS.gene40419.t1 MTR_5g045560 41.667 72 42 0 1 72 1 72 7.33e-14 68.2
MS.gene40419.t1 MTR_3g030770 40.278 72 43 0 1 72 1 72 8.99e-14 67.8
MS.gene40419.t1 MTR_1g075600 36.585 82 52 0 1 82 1 82 2.92e-13 66.6
MS.gene40419.t1 MTR_4g094632 35.354 99 60 1 9 107 2 96 3.15e-13 65.1
MS.gene40419.t1 MTR_3g030780 38.889 72 44 0 1 72 1 72 7.09e-13 63.5
MS.gene40419.t1 MTR_0121s0100 35.065 77 50 0 1 77 1 77 1.27e-12 62.8
MS.gene40419.t1 MTR_2g105290 28.144 167 106 5 4 158 7 171 1.52e-12 63.5
MS.gene40419.t1 MTR_2g093190 28.750 160 97 4 1 148 1 155 1.60e-12 64.3
MS.gene40419.t1 MTR_4g094638 37.143 70 44 0 9 78 2 71 2.68e-12 63.2
MS.gene40419.t1 MTR_8g086290 34.667 75 49 0 4 78 7 81 3.58e-12 62.8
MS.gene40419.t1 MTR_0121s0080 35.897 78 50 0 5 82 5 82 1.65e-11 61.6
MS.gene40419.t1 MTR_8g079502 33.735 83 47 1 9 83 2 84 3.16e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40419.t1 AT4G36590 44.444 81 44 1 5 84 3 83 1.18e-15 73.6
MS.gene40419.t1 AT1G29962 42.500 80 45 1 1 80 1 79 7.81e-15 70.1
MS.gene40419.t1 AT2G34440 35.135 111 66 3 9 114 2 111 2.32e-14 68.6
MS.gene40419.t1 AT5G60440 42.308 78 44 1 5 82 3 79 2.40e-14 70.5
MS.gene40419.t1 AT2G24840 40.000 80 48 0 7 86 61 140 4.58e-14 69.3
MS.gene40419.t1 AT1G28460 28.108 185 109 5 1 167 1 179 1.64e-12 63.5
MS.gene40419.t1 AT3G04100 35.714 84 51 1 5 88 10 90 8.03e-12 62.4
MS.gene40419.t1 AT3G66656 40.000 65 39 0 9 73 2 66 4.02e-11 59.7
MS.gene40419.t1 AT1G01530 24.706 170 111 4 5 157 3 172 6.79e-11 60.1

Find 27 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGAGTTAACAACACTTTC+AGG 0.202264 6.3:+71034729 MS.gene40419:CDS
ACACAAGGAGTCAACCTTAT+TGG 0.323352 6.3:+71035646 MS.gene40419:CDS
ATCATTTCCTCTTCTATTGA+AGG 0.331143 6.3:-71034855 None:intergenic
ATCCTCCGCTTGCACCAATA+AGG 0.357163 6.3:-71035660 None:intergenic
TTTCTTTCACTTGATCATAC+TGG 0.398154 6.3:-71035019 None:intergenic
TTTATTTGTGACAGCAACTA+AGG 0.402905 6.3:-71035051 None:intergenic
TTTGTTATAGATTCAGAAGA+TGG 0.410640 6.3:-71034810 None:intergenic
TTTCCTCTTGATGACCTCTT+CGG 0.445330 6.3:-71034618 None:intergenic
GCATTTACAACGAGAAAGTC+TGG 0.455029 6.3:+71034690 MS.gene40419:CDS
TGTTGGAAAGATCTAGATAT+TGG 0.477616 6.3:+71034967 MS.gene40419:CDS
CTGAGTTAACAACACTTTCA+GGG 0.482866 6.3:+71034730 MS.gene40419:CDS
TATTCTCATGCTTTCTCCAA+CGG 0.500320 6.3:+71034764 MS.gene40419:CDS
TGATCCAAAAGGTAAAGGTA+TGG 0.511773 6.3:+71035597 MS.gene40419:intron
TGAAAATCCTTCAATAGAAG+AGG 0.547647 6.3:+71034848 MS.gene40419:CDS
GAGTAAGAATGCCGCCGAAG+AGG 0.583357 6.3:+71034604 None:intergenic
GTCAACCTTATTGGTGCAAG+CGG 0.586884 6.3:+71035655 MS.gene40419:CDS
AACCTTATTGGTGCAAGCGG+AGG 0.596051 6.3:+71035658 MS.gene40419:CDS
TAGATATTGGTCAATTCAAG+AGG 0.600081 6.3:+71034980 MS.gene40419:CDS
CCTCTTGATGACCTCTTCGG+CGG 0.600952 6.3:-71034615 None:intergenic
TGAGTTAACAACACTTTCAG+GGG 0.607847 6.3:+71034731 MS.gene40419:CDS
CCGCCGAAGAGGTCATCAAG+AGG 0.664394 6.3:+71034615 MS.gene40419:CDS
TGAAAGTGTTGTTAACTCAG+AGG 0.669188 6.3:-71034727 None:intergenic
GGAGGAGATCTTAACCCTCG+TGG 0.672202 6.3:+71035098 MS.gene40419:CDS
AAGCATGAGAATATCAACTG+AGG 0.718686 6.3:-71034754 None:intergenic
TCTTATGATATAGAAACACA+AGG 0.719882 6.3:+71035631 MS.gene40419:CDS
AAGATGTACACATACCACGA+GGG 0.757349 6.3:-71035112 None:intergenic
AAAGTCTGGAATTTACAACA+AGG 0.757794 6.3:+71034704 MS.gene40419:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACAAAAAATTAAAAAC+AGG - chr6.3:71035348-71035367 None:intergenic 10.0%
!!! TTTAAAATAATTAGACAAAA+AGG - chr6.3:71035195-71035214 None:intergenic 10.0%
!! ATAAATAAAGTCTTGAAAAA+TGG + chr6.3:71035077-71035096 MS.gene40419:CDS 15.0%
!!! CTAATTATTTTAAATGAATC+TGG + chr6.3:71035201-71035220 MS.gene40419:intron 15.0%
!! TCTTCTTAATTTCTATTACT+AGG + chr6.3:71035490-71035509 MS.gene40419:intron 20.0%
!!! TCATTTTGCTGTATAATATT+CGG - chr6.3:71034885-71034904 None:intergenic 20.0%
! AAAAAGATTGAATCCATGAA+AGG - chr6.3:71035578-71035597 None:intergenic 25.0%
! AAACTATAATGGTAAAAGCT+GGG - chr6.3:71035442-71035461 None:intergenic 25.0%
! AACAGAAAAGATCATGAAAT+TGG + chr6.3:71035302-71035321 MS.gene40419:intron 25.0%
! AATAAAGTCTTGAAAAATGG+AGG + chr6.3:71035080-71035099 MS.gene40419:CDS 25.0%
! ACCATTATAGTTTCACTTAT+GGG + chr6.3:71035449-71035468 MS.gene40419:intron 25.0%
! ACGTAAAAATTTGAAGATGT+TGG + chr6.3:71034950-71034969 MS.gene40419:CDS 25.0%
! TACCATTATAGTTTCACTTA+TGG + chr6.3:71035448-71035467 MS.gene40419:intron 25.0%
! TCTTATGATATAGAAACACA+AGG + chr6.3:71035631-71035650 MS.gene40419:CDS 25.0%
!! TTCAATCTTTTTGATCCAAA+AGG + chr6.3:71035586-71035605 MS.gene40419:intron 25.0%
!! TTTGAATAAAAAGCATGTTG+CGG + chr6.3:71034920-71034939 MS.gene40419:CDS 25.0%
!! TTTGTTATAGATTCAGAAGA+TGG - chr6.3:71034813-71034832 None:intergenic 25.0%
!! TTTTGCTTGAAATATTCTAG+CGG + chr6.3:71035364-71035383 MS.gene40419:intron 25.0%
!!! AAATCATGCTTATGTTTTTG+AGG + chr6.3:71035277-71035296 MS.gene40419:intron 25.0%
ATCAAGAGGAAAACAAAAAC+TGG + chr6.3:71034629-71034648 MS.gene40419:CDS 30.0%
ATCATTTCCTCTTCTATTGA+AGG - chr6.3:71034858-71034877 None:intergenic 30.0%
GAAACTATAATGGTAAAAGC+TGG - chr6.3:71035443-71035462 None:intergenic 30.0%
TAGATATTGGTCAATTCAAG+AGG + chr6.3:71034980-71034999 MS.gene40419:CDS 30.0%
TATGTATTGTCTTCCTTTCA+TGG + chr6.3:71035562-71035581 MS.gene40419:intron 30.0%
TCCCATAAGTGAAACTATAA+TGG - chr6.3:71035453-71035472 None:intergenic 30.0%
TGAAAATCCTTCAATAGAAG+AGG + chr6.3:71034848-71034867 MS.gene40419:CDS 30.0%
TGTAGTAATTTCTACTATCG+AGG + chr6.3:71035235-71035254 MS.gene40419:intron 30.0%
TGTTGGAAAGATCTAGATAT+TGG + chr6.3:71034967-71034986 MS.gene40419:CDS 30.0%
TTTATTTGTGACAGCAACTA+AGG - chr6.3:71035054-71035073 None:intergenic 30.0%
TTTCTTTCACTTGATCATAC+TGG - chr6.3:71035022-71035041 None:intergenic 30.0%
! AAAGTCTGGAATTTACAACA+AGG + chr6.3:71034704-71034723 MS.gene40419:CDS 30.0%
! ACACTCACACATTAAACTTT+TGG + chr6.3:71035389-71035408 MS.gene40419:intron 30.0%
! ACGGTAAAACCATTTTGTTA+TGG + chr6.3:71034783-71034802 MS.gene40419:CDS 30.0%
! CTTTTTGATCCAAAAGGTAA+AGG + chr6.3:71035592-71035611 MS.gene40419:intron 30.0%
! GATGGTTTTCCATAACAAAA+TGG - chr6.3:71034795-71034814 None:intergenic 30.0%
!! TAACAAAATGGTTTTACCGT+TGG - chr6.3:71034783-71034802 None:intergenic 30.0%
AAGCATGAGAATATCAACTG+AGG - chr6.3:71034757-71034776 None:intergenic 35.0%
CTGAGTTAACAACACTTTCA+GGG + chr6.3:71034730-71034749 MS.gene40419:CDS 35.0%
TATTCTCATGCTTTCTCCAA+CGG + chr6.3:71034764-71034783 MS.gene40419:CDS 35.0%
TCTGAGTTAACAACACTTTC+AGG + chr6.3:71034729-71034748 MS.gene40419:CDS 35.0%
TGAGTTAACAACACTTTCAG+GGG + chr6.3:71034731-71034750 MS.gene40419:CDS 35.0%
TGATCCAAAAGGTAAAGGTA+TGG + chr6.3:71035597-71035616 MS.gene40419:intron 35.0%
! TTTTGGACAAGAGATGTTGT+TGG + chr6.3:71035406-71035425 MS.gene40419:intron 35.0%
!! TGAAAGTGTTGTTAACTCAG+AGG - chr6.3:71034730-71034749 None:intergenic 35.0%
AAGATGTACACATACCACGA+GGG - chr6.3:71035115-71035134 None:intergenic 40.0%
ACACAAGGAGTCAACCTTAT+TGG + chr6.3:71035646-71035665 MS.gene40419:CDS 40.0%
GCATTTACAACGAGAAAGTC+TGG + chr6.3:71034690-71034709 MS.gene40419:CDS 40.0%
! GCAACCATACCTTTACCTTT+TGG - chr6.3:71035604-71035623 None:intergenic 40.0%
! TTTCCTCTTGATGACCTCTT+CGG - chr6.3:71034621-71034640 None:intergenic 40.0%
GAAGATGTACACATACCACG+AGG - chr6.3:71035116-71035135 None:intergenic 45.0%
GTCAACCTTATTGGTGCAAG+CGG + chr6.3:71035655-71035674 MS.gene40419:CDS 45.0%
AACCTTATTGGTGCAAGCGG+AGG + chr6.3:71035658-71035677 MS.gene40419:CDS 50.0%
ATCCTCCGCTTGCACCAATA+AGG - chr6.3:71035663-71035682 None:intergenic 50.0%
GGAGGAGATCTTAACCCTCG+TGG + chr6.3:71035098-71035117 MS.gene40419:CDS 55.0%
! CCTCTTGATGACCTCTTCGG+CGG - chr6.3:71034618-71034637 None:intergenic 55.0%
CCGCCGAAGAGGTCATCAAG+AGG + chr6.3:71034615-71034634 MS.gene40419:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 71034612 71035720 71034612 ID=MS.gene40419
chr6.3 mRNA 71034612 71035720 71034612 ID=MS.gene40419.t1;Parent=MS.gene40419
chr6.3 exon 71034612 71035119 71034612 ID=MS.gene40419.t1.exon1;Parent=MS.gene40419.t1
chr6.3 CDS 71034612 71035119 71034612 ID=cds.MS.gene40419.t1;Parent=MS.gene40419.t1
chr6.3 exon 71035608 71035720 71035608 ID=MS.gene40419.t1.exon2;Parent=MS.gene40419.t1
chr6.3 CDS 71035608 71035720 71035608 ID=cds.MS.gene40419.t1;Parent=MS.gene40419.t1
Gene Sequence

>MS.gene40419

ATGCCGCCGAAGAGGTCATCAAGAGGAAAACAAAAACTGGAGCTAAAAAAAATTGAGAGTAAGAATGATCTCTTTGTTGCATTTACAACGAGAAAGTCTGGAATTTACAACAAGGCCTCTGAGTTAACAACACTTTCAGGGGCCTCAGTTGATATTCTCATGCTTTCTCCAACGGTAAAACCATTTTGTTATGGAAAACCATCTTCTGAATCTATAACAAAAACTAGTTTGAATGATGAAAATCCTTCAATAGAAGAGGAAATGATGAAACCGAATATTATACAGCAAAATGAAAAAAATGATAATCTTTTGAATAAAAAGCATGTTGCGGAAGCACAACGTAAAAATTTGAAGATGTTGGAAAGATCTAGATATTGGTCAATTCAAGAGGAAGATGATAAAAGCTGCCAGTATGATCAAGTGAAAGAAATTGACAAATCCTTAGTTGCTGTCACAAATAAATTGATAAATAAAGTCTTGAAAAATGGAGGAGATCTTAACCCTCGTGGTATGTGTACATCTTCTAACTAACTATGTGTTATATTTGATCTATTAATGACGTCAAATGATTTCATGTCATCCTTTTTGTCTAATTATTTTAAATGAATCTGGTTATAATTTTTTGTAGTAATTTCTACTATCGAGGAACTGAATGCAGTCTAAACAAATCATGCTTATGTTTTTGAGGACAACAGAAAAGATCATGAAATTGGTGCAAGTAAGAATTCTCATTCCTGTTTTTAATTTTTTGTTTTTGCTTGAAATATTCTAGCGGTGACACTCACACATTAAACTTTTGGACAAGAGATGTTGTTGGTTAATCGTGTCCCAGCTTTTACCATTATAGTTTCACTTATGGGAAAAATTTCAATTACTTTTCTTCTTAATTTCTATTACTAGGCATTCAAACATTTACTTATAATATTTCATGCGAAAAATCTAACATATGTTATGTATTGTCTTCCTTTCATGGATTCAATCTTTTTGATCCAAAAGGTAAAGGTATGGTTGCTAATGCTTCTTATGATATAGAAACACAAGGAGTCAACCTTATTGGTGCAAGCGGAGGATATGAAAGTGTTGTTGATCATGCTTCTCGAGATATATGA
Protein sequence

>MS.gene40419.t1

MPPKRSSRGKQKLELKKIESKNDLFVAFTTRKSGIYNKASELTTLSGASVDILMLSPTVKPFCYGKPSSESITKTSLNDENPSIEEEMMKPNIIQQNEKNDNLLNKKHVAEAQRKNLKMLERSRYWSIQEEDDKSCQYDQVKEIDKSLVAVTNKLINKVLKNGGDLNPRGKGMVANASYDIETQGVNLIGASGGYESVVDHASRDI