AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028165

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028165.t1 MTR_1g033340 51.765 255 80 8 1 217 2 251 4.69e-78 234
MS.gene028165.t1 MTR_3g065020 48.000 200 93 6 21 217 47 238 4.57e-57 181
MS.gene028165.t1 MTR_5g077370 45.588 204 92 6 23 217 44 237 1.78e-50 164
MS.gene028165.t1 MTR_2g104900 45.333 150 63 6 2 133 10 158 5.04e-30 111
MS.gene028165.t1 MTR_1g107055 45.763 118 58 3 62 179 64 175 7.07e-25 97.1
MS.gene028165.t1 MTR_1g013130 40.278 144 60 4 15 132 37 180 3.11e-24 97.1
MS.gene028165.t1 MTR_4g006575 40.876 137 63 4 2 132 6 130 2.43e-23 93.6
MS.gene028165.t1 MTR_4g006600 40.876 137 63 4 2 132 6 130 2.43e-23 93.6
MS.gene028165.t1 MTR_3g106230 50.562 89 26 4 61 132 71 158 9.68e-20 84.3
MS.gene028165.t1 MTR_4g128340 62.295 61 21 1 59 119 42 100 5.45e-18 78.2
MS.gene028165.t1 MTR_8g466760 43.038 79 36 3 62 134 98 173 4.06e-12 64.3
MS.gene028165.t1 MTR_7g083210 75.758 33 8 0 62 94 39 71 4.47e-12 62.8
MS.gene028165.t1 MTR_7g086860 61.905 42 16 0 57 98 25 66 5.02e-12 62.0
MS.gene028165.t1 MTR_3g011990 43.421 76 36 2 62 132 98 171 3.83e-11 61.6
MS.gene028165.t1 MTR_5g008280 46.753 77 35 4 62 132 46 122 5.12e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028165.t1 AT1G66140 47.059 187 69 7 57 217 78 260 2.64e-45 151
MS.gene028165.t1 AT1G24625 44.970 169 66 7 61 217 56 209 8.89e-33 117
MS.gene028165.t1 AT1G80730 42.484 153 66 4 2 132 1 153 9.63e-26 100
MS.gene028165.t1 AT5G25160 46.226 106 49 3 32 132 32 134 1.06e-22 92.4
MS.gene028165.t1 AT5G10970 42.105 133 67 6 9 132 44 175 1.85e-22 92.4
MS.gene028165.t1 AT5G57520 76.923 39 9 0 61 99 49 87 1.08e-16 74.3
MS.gene028165.t1 AT5G14010 72.222 36 10 0 62 97 36 71 3.77e-13 65.1
MS.gene028165.t1 AT5G01860 57.500 40 17 0 62 101 65 104 2.34e-11 61.2
MS.gene028165.t1 AT5G27880 44.928 69 36 1 33 99 47 115 7.94e-11 60.5

Find 54 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATTTGATAGAAACCATTT+TGG 0.216847 4.2:+15901627 MS.gene028165:CDS
TTCGAGTGAGGCCGAGTTAA+TGG 0.228364 4.2:+15901272 MS.gene028165:CDS
GTCCACCTGTCTAAAACTTC+CGG 0.315216 4.2:-15901694 None:intergenic
TTCGCAGCAGCTCTCATATC+TGG 0.318459 4.2:-15901606 None:intergenic
CTTGCATCTCTACCTCTTCA+TGG 0.342785 4.2:+15901501 MS.gene028165:CDS
TCAGGTTCCAAGTTCAAGTT+TGG 0.345240 4.2:-15901186 None:intergenic
ATGATGATGCAGGTAGCTTT+TGG 0.346841 4.2:+15901670 MS.gene028165:CDS
CGAAAACTAGCGATCCAAAA+TGG 0.355731 4.2:-15901641 None:intergenic
TGCAAGGCTTGTATACCTTT+CGG 0.407124 4.2:-15901484 None:intergenic
TCCACCTGTCTAAAACTTCC+GGG 0.407344 4.2:-15901693 None:intergenic
AAACTCGAATTTGAAGTTTG+AGG 0.421800 4.2:-15901744 None:intergenic
GATGCAGATGCTTGAGGTGG+AGG 0.428693 4.2:-15901783 None:intergenic
TCGAGTGAGGCCGAGTTAAT+GGG 0.432246 4.2:+15901273 MS.gene028165:CDS
GTCATCAGAACGCTCACAAA+AGG 0.433204 4.2:+15901418 MS.gene028165:CDS
GGTCATAGGATCTAGATCTT+GGG 0.441405 4.2:-15901226 None:intergenic
CTATATTAACACTTCCTCCT+TGG 0.445595 4.2:-15901716 None:intergenic
GGGTCATAGGATCTAGATCT+TGG 0.448749 4.2:-15901227 None:intergenic
GGCTAAACGTGCAATGCGAA+TGG 0.452909 4.2:+15901452 MS.gene028165:CDS
TTCTATAGCTCGCAAGCATT+AGG 0.456033 4.2:+15901393 MS.gene028165:CDS
CAAGGAGGAAGTGTTAATAT+AGG 0.461179 4.2:+15901717 MS.gene028165:CDS
GATGACTCCAAACTTGAACT+TGG 0.465674 4.2:+15901179 MS.gene028165:CDS
AGTGATGCTAGTAGTGAAGT+AGG 0.485652 4.2:+15901300 MS.gene028165:CDS
TAATTACAAGAGAATATCCT+TGG 0.504702 4.2:-15901357 None:intergenic
AGTGTCAAGTCAAGGGTCAT+AGG 0.518887 4.2:-15901240 None:intergenic
TGAGGTGGAGGAGGTGCCAT+TGG 0.521384 4.2:-15901771 None:intergenic
TATAGCTTCAGTGTAAGATC+AGG 0.528823 4.2:-15901807 None:intergenic
TCTCTTGTAATTACTGCAAG+AGG 0.530679 4.2:+15901367 MS.gene028165:CDS
GCTAAACGTGCAATGCGAAT+GGG 0.536618 4.2:+15901453 MS.gene028165:CDS
TGAAATTGAGTGTCAAGTCA+AGG 0.555713 4.2:-15901248 None:intergenic
TCATCAGAACGCTCACAAAA+GGG 0.564572 4.2:+15901419 MS.gene028165:CDS
TCAACACCAAGGGACCGAAA+AGG 0.568839 4.2:-15901528 None:intergenic
GCAGATGCTTGAGGTGGAGG+AGG 0.582836 4.2:-15901780 None:intergenic
TTCGTGGAAGATGATGATGC+AGG 0.588719 4.2:+15901660 MS.gene028165:CDS
GAAATTGAGTGTCAAGTCAA+GGG 0.590766 4.2:-15901247 None:intergenic
GTCATAGGATCTAGATCTTG+GGG 0.590838 4.2:-15901225 None:intergenic
CTTCGCCATCGGTAACTCCA+AGG 0.598331 4.2:+15901340 MS.gene028165:CDS
TGCAACCATCGTCAACAATG+AGG 0.600965 4.2:+15901580 MS.gene028165:CDS
GCAACCATCGTCAACAATGA+GGG 0.605847 4.2:+15901581 MS.gene028165:CDS
TCAGGAGATGCAGATGCTTG+AGG 0.608142 4.2:-15901789 None:intergenic
ACTCAATTTCAGTTCGAGTG+AGG 0.611871 4.2:+15901260 MS.gene028165:CDS
TGAAGTTCATGCTTCGCCAT+CGG 0.612721 4.2:+15901329 MS.gene028165:CDS
ATCACTTGAACCCATTAACT+CGG 0.613671 4.2:-15901283 None:intergenic
GGAGATGCAGATGCTTGAGG+TGG 0.634898 4.2:-15901786 None:intergenic
AGAACGCTCACAAAAGGGAG+AGG 0.635123 4.2:+15901424 MS.gene028165:CDS
CAGAATGAGCTTCAACACCA+AGG 0.638470 4.2:-15901539 None:intergenic
CATGAAGAGGTAGAGATGCA+AGG 0.640521 4.2:-15901500 None:intergenic
AATATCCTTGGAGTTACCGA+TGG 0.642699 4.2:-15901345 None:intergenic
GAATGGGAATGTTCACCGAA+AGG 0.647190 4.2:+15901469 MS.gene028165:CDS
CGAAAAGGCGAACCATGAAG+AGG 0.651068 4.2:-15901513 None:intergenic
AGAATGAGCTTCAACACCAA+GGG 0.655962 4.2:-15901538 None:intergenic
TATAGCTCGCAAGCATTAGG+CGG 0.663928 4.2:+15901396 MS.gene028165:CDS
GGAGCCCTCATTGTTGACGA+TGG 0.667173 4.2:-15901585 None:intergenic
TTTAGACAGGTGGACCAAGG+AGG 0.688046 4.2:+15901702 MS.gene028165:CDS
TCACAAAAGGGAGAGGACGA+TGG 0.689083 4.2:+15901431 MS.gene028165:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTGATAGAAACCATTT+TGG + chr4.2:15901627-15901646 MS.gene028165:CDS 20.0%
! TAATTACAAGAGAATATCCT+TGG - chr4.2:15901360-15901379 None:intergenic 25.0%
! AAACTCGAATTTGAAGTTTG+AGG - chr4.2:15901747-15901766 None:intergenic 30.0%
!!! AAATTCGAGTTTTGTTCCAA+TGG + chr4.2:15901755-15901774 MS.gene028165:CDS 30.0%
ATCACTTGAACCCATTAACT+CGG - chr4.2:15901286-15901305 None:intergenic 35.0%
CTATATTAACACTTCCTCCT+TGG - chr4.2:15901719-15901738 None:intergenic 35.0%
GAAATTGAGTGTCAAGTCAA+GGG - chr4.2:15901250-15901269 None:intergenic 35.0%
TATAGCTTCAGTGTAAGATC+AGG - chr4.2:15901810-15901829 None:intergenic 35.0%
TCTCTTGTAATTACTGCAAG+AGG + chr4.2:15901367-15901386 MS.gene028165:CDS 35.0%
TGAAATTGAGTGTCAAGTCA+AGG - chr4.2:15901251-15901270 None:intergenic 35.0%
!! CAAGGAGGAAGTGTTAATAT+AGG + chr4.2:15901717-15901736 MS.gene028165:CDS 35.0%
AATATCCTTGGAGTTACCGA+TGG - chr4.2:15901348-15901367 None:intergenic 40.0%
ACTCAATTTCAGTTCGAGTG+AGG + chr4.2:15901260-15901279 MS.gene028165:CDS 40.0%
AGAATGAGCTTCAACACCAA+GGG - chr4.2:15901541-15901560 None:intergenic 40.0%
AGTGATGCTAGTAGTGAAGT+AGG + chr4.2:15901300-15901319 MS.gene028165:CDS 40.0%
CGAAAACTAGCGATCCAAAA+TGG - chr4.2:15901644-15901663 None:intergenic 40.0%
GATGACTCCAAACTTGAACT+TGG + chr4.2:15901179-15901198 MS.gene028165:CDS 40.0%
GGTCATAGGATCTAGATCTT+GGG - chr4.2:15901229-15901248 None:intergenic 40.0%
GTCATAGGATCTAGATCTTG+GGG - chr4.2:15901228-15901247 None:intergenic 40.0%
TCATCAGAACGCTCACAAAA+GGG + chr4.2:15901419-15901438 MS.gene028165:CDS 40.0%
TGCAAGGCTTGTATACCTTT+CGG - chr4.2:15901487-15901506 None:intergenic 40.0%
TTCTATAGCTCGCAAGCATT+AGG + chr4.2:15901393-15901412 MS.gene028165:CDS 40.0%
! TCAGGTTCCAAGTTCAAGTT+TGG - chr4.2:15901189-15901208 None:intergenic 40.0%
!! ATGATGATGCAGGTAGCTTT+TGG + chr4.2:15901670-15901689 MS.gene028165:CDS 40.0%
!!! TTTTGGATCGCTAGTTTTCG+TGG + chr4.2:15901644-15901663 MS.gene028165:CDS 40.0%
AGTGTCAAGTCAAGGGTCAT+AGG - chr4.2:15901243-15901262 None:intergenic 45.0%
CAGAATGAGCTTCAACACCA+AGG - chr4.2:15901542-15901561 None:intergenic 45.0%
CATGAAGAGGTAGAGATGCA+AGG - chr4.2:15901503-15901522 None:intergenic 45.0%
CTTGCATCTCTACCTCTTCA+TGG + chr4.2:15901501-15901520 MS.gene028165:CDS 45.0%
GAATGGGAATGTTCACCGAA+AGG + chr4.2:15901469-15901488 MS.gene028165:CDS 45.0%
GCAACCATCGTCAACAATGA+GGG + chr4.2:15901581-15901600 MS.gene028165:CDS 45.0%
GCTAAACGTGCAATGCGAAT+GGG + chr4.2:15901453-15901472 MS.gene028165:CDS 45.0%
GGGTCATAGGATCTAGATCT+TGG - chr4.2:15901230-15901249 None:intergenic 45.0%
GTCATCAGAACGCTCACAAA+AGG + chr4.2:15901418-15901437 MS.gene028165:CDS 45.0%
TATAGCTCGCAAGCATTAGG+CGG + chr4.2:15901396-15901415 MS.gene028165:CDS 45.0%
TGAAGTTCATGCTTCGCCAT+CGG + chr4.2:15901329-15901348 MS.gene028165:CDS 45.0%
TGCAACCATCGTCAACAATG+AGG + chr4.2:15901580-15901599 MS.gene028165:CDS 45.0%
! CTCTTCATGGTTCGCCTTTT+CGG + chr4.2:15901514-15901533 MS.gene028165:CDS 45.0%
! GTCCACCTGTCTAAAACTTC+CGG - chr4.2:15901697-15901716 None:intergenic 45.0%
! TCCACCTGTCTAAAACTTCC+GGG - chr4.2:15901696-15901715 None:intergenic 45.0%
! TTCGTGGAAGATGATGATGC+AGG + chr4.2:15901660-15901679 MS.gene028165:CDS 45.0%
!! GGTGCTTCTGACTGATTTTC+AGG - chr4.2:15901207-15901226 None:intergenic 45.0%
!!! AGTTTTAGACAGGTGGACCA+AGG + chr4.2:15901699-15901718 MS.gene028165:CDS 45.0%
AGAACGCTCACAAAAGGGAG+AGG + chr4.2:15901424-15901443 MS.gene028165:CDS 50.0%
CGAAAAGGCGAACCATGAAG+AGG - chr4.2:15901516-15901535 None:intergenic 50.0%
GGCTAAACGTGCAATGCGAA+TGG + chr4.2:15901452-15901471 MS.gene028165:CDS 50.0%
TCAACACCAAGGGACCGAAA+AGG - chr4.2:15901531-15901550 None:intergenic 50.0%
TCACAAAAGGGAGAGGACGA+TGG + chr4.2:15901431-15901450 MS.gene028165:CDS 50.0%
TCAGGAGATGCAGATGCTTG+AGG - chr4.2:15901792-15901811 None:intergenic 50.0%
TCGAGTGAGGCCGAGTTAAT+GGG + chr4.2:15901273-15901292 MS.gene028165:CDS 50.0%
TTCGAGTGAGGCCGAGTTAA+TGG + chr4.2:15901272-15901291 MS.gene028165:CDS 50.0%
TTCGCAGCAGCTCTCATATC+TGG - chr4.2:15901609-15901628 None:intergenic 50.0%
TTTAGACAGGTGGACCAAGG+AGG + chr4.2:15901702-15901721 MS.gene028165:CDS 50.0%
!!! TTGGCCCGGAAGTTTTAGAC+AGG + chr4.2:15901689-15901708 MS.gene028165:CDS 50.0%
CTTCGCCATCGGTAACTCCA+AGG + chr4.2:15901340-15901359 MS.gene028165:CDS 55.0%
GATGCAGATGCTTGAGGTGG+AGG - chr4.2:15901786-15901805 None:intergenic 55.0%
GGAGATGCAGATGCTTGAGG+TGG - chr4.2:15901789-15901808 None:intergenic 55.0%
GGAGCCCTCATTGTTGACGA+TGG - chr4.2:15901588-15901607 None:intergenic 55.0%
! GATGCAGGTAGCTTTTGGCC+CGG + chr4.2:15901675-15901694 MS.gene028165:CDS 55.0%
!!! GCCCGGAAGTTTTAGACAGG+TGG + chr4.2:15901692-15901711 MS.gene028165:CDS 55.0%
GCAGATGCTTGAGGTGGAGG+AGG - chr4.2:15901783-15901802 None:intergenic 60.0%
! GGTTCGCCTTTTCGGTCCCT+TGG + chr4.2:15901522-15901541 MS.gene028165:CDS 60.0%
!! TGAGGTGGAGGAGGTGCCAT+TGG - chr4.2:15901774-15901793 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 15901177 15901830 15901177 ID=MS.gene028165
chr4.2 mRNA 15901177 15901830 15901177 ID=MS.gene028165.t1;Parent=MS.gene028165
chr4.2 exon 15901177 15901830 15901177 ID=MS.gene028165.t1.exon1;Parent=MS.gene028165.t1
chr4.2 CDS 15901177 15901830 15901177 ID=cds.MS.gene028165.t1;Parent=MS.gene028165.t1
Gene Sequence

>MS.gene028165

ATGATGACTCCAAACTTGAACTTGGAACCTGAAAATCAGTCAGAAGCACCCCAAGATCTAGATCCTATGACCCTTGACTTGACACTCAATTTCAGTTCGAGTGAGGCCGAGTTAATGGGTTCAAGTGATGCTAGTAGTGAAGTAGGAGCTGCTGAAGTTCATGCTTCGCCATCGGTAACTCCAAGGATATTCTCTTGTAATTACTGCAAGAGGAAGTTCTATAGCTCGCAAGCATTAGGCGGTCATCAGAACGCTCACAAAAGGGAGAGGACGATGGCTAAACGTGCAATGCGAATGGGAATGTTCACCGAAAGGTATACAAGCCTTGCATCTCTACCTCTTCATGGTTCGCCTTTTCGGTCCCTTGGTGTTGAAGCTCATTCTGCAATGCATCAAAGACATATGCAACCATCGTCAACAATGAGGGCTCCAGATATGAGAGCTGCTGCGAAATTTGATAGAAACCATTTTGGATCGCTAGTTTTCGTGGAAGATGATGATGCAGGTAGCTTTTGGCCCGGAAGTTTTAGACAGGTGGACCAAGGAGGAAGTGTTAATATAGGATATCCTCAAACTTCAAATTCGAGTTTTGTTCCAATGGCACCTCCTCCACCTCAAGCATCTGCATCTCCTGATCTTACACTGAAGCTATAA
Protein sequence

>MS.gene028165.t1

MMTPNLNLEPENQSEAPQDLDPMTLDLTLNFSSSEAELMGSSDASSEVGAAEVHASPSVTPRIFSCNYCKRKFYSSQALGGHQNAHKRERTMAKRAMRMGMFTERYTSLASLPLHGSPFRSLGVEAHSAMHQRHMQPSSTMRAPDMRAAAKFDRNHFGSLVFVEDDDAGSFWPGSFRQVDQGGSVNIGYPQTSNSSFVPMAPPPPQASASPDLTLKL