AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene08335

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene08335.t1 MTR_1g033340 52.157 255 79 8 1 217 2 251 9.33e-79 236
MS.gene08335.t1 MTR_3g065020 48.500 200 92 6 21 217 47 238 2.18e-57 182
MS.gene08335.t1 MTR_5g077370 46.078 204 91 7 23 217 44 237 2.27e-49 161
MS.gene08335.t1 MTR_2g104900 66.667 81 21 2 59 133 78 158 6.57e-30 111
MS.gene08335.t1 MTR_1g013130 40.972 144 59 4 15 132 37 180 6.60e-25 98.6
MS.gene08335.t1 MTR_1g107055 45.763 118 58 3 62 179 64 175 7.38e-25 97.1
MS.gene08335.t1 MTR_4g006575 40.146 137 64 4 2 132 6 130 8.48e-23 92.4
MS.gene08335.t1 MTR_4g006600 40.146 137 64 4 2 132 6 130 8.48e-23 92.4
MS.gene08335.t1 MTR_3g106230 50.562 89 26 4 61 132 71 158 1.07e-19 84.3
MS.gene08335.t1 MTR_4g128340 62.295 61 21 1 59 119 42 100 4.80e-18 78.6
MS.gene08335.t1 MTR_8g466760 43.038 79 36 3 62 134 98 173 4.52e-12 64.3
MS.gene08335.t1 MTR_7g083210 75.758 33 8 0 62 94 39 71 4.56e-12 62.8
MS.gene08335.t1 MTR_7g086860 61.905 42 16 0 57 98 25 66 4.77e-12 62.0
MS.gene08335.t1 MTR_3g011990 43.421 76 36 2 62 132 98 171 3.51e-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.gene08335.t1 AT1G66140 46.524 187 70 7 57 217 78 260 1.85e-44 149
MS.gene08335.t1 AT1G24625 39.450 218 90 8 12 217 22 209 2.11e-33 119
MS.gene08335.t1 AT1G80730 55.056 89 23 2 61 132 65 153 1.55e-25 99.8
MS.gene08335.t1 AT5G25160 53.012 83 34 2 55 132 52 134 1.76e-22 91.7
MS.gene08335.t1 AT5G10970 42.105 133 67 5 9 132 44 175 4.29e-22 91.7
MS.gene08335.t1 AT5G57520 76.923 39 9 0 61 99 49 87 1.10e-16 74.3
MS.gene08335.t1 AT5G14010 72.222 36 10 0 62 97 36 71 3.69e-13 65.1
MS.gene08335.t1 AT5G01860 57.500 40 17 0 62 101 65 104 2.24e-11 61.2

Find 55 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCGAGTGACGCCGAGTTAA+TGG 0.183956 4.1:+16857162 MS.gene08335:CDS
AAATTTGATAGAAACCATTT+TGG 0.216847 4.1:+16857517 MS.gene08335:CDS
ATATCCTCAAACTTCAAATT+CGG 0.284335 4.1:+16857630 MS.gene08335:CDS
GTCCACCTGTCTAAAACTTC+CGG 0.315216 4.1:-16857584 None:intergenic
TTCGCAGCAGCTCTCATATC+TGG 0.318459 4.1:-16857496 None:intergenic
CTTGCATCTCTACCTCTTCA+TGG 0.342785 4.1:+16857391 MS.gene08335:CDS
TCAGGTTCCAAGTTCAAGTT+TGG 0.345240 4.1:-16857076 None:intergenic
CGAAAACTAGCGATCCAAAA+TGG 0.355731 4.1:-16857531 None:intergenic
TATCCTCAAACTTCAAATTC+GGG 0.357303 4.1:+16857631 MS.gene08335:CDS
ATGATGATGTAGGTAGCTTT+TGG 0.366343 4.1:+16857560 MS.gene08335:CDS
TCGAGTGACGCCGAGTTAAT+GGG 0.376026 4.1:+16857163 MS.gene08335:CDS
TGCAAGGCTTGTATACCTTT+CGG 0.407124 4.1:-16857374 None:intergenic
TCCACCTGTCTAAAACTTCC+GGG 0.407344 4.1:-16857583 None:intergenic
GATGCAGATGCTTGAGGTGG+AGG 0.428693 4.1:-16857673 None:intergenic
GTCATCAGAACGCTCACAAA+AGG 0.433204 4.1:+16857308 MS.gene08335:CDS
GGTCATAGGATCTAGATCTT+GGG 0.441405 4.1:-16857116 None:intergenic
CTATATTAACACTTCCTCCT+TGG 0.445595 4.1:-16857606 None:intergenic
GGGTCATAGGATCTAGATCT+TGG 0.448749 4.1:-16857117 None:intergenic
AAACCCGAATTTGAAGTTTG+AGG 0.449808 4.1:-16857634 None:intergenic
GGCTAAACGTGCAATGCGAA+TGG 0.452909 4.1:+16857342 MS.gene08335:CDS
TTCTATAGCTCGCAAGCATT+AGG 0.456033 4.1:+16857283 MS.gene08335:CDS
CAAGGAGGAAGTGTTAATAT+AGG 0.461179 4.1:+16857607 MS.gene08335:CDS
GATGACTCCAAACTTGAACT+TGG 0.465674 4.1:+16857069 MS.gene08335:CDS
AGTGATGCTAGTAGTGAAGT+AGG 0.485652 4.1:+16857190 MS.gene08335:CDS
TAATTACAAGAGAATATCCT+TGG 0.504702 4.1:-16857247 None:intergenic
AGTGTCAAGTCAAGGGTCAT+AGG 0.518887 4.1:-16857130 None:intergenic
TGAGGTGGAGGAGGTGCCAT+TGG 0.521384 4.1:-16857661 None:intergenic
TATAGCTTCAGTGTAAGATC+AGG 0.528823 4.1:-16857697 None:intergenic
TCTCTTGTAATTACTGCAAG+AGG 0.530679 4.1:+16857257 MS.gene08335:CDS
GCTAAACGTGCAATGCGAAT+GGG 0.536618 4.1:+16857343 MS.gene08335:CDS
TGAAATTGAGTGTCAAGTCA+AGG 0.555713 4.1:-16857138 None:intergenic
TCATCAGAACGCTCACAAAA+GGG 0.564572 4.1:+16857309 MS.gene08335:CDS
TCAACACCAAGGGACCGAAA+AGG 0.568839 4.1:-16857418 None:intergenic
GCAGATGCTTGAGGTGGAGG+AGG 0.582836 4.1:-16857670 None:intergenic
GAAATTGAGTGTCAAGTCAA+GGG 0.590766 4.1:-16857137 None:intergenic
GTCATAGGATCTAGATCTTG+GGG 0.590838 4.1:-16857115 None:intergenic
CTTCGCCATCGGTAACTCCA+AGG 0.598331 4.1:+16857230 MS.gene08335:CDS
TGCAACCATCGTCAACAATG+AGG 0.600965 4.1:+16857470 MS.gene08335:CDS
TTCGTGGAAGATGATGATGT+AGG 0.604810 4.1:+16857550 MS.gene08335:CDS
GCAACCATCGTCAACAATGA+GGG 0.605847 4.1:+16857471 MS.gene08335:CDS
TCAGGAGATGCAGATGCTTG+AGG 0.608142 4.1:-16857679 None:intergenic
TGAAGTTCATGCTTCGCCAT+CGG 0.612721 4.1:+16857219 MS.gene08335:CDS
ATCACTTGAACCCATTAACT+CGG 0.620524 4.1:-16857173 None:intergenic
GGAGATGCAGATGCTTGAGG+TGG 0.634898 4.1:-16857676 None:intergenic
AGAACGCTCACAAAAGGGAG+AGG 0.635123 4.1:+16857314 MS.gene08335:CDS
CAGAATGAGCTTCAACACCA+AGG 0.638470 4.1:-16857429 None:intergenic
CATGAAGAGGTAGAGATGCA+AGG 0.640521 4.1:-16857390 None:intergenic
AATATCCTTGGAGTTACCGA+TGG 0.642699 4.1:-16857235 None:intergenic
GAATGGGAATGTTCACCGAA+AGG 0.647190 4.1:+16857359 MS.gene08335:CDS
CGAAAAGGCGAACCATGAAG+AGG 0.651068 4.1:-16857403 None:intergenic
AGAATGAGCTTCAACACCAA+GGG 0.655962 4.1:-16857428 None:intergenic
TATAGCTCGCAAGCATTAGG+CGG 0.663928 4.1:+16857286 MS.gene08335:CDS
GGAGCCCTCATTGTTGACGA+TGG 0.667173 4.1:-16857475 None:intergenic
TTTAGACAGGTGGACCAAGG+AGG 0.688046 4.1:+16857592 MS.gene08335:CDS
TCACAAAAGGGAGAGGACGA+TGG 0.689083 4.1:+16857321 MS.gene08335:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTGATAGAAACCATTT+TGG + chr4.1:16857517-16857536 MS.gene08335:CDS 20.0%
! ATATCCTCAAACTTCAAATT+CGG + chr4.1:16857630-16857649 MS.gene08335:CDS 25.0%
! TAATTACAAGAGAATATCCT+TGG - chr4.1:16857250-16857269 None:intergenic 25.0%
TATCCTCAAACTTCAAATTC+GGG + chr4.1:16857631-16857650 MS.gene08335:CDS 30.0%
ATCACTTGAACCCATTAACT+CGG - chr4.1:16857176-16857195 None:intergenic 35.0%
CTATATTAACACTTCCTCCT+TGG - chr4.1:16857609-16857628 None:intergenic 35.0%
GAAATTGAGTGTCAAGTCAA+GGG - chr4.1:16857140-16857159 None:intergenic 35.0%
TATAGCTTCAGTGTAAGATC+AGG - chr4.1:16857700-16857719 None:intergenic 35.0%
TCTCTTGTAATTACTGCAAG+AGG + chr4.1:16857257-16857276 MS.gene08335:CDS 35.0%
TGAAATTGAGTGTCAAGTCA+AGG - chr4.1:16857141-16857160 None:intergenic 35.0%
! AAACCCGAATTTGAAGTTTG+AGG - chr4.1:16857637-16857656 None:intergenic 35.0%
!! ATGATGATGTAGGTAGCTTT+TGG + chr4.1:16857560-16857579 MS.gene08335:CDS 35.0%
!! CAAGGAGGAAGTGTTAATAT+AGG + chr4.1:16857607-16857626 MS.gene08335:CDS 35.0%
!!! AAATTCGGGTTTTGTTCCAA+TGG + chr4.1:16857645-16857664 MS.gene08335:CDS 35.0%
AATATCCTTGGAGTTACCGA+TGG - chr4.1:16857238-16857257 None:intergenic 40.0%
AGAATGAGCTTCAACACCAA+GGG - chr4.1:16857431-16857450 None:intergenic 40.0%
AGTGATGCTAGTAGTGAAGT+AGG + chr4.1:16857190-16857209 MS.gene08335:CDS 40.0%
CGAAAACTAGCGATCCAAAA+TGG - chr4.1:16857534-16857553 None:intergenic 40.0%
GATGACTCCAAACTTGAACT+TGG + chr4.1:16857069-16857088 MS.gene08335:CDS 40.0%
GGTCATAGGATCTAGATCTT+GGG - chr4.1:16857119-16857138 None:intergenic 40.0%
GTCATAGGATCTAGATCTTG+GGG - chr4.1:16857118-16857137 None:intergenic 40.0%
TCATCAGAACGCTCACAAAA+GGG + chr4.1:16857309-16857328 MS.gene08335:CDS 40.0%
TGCAAGGCTTGTATACCTTT+CGG - chr4.1:16857377-16857396 None:intergenic 40.0%
TTCTATAGCTCGCAAGCATT+AGG + chr4.1:16857283-16857302 MS.gene08335:CDS 40.0%
! TCAGGTTCCAAGTTCAAGTT+TGG - chr4.1:16857079-16857098 None:intergenic 40.0%
! TTCGTGGAAGATGATGATGT+AGG + chr4.1:16857550-16857569 MS.gene08335:CDS 40.0%
!!! TTTTGGATCGCTAGTTTTCG+TGG + chr4.1:16857534-16857553 MS.gene08335:CDS 40.0%
AGTGTCAAGTCAAGGGTCAT+AGG - chr4.1:16857133-16857152 None:intergenic 45.0%
CAGAATGAGCTTCAACACCA+AGG - chr4.1:16857432-16857451 None:intergenic 45.0%
CATGAAGAGGTAGAGATGCA+AGG - chr4.1:16857393-16857412 None:intergenic 45.0%
CTTGCATCTCTACCTCTTCA+TGG + chr4.1:16857391-16857410 MS.gene08335:CDS 45.0%
GAATGGGAATGTTCACCGAA+AGG + chr4.1:16857359-16857378 MS.gene08335:CDS 45.0%
GCAACCATCGTCAACAATGA+GGG + chr4.1:16857471-16857490 MS.gene08335:CDS 45.0%
GCTAAACGTGCAATGCGAAT+GGG + chr4.1:16857343-16857362 MS.gene08335:CDS 45.0%
GGGTCATAGGATCTAGATCT+TGG - chr4.1:16857120-16857139 None:intergenic 45.0%
GTCATCAGAACGCTCACAAA+AGG + chr4.1:16857308-16857327 MS.gene08335:CDS 45.0%
TATAGCTCGCAAGCATTAGG+CGG + chr4.1:16857286-16857305 MS.gene08335:CDS 45.0%
TGAAGTTCATGCTTCGCCAT+CGG + chr4.1:16857219-16857238 MS.gene08335:CDS 45.0%
TGCAACCATCGTCAACAATG+AGG + chr4.1:16857470-16857489 MS.gene08335:CDS 45.0%
! CTCTTCATGGTTCGCCTTTT+CGG + chr4.1:16857404-16857423 MS.gene08335:CDS 45.0%
! GTCCACCTGTCTAAAACTTC+CGG - chr4.1:16857587-16857606 None:intergenic 45.0%
! TCCACCTGTCTAAAACTTCC+GGG - chr4.1:16857586-16857605 None:intergenic 45.0%
!! GGTGCTTCTGACTGATTTTC+AGG - chr4.1:16857097-16857116 None:intergenic 45.0%
!!! AGTTTTAGACAGGTGGACCA+AGG + chr4.1:16857589-16857608 MS.gene08335:CDS 45.0%
AGAACGCTCACAAAAGGGAG+AGG + chr4.1:16857314-16857333 MS.gene08335:CDS 50.0%
CGAAAAGGCGAACCATGAAG+AGG - chr4.1:16857406-16857425 None:intergenic 50.0%
GGCTAAACGTGCAATGCGAA+TGG + chr4.1:16857342-16857361 MS.gene08335:CDS 50.0%
TCAACACCAAGGGACCGAAA+AGG - chr4.1:16857421-16857440 None:intergenic 50.0%
TCACAAAAGGGAGAGGACGA+TGG + chr4.1:16857321-16857340 MS.gene08335:CDS 50.0%
TCAGGAGATGCAGATGCTTG+AGG - chr4.1:16857682-16857701 None:intergenic 50.0%
TCGAGTGACGCCGAGTTAAT+GGG + chr4.1:16857163-16857182 MS.gene08335:CDS 50.0%
TTCGAGTGACGCCGAGTTAA+TGG + chr4.1:16857162-16857181 MS.gene08335:CDS 50.0%
TTCGCAGCAGCTCTCATATC+TGG - chr4.1:16857499-16857518 None:intergenic 50.0%
TTTAGACAGGTGGACCAAGG+AGG + chr4.1:16857592-16857611 MS.gene08335:CDS 50.0%
! GATGTAGGTAGCTTTTGGCC+CGG + chr4.1:16857565-16857584 MS.gene08335:CDS 50.0%
!!! TTGGCCCGGAAGTTTTAGAC+AGG + chr4.1:16857579-16857598 MS.gene08335:CDS 50.0%
CTTCGCCATCGGTAACTCCA+AGG + chr4.1:16857230-16857249 MS.gene08335:CDS 55.0%
GATGCAGATGCTTGAGGTGG+AGG - chr4.1:16857676-16857695 None:intergenic 55.0%
GGAGATGCAGATGCTTGAGG+TGG - chr4.1:16857679-16857698 None:intergenic 55.0%
GGAGCCCTCATTGTTGACGA+TGG - chr4.1:16857478-16857497 None:intergenic 55.0%
!!! GCCCGGAAGTTTTAGACAGG+TGG + chr4.1:16857582-16857601 MS.gene08335:CDS 55.0%
GCAGATGCTTGAGGTGGAGG+AGG - chr4.1:16857673-16857692 None:intergenic 60.0%
! GGTTCGCCTTTTCGGTCCCT+TGG + chr4.1:16857412-16857431 MS.gene08335:CDS 60.0%
!! TGAGGTGGAGGAGGTGCCAT+TGG - chr4.1:16857664-16857683 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 16857067 16857720 16857067 ID=MS.gene08335
chr4.1 mRNA 16857067 16857720 16857067 ID=MS.gene08335.t1;Parent=MS.gene08335
chr4.1 exon 16857067 16857720 16857067 ID=MS.gene08335.t1.exon1;Parent=MS.gene08335.t1
chr4.1 CDS 16857067 16857720 16857067 ID=cds.MS.gene08335.t1;Parent=MS.gene08335.t1
Gene Sequence

>MS.gene08335

ATGATGACTCCAAACTTGAACTTGGAACCTGAAAATCAGTCAGAAGCACCCCAAGATCTAGATCCTATGACCCTTGACTTGACACTCAATTTCAGTTCGAGTGACGCCGAGTTAATGGGTTCAAGTGATGCTAGTAGTGAAGTAGGAGCTGCTGAAGTTCATGCTTCGCCATCGGTAACTCCAAGGATATTCTCTTGTAATTACTGCAAGAGGAAGTTCTATAGCTCGCAAGCATTAGGCGGTCATCAGAACGCTCACAAAAGGGAGAGGACGATGGCTAAACGTGCAATGCGAATGGGAATGTTCACCGAAAGGTATACAAGCCTTGCATCTCTACCTCTTCATGGTTCGCCTTTTCGGTCCCTTGGTGTTGAAGCTCATTCTGCAATGCATCAAAGACATATGCAACCATCGTCAACAATGAGGGCTCCAGATATGAGAGCTGCTGCGAAATTTGATAGAAACCATTTTGGATCGCTAGTTTTCGTGGAAGATGATGATGTAGGTAGCTTTTGGCCCGGAAGTTTTAGACAGGTGGACCAAGGAGGAAGTGTTAATATAGGATATCCTCAAACTTCAAATTCGGGTTTTGTTCCAATGGCACCTCCTCCACCTCAAGCATCTGCATCTCCTGATCTTACACTGAAGCTATAA
Protein sequence

>MS.gene08335.t1

MMTPNLNLEPENQSEAPQDLDPMTLDLTLNFSSSDAELMGSSDASSEVGAAEVHASPSVTPRIFSCNYCKRKFYSSQALGGHQNAHKRERTMAKRAMRMGMFTERYTSLASLPLHGSPFRSLGVEAHSAMHQRHMQPSSTMRAPDMRAAAKFDRNHFGSLVFVEDDDVGSFWPGSFRQVDQGGSVNIGYPQTSNSGFVPMAPPPPQASASPDLTLKL