AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene000605

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000605.t1 MTR_4g006575 97.333 225 5 1 1 225 1 224 6.60e-162 446
MS.gene000605.t1 MTR_4g006600 97.333 225 5 1 1 225 1 224 6.60e-162 446
MS.gene000605.t1 MTR_2g104900 52.083 240 81 11 9 225 19 247 8.38e-60 188
MS.gene000605.t1 MTR_1g013130 38.136 236 96 10 21 225 46 262 1.99e-34 124
MS.gene000605.t1 MTR_3g106230 35.610 205 99 6 24 198 25 226 5.44e-27 103
MS.gene000605.t1 MTR_5g077370 49.580 119 50 3 16 127 38 153 4.98e-21 88.2
MS.gene000605.t1 MTR_1g107055 44.231 104 55 1 32 132 29 132 2.38e-19 82.8
MS.gene000605.t1 MTR_1g033340 56.944 72 24 2 67 131 97 168 6.14e-19 82.8
MS.gene000605.t1 MTR_3g065020 60.274 73 21 3 62 127 80 151 2.60e-18 80.9
MS.gene000605.t1 MTR_4g128340 65.385 52 16 1 64 115 42 91 4.85e-16 73.2
MS.gene000605.t1 MTR_5g008280 40.909 110 41 3 46 137 25 128 8.14e-16 75.9
MS.gene000605.t1 MTR_5g008320 35.294 136 54 5 59 178 64 181 9.13e-15 72.4
MS.gene000605.t1 MTR_5g008390 46.753 77 38 1 61 137 8 81 1.21e-14 67.4
MS.gene000605.t1 MTR_8g466760 41.346 104 47 4 46 137 76 177 5.21e-14 70.1
MS.gene000605.t1 MTR_3g011990 42.157 102 49 3 46 137 76 177 7.43e-14 69.3
MS.gene000605.t1 MTR_5g008310 41.935 93 34 3 61 137 66 154 1.50e-13 68.9
MS.gene000605.t1 MTR_3g012010 40.000 110 44 3 47 137 77 183 4.50e-13 67.4
MS.gene000605.t1 MTR_7g086860 76.471 34 8 0 67 100 30 63 3.93e-12 62.4
MS.gene000605.t1 MTR_7g083210 75.758 33 8 0 67 99 39 71 4.27e-12 63.2
MS.gene000605.t1 MTR_3g011970 40.909 88 37 2 65 137 96 183 1.14e-11 63.2
MS.gene000605.t1 MTR_7g022960 28.436 211 106 10 6 185 27 223 5.19e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000605.t1 AT1G80730 38.428 229 92 7 24 225 22 228 4.36e-33 119
MS.gene000605.t1 AT5G25160 42.593 216 87 10 36 225 31 235 1.68e-31 115
MS.gene000605.t1 AT5G10970 39.726 219 113 8 22 225 58 272 3.12e-31 115
MS.gene000605.t1 AT1G24625 62.121 66 24 1 63 127 53 118 3.76e-20 85.1
MS.gene000605.t1 AT1G66140 48.485 99 23 3 67 137 83 181 1.95e-17 79.0
MS.gene000605.t1 AT5G57520 70.833 48 14 0 66 113 49 96 2.72e-16 73.6
MS.gene000605.t1 AT5G14010 79.412 34 7 0 67 100 36 69 2.25e-13 65.9
MS.gene000605.t1 AT5G01860 62.222 45 17 0 56 100 54 98 7.95e-13 65.5

Find 34 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTTCACTACCTTCTTA+TGG 0.229495 4.3:+88671920 MS.gene000605:CDS
GGGTAGCCATGTTTCCTAAA+AGG 0.278959 4.3:+88672149 MS.gene000605:CDS
TTTCGCGCTTGTGTGCATTC+TGG 0.297005 4.3:-88671859 None:intergenic
GAGAACTATAAAACTTTCTT+TGG 0.300653 4.3:-88671820 None:intergenic
TTGTTTCCATGCAAATTTAT+CGG 0.310453 4.3:+88671733 MS.gene000605:CDS
AGGACTTGGAGGTTACTTAT+TGG 0.313639 4.3:+88672183 MS.gene000605:CDS
TCAATGCCTAAAACCTTCTA+TGG 0.314982 4.3:+88671607 MS.gene000605:CDS
AATGGAAGCTTTCCAATTGC+TGG 0.351292 4.3:-88672070 None:intergenic
AAAACAGGTGTTTGATAAGA+AGG 0.353585 4.3:-88671992 None:intergenic
TTTGATTCACAGCCAGCAAT+TGG 0.385219 4.3:+88672058 MS.gene000605:CDS
CTCACATGAAAATTTCCTAA+TGG 0.404461 4.3:-88672088 None:intergenic
GCAATTGGAAAGCTTCCATT+AGG 0.416438 4.3:+88672073 MS.gene000605:CDS
CCTTTGGTGGTAGCATTTCA+AGG 0.427189 4.3:+88672128 MS.gene000605:CDS
CCTAAAAGGCTTGCAAATGA+AGG 0.436826 4.3:+88672163 MS.gene000605:CDS
GATGAAGTTGAATCATCCTT+TGG 0.437021 4.3:+88672112 MS.gene000605:CDS
AGGCTTGCAAATGAAGGACT+TGG 0.478799 4.3:+88672169 MS.gene000605:CDS
GTTCAAATGGACAAAATGGA+TGG 0.492994 4.3:+88672023 MS.gene000605:CDS
TTGTTACACAAGCCATAAGA+AGG 0.503153 4.3:-88671932 None:intergenic
CTTGCAAATGAAGGACTTGG+AGG 0.517674 4.3:+88672172 MS.gene000605:CDS
AATTTGCATGGAAACAATTG+AGG 0.530917 4.3:-88671727 None:intergenic
GGCTTGTGTAACAAATCACT+TGG 0.540135 4.3:+88671941 MS.gene000605:CDS
ACACAAGCGCGAAAGAACTT+TGG 0.541231 4.3:+88671868 MS.gene000605:CDS
AGCTTTCCGATAAATTTGCA+TGG 0.561003 4.3:-88671739 None:intergenic
CCTTGAAATGCTACCACCAA+AGG 0.566032 4.3:-88672128 None:intergenic
TCTGACTTTGAATCACTACA+TGG 0.579513 4.3:-88671695 None:intergenic
AAATTTATCGGAAAGCTCCT+CGG 0.581574 4.3:+88671745 MS.gene000605:CDS
TTGCATGGAAACAATTGAGG+AGG 0.582251 4.3:-88671724 None:intergenic
GAAAGAACTTTGGCGAGAAG+AGG 0.587899 4.3:+88671878 MS.gene000605:CDS
TGATCTAAGTCTCTCTAGCA+AGG 0.597107 4.3:+88671670 MS.gene000605:CDS
CTTTGGTGGTAGCATTTCAA+GGG 0.599828 4.3:+88672129 MS.gene000605:CDS
GAAGTTGAATCATCCTTTGG+TGG 0.613485 4.3:+88672115 MS.gene000605:CDS
AAGAGGCTATACAACTAGCA+TGG 0.636438 4.3:+88671895 MS.gene000605:CDS
ATTCTCATGACTAGATTCCG+AGG 0.661115 4.3:-88671762 None:intergenic
TATAGTTCTCAAGCACTCGG+AGG 0.694468 4.3:+88671833 MS.gene000605:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAGAACTATAAAACTTTCTT+TGG - chr4.3:88671823-88671842 None:intergenic 25.0%
! TTGTTTCCATGCAAATTTAT+CGG + chr4.3:88671733-88671752 MS.gene000605:CDS 25.0%
! TTTGAACAAAATCCAAAAAC+AGG - chr4.3:88672010-88672029 None:intergenic 25.0%
!! ATTAGGAAATTTTCATGTGA+GGG + chr4.3:88672090-88672109 MS.gene000605:CDS 25.0%
!! TTTTGTTCAAATGGACAAAA+TGG + chr4.3:88672019-88672038 MS.gene000605:CDS 25.0%
!!! GTTTTTGGATTTTGTTCAAA+TGG + chr4.3:88672010-88672029 MS.gene000605:CDS 25.0%
AAAACAGGTGTTTGATAAGA+AGG - chr4.3:88671995-88672014 None:intergenic 30.0%
AATTTGCATGGAAACAATTG+AGG - chr4.3:88671730-88671749 None:intergenic 30.0%
CTCACATGAAAATTTCCTAA+TGG - chr4.3:88672091-88672110 None:intergenic 30.0%
TAGTTGCATGAAAAAACTCT+CGG - chr4.3:88671797-88671816 None:intergenic 30.0%
! CATTAGGAAATTTTCATGTG+AGG + chr4.3:88672089-88672108 MS.gene000605:CDS 30.0%
! TCTTATCAAACACCTGTTTT+TGG + chr4.3:88671995-88672014 MS.gene000605:CDS 30.0%
! TTCTATCCATAGAAGGTTTT+AGG - chr4.3:88671616-88671635 None:intergenic 30.0%
! TTGTGTTTTCTATCCATAGA+AGG - chr4.3:88671623-88671642 None:intergenic 30.0%
! TTTTATAGTTCTCAAGCACT+CGG + chr4.3:88671830-88671849 MS.gene000605:CDS 30.0%
AAATTTATCGGAAAGCTCCT+CGG + chr4.3:88671745-88671764 MS.gene000605:CDS 35.0%
AGCTTTCCGATAAATTTGCA+TGG - chr4.3:88671742-88671761 None:intergenic 35.0%
GATGAAGTTGAATCATCCTT+TGG + chr4.3:88672112-88672131 MS.gene000605:CDS 35.0%
GTTCAAATGGACAAAATGGA+TGG + chr4.3:88672023-88672042 MS.gene000605:CDS 35.0%
TCAATGCCTAAAACCTTCTA+TGG + chr4.3:88671607-88671626 MS.gene000605:CDS 35.0%
TCTGACTTTGAATCACTACA+TGG - chr4.3:88671698-88671717 None:intergenic 35.0%
TCTTCTTCACTACCTTCTTA+TGG + chr4.3:88671920-88671939 MS.gene000605:CDS 35.0%
TTGTTACACAAGCCATAAGA+AGG - chr4.3:88671935-88671954 None:intergenic 35.0%
AAGAGGCTATACAACTAGCA+TGG + chr4.3:88671895-88671914 MS.gene000605:CDS 40.0%
AATGGAAGCTTTCCAATTGC+TGG - chr4.3:88672073-88672092 None:intergenic 40.0%
AGGACTTGGAGGTTACTTAT+TGG + chr4.3:88672183-88672202 MS.gene000605:CDS 40.0%
ATTCTCATGACTAGATTCCG+AGG - chr4.3:88671765-88671784 None:intergenic 40.0%
CCTAAAAGGCTTGCAAATGA+AGG + chr4.3:88672163-88672182 MS.gene000605:CDS 40.0%
GAAGTTGAATCATCCTTTGG+TGG + chr4.3:88672115-88672134 MS.gene000605:CDS 40.0%
GCAATTGGAAAGCTTCCATT+AGG + chr4.3:88672073-88672092 MS.gene000605:CDS 40.0%
GGCTTGTGTAACAAATCACT+TGG + chr4.3:88671941-88671960 MS.gene000605:CDS 40.0%
TGATCTAAGTCTCTCTAGCA+AGG + chr4.3:88671670-88671689 MS.gene000605:CDS 40.0%
TTGCATGGAAACAATTGAGG+AGG - chr4.3:88671727-88671746 None:intergenic 40.0%
TTTGATTCACAGCCAGCAAT+TGG + chr4.3:88672058-88672077 MS.gene000605:CDS 40.0%
! CCTTCATTTGCAAGCCTTTT+AGG - chr4.3:88672166-88672185 None:intergenic 40.0%
! CTTTGGTGGTAGCATTTCAA+GGG + chr4.3:88672129-88672148 MS.gene000605:CDS 40.0%
!! TGCAAGCCTTTTAGGAAACA+TGG - chr4.3:88672158-88672177 None:intergenic 40.0%
ACACAAGCGCGAAAGAACTT+TGG + chr4.3:88671868-88671887 MS.gene000605:CDS 45.0%
AGGCTTGCAAATGAAGGACT+TGG + chr4.3:88672169-88672188 MS.gene000605:CDS 45.0%
CCTTGAAATGCTACCACCAA+AGG - chr4.3:88672131-88672150 None:intergenic 45.0%
CTTGCAAATGAAGGACTTGG+AGG + chr4.3:88672172-88672191 MS.gene000605:CDS 45.0%
GAAAGAACTTTGGCGAGAAG+AGG + chr4.3:88671878-88671897 MS.gene000605:CDS 45.0%
GGGTAGCCATGTTTCCTAAA+AGG + chr4.3:88672149-88672168 MS.gene000605:CDS 45.0%
TATAGTTCTCAAGCACTCGG+AGG + chr4.3:88671833-88671852 MS.gene000605:CDS 45.0%
! CCTTTGGTGGTAGCATTTCA+AGG + chr4.3:88672128-88672147 MS.gene000605:CDS 45.0%
TTTCGCGCTTGTGTGCATTC+TGG - chr4.3:88671862-88671881 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 88671599 88672276 88671599 ID=MS.gene000605
chr4.3 mRNA 88671599 88672276 88671599 ID=MS.gene000605.t1;Parent=MS.gene000605
chr4.3 exon 88671599 88672276 88671599 ID=MS.gene000605.t1.exon1;Parent=MS.gene000605.t1
chr4.3 CDS 88671599 88672276 88671599 ID=cds.MS.gene000605.t1;Parent=MS.gene000605.t1
Gene Sequence

>MS.gene000605

ATGAATCTTCAATGCCTAAAACCTTCTATGGATAGAAAACACAAAAATGATTCATCTTCTCAACTTGTACTTGATCTAAGTCTCTCTAGCAAGGATCCATGTAGTGATTCAAAGTCAGAACTTAACCTCCTCAATTGTTTCCATGCAAATTTATCGGAAAGCTCCTCGGAATCTAGTCATGAGAATGAACTTGATCCGAGAGTTTTTTCATGCAACTACTGCCAAAGAAAGTTTTATAGTTCTCAAGCACTCGGAGGACACCAGAATGCACACAAGCGCGAAAGAACTTTGGCGAGAAGAGGCTATACAACTAGCATGGCTTCTTCTTCACTACCTTCTTATGGCTTGTGTAACAAATCACTTGGCATTCAAGTGCATTCTATGATTAACAAACCTTCTTATCAAACACCTGTTTTTGGATTTTGTTCAAATGGACAAAATGGATGGAGAAGACAAAACTTTGATTCACAGCCAGCAATTGGAAAGCTTCCATTAGGAAATTTTCATGTGAGGGATGAAGTTGAATCATCCTTTGGTGGTAGCATTTCAAGGGTAGCCATGTTTCCTAAAAGGCTTGCAAATGAAGGACTTGGAGGTTACTTATTGGATAGTAACACTTCTCATTTGCAGTCTAAACAAGAGAAGTTGCAAAAACTTGACTTATCTCTTAAGCTCTAA
Protein sequence

>MS.gene000605.t1

MNLQCLKPSMDRKHKNDSSSQLVLDLSLSSKDPCSDSKSELNLLNCFHANLSESSSESSHENELDPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLARRGYTTSMASSSLPSYGLCNKSLGIQVHSMINKPSYQTPVFGFCSNGQNGWRRQNFDSQPAIGKLPLGNFHVRDEVESSFGGSISRVAMFPKRLANEGLGGYLLDSNTSHLQSKQEKLQKLDLSLKL