AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1171380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1171380 MtrunA17_Chr7g0266581 95.385 130 6 0 1 130 1 130 1.69e-89 255
Msa1171380 MtrunA17_Chr7g0266571 90.769 130 12 0 1 130 1 130 8.47e-69 203
Msa1171380 MtrunA17_Chr1g0178451 65.185 135 36 3 1 130 1 129 1.69e-47 149
Msa1171380 MtrunA17_Chr2g0301531 54.839 62 28 0 53 114 79 140 3.86e-20 80.9
Msa1171380 MtrunA17_Chr4g0070071 42.353 85 49 0 37 121 56 140 2.06e-19 78.6
Msa1171380 MtrunA17_Chr3g0145371 45.902 61 33 0 53 113 48 108 8.93e-16 68.2
Msa1171380 MtrunA17_Chr7g0214201 43.056 72 37 1 53 120 70 141 1.12e-15 69.3
Msa1171380 MtrunA17_Chr4g0036161 45.902 61 33 0 53 113 39 99 2.16e-15 66.6
Msa1171380 MtrunA17_Chr4g0036841 40.260 77 45 1 38 113 23 99 3.02e-15 66.6
Msa1171380 MtrunA17_Chr1g0147571 44.776 67 37 0 48 114 102 168 3.11e-15 68.9
Msa1171380 MtrunA17_Chr5g0405301 42.623 61 35 0 53 113 43 103 6.22e-15 65.9
Msa1171380 MtrunA17_Chr8g0372061 47.541 61 32 0 53 113 88 148 7.73e-15 66.6
Msa1171380 MtrunA17_Chr3g0142421 44.262 61 34 0 53 113 45 105 3.15e-14 63.9
Msa1171380 MtrunA17_Chr8g0386111 41.176 85 46 1 30 114 29 109 4.36e-14 64.7
Msa1171380 MtrunA17_Chr3g0131991 41.270 63 37 0 52 114 55 117 5.04e-14 64.7
Msa1171380 MtrunA17_Chr6g0481791 42.857 63 35 1 53 114 37 99 6.43e-14 63.2
Msa1171380 MtrunA17_Chr8g0389141 31.624 117 72 1 4 120 12 120 8.38e-14 64.3
Msa1171380 MtrunA17_Chr4g0036611 38.158 76 42 2 43 113 14 89 1.02e-13 62.4
Msa1171380 MtrunA17_Chr4g0000251 41.935 62 36 0 53 114 73 134 1.35e-13 63.9
Msa1171380 MtrunA17_Chr4g0036751 37.838 74 45 1 43 115 13 86 2.15e-13 61.2
Msa1171380 MtrunA17_Chr8g0346181 46.429 56 30 0 59 114 38 93 2.16e-13 62.0
Msa1171380 MtrunA17_Chr8g0386121 43.548 62 35 0 53 114 49 110 3.04e-13 61.6
Msa1171380 MtrunA17_Chr4g0036461 43.548 62 34 1 53 113 28 89 3.34e-13 60.8
Msa1171380 MtrunA17_Chr3g0139171 30.894 123 73 2 4 114 11 133 3.53e-13 62.8
Msa1171380 MtrunA17_Chr4g0036431 41.667 72 41 1 43 113 18 89 4.01e-13 60.8
Msa1171380 MtrunA17_Chr8g0386131 45.161 62 34 0 53 114 52 113 4.82e-13 62.0
Msa1171380 MtrunA17_Chr2g0281291 40.278 72 42 1 43 113 19 90 5.15e-13 60.5
Msa1171380 MtrunA17_Chr4g0036491 43.548 62 34 1 53 113 28 89 5.56e-13 60.5
Msa1171380 MtrunA17_Chr4g0036531 36.842 76 42 2 44 113 14 89 9.89e-13 59.7
Msa1171380 MtrunA17_Chr4g0036821 43.333 60 33 1 53 111 29 88 1.02e-12 59.7
Msa1171380 MtrunA17_Chr5g0396091 36.842 76 43 2 43 113 18 93 1.16e-12 59.7
Msa1171380 MtrunA17_Chr3g0127561 33.708 89 48 2 28 114 20 99 1.81e-12 59.7
Msa1171380 MtrunA17_Chr4g0009931 38.462 78 47 1 38 114 14 91 2.56e-12 58.9
Msa1171380 MtrunA17_Chr4g0036581 38.889 72 43 1 43 113 18 89 2.93e-12 58.5
Msa1171380 MtrunA17_Chr7g0276101 41.818 55 32 0 60 114 35 89 6.04e-12 58.2
Msa1171380 MtrunA17_Chr4g0036651 38.889 72 42 2 43 113 19 89 6.49e-12 57.8
Msa1171380 MtrunA17_Chr4g0036401 38.889 72 42 2 43 113 19 89 7.62e-12 57.4
Msa1171380 MtrunA17_Chr4g0036811 38.158 76 41 2 44 113 15 90 7.94e-12 57.4
Msa1171380 MtrunA17_Chr4g0036631 40.625 64 37 1 51 113 21 84 1.01e-11 57.0
Msa1171380 MtrunA17_Chr3g0121721 39.130 69 41 1 44 111 19 87 1.53e-11 56.6
Msa1171380 MtrunA17_Chr3g0121731 34.118 85 54 2 28 111 4 87 1.76e-11 56.6
Msa1171380 MtrunA17_Chr4g0036791 37.681 69 42 1 46 113 23 91 1.79e-11 56.6
Msa1171380 MtrunA17_Chr4g0036521 46.875 64 32 2 53 114 35 98 1.88e-11 56.6
Msa1171380 MtrunA17_Chr4g0036681 37.500 64 39 1 51 113 26 89 1.92e-11 56.2
Msa1171380 MtrunA17_Chr8g0389151 37.500 64 40 0 51 114 41 104 2.03e-11 57.8
Msa1171380 MtrunA17_Chr4g0036711 39.683 63 37 1 53 114 18 80 2.15e-11 55.8
Msa1171380 MtrunA17_Chr3g0145401 37.143 70 43 1 43 111 38 107 2.20e-11 56.6
Msa1171380 MtrunA17_Chr4g0036561 38.710 62 37 1 53 113 23 84 2.40e-11 55.8
Msa1171380 MtrunA17_Chr8g0359011 45.455 55 29 1 53 106 6 60 2.82e-11 55.5
Msa1171380 MtrunA17_Chr3g0121801 45.455 55 29 1 53 106 28 82 3.49e-11 55.8
Msa1171380 MtrunA17_Chr4g0036241 38.710 62 37 1 53 113 29 90 4.68e-11 55.5
Msa1171380 MtrunA17_Chr8g0358981 39.130 69 41 1 44 111 19 87 5.19e-11 55.5
Msa1171380 MtrunA17_Chr1g0156341 32.927 82 54 1 30 110 16 97 8.34e-11 56.2
Msa1171380 MtrunA17_Chr3g0121701 40.000 60 35 1 53 111 28 87 9.36e-11 54.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1171380 AT2G36210.1 45.185 135 69 2 1 130 1 135 1.57e-32 112
Msa1171380 AT5G20810.1 51.562 64 31 0 53 116 82 145 3.01e-18 76.3
Msa1171380 AT5G20810.2 51.562 64 31 0 53 116 82 145 6.07e-18 75.9
Msa1171380 AT3G51200.1 43.421 76 35 1 38 113 36 103 1.05e-17 73.2
Msa1171380 AT5G66260.1 45.902 61 33 0 53 113 37 97 4.94e-17 71.2
Msa1171380 AT3G43120.1 46.479 71 37 1 53 123 82 151 1.05e-16 72.0
Msa1171380 AT4G34760.1 45.902 61 33 0 53 113 46 106 9.61e-16 68.2
Msa1171380 AT4G34780.1 40.964 83 45 2 38 116 16 98 1.11e-15 68.2
Msa1171380 AT2G21220.1 47.541 61 32 0 53 113 43 103 1.17e-15 67.8
Msa1171380 AT3G20220.1 42.029 69 38 2 53 119 50 118 9.10e-15 65.9
Msa1171380 AT4G00880.1 36.000 100 53 2 30 127 17 107 1.05e-14 65.9
Msa1171380 AT2G24400.1 46.154 65 35 0 53 117 67 131 3.06e-14 66.2
Msa1171380 AT4G31320.1 46.875 64 34 0 53 116 83 146 4.08e-14 65.9
Msa1171380 AT1G75580.1 44.262 61 34 0 53 113 47 107 4.56e-14 63.9
Msa1171380 AT1G19830.1 42.623 61 35 0 53 113 51 111 7.78e-14 63.5
Msa1171380 AT3G61900.1 46.875 64 31 1 53 113 33 96 1.51e-13 63.2
Msa1171380 AT4G34750.2 34.940 83 52 1 30 110 15 97 2.60e-13 63.2
Msa1171380 AT4G34750.1 34.940 83 52 1 30 110 15 97 2.60e-13 63.2
Msa1171380 AT4G36110.1 45.763 59 32 0 53 111 43 101 2.69e-13 62.0
Msa1171380 AT4G38850.1 43.243 74 38 2 45 114 16 89 3.34e-13 61.2
Msa1171380 AT4G38860.1 45.161 62 33 1 53 113 43 104 4.10e-13 61.6
Msa1171380 AT3G03820.1 44.000 75 38 2 44 114 21 95 4.66e-13 61.2
Msa1171380 AT2G46690.1 35.714 98 58 2 30 124 6 101 4.68e-13 61.6
Msa1171380 AT3G60690.1 32.479 117 67 3 16 127 61 170 6.03e-13 62.4
Msa1171380 AT5G18050.1 39.189 74 43 2 43 114 17 90 8.64e-13 60.1
Msa1171380 AT2G21210.1 42.647 68 36 2 53 117 31 98 8.73e-13 60.5
Msa1171380 AT5G10990.1 34.884 86 54 1 30 113 19 104 9.32e-13 61.6
Msa1171380 AT5G50760.1 42.647 68 39 0 49 116 54 121 9.67e-13 62.4
Msa1171380 AT5G18030.1 35.227 88 55 2 29 114 1 88 1.21e-12 59.7
Msa1171380 AT4G38825.1 42.647 68 37 2 49 114 22 89 2.11e-12 59.3
Msa1171380 AT3G03840.1 43.836 73 38 2 45 114 22 94 2.14e-12 59.3
Msa1171380 AT2G21210.2 34.783 115 62 4 7 117 60 165 3.42e-12 60.5
Msa1171380 AT3G03850.1 43.077 65 34 2 53 114 28 92 3.68e-12 58.5
Msa1171380 AT2G18010.1 36.364 77 44 1 35 111 38 109 3.77e-12 59.3
Msa1171380 AT1G75590.1 35.632 87 53 2 30 113 19 105 5.22e-12 59.7
Msa1171380 AT4G34800.1 44.776 67 33 2 53 115 24 90 6.80e-12 58.2
Msa1171380 AT2G16580.1 40.984 61 36 0 53 113 47 107 6.91e-12 58.2
Msa1171380 AT2G37030.1 32.381 105 64 3 9 112 13 111 7.62e-12 58.5
Msa1171380 AT2G21200.1 43.077 65 35 2 44 106 15 79 7.76e-12 57.8
Msa1171380 AT5G18010.1 39.189 74 43 2 43 114 17 90 1.48e-11 57.0
Msa1171380 AT5G18020.1 37.838 74 44 2 43 114 17 90 1.48e-11 57.0
Msa1171380 AT4G13790.1 44.595 74 37 3 43 113 19 91 2.21e-11 56.6
Msa1171380 AT5G18080.1 37.838 74 44 2 43 114 17 90 2.24e-11 56.6
Msa1171380 AT3G12830.1 35.211 71 46 0 43 113 43 113 2.27e-11 57.8
Msa1171380 AT5G18060.1 39.437 71 41 2 43 111 17 87 2.37e-11 56.6
Msa1171380 AT4G34770.1 43.077 65 34 2 53 114 38 102 3.28e-11 56.6
Msa1171380 AT1G19840.1 32.558 86 56 1 30 113 19 104 4.23e-11 57.4
Msa1171380 AT1G16510.1 31.461 89 59 1 44 130 48 136 4.26e-11 57.4
Msa1171380 AT1G56150.1 28.571 105 71 1 9 113 1 101 4.40e-11 56.2

Find 23 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGAAAGCATACAATGAATT+TGG 0.161291 8_1:+1000675 Msa1171380:CDS
TCCAACAACATCTTGAATAA+TGG 0.266822 8_1:-1000654 None:intergenic
GTTACAATTAACAAGATGTT+AGG 0.272598 8_1:+1000414 None:intergenic
AAAGTTGTTGAAGGAATATA+AGG 0.315149 8_1:+1000515 Msa1171380:CDS
AGAAAGCATACAATGAATTT+GGG 0.366303 8_1:+1000676 Msa1171380:CDS
TCCATTATTCAAGATGTTGT+TGG 0.366607 8_1:+1000653 Msa1171380:CDS
TTCAACAACTTTAAGTGAGC+AGG 0.391696 8_1:-1000504 None:intergenic
TGCTCACTTAAAGTTGTTGA+AGG 0.443749 8_1:+1000506 Msa1171380:CDS
TTACAATTAACAAGATGTTA+GGG 0.491456 8_1:+1000415 None:intergenic
TGTTTCAGCATTTCATGAAG+TGG 0.514250 8_1:+1000734 Msa1171380:CDS
ATAATGGATGAGAGAGGTAC+CGG 0.538476 8_1:-1000638 None:intergenic
TTTGGGTTTGAACAGAGGAA+TGG 0.555355 8_1:+1000693 Msa1171380:CDS
ATGAATTTGGGTTTGAACAG+AGG 0.563400 8_1:+1000688 Msa1171380:CDS
TGAAATGCTGAAACACTACA+TGG 0.566399 8_1:-1000726 None:intergenic
GTTTGAACAGAGGAATGGCT+TGG 0.578047 8_1:+1000698 Msa1171380:CDS
AACAATTGTAAGTTTGACAT+GGG 0.582976 8_1:+1000774 Msa1171380:CDS
TAACAATTGTAAGTTTGACA+TGG 0.588948 8_1:+1000773 Msa1171380:CDS
TCAACAACTTTAAGTGAGCA+GGG 0.593542 8_1:-1000503 None:intergenic
AGAGATACGTGGTTCCAACC+CGG 0.610242 8_1:+1000619 Msa1171380:CDS
GGATGAGAGAGGTACCGGGT+TGG 0.623880 8_1:-1000633 None:intergenic
TAATGGATGAGAGAGGTACC+GGG 0.654606 8_1:-1000637 None:intergenic
TCTTGAATAATGGATGAGAG+AGG 0.689267 8_1:-1000644 None:intergenic
GGAGGAACGACAGAGATACG+TGG 0.777826 8_1:+1000608 Msa1171380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGTTGTTGAAGGAATATA+AGG + chr8_1:1000515-1000534 Msa1171380:CDS 25.0%
!! AGAAAGCATACAATGAATTT+GGG + chr8_1:1000676-1000695 Msa1171380:CDS 25.0%
! TAACAATTGTAAGTTTGACA+TGG + chr8_1:1000773-1000792 Msa1171380:CDS 25.0%
! AACAATTGTAAGTTTGACAT+GGG + chr8_1:1000774-1000793 Msa1171380:CDS 25.0%
GATCAAGAAACTTGCAAAAA+AGG + chr8_1:1000452-1000471 Msa1171380:CDS 30.0%
GAAACTTGCAAAAAAGGTAA+AGG + chr8_1:1000458-1000477 Msa1171380:CDS 30.0%
ATTCCAACCACAAAAAAAGT+TGG + chr8_1:1000549-1000568 Msa1171380:CDS 30.0%
TTCCAACCACAAAAAAAGTT+GGG + chr8_1:1000550-1000569 Msa1171380:CDS 30.0%
!!! TGCAAAAACACCACTTTTTT+TGG - chr8_1:1000577-1000596 None:intergenic 30.0%
!! GTGTTTTTGCACTATATGTT+GGG + chr8_1:1000586-1000605 Msa1171380:CDS 30.0%
!! TGTTTTTGCACTATATGTTG+GGG + chr8_1:1000587-1000606 Msa1171380:CDS 30.0%
TCCATTATTCAAGATGTTGT+TGG + chr8_1:1000653-1000672 Msa1171380:CDS 30.0%
TCCAACAACATCTTGAATAA+TGG - chr8_1:1000657-1000676 None:intergenic 30.0%
! GAGAAAGCATACAATGAATT+TGG + chr8_1:1000675-1000694 Msa1171380:CDS 30.0%
GCAAAAAAGGTAAAGGTTGT+AGG + chr8_1:1000465-1000484 Msa1171380:CDS 35.0%
TCAACAACTTTAAGTGAGCA+GGG - chr8_1:1000506-1000525 None:intergenic 35.0%
TTCAACAACTTTAAGTGAGC+AGG - chr8_1:1000507-1000526 None:intergenic 35.0%
TGCTCACTTAAAGTTGTTGA+AGG + chr8_1:1000506-1000525 Msa1171380:CDS 35.0%
!!! TTTGGACCCAACTTTTTTTG+TGG - chr8_1:1000559-1000578 None:intergenic 35.0%
AAAGTTGGGTCCAAAAAAAG+TGG + chr8_1:1000564-1000583 Msa1171380:CDS 35.0%
!! GGTGTTTTTGCACTATATGT+TGG + chr8_1:1000585-1000604 Msa1171380:CDS 35.0%
!! TCTTGAATAATGGATGAGAG+AGG - chr8_1:1000647-1000666 None:intergenic 35.0%
! ATGAATTTGGGTTTGAACAG+AGG + chr8_1:1000688-1000707 Msa1171380:CDS 35.0%
TGAAATGCTGAAACACTACA+TGG - chr8_1:1000729-1000748 None:intergenic 35.0%
TGTTTCAGCATTTCATGAAG+TGG + chr8_1:1000734-1000753 Msa1171380:CDS 35.0%
!!! GACCCAACTTTTTTTGTGGT+TGG - chr8_1:1000555-1000574 None:intergenic 40.0%
! TTTTGCACTATATGTTGGGG+AGG + chr8_1:1000590-1000609 Msa1171380:CDS 40.0%
!! ATAATGGATGAGAGAGGTAC+CGG - chr8_1:1000641-1000660 None:intergenic 40.0%
! TTTGGGTTTGAACAGAGGAA+TGG + chr8_1:1000693-1000712 Msa1171380:CDS 40.0%
!! TAATGGATGAGAGAGGTACC+GGG - chr8_1:1000640-1000659 None:intergenic 45.0%
GTTTGAACAGAGGAATGGCT+TGG + chr8_1:1000698-1000717 Msa1171380:CDS 45.0%
AGAGATACGTGGTTCCAACC+CGG + chr8_1:1000619-1000638 Msa1171380:CDS 50.0%
GGAGGAACGACAGAGATACG+TGG + chr8_1:1000608-1000627 Msa1171380:CDS 55.0%
!! GGATGAGAGAGGTACCGGGT+TGG - chr8_1:1000636-1000655 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 1000429 1000821 1000429 ID=Msa1171380;Name=Msa1171380
chr8_1 mRNA 1000429 1000821 1000429 ID=Msa1171380-mRNA-1;Parent=Msa1171380;Name=Msa1171380-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|130
chr8_1 exon 1000429 1000821 1000429 ID=Msa1171380-mRNA-1:exon:350;Parent=Msa1171380-mRNA-1
chr8_1 CDS 1000429 1000821 1000429 ID=Msa1171380-mRNA-1:cds;Parent=Msa1171380-mRNA-1
Gene Sequence

>Msa1171380

ATGTTAGGGAAAAAGATTGTATCGATCAAGAAACTTGCAAAAAAGGTAAAGGTTGTAGGTAGAGTTGACTCTGACCCTGCTCACTTAAAGTTGTTGAAGGAATATAAGGAAGAAGAAAAAATTCCAACCACAAAAAAAGTTGGGTCCAAAAAAAGTGGTGTTTTTGCACTATATGTTGGGGAGGAACGACAGAGATACGTGGTTCCAACCCGGTACCTCTCTCATCCATTATTCAAGATGTTGTTGGAGAAAGCATACAATGAATTTGGGTTTGAACAGAGGAATGGCTTGGTAGTTCCATGTAGTGTTTCAGCATTTCATGAAGTGGTTAATGCTATAGAATGTAACAATTGTAAGTTTGACATGGGAAATATTTTTGATGAATTGATTTGA
Protein sequence

>Msa1171380

MLGKKIVSIKKLAKKVKVVGRVDSDPAHLKLLKEYKEEEKIPTTKKVGSKKSGVFALYVGEERQRYVVPTRYLSHPLFKMLLEKAYNEFGFEQRNGLVVPCSVSAFHEVVNAIECNNCKFDMGNIFDELI*