AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0586010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0586010 MtrunA17_Chr5g0444351 68.800 125 37 1 1 125 1 123 4.68e-58 177
Msa0586010 MtrunA17_Chr7g0225111 64.407 118 40 1 1 118 1 116 2.44e-54 167
Msa0586010 MtrunA17_Chr2g0311601 42.735 117 60 2 6 122 14 123 3.12e-32 112
Msa0586010 MtrunA17_Chr4g0043421 41.880 117 61 2 6 122 16 125 1.40e-30 108
Msa0586010 MtrunA17_Chr5g0437571 57.143 77 33 0 6 82 7 83 2.90e-30 107
Msa0586010 MtrunA17_Chr3g0106101 41.880 117 61 2 6 122 8 117 2.95e-30 107
Msa0586010 MtrunA17_Chr3g0114061 42.276 123 70 1 6 127 9 131 3.65e-30 107
Msa0586010 MtrunA17_Chr3g0115431 50.588 85 42 0 6 90 10 94 1.13e-28 105
Msa0586010 MtrunA17_Chr7g0227511 57.143 77 33 0 6 82 12 88 1.27e-28 103
Msa0586010 MtrunA17_Chr6g0449651 54.545 77 35 0 6 82 68 144 3.47e-28 103
Msa0586010 MtrunA17_Chr6g0449641 54.545 77 35 0 6 82 10 86 6.75e-28 100
Msa0586010 MtrunA17_Chr4g0058651 55.844 77 34 0 6 82 12 88 2.57e-27 100
Msa0586010 MtrunA17_Chr8g0353981 55.128 78 35 0 6 83 8 85 2.93e-27 101
Msa0586010 MtrunA17_Chr3g0117121 55.844 77 34 0 6 82 11 87 3.59e-27 100
Msa0586010 MtrunA17_Chr5g0438091 54.545 77 35 0 6 82 40 116 4.70e-27 100
Msa0586010 MtrunA17_Chr5g0402611 42.478 113 51 2 6 118 9 107 5.49e-27 102
Msa0586010 MtrunA17_Chr3g0129071 54.545 77 35 0 6 82 48 124 3.89e-26 99.0
Msa0586010 MtrunA17_Chr5g0432451 51.948 77 37 0 6 82 44 120 5.53e-26 98.2
Msa0586010 MtrunA17_Chr3g0097221 55.128 78 35 0 6 83 8 85 6.88e-26 99.4
Msa0586010 MtrunA17_Chr4g0030001 37.302 126 71 3 1 125 20 138 7.40e-26 97.1
Msa0586010 MtrunA17_Chr3g0113891 43.820 89 49 1 6 94 15 102 9.87e-26 96.7
Msa0586010 MtrunA17_Chr5g0437401 42.697 89 50 1 6 94 12 99 1.39e-24 93.2
Msa0586010 MtrunA17_Chr1g0200201 48.052 77 40 0 6 82 73 149 3.73e-23 90.9
Msa0586010 MtrunA17_Chr6g0452671 42.500 80 46 0 6 85 12 91 1.36e-22 89.0
Msa0586010 MtrunA17_Chr7g0260971 50.649 77 37 1 6 81 15 91 2.18e-22 88.6
Msa0586010 MtrunA17_Chr6g0452691 37.273 110 66 2 6 114 10 117 4.01e-22 87.0
Msa0586010 MtrunA17_Chr1g0184281 51.948 77 36 1 6 81 16 92 1.13e-21 86.7
Msa0586010 MtrunA17_Chr8g0374601 46.753 77 41 0 6 82 27 103 1.55e-21 87.8
Msa0586010 MtrunA17_Chr6g0460951 48.148 81 41 1 6 85 41 121 5.15e-21 85.1
Msa0586010 MtrunA17_Chr6g0452661 33.588 131 83 3 6 135 10 137 1.02e-20 85.1
Msa0586010 MtrunA17_Chr5g0435641 48.052 77 39 1 6 81 8 84 1.10e-20 83.6
Msa0586010 MtrunA17_Chr8g0374591 42.857 77 44 0 6 82 9 85 2.41e-20 81.3
Msa0586010 MtrunA17_Chr8g0374581 47.436 78 40 1 6 82 9 86 1.27e-19 81.6
Msa0586010 MtrunA17_Chr8g0351701 41.837 98 54 2 4 98 22 119 1.73e-19 81.3
Msa0586010 MtrunA17_Chr7g0261031 47.436 78 40 1 6 82 9 86 4.04e-19 80.1
Msa0586010 MtrunA17_Chr6g0460941 44.156 77 42 1 6 81 8 84 5.20e-19 76.6
Msa0586010 MtrunA17_Chr1g0184271 44.872 78 42 1 6 82 13 90 6.72e-19 79.7
Msa0586010 MtrunA17_Chr7g0245871 46.154 78 41 1 6 82 28 105 6.90e-19 80.1
Msa0586010 MtrunA17_Chr8g0351721 45.000 80 43 1 4 82 17 96 3.59e-18 77.4
Msa0586010 MtrunA17_Chr4g0055441 39.241 79 47 1 6 83 3 81 1.12e-17 74.7
Msa0586010 MtrunA17_Chr4g0059901 41.333 75 44 0 6 80 11 85 2.13e-17 76.3
Msa0586010 MtrunA17_Chr7g0245861 44.444 81 42 2 4 81 11 91 3.35e-17 73.2
Msa0586010 MtrunA17_Chr4g0040831 35.802 81 52 0 2 82 12 92 5.24e-17 74.3
Msa0586010 MtrunA17_Chr5g0439111 37.805 82 50 1 6 86 10 91 5.53e-17 74.7
Msa0586010 MtrunA17_Chr8g0342351 40.000 75 45 0 6 80 13 87 3.04e-16 73.2
Msa0586010 MtrunA17_Chr2g0330201 34.667 75 49 0 6 80 20 94 2.84e-15 70.9
Msa0586010 MtrunA17_Chr2g0326041 45.098 51 28 0 1 51 29 79 8.53e-14 63.2
Msa0586010 MtrunA17_Chr4g0046201 31.765 85 58 0 6 90 7 91 3.02e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0586010 AT3G26620.1 53.043 115 50 2 5 117 5 117 1.01e-38 128
Msa0586010 AT3G26660.1 53.509 114 49 2 5 116 5 116 1.21e-38 127
Msa0586010 AT1G31320.1 59.740 77 31 0 6 82 14 90 2.05e-31 110
Msa0586010 AT2G30130.1 57.143 77 33 0 6 82 9 85 3.27e-30 108
Msa0586010 AT3G27650.1 55.844 77 34 0 6 82 40 116 3.32e-29 105
Msa0586010 AT2G23660.2 53.846 78 36 0 6 83 6 83 9.21e-28 105
Msa0586010 AT2G23660.3 53.846 78 36 0 6 83 6 83 9.21e-28 105
Msa0586010 AT2G23660.1 53.846 78 36 0 6 83 6 83 9.21e-28 105
Msa0586010 AT5G66870.1 52.564 78 37 0 6 83 8 85 2.78e-27 103
Msa0586010 AT1G65620.1 52.564 78 37 0 6 83 10 87 6.89e-27 100
Msa0586010 AT1G65620.4 52.564 78 37 0 6 83 10 87 6.89e-27 100
Msa0586010 AT1G65620.3 52.564 78 37 0 6 83 10 87 6.89e-27 100
Msa0586010 AT1G65620.5 52.564 78 37 0 6 83 10 87 6.89e-27 100
Msa0586010 AT1G65620.2 52.564 78 37 0 6 83 10 87 6.89e-27 100
Msa0586010 AT2G40470.2 54.545 77 35 0 6 82 21 97 1.30e-26 99.4
Msa0586010 AT2G40470.1 54.545 77 35 0 6 82 46 122 2.38e-26 99.4
Msa0586010 AT1G16530.1 50.000 88 42 2 6 92 15 101 2.69e-26 97.8
Msa0586010 AT5G63090.4 54.545 77 35 0 6 82 12 88 4.76e-26 97.8
Msa0586010 AT5G63090.3 54.545 77 35 0 6 82 12 88 4.76e-26 97.8
Msa0586010 AT5G63090.2 54.545 77 35 0 6 82 12 88 4.76e-26 97.8
Msa0586010 AT5G63090.1 54.545 77 35 0 6 82 12 88 4.76e-26 97.8
Msa0586010 AT1G07900.1 46.341 82 44 0 1 82 29 110 1.03e-25 97.1
Msa0586010 AT3G11090.1 39.286 112 67 1 6 117 12 122 4.40e-25 94.7
Msa0586010 AT2G28500.1 45.122 82 45 0 1 82 51 132 1.07e-24 95.5
Msa0586010 AT2G30340.1 50.649 77 38 0 6 82 53 129 1.05e-23 93.6
Msa0586010 AT2G30340.2 50.649 77 38 0 6 82 54 130 1.07e-23 93.6
Msa0586010 AT2G42440.1 37.607 117 67 2 6 121 8 119 4.62e-21 86.3
Msa0586010 AT3G47870.1 43.210 81 46 0 4 84 35 115 7.39e-21 87.0
Msa0586010 AT2G42430.1 49.351 77 38 1 6 81 16 92 7.40e-21 85.5
Msa0586010 AT5G06080.1 48.718 78 39 1 6 82 8 85 2.81e-20 82.4
Msa0586010 AT3G50510.1 38.462 104 62 1 2 103 9 112 2.97e-20 82.8
Msa0586010 AT3G50510.2 38.462 104 62 1 2 103 9 112 2.97e-20 82.8
Msa0586010 AT3G03760.1 38.053 113 62 3 6 117 52 157 3.54e-20 84.3
Msa0586010 AT4G00210.1 45.000 80 43 1 4 82 10 89 7.46e-20 82.4
Msa0586010 AT5G35900.1 33.594 128 71 1 6 133 6 119 5.98e-19 79.7
Msa0586010 AT3G58190.1 45.455 77 41 1 6 81 12 88 6.06e-19 80.1
Msa0586010 AT4G00220.1 38.235 102 60 2 8 106 20 121 9.11e-19 79.7
Msa0586010 AT2G45410.1 41.176 102 59 1 8 108 19 120 9.23e-19 79.0
Msa0586010 AT1G06280.1 41.558 77 45 0 6 82 25 101 1.97e-17 75.9
Msa0586010 AT2G45420.1 46.053 76 40 1 8 82 40 115 2.25e-17 76.6
Msa0586010 AT3G13850.1 38.462 78 48 0 6 83 37 114 5.43e-17 75.9
Msa0586010 AT2G31310.1 38.961 77 46 1 6 81 8 84 1.77e-16 72.8
Msa0586010 AT1G72980.1 37.838 74 46 0 6 79 14 87 1.95e-14 68.2
Msa0586010 AT2G19820.1 31.915 94 54 2 6 98 13 97 4.44e-14 65.1
Msa0586010 AT5G15060.1 42.667 75 39 2 5 76 17 90 1.53e-13 63.9
Msa0586010 AT4G22700.1 39.535 86 50 2 1 85 1 85 2.65e-12 62.0
Msa0586010 AT1G36000.1 27.957 93 58 1 6 98 10 93 2.70e-11 57.8

Find 33 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTTCATATTGTTGATTT+TGG 0.095309 4_2:-7113493 None:intergenic
AGGATTCAAAATCCAGTTTA+TGG 0.187774 4_2:+7113378 Msa0586010:CDS
ACTCCTAATTGGTTTAATTA+AGG 0.204559 4_2:+7113581 Msa0586010:CDS
AGCAAATCTTTGAGGATTAT+TGG 0.230583 4_2:-7113118 None:intergenic
GGCCTAATCAAACTCCTAAT+TGG 0.237196 4_2:+7113570 Msa0586010:CDS
AGCAATCTGAGTCTGAATTT+TGG 0.276155 4_2:-7113459 None:intergenic
GGATTATTGGCAGGAAAATA+TGG 0.286711 4_2:-7113105 None:intergenic
AGTCCTTAATTAAACCAATT+AGG 0.327340 4_2:-7113584 None:intergenic
GCTTCTGTCCACCGAATCTA+TGG 0.338967 4_2:+7113138 Msa0586010:CDS
ATCCCAACACATCCATAAAC+TGG 0.380377 4_2:-7113390 None:intergenic
CCAGCTCAGCTTCTGTATCA+TGG 0.391779 4_2:-7113436 None:intergenic
ATCCAGTTTATGGATGTGTT+GGG 0.435692 4_2:+7113388 Msa0586010:CDS
AACCAATTAGGAGTTTGATT+AGG 0.441199 4_2:-7113572 None:intergenic
TGCTCCATGCTGCTACTTTG+TGG 0.452878 4_2:-7113539 None:intergenic
AATCTTTGAGGATTATTGGC+AGG 0.458959 4_2:-7113114 None:intergenic
AATCCAGTTTATGGATGTGT+TGG 0.478419 4_2:+7113387 Msa0586010:CDS
CCATGATACAGAAGCTGAGC+TGG 0.490473 4_2:+7113436 Msa0586010:CDS
TGTATTTAGAAGCACAATGT+AGG 0.494601 4_2:+7113358 Msa0586010:CDS
TGGACAGAAGCAAATCTTTG+AGG 0.503992 4_2:-7113126 None:intergenic
CAAAATCAACAATATGAAGC+TGG 0.506425 4_2:+7113494 Msa0586010:CDS
TGCTACTTTGTGGAGGCAAA+AGG 0.516646 4_2:-7113529 None:intergenic
ATCTATGGTGGTGCCAATGT+TGG 0.519520 4_2:+7113153 Msa0586010:CDS
CATTGGCACCACCATAGATT+CGG 0.530883 4_2:-7113149 None:intergenic
TTGACATCATGATTTATGGT+AGG 0.535888 4_2:+7113028 None:intergenic
GCAGCATGGAGCAGTTTCAA+TGG 0.542505 4_2:+7113549 Msa0586010:CDS
GGAGAGAAAATGCAATCAGA+AGG 0.551169 4_2:-7113084 None:intergenic
CTTGCAAGAGTCAAAGAAGA+AGG 0.555730 4_2:+7113058 Msa0586010:CDS
GCCTCCACAAAGTAGCAGCA+TGG 0.580606 4_2:+7113535 Msa0586010:CDS
GAGAGAAAATGCAATCAGAA+GGG 0.619697 4_2:-7113083 None:intergenic
TCCATGCTGCTACTTTGTGG+AGG 0.624030 4_2:-7113536 None:intergenic
GCTTGTTCTCTTGCATAGTG+AGG 0.625490 4_2:-7113324 None:intergenic
TGGCACCACCATAGATTCGG+TGG 0.632816 4_2:-7113146 None:intergenic
TCTGTCCACCGAATCTATGG+TGG 0.637607 4_2:+7113141 Msa0586010:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATAATATAATTATAATA+TGG + chr4_2:7113233-7113252 Msa0586010:intron 0.0%
!!! TTCTTATCTAGTATTTTTAT+TGG + chr4_2:7113290-7113309 Msa0586010:intron 15.0%
!! ACTCCTAATTGGTTTAATTA+AGG + chr4_2:7113581-7113600 Msa0586010:CDS 25.0%
! AGTCCTTAATTAAACCAATT+AGG - chr4_2:7113587-7113606 None:intergenic 25.0%
! AGCAAATCTTTGAGGATTAT+TGG - chr4_2:7113121-7113140 None:intergenic 30.0%
! TGTATTTAGAAGCACAATGT+AGG + chr4_2:7113358-7113377 Msa0586010:CDS 30.0%
AGGATTCAAAATCCAGTTTA+TGG + chr4_2:7113378-7113397 Msa0586010:CDS 30.0%
!!! CAGCTTCATATTGTTGATTT+TGG - chr4_2:7113496-7113515 None:intergenic 30.0%
CAAAATCAACAATATGAAGC+TGG + chr4_2:7113494-7113513 Msa0586010:CDS 30.0%
AACCAATTAGGAGTTTGATT+AGG - chr4_2:7113575-7113594 None:intergenic 30.0%
GAGAGAAAATGCAATCAGAA+GGG - chr4_2:7113086-7113105 None:intergenic 35.0%
GGATTATTGGCAGGAAAATA+TGG - chr4_2:7113108-7113127 None:intergenic 35.0%
! AATCTTTGAGGATTATTGGC+AGG - chr4_2:7113117-7113136 None:intergenic 35.0%
!! CTGAAGCATTTTTCCAACAT+TGG - chr4_2:7113169-7113188 None:intergenic 35.0%
CAATGTTGGAAAAATGCTTC+AGG + chr4_2:7113167-7113186 Msa0586010:CDS 35.0%
AATCCAGTTTATGGATGTGT+TGG + chr4_2:7113387-7113406 Msa0586010:CDS 35.0%
ATCCAGTTTATGGATGTGTT+GGG + chr4_2:7113388-7113407 Msa0586010:CDS 35.0%
! AGCAATCTGAGTCTGAATTT+TGG - chr4_2:7113462-7113481 None:intergenic 35.0%
CTTGCAAGAGTCAAAGAAGA+AGG + chr4_2:7113058-7113077 Msa0586010:CDS 40.0%
GGAGAGAAAATGCAATCAGA+AGG - chr4_2:7113087-7113106 None:intergenic 40.0%
TGGACAGAAGCAAATCTTTG+AGG - chr4_2:7113129-7113148 None:intergenic 40.0%
ATCCCAACACATCCATAAAC+TGG - chr4_2:7113393-7113412 None:intergenic 40.0%
GGCCTAATCAAACTCCTAAT+TGG + chr4_2:7113570-7113589 Msa0586010:CDS 40.0%
CATTGGCACCACCATAGATT+CGG - chr4_2:7113152-7113171 None:intergenic 45.0%
! ATCTATGGTGGTGCCAATGT+TGG + chr4_2:7113153-7113172 Msa0586010:CDS 45.0%
GCTTGTTCTCTTGCATAGTG+AGG - chr4_2:7113327-7113346 None:intergenic 45.0%
!! TGCTACTTTGTGGAGGCAAA+AGG - chr4_2:7113532-7113551 None:intergenic 45.0%
GCTTCTGTCCACCGAATCTA+TGG + chr4_2:7113138-7113157 Msa0586010:CDS 50.0%
TCTGTCCACCGAATCTATGG+TGG + chr4_2:7113141-7113160 Msa0586010:CDS 50.0%
CCAGCTCAGCTTCTGTATCA+TGG - chr4_2:7113439-7113458 None:intergenic 50.0%
CCATGATACAGAAGCTGAGC+TGG + chr4_2:7113436-7113455 Msa0586010:CDS 50.0%
!! TCCATGCTGCTACTTTGTGG+AGG - chr4_2:7113539-7113558 None:intergenic 50.0%
!! TGCTCCATGCTGCTACTTTG+TGG - chr4_2:7113542-7113561 None:intergenic 50.0%
GCAGCATGGAGCAGTTTCAA+TGG + chr4_2:7113549-7113568 Msa0586010:CDS 50.0%
TGGCACCACCATAGATTCGG+TGG - chr4_2:7113149-7113168 None:intergenic 55.0%
GCCTCCACAAAGTAGCAGCA+TGG + chr4_2:7113535-7113554 Msa0586010:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 7113036 7113620 7113036 ID=Msa0586010;Name=Msa0586010
chr4_2 mRNA 7113036 7113620 7113036 ID=Msa0586010-mRNA-1;Parent=Msa0586010;Name=Msa0586010-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|2|0|151
chr4_2 exon 7113036 7113188 7113036 ID=Msa0586010-mRNA-1:exon:1789;Parent=Msa0586010-mRNA-1
chr4_2 exon 7113318 7113620 7113318 ID=Msa0586010-mRNA-1:exon:1790;Parent=Msa0586010-mRNA-1
chr4_2 CDS 7113036 7113188 7113036 ID=Msa0586010-mRNA-1:cds;Parent=Msa0586010-mRNA-1
chr4_2 CDS 7113318 7113620 7113318 ID=Msa0586010-mRNA-1:cds;Parent=Msa0586010-mRNA-1
Gene Sequence

>Msa0586010

ATGATTTATGGTAGGTGTGCTGCTTGCAAGAGTCAAAGAAGAAGGTGCCCTTCTGATTGCATTTTCTCTCCATATTTTCCTGCCAATAATCCTCAAAGATTTGCTTCTGTCCACCGAATCTATGGTGGTGCCAATGTTGGAAAAATGCTTCAGCAATTACCTCACTATGCAAGAGAACAAGCTGCAAATACTTTGTATTTAGAAGCACAATGTAGGATTCAAAATCCAGTTTATGGATGTGTTGGGATTACTCTAAATTGTATCAACAAATCCATGATACAGAAGCTGAGCTGGCCAAAATTCAGACTCAGATTGCTTGTCATAAGCTCCAAAATCAACAATATGAAGCTGGATCAAACTTCAACCTTTTGCCTCCACAAAGTAGCAGCATGGAGCAGTTTCAATGGCCTAATCAAACTCCTAATTGGTTTAATTAAGGACTTGTTTTCCAATTGA
Protein sequence

>Msa0586010

MIYGRCAACKSQRRRCPSDCIFSPYFPANNPQRFASVHRIYGGANVGKMLQQLPHYAREQAANTLYLEAQCRIQNPVYGCVGITLNCINKSMIQKLSWPKFRLRLLVISSKINNMKLDQTSTFCLHKVAAWSSFNGLIKLLIGLIKDLFSN*