AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0779620

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0779620 MtrunA17_Chr5g0444351 97.241 145 4 0 1 145 1 145 1.52e-105 297
Msa0779620 MtrunA17_Chr7g0225111 82.051 117 21 0 1 117 1 117 1.05e-70 208
Msa0779620 MtrunA17_Chr5g0437571 51.376 109 53 0 6 114 7 115 7.88e-39 129
Msa0779620 MtrunA17_Chr3g0106101 45.833 120 62 1 6 125 8 124 1.57e-37 126
Msa0779620 MtrunA17_Chr2g0311601 48.571 105 54 0 6 110 14 118 2.27e-37 125
Msa0779620 MtrunA17_Chr3g0114061 42.143 140 73 2 6 145 9 140 3.95e-37 124
Msa0779620 MtrunA17_Chr4g0043421 52.525 99 47 0 6 104 16 114 2.90e-35 120
Msa0779620 MtrunA17_Chr3g0115431 46.602 103 55 0 6 108 10 112 3.62e-33 116
Msa0779620 MtrunA17_Chr5g0438091 44.882 127 67 1 6 129 40 166 4.11e-33 115
Msa0779620 MtrunA17_Chr3g0097221 49.074 108 55 0 6 113 8 115 2.87e-32 115
Msa0779620 MtrunA17_Chr4g0030001 42.857 112 63 1 1 111 20 131 3.23e-32 113
Msa0779620 MtrunA17_Chr5g0402611 46.602 103 55 0 6 108 9 111 4.27e-32 115
Msa0779620 MtrunA17_Chr3g0129071 49.057 106 54 0 6 111 48 153 4.40e-32 114
Msa0779620 MtrunA17_Chr7g0227511 45.690 116 59 1 6 117 12 127 1.48e-31 110
Msa0779620 MtrunA17_Chr4g0058651 47.664 107 56 0 6 112 12 118 1.82e-31 110
Msa0779620 MtrunA17_Chr6g0449641 48.000 100 52 0 6 105 10 109 1.47e-30 107
Msa0779620 MtrunA17_Chr3g0117121 49.000 100 51 0 6 105 11 110 3.36e-30 107
Msa0779620 MtrunA17_Chr6g0449651 40.876 137 74 2 6 142 68 197 5.79e-30 107
Msa0779620 MtrunA17_Chr1g0200201 43.564 101 57 0 6 106 73 173 4.65e-29 105
Msa0779620 MtrunA17_Chr5g0432451 48.077 104 54 0 6 109 44 147 2.11e-28 104
Msa0779620 MtrunA17_Chr6g0452691 37.879 132 79 2 6 134 10 141 3.38e-28 102
Msa0779620 MtrunA17_Chr3g0113891 44.681 94 52 0 6 99 15 108 3.70e-28 102
Msa0779620 MtrunA17_Chr8g0353981 56.250 80 35 0 6 85 8 87 5.23e-28 103
Msa0779620 MtrunA17_Chr5g0437401 41.584 101 59 0 6 106 12 112 1.66e-27 100
Msa0779620 MtrunA17_Chr6g0460951 44.340 106 58 1 6 110 41 146 2.04e-27 101
Msa0779620 MtrunA17_Chr7g0260971 45.098 102 55 1 6 106 15 116 6.77e-27 100
Msa0779620 MtrunA17_Chr6g0452671 41.237 97 57 0 6 102 12 108 1.34e-26 99.0
Msa0779620 MtrunA17_Chr1g0184281 43.478 115 60 2 6 119 16 126 2.17e-26 98.6
Msa0779620 MtrunA17_Chr8g0351701 41.667 108 62 1 4 110 22 129 3.40e-25 95.9
Msa0779620 MtrunA17_Chr7g0245871 44.554 101 55 1 6 105 28 128 7.37e-25 95.5
Msa0779620 MtrunA17_Chr8g0374601 39.604 101 61 0 6 106 27 127 1.51e-24 95.5
Msa0779620 MtrunA17_Chr7g0261031 41.732 127 67 3 6 125 9 135 2.20e-24 93.6
Msa0779620 MtrunA17_Chr8g0374581 42.574 101 57 1 6 105 9 109 3.98e-24 93.2
Msa0779620 MtrunA17_Chr8g0351721 43.269 104 58 1 4 106 17 120 4.70e-24 92.8
Msa0779620 MtrunA17_Chr1g0184271 37.857 140 78 4 6 144 13 144 8.60e-24 92.4
Msa0779620 MtrunA17_Chr8g0374591 36.634 101 64 0 6 106 9 109 1.99e-23 89.0
Msa0779620 MtrunA17_Chr5g0435641 41.176 102 59 1 6 106 8 109 4.57e-23 89.7
Msa0779620 MtrunA17_Chr6g0452661 35.294 102 65 1 6 106 10 111 7.11e-22 87.8
Msa0779620 MtrunA17_Chr5g0439111 33.333 144 87 4 6 144 10 149 2.26e-21 86.3
Msa0779620 MtrunA17_Chr6g0460941 42.529 87 49 1 6 91 8 94 1.34e-20 80.5
Msa0779620 MtrunA17_Chr4g0059901 40.000 100 60 0 6 105 11 110 1.89e-20 84.3
Msa0779620 MtrunA17_Chr8g0342351 36.538 104 66 0 6 109 13 116 4.90e-20 83.2
Msa0779620 MtrunA17_Chr4g0055441 34.314 102 66 1 6 106 3 104 5.60e-20 80.5
Msa0779620 MtrunA17_Chr2g0330201 33.663 101 67 0 6 106 20 120 1.24e-18 80.1
Msa0779620 MtrunA17_Chr7g0245861 42.857 91 49 2 4 91 11 101 3.12e-18 75.9
Msa0779620 MtrunA17_Chr4g0040831 34.831 89 58 0 2 90 12 100 3.27e-18 77.0
Msa0779620 MtrunA17_Chr2g0326041 42.105 57 33 0 1 57 29 85 3.18e-14 63.9
Msa0779620 MtrunA17_Chr4g0046201 31.395 86 59 0 6 91 7 92 1.28e-13 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0779620 AT3G26660.1 64.706 102 36 0 5 106 5 106 2.24e-45 144
Msa0779620 AT3G26620.1 64.706 102 36 0 5 106 5 106 2.70e-45 144
Msa0779620 AT2G30130.1 50.926 108 53 0 6 113 9 116 5.60e-38 128
Msa0779620 AT1G31320.1 60.465 86 34 0 6 91 14 99 1.06e-34 119
Msa0779620 AT5G63090.4 42.647 136 78 0 6 141 12 147 5.25e-32 112
Msa0779620 AT5G63090.3 42.647 136 78 0 6 141 12 147 5.25e-32 112
Msa0779620 AT5G63090.2 42.647 136 78 0 6 141 12 147 5.25e-32 112
Msa0779620 AT5G63090.1 42.647 136 78 0 6 141 12 147 5.25e-32 112
Msa0779620 AT2G28500.1 42.342 111 64 0 1 111 51 161 7.44e-32 113
Msa0779620 AT3G27650.1 49.000 100 51 0 6 105 40 139 7.80e-32 111
Msa0779620 AT1G07900.1 42.342 111 64 0 1 111 29 139 8.43e-32 112
Msa0779620 AT1G16530.1 49.505 101 50 1 6 105 15 115 1.07e-31 111
Msa0779620 AT2G23660.2 45.631 103 56 0 6 108 6 108 1.11e-31 115
Msa0779620 AT2G23660.3 45.631 103 56 0 6 108 6 108 1.11e-31 115
Msa0779620 AT2G23660.1 45.631 103 56 0 6 108 6 108 1.11e-31 115
Msa0779620 AT5G66870.1 44.660 103 57 0 6 108 8 110 1.44e-31 114
Msa0779620 AT2G30340.1 47.170 106 56 0 6 111 53 158 6.00e-31 112
Msa0779620 AT2G30340.2 47.170 106 56 0 6 111 54 159 6.20e-31 112
Msa0779620 AT2G40470.2 44.615 130 66 2 6 135 21 144 1.81e-29 106
Msa0779620 AT2G40470.1 44.961 129 65 2 6 134 46 168 2.94e-29 106
Msa0779620 AT3G11090.1 35.294 136 80 1 6 141 12 139 1.44e-28 103
Msa0779620 AT1G65620.1 45.545 101 55 0 6 106 10 110 1.28e-27 102
Msa0779620 AT1G65620.4 45.545 101 55 0 6 106 10 110 1.28e-27 102
Msa0779620 AT1G65620.3 45.545 101 55 0 6 106 10 110 1.28e-27 102
Msa0779620 AT1G65620.5 45.545 101 55 0 6 106 10 110 1.28e-27 102
Msa0779620 AT1G65620.2 45.545 101 55 0 6 106 10 110 1.28e-27 102
Msa0779620 AT4G00210.1 39.416 137 73 3 4 132 10 144 2.79e-27 101
Msa0779620 AT3G03760.1 45.545 101 54 1 6 105 52 152 9.33e-27 101
Msa0779620 AT2G42430.1 43.810 105 58 1 6 109 16 120 3.01e-26 99.4
Msa0779620 AT3G50510.1 41.905 105 61 0 2 106 9 113 9.38e-26 97.1
Msa0779620 AT3G50510.2 41.905 105 61 0 2 106 9 113 9.38e-26 97.1
Msa0779620 AT5G06080.1 41.322 121 67 2 6 125 8 125 6.37e-25 94.4
Msa0779620 AT2G45410.1 45.000 100 54 1 8 106 19 118 2.24e-24 93.2
Msa0779620 AT4G00220.1 40.385 104 61 1 8 110 20 123 1.34e-23 92.0
Msa0779620 AT3G58190.1 43.137 102 57 1 6 106 12 113 1.49e-23 91.7
Msa0779620 AT2G42440.1 43.000 100 56 1 6 104 8 107 2.18e-23 92.0
Msa0779620 AT3G47870.1 37.736 106 66 0 4 109 35 140 6.99e-23 92.0
Msa0779620 AT2G45420.1 42.308 104 59 1 8 110 40 143 1.08e-22 90.5
Msa0779620 AT3G13850.1 33.766 154 82 2 6 139 37 190 2.86e-22 89.4
Msa0779620 AT5G35900.1 40.777 103 54 1 6 101 6 108 1.55e-20 83.6
Msa0779620 AT2G31310.1 31.206 141 89 3 6 145 8 141 7.98e-20 81.3
Msa0779620 AT1G72980.1 33.077 130 83 2 6 134 14 140 2.15e-17 75.5
Msa0779620 AT1G06280.1 37.209 86 54 0 6 91 25 110 2.75e-17 75.1
Msa0779620 AT2G19820.1 34.021 97 58 2 6 101 13 104 1.41e-14 66.2
Msa0779620 AT4G22700.1 31.579 114 76 2 1 113 1 113 2.01e-13 64.7
Msa0779620 AT5G15060.1 43.243 74 38 2 6 76 18 90 1.94e-12 61.2
Msa0779620 AT1G36000.1 26.882 93 68 0 6 98 10 102 6.99e-11 56.6

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 5_2:+60898881 None:intergenic
AGGATTCAAAATCCTGTTTA+TGG 0.168254 5_2:-60898997 Msa0779620:CDS
AGCAAATCTTTGAGGATTAT+TGG 0.218212 5_2:+60899259 None:intergenic
AGCAATCTGAGTTTGGATTT+TGG 0.249357 5_2:+60898915 None:intergenic
GGATTATTGGCAGGGAAATA+TGG 0.290635 5_2:+60899272 None:intergenic
GCTTATGTCCACCGAATCTA+TGG 0.297656 5_2:-60899239 Msa0779620:CDS
GGCCCAATCAAACACCTAAT+TGG 0.314557 5_2:-60898804 Msa0779620:CDS
TATGACAAGCAATCTGAGTT+TGG 0.340516 5_2:+60898908 None:intergenic
AAGTCTTAATTGAACCAATT+AGG 0.341976 5_2:+60898790 None:intergenic
GAACCAATTAGGTGTTTGAT+TGG 0.385252 5_2:+60898801 None:intergenic
CCAGCTCAGCTTCTGTATCA+TGG 0.391779 5_2:+60898938 None:intergenic
ATCCCAACACATCCATAAAC+AGG 0.441067 5_2:+60898985 None:intergenic
AATCTTTGAGGATTATTGGC+AGG 0.455276 5_2:+60899263 None:intergenic
TGCTCCATGCTGCTACTTTG+TGG 0.458851 5_2:+60898835 None:intergenic
AACCAATTAGGTGTTTGATT+GGG 0.459934 5_2:+60898802 None:intergenic
CCATGATACAGAAGCTGAGC+TGG 0.490473 5_2:-60898938 Msa0779620:CDS
TGTATTTAGAAGCACAATGT+AGG 0.494601 5_2:-60899017 Msa0779620:CDS
TGGACATAAGCAAATCTTTG+AGG 0.504910 5_2:+60899251 None:intergenic
CAAAATCAACAATATGAAGC+TGG 0.506425 5_2:-60898880 Msa0779620:CDS
ATCTATGGTGGTGCCAATGT+TGG 0.519520 5_2:-60899224 Msa0779620:CDS
CATTGGCACCACCATAGATT+CGG 0.530883 5_2:+60899228 None:intergenic
TTGACATCATGATTTATGGT+AGG 0.535888 5_2:-60899349 None:intergenic
AATCCTGTTTATGGATGTGT+TGG 0.538555 5_2:-60898988 Msa0779620:CDS
GGAGAGAAAATGCAATCAGA+AGG 0.551169 5_2:+60899293 None:intergenic
CTTGCAAGAGTCAAAGAAGA+AGG 0.555730 5_2:-60899319 Msa0779620:CDS
ATCTTTGAGGATTATTGGCA+GGG 0.557843 5_2:+60899264 None:intergenic
GCCTCCACAAAGTAGCAGCA+TGG 0.580606 5_2:-60898839 Msa0779620:CDS
ATCCTGTTTATGGATGTGTT+GGG 0.594258 5_2:-60898987 Msa0779620:CDS
GCTTGTTCTCTTACATAGTG+AGG 0.601870 5_2:+60899051 None:intergenic
GAGAGAAAATGCAATCAGAA+GGG 0.619697 5_2:+60899294 None:intergenic
TGGCACCACCATAGATTCGG+TGG 0.632816 5_2:+60899231 None:intergenic
TCCATGCTGCTACTTTGTGG+AGG 0.665689 5_2:+60898838 None:intergenic
TATGTCCACCGAATCTATGG+TGG 0.669495 5_2:-60899236 Msa0779620:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTAATATAATTATAACATA+TGG - chr5_2:60898994-60899013 Msa0779620:CDS 10.0%
!!! TTCTTATCTAGTATTTTTAT+TGG - chr5_2:60899051-60899070 Msa0779620:CDS 15.0%
! AGCAAATCTTTGAGGATTAT+TGG + chr5_2:60898880-60898899 None:intergenic 30.0%
! TGTATTTAGAAGCACAATGT+AGG - chr5_2:60899119-60899138 Msa0779620:intron 30.0%
AGGATTCAAAATCCTGTTTA+TGG - chr5_2:60899139-60899158 Msa0779620:intron 30.0%
!!! CAGCTTCATATTGTTGATTT+TGG + chr5_2:60899258-60899277 None:intergenic 30.0%
CAAAATCAACAATATGAAGC+TGG - chr5_2:60899256-60899275 Msa0779620:CDS 30.0%
AACCAATTAGGTGTTTGATT+GGG + chr5_2:60899337-60899356 None:intergenic 30.0%
GAGAGAAAATGCAATCAGAA+GGG + chr5_2:60898845-60898864 None:intergenic 35.0%
! ATCTTTGAGGATTATTGGCA+GGG + chr5_2:60898875-60898894 None:intergenic 35.0%
! AATCTTTGAGGATTATTGGC+AGG + chr5_2:60898876-60898895 None:intergenic 35.0%
TGGACATAAGCAAATCTTTG+AGG + chr5_2:60898888-60898907 None:intergenic 35.0%
!! CTGAAGCATTTTTCCAACAT+TGG + chr5_2:60898928-60898947 None:intergenic 35.0%
CAATGTTGGAAAAATGCTTC+AGG - chr5_2:60898926-60898945 Msa0779620:CDS 35.0%
AATCCTGTTTATGGATGTGT+TGG - chr5_2:60899148-60899167 Msa0779620:intron 35.0%
ATCCTGTTTATGGATGTGTT+GGG - chr5_2:60899149-60899168 Msa0779620:intron 35.0%
! AGCAATCTGAGTTTGGATTT+TGG + chr5_2:60899224-60899243 None:intergenic 35.0%
TATGACAAGCAATCTGAGTT+TGG + chr5_2:60899231-60899250 None:intergenic 35.0%
GAACCAATTAGGTGTTTGAT+TGG + chr5_2:60899338-60899357 None:intergenic 35.0%
CTTGCAAGAGTCAAAGAAGA+AGG - chr5_2:60898817-60898836 Msa0779620:CDS 40.0%
GGAGAGAAAATGCAATCAGA+AGG + chr5_2:60898846-60898865 None:intergenic 40.0%
GGATTATTGGCAGGGAAATA+TGG + chr5_2:60898867-60898886 None:intergenic 40.0%
GCTTGTTCTCTTACATAGTG+AGG + chr5_2:60899088-60899107 None:intergenic 40.0%
ATCCCAACACATCCATAAAC+AGG + chr5_2:60899154-60899173 None:intergenic 40.0%
GCTTATGTCCACCGAATCTA+TGG - chr5_2:60898897-60898916 Msa0779620:CDS 45.0%
TATGTCCACCGAATCTATGG+TGG - chr5_2:60898900-60898919 Msa0779620:CDS 45.0%
CATTGGCACCACCATAGATT+CGG + chr5_2:60898911-60898930 None:intergenic 45.0%
! ATCTATGGTGGTGCCAATGT+TGG - chr5_2:60898912-60898931 Msa0779620:CDS 45.0%
!! GCAGCATGGAGCATTTTCAA+TGG - chr5_2:60899311-60899330 Msa0779620:CDS 45.0%
GGCCCAATCAAACACCTAAT+TGG - chr5_2:60899332-60899351 Msa0779620:CDS 45.0%
CCAGCTCAGCTTCTGTATCA+TGG + chr5_2:60899201-60899220 None:intergenic 50.0%
CCATGATACAGAAGCTGAGC+TGG - chr5_2:60899198-60899217 Msa0779620:intron 50.0%
!! TCCATGCTGCTACTTTGTGG+AGG + chr5_2:60899301-60899320 None:intergenic 50.0%
!! TGCTCCATGCTGCTACTTTG+TGG + chr5_2:60899304-60899323 None:intergenic 50.0%
TGGCACCACCATAGATTCGG+TGG + chr5_2:60898908-60898927 None:intergenic 55.0%
GCCTCCACAAAGTAGCAGCA+TGG - chr5_2:60899297-60899316 Msa0779620:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 60898795 60899363 60898795 ID=Msa0779620;Name=Msa0779620
chr5_2 mRNA 60898795 60899363 60898795 ID=Msa0779620-mRNA-1;Parent=Msa0779620;Name=Msa0779620-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|2|0|145
chr5_2 exon 60899211 60899363 60899211 ID=Msa0779620-mRNA-1:exon:17929;Parent=Msa0779620-mRNA-1
chr5_2 exon 60898795 60899079 60898795 ID=Msa0779620-mRNA-1:exon:17928;Parent=Msa0779620-mRNA-1
chr5_2 CDS 60899211 60899363 60899211 ID=Msa0779620-mRNA-1:cds;Parent=Msa0779620-mRNA-1
chr5_2 CDS 60898795 60899079 60898795 ID=Msa0779620-mRNA-1:cds;Parent=Msa0779620-mRNA-1
Gene Sequence

>Msa0779620

ATGATTTATGGTAGGTGTGCTGCTTGCAAGAGTCAAAGAAGAAGGTGCCCTTCTGATTGCATTTTCTCTCCATATTTCCCTGCCAATAATCCTCAAAGATTTGCTTATGTCCACCGAATCTATGGTGGTGCCAATGTTGGAAAAATGCTTCAGCAATTGCCTCACTATGTAAGAGAACAAGCTGCAAATACTTTGTATTTAGAAGCACAATGTAGGATTCAAAATCCTGTTTATGGATGTGTTGGGATCATCTCTAAATTGTATCAACAAATCCATGATACAGAAGCTGAGCTGGCCAAAATCCAAACTCAGATTGCTTGTCATAAGCTCCAAAATCAACAATATGAAGCTGGATCAAACTTCAATCTTTTGCCTCCACAAAGTAGCAGCATGGAGCATTTTCAATGGCCCAATCAAACACCTAATTGGTTCAATTAA
Protein sequence

>Msa0779620

MIYGRCAACKSQRRRCPSDCIFSPYFPANNPQRFAYVHRIYGGANVGKMLQQLPHYVREQAANTLYLEAQCRIQNPVYGCVGIISKLYQQIHDTEAELAKIQTQIACHKLQNQQYEAGSNFNLLPPQSSSMEHFQWPNQTPNWFN*