AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1084450

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1084450 MtrunA17_Chr7g0266581 91.935 124 10 0 1 124 1 124 3.69e-81 234
Msa1084450 MtrunA17_Chr7g0266571 88.710 124 14 0 1 124 1 124 4.00e-62 186
Msa1084450 MtrunA17_Chr1g0178451 68.504 127 29 3 1 122 1 121 1.44e-45 144
Msa1084450 MtrunA17_Chr2g0301531 54.839 62 28 0 53 114 79 140 1.75e-20 81.3
Msa1084450 MtrunA17_Chr4g0070071 53.226 62 29 0 53 114 72 133 7.22e-20 79.7
Msa1084450 MtrunA17_Chr4g0036161 47.541 61 32 0 53 113 39 99 2.50e-16 68.9
Msa1084450 MtrunA17_Chr3g0145371 45.902 61 33 0 53 113 48 108 3.59e-16 68.9
Msa1084450 MtrunA17_Chr4g0036841 40.260 77 45 1 38 113 23 99 9.71e-16 67.4
Msa1084450 MtrunA17_Chr1g0147571 44.776 67 37 0 48 114 102 168 1.56e-15 69.7
Msa1084450 MtrunA17_Chr5g0405301 42.623 61 35 0 53 113 43 103 1.58e-15 67.0
Msa1084450 MtrunA17_Chr8g0372061 47.541 61 32 0 53 113 88 148 2.14e-15 67.8
Msa1084450 MtrunA17_Chr7g0214201 42.466 73 38 1 53 121 70 142 3.01e-15 67.8
Msa1084450 MtrunA17_Chr3g0142421 44.262 61 34 0 53 113 45 105 6.59e-15 65.5
Msa1084450 MtrunA17_Chr4g0036611 40.000 75 40 2 44 113 15 89 1.22e-14 64.3
Msa1084450 MtrunA17_Chr8g0386111 41.176 85 46 1 30 114 29 109 2.47e-14 65.1
Msa1084450 MtrunA17_Chr6g0481791 42.857 63 35 1 53 114 37 99 2.72e-14 63.9
Msa1084450 MtrunA17_Chr4g0036461 45.161 62 33 1 53 113 28 89 3.75e-14 63.2
Msa1084450 MtrunA17_Chr8g0389141 31.356 118 73 1 4 121 12 121 4.46e-14 64.7
Msa1084450 MtrunA17_Chr3g0139171 29.197 137 79 3 4 122 11 147 4.83e-14 64.7
Msa1084450 MtrunA17_Chr4g0000251 41.935 62 36 0 53 114 73 134 5.76e-14 64.7
Msa1084450 MtrunA17_Chr4g0036431 43.056 72 40 1 43 113 18 89 5.78e-14 62.8
Msa1084450 MtrunA17_Chr4g0036491 45.161 62 33 1 53 113 28 89 6.68e-14 62.4
Msa1084450 MtrunA17_Chr8g0346181 46.429 56 30 0 59 114 38 93 8.24e-14 62.8
Msa1084450 MtrunA17_Chr3g0131991 41.270 63 37 0 52 114 55 117 1.22e-13 63.5
Msa1084450 MtrunA17_Chr4g0036821 45.000 60 32 1 53 111 29 88 1.33e-13 62.0
Msa1084450 MtrunA17_Chr8g0386121 43.548 62 35 0 53 114 49 110 1.55e-13 62.0
Msa1084450 MtrunA17_Chr4g0036751 37.838 74 45 1 43 115 13 86 1.56e-13 61.6
Msa1084450 MtrunA17_Chr4g0036531 38.158 76 41 2 44 113 14 89 1.68e-13 61.6
Msa1084450 MtrunA17_Chr5g0396091 38.158 76 42 2 43 113 18 93 1.98e-13 61.6
Msa1084450 MtrunA17_Chr8g0386131 45.161 62 34 0 53 114 52 113 2.37e-13 62.8
Msa1084450 MtrunA17_Chr2g0281291 40.278 72 42 1 43 113 19 90 2.65e-13 61.2
Msa1084450 MtrunA17_Chr3g0127561 33.708 89 48 2 28 114 20 99 2.84e-13 61.6
Msa1084450 MtrunA17_Chr4g0036581 40.278 72 42 1 43 113 18 89 3.46e-13 60.8
Msa1084450 MtrunA17_Chr4g0036651 40.278 72 41 2 43 113 19 89 7.36e-13 60.1
Msa1084450 MtrunA17_Chr4g0036401 40.278 72 41 2 43 113 19 89 8.65e-13 59.7
Msa1084450 MtrunA17_Chr4g0009931 38.462 78 47 1 38 114 14 91 1.10e-12 59.7
Msa1084450 MtrunA17_Chr4g0036631 42.188 64 36 1 51 113 21 84 1.14e-12 59.3
Msa1084450 MtrunA17_Chr7g0276101 41.818 55 32 0 60 114 35 89 1.85e-12 59.3
Msa1084450 MtrunA17_Chr4g0036681 39.062 64 38 1 51 113 26 89 2.14e-12 58.5
Msa1084450 MtrunA17_Chr4g0036791 40.299 67 39 1 46 111 23 89 2.32e-12 58.5
Msa1084450 MtrunA17_Chr4g0036811 38.158 76 41 2 44 113 15 90 4.48e-12 57.8
Msa1084450 MtrunA17_Chr4g0036241 40.323 62 36 1 53 113 29 90 5.70e-12 57.8
Msa1084450 MtrunA17_Chr8g0389151 38.095 63 39 0 51 113 41 103 6.87e-12 58.5
Msa1084450 MtrunA17_Chr3g0121721 39.130 69 41 1 44 111 19 87 8.38e-12 57.0
Msa1084450 MtrunA17_Chr4g0036521 46.154 65 33 2 53 115 35 99 9.77e-12 57.4
Msa1084450 MtrunA17_Chr4g0036711 39.683 63 37 1 53 114 18 80 1.05e-11 56.6
Msa1084450 MtrunA17_Chr3g0121731 34.118 85 54 2 28 111 4 87 1.05e-11 57.0
Msa1084450 MtrunA17_Chr4g0036561 38.710 62 37 1 53 113 23 84 1.37e-11 56.6
Msa1084450 MtrunA17_Chr4g0036201 38.710 62 37 1 53 113 29 90 1.42e-11 56.6
Msa1084450 MtrunA17_Chr4g0036191 43.333 60 31 2 53 111 29 86 1.68e-11 56.2
Msa1084450 MtrunA17_Chr4g0036801 36.111 72 45 1 43 113 19 90 1.88e-11 56.2
Msa1084450 MtrunA17_Chr8g0359011 45.455 55 29 1 53 106 6 60 2.19e-11 55.5
Msa1084450 MtrunA17_Chr4g0036181 40.323 62 36 1 53 113 86 147 2.52e-11 57.4
Msa1084450 MtrunA17_Chr3g0121801 45.455 55 29 1 53 106 28 82 2.56e-11 55.8
Msa1084450 MtrunA17_Chr8g0358981 39.130 69 41 1 44 111 19 87 2.76e-11 55.8
Msa1084450 MtrunA17_Chr4g0036861 37.879 66 40 1 46 110 53 118 2.93e-11 56.6
Msa1084450 MtrunA17_Chr3g0145401 37.143 70 43 1 43 111 38 107 3.19e-11 56.2
Msa1084450 MtrunA17_Chr7g0230411 30.435 138 73 6 2 117 9 145 3.53e-11 57.0
Msa1084450 MtrunA17_Chr1g0156341 32.927 82 54 1 30 110 16 97 3.61e-11 57.0
Msa1084450 MtrunA17_Chr3g0121701 40.000 60 35 1 53 111 28 87 4.11e-11 55.5
Msa1084450 MtrunA17_Chr5g0396071 33.803 71 46 1 44 113 15 85 5.16e-11 55.1
Msa1084450 MtrunA17_Chr2g0311341 40.984 61 36 0 53 113 61 121 6.19e-11 56.2
Msa1084450 MtrunA17_Chr4g0011821 39.706 68 38 1 53 117 82 149 8.68e-11 56.2
Msa1084450 MtrunA17_Chr4g0036331 38.710 62 37 1 53 113 26 87 8.96e-11 54.3
Msa1084450 MtrunA17_Chr8g0358971 36.232 69 43 1 44 111 19 87 8.99e-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
Msa1084450 AT2G36210.1 45.385 130 66 2 1 125 1 130 1.45e-30 106
Msa1084450 AT5G20810.1 50.000 72 35 1 53 124 82 152 7.22e-19 77.8
Msa1084450 AT5G20810.2 50.000 72 35 1 53 124 82 152 1.55e-18 77.4
Msa1084450 AT3G51200.1 43.421 76 35 1 38 113 36 103 3.83e-18 74.3
Msa1084450 AT5G66260.1 45.902 61 33 0 53 113 37 97 1.24e-17 72.8
Msa1084450 AT3G43120.1 48.387 62 32 0 53 114 82 143 4.65e-17 72.8
Msa1084450 AT4G34760.1 47.541 61 32 0 53 113 46 106 9.27e-17 70.9
Msa1084450 AT2G21220.1 47.541 61 32 0 53 113 43 103 5.06e-16 68.6
Msa1084450 AT4G34780.1 40.964 83 45 2 38 116 16 98 5.32e-16 68.6
Msa1084450 AT3G20220.1 42.424 66 36 2 53 116 50 115 2.24e-15 67.4
Msa1084450 AT4G31320.1 46.875 64 34 0 53 116 83 146 1.17e-14 67.4
Msa1084450 AT2G24400.1 46.154 65 35 0 53 117 67 131 1.31e-14 67.0
Msa1084450 AT1G75580.1 44.262 61 34 0 53 113 47 107 2.03e-14 64.7
Msa1084450 AT4G00880.1 36.082 97 51 2 30 124 17 104 2.18e-14 65.1
Msa1084450 AT1G19830.1 42.623 61 35 0 53 113 51 111 2.52e-14 64.7
Msa1084450 AT3G61900.1 46.875 64 31 1 53 113 33 96 6.00e-14 64.3
Msa1084450 AT4G34750.2 34.940 83 52 1 30 110 15 97 7.24e-14 64.3
Msa1084450 AT4G34750.1 34.940 83 52 1 30 110 15 97 7.24e-14 64.3
Msa1084450 AT4G36110.1 45.763 59 32 0 53 111 43 101 7.65e-14 63.2
Msa1084450 AT3G60690.1 33.043 115 65 3 13 122 58 165 2.14e-13 63.5
Msa1084450 AT4G38860.1 45.161 62 33 1 53 113 43 104 2.25e-13 62.0
Msa1084450 AT2G46690.1 38.636 88 49 2 30 114 6 91 2.58e-13 62.4
Msa1084450 AT3G03820.1 42.308 78 41 2 41 114 18 95 4.02e-13 61.2
Msa1084450 AT5G10990.1 34.884 86 54 1 30 113 19 104 4.43e-13 62.4
Msa1084450 AT2G21210.1 42.647 68 36 2 53 117 31 98 4.55e-13 60.8
Msa1084450 AT2G16580.1 42.623 61 35 0 53 113 47 107 5.07e-13 61.2
Msa1084450 AT5G18050.1 39.189 74 43 2 43 114 17 90 6.22e-13 60.5
Msa1084450 AT4G38850.1 43.243 74 38 2 45 114 16 89 6.84e-13 60.1
Msa1084450 AT5G50760.1 42.647 68 39 0 49 116 54 121 1.14e-12 62.0
Msa1084450 AT2G18010.1 36.364 77 44 1 35 111 38 109 1.15e-12 60.5
Msa1084450 AT5G18030.1 35.227 88 55 2 29 114 1 88 1.18e-12 59.7
Msa1084450 AT4G38825.1 42.647 68 37 2 49 114 22 89 1.88e-12 59.3
Msa1084450 AT2G21210.2 34.783 115 62 4 7 117 60 165 1.96e-12 60.8
Msa1084450 AT3G03840.1 43.836 73 38 2 45 114 22 94 2.08e-12 59.3
Msa1084450 AT1G75590.1 35.632 87 53 2 30 113 19 105 2.29e-12 60.5
Msa1084450 AT3G03850.1 43.077 65 34 2 53 114 28 92 2.41e-12 58.9
Msa1084450 AT4G34800.1 44.776 67 33 2 53 115 24 90 4.46e-12 58.2
Msa1084450 AT2G37030.1 32.381 105 64 3 9 112 13 111 4.69e-12 58.9
Msa1084450 AT2G21200.1 43.077 65 35 2 44 106 15 79 6.59e-12 57.8
Msa1084450 AT4G34770.1 43.077 65 34 2 53 114 38 102 9.96e-12 57.8
Msa1084450 AT3G12830.1 35.211 71 46 0 43 113 43 113 1.02e-11 58.2
Msa1084450 AT5G18020.1 37.838 74 44 2 43 114 17 90 1.40e-11 57.0
Msa1084450 AT1G16510.1 35.714 70 45 0 44 113 48 117 1.46e-11 58.2
Msa1084450 AT5G18010.1 39.189 74 43 2 43 114 17 90 1.68e-11 56.6
Msa1084450 AT1G56150.1 28.571 105 71 1 9 113 1 101 1.70e-11 57.4
Msa1084450 AT5G18080.1 42.188 64 35 2 53 114 27 90 2.04e-11 56.6
Msa1084450 AT5G18060.1 37.838 74 44 2 43 114 17 90 2.06e-11 56.6
Msa1084450 AT1G19840.1 32.558 86 56 1 30 113 19 104 2.19e-11 57.8
Msa1084450 AT4G09530.1 38.028 71 40 2 53 119 31 101 4.32e-11 55.8
Msa1084450 AT4G13790.1 44.595 74 37 3 43 113 19 91 5.04e-11 55.5
Msa1084450 AT1G79130.1 38.462 65 40 0 49 113 47 111 5.45e-11 56.6
Msa1084450 AT4G38840.1 45.902 61 31 2 53 111 36 96 8.71e-11 55.1

Find 25 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTACAATTGTTACATTCTA+TGG 0.154919 7_2:+84824249 None:intergenic
GAGAAAGCATACAATGAATT+TGG 0.161291 7_2:-84824337 Msa1084450:CDS
TCCAACAACATCTTGAATAA+TGG 0.266822 7_2:+84824358 None:intergenic
GTTACAATTAACAAGATGTT+AGG 0.272598 7_2:-84824598 None:intergenic
CACTTGTACCACTAGTAATT+TGG 0.273994 7_2:+84824217 None:intergenic
AAAGTTGTTGAAGGAATATA+AGG 0.315149 7_2:-84824497 Msa1084450:CDS
AGAAAGCATACAATGAATTT+GGG 0.366303 7_2:-84824336 Msa1084450:CDS
TCCATTATTCAAGATGTTGT+TGG 0.366607 7_2:-84824359 Msa1084450:CDS
TTCAACAACTTTAAGTGAGC+AGG 0.391696 7_2:+84824508 None:intergenic
TGCTCACTTAAAGTTGTTGA+AGG 0.443749 7_2:-84824506 Msa1084450:CDS
TTACAATTAACAAGATGTTA+GGG 0.491456 7_2:-84824597 None:intergenic
ATAATGGATGAGAGAGGTAC+CGG 0.538476 7_2:+84824374 None:intergenic
TTTGGGTTTGAACAGAGGAA+TGG 0.555355 7_2:-84824319 Msa1084450:CDS
ATGAATTTGGGTTTGAACAG+AGG 0.563400 7_2:-84824324 Msa1084450:CDS
GTTTGAACAGAGGAATGGCT+TGG 0.578047 7_2:-84824314 Msa1084450:CDS
TGTTTCAGCATTTCAAGAGG+TGG 0.578415 7_2:-84824278 Msa1084450:CDS
CAGTGTTTCAGCATTTCAAG+AGG 0.583042 7_2:-84824281 Msa1084450:CDS
TCAACAACTTTAAGTGAGCA+GGG 0.593542 7_2:+84824509 None:intergenic
TGAAATGCTGAAACACTGCA+TGG 0.603670 7_2:+84824286 None:intergenic
TTGCGTTGCCAAATTACTAG+TGG 0.605986 7_2:-84824225 None:intergenic
AGAGATACGTGGTTCCAACC+CGG 0.610242 7_2:-84824393 Msa1084450:CDS
GGATGAGAGAGGTACCGGGT+TGG 0.623880 7_2:+84824379 None:intergenic
TAATGGATGAGAGAGGTACC+GGG 0.654606 7_2:+84824375 None:intergenic
TCTTGAATAATGGATGAGAG+AGG 0.689267 7_2:+84824368 None:intergenic
GGAGGAACGACAGAGATACG+TGG 0.777826 7_2:-84824404 Msa1084450:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGTTGTTGAAGGAATATA+AGG - chr7_2:84824314-84824333 Msa1084450:CDS 25.0%
!! AGAAAGCATACAATGAATTT+GGG - chr7_2:84824475-84824494 Msa1084450:CDS 25.0%
! CTTACAATTGTTACATTCTA+TGG + chr7_2:84824565-84824584 None:intergenic 25.0%
GATCAAGAAACTTGCAAAAA+AGG - chr7_2:84824251-84824270 Msa1084450:CDS 30.0%
GAAACTTGCAAAAAAGGTAA+AGG - chr7_2:84824257-84824276 Msa1084450:CDS 30.0%
ATTCCAACCACAAAAAAAGT+TGG - chr7_2:84824348-84824367 Msa1084450:CDS 30.0%
TTCCAACCACAAAAAAAGTT+GGG - chr7_2:84824349-84824368 Msa1084450:CDS 30.0%
!!! TGCAAAAACACCACTTTTTT+TGG + chr7_2:84824376-84824395 None:intergenic 30.0%
!! GTGTTTTTGCACTATATGTT+GGG - chr7_2:84824385-84824404 Msa1084450:CDS 30.0%
!! TGTTTTTGCACTATATGTTG+GGG - chr7_2:84824386-84824405 Msa1084450:CDS 30.0%
TCCATTATTCAAGATGTTGT+TGG - chr7_2:84824452-84824471 Msa1084450:CDS 30.0%
TCCAACAACATCTTGAATAA+TGG + chr7_2:84824456-84824475 None:intergenic 30.0%
! GAGAAAGCATACAATGAATT+TGG - chr7_2:84824474-84824493 Msa1084450:CDS 30.0%
GCAAAAAAGGTAAAGGTTGT+AGG - chr7_2:84824264-84824283 Msa1084450:CDS 35.0%
TCAACAACTTTAAGTGAGCA+GGG + chr7_2:84824305-84824324 None:intergenic 35.0%
TTCAACAACTTTAAGTGAGC+AGG + chr7_2:84824306-84824325 None:intergenic 35.0%
TGCTCACTTAAAGTTGTTGA+AGG - chr7_2:84824305-84824324 Msa1084450:CDS 35.0%
!!! TTTGGACCCAACTTTTTTTG+TGG + chr7_2:84824358-84824377 None:intergenic 35.0%
AAAGTTGGGTCCAAAAAAAG+TGG - chr7_2:84824363-84824382 Msa1084450:CDS 35.0%
!! GGTGTTTTTGCACTATATGT+TGG - chr7_2:84824384-84824403 Msa1084450:CDS 35.0%
!! TCTTGAATAATGGATGAGAG+AGG + chr7_2:84824446-84824465 None:intergenic 35.0%
! ATGAATTTGGGTTTGAACAG+AGG - chr7_2:84824487-84824506 Msa1084450:CDS 35.0%
!!! GACCCAACTTTTTTTGTGGT+TGG + chr7_2:84824354-84824373 None:intergenic 40.0%
! TTTTGCACTATATGTTGGGG+AGG - chr7_2:84824389-84824408 Msa1084450:CDS 40.0%
!! ATAATGGATGAGAGAGGTAC+CGG + chr7_2:84824440-84824459 None:intergenic 40.0%
! TTTGGGTTTGAACAGAGGAA+TGG - chr7_2:84824492-84824511 Msa1084450:CDS 40.0%
TGAAATGCTGAAACACTGCA+TGG + chr7_2:84824528-84824547 None:intergenic 40.0%
CAGTGTTTCAGCATTTCAAG+AGG - chr7_2:84824530-84824549 Msa1084450:CDS 40.0%
TGTTTCAGCATTTCAAGAGG+TGG - chr7_2:84824533-84824552 Msa1084450:CDS 40.0%
!! TAATGGATGAGAGAGGTACC+GGG + chr7_2:84824439-84824458 None:intergenic 45.0%
GTTTGAACAGAGGAATGGCT+TGG - chr7_2:84824497-84824516 Msa1084450:CDS 45.0%
AGAGATACGTGGTTCCAACC+CGG - chr7_2:84824418-84824437 Msa1084450:CDS 50.0%
GGAGGAACGACAGAGATACG+TGG - chr7_2:84824407-84824426 Msa1084450:CDS 55.0%
!! GGATGAGAGAGGTACCGGGT+TGG + chr7_2:84824435-84824454 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 84824228 84824605 84824228 ID=Msa1084450;Name=Msa1084450
chr7_2 mRNA 84824228 84824605 84824228 ID=Msa1084450-mRNA-1;Parent=Msa1084450;Name=Msa1084450-mRNA-1;_AED=0.27;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|125
chr7_2 exon 84824228 84824605 84824228 ID=Msa1084450-mRNA-1:exon:22815;Parent=Msa1084450-mRNA-1
chr7_2 CDS 84824228 84824605 84824228 ID=Msa1084450-mRNA-1:cds;Parent=Msa1084450-mRNA-1
Gene Sequence

>Msa1084450

ATGTTAGGGAAAAAGATTGTATCGATCAAGAAACTTGCAAAAAAGGTAAAGGTTGTAGGTAGAGTTGACTCTGACCCTGCTCACTTAAAGTTGTTGAAGGAATATAAGGAAGAAGAAAAAATTCCAACCACAAAAAAAGTTGGGTCCAAAAAAAGTGGTGTTTTTGCACTATATGTTGGGGAGGAACGACAGAGATACGTGGTTCCAACCCGGTACCTCTCTCATCCATTATTCAAGATGTTGTTGGAGAAAGCATACAATGAATTTGGGTTTGAACAGAGGAATGGCTTGGTAGTTCCATGCAGTGTTTCAGCATTTCAAGAGGTGGTTAATGCCATAGAATGTAACAATTGTAAGTTTGCGTTGCCAAATTACTAG
Protein sequence

>Msa1084450

MLGKKIVSIKKLAKKVKVVGRVDSDPAHLKLLKEYKEEEKIPTTKKVGSKKSGVFALYVGEERQRYVVPTRYLSHPLFKMLLEKAYNEFGFEQRNGLVVPCSVSAFQEVVNAIECNNCKFALPNY*