AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0269330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0269330 MtrunA17_Chr6g0449311 89.431 123 12 1 37 159 1 122 5.06e-65 195
Msa0269330 MtrunA17_Chr5g0439111 63.473 167 49 5 1 162 1 160 1.07e-61 190
Msa0269330 MtrunA17_Chr6g0452661 58.788 165 55 3 1 162 1 155 1.51e-60 187
Msa0269330 MtrunA17_Chr4g0055441 62.590 139 39 3 10 146 3 130 2.18e-53 166
Msa0269330 MtrunA17_Chr6g0452691 57.554 139 49 2 1 136 1 132 3.02e-52 164
Msa0269330 MtrunA17_Chr6g0452671 56.338 142 55 3 1 140 1 137 6.71e-48 154
Msa0269330 MtrunA17_Chr4g0059901 51.402 107 51 1 8 114 9 114 7.76e-33 117
Msa0269330 MtrunA17_Chr8g0342351 52.336 107 50 1 8 114 11 116 1.95e-31 113
Msa0269330 MtrunA17_Chr3g0097221 45.536 112 60 1 7 118 5 115 1.61e-27 103
Msa0269330 MtrunA17_Chr7g0227511 45.918 98 52 1 7 104 9 105 1.43e-26 98.6
Msa0269330 MtrunA17_Chr2g0330201 44.954 109 59 1 8 116 18 125 3.51e-26 100
Msa0269330 MtrunA17_Chr4g0058651 36.184 152 85 2 7 158 9 148 9.87e-26 97.1
Msa0269330 MtrunA17_Chr5g0402611 43.810 105 58 1 7 111 6 109 1.72e-25 99.4
Msa0269330 MtrunA17_Chr3g0115431 44.118 102 56 1 10 111 10 110 2.69e-25 96.7
Msa0269330 MtrunA17_Chr8g0353981 50.602 83 40 1 7 89 5 86 3.59e-25 96.7
Msa0269330 MtrunA17_Chr6g0449641 39.259 135 75 3 7 137 7 138 3.66e-25 94.4
Msa0269330 MtrunA17_Chr3g0117121 44.898 98 53 1 7 104 8 104 5.66e-25 95.1
Msa0269330 MtrunA17_Chr4g0043421 38.931 131 78 2 10 140 16 144 6.04e-24 92.0
Msa0269330 MtrunA17_Chr6g0449651 38.393 112 66 2 7 118 65 173 6.72e-23 89.7
Msa0269330 MtrunA17_Chr2g0311601 39.796 98 58 1 10 107 14 110 1.46e-22 87.8
Msa0269330 MtrunA17_Chr5g0438091 34.074 135 87 2 10 143 40 173 2.21e-22 88.6
Msa0269330 MtrunA17_Chr5g0437401 36.697 109 68 1 5 113 7 114 2.42e-22 87.8
Msa0269330 MtrunA17_Chr5g0437571 40.187 107 62 2 7 113 4 108 3.48e-22 87.4
Msa0269330 MtrunA17_Chr7g0225111 37.273 110 68 1 10 119 6 114 3.86e-22 85.9
Msa0269330 MtrunA17_Chr4g0030001 40.351 114 65 3 10 122 25 136 1.15e-21 86.7
Msa0269330 MtrunA17_Chr8g0374591 39.423 104 62 1 8 111 7 109 2.71e-21 84.0
Msa0269330 MtrunA17_Chr5g0444351 34.545 110 71 1 10 119 6 114 3.10e-21 84.3
Msa0269330 MtrunA17_Chr3g0106101 39.362 94 56 1 10 103 8 100 8.50e-21 84.0
Msa0269330 MtrunA17_Chr3g0113891 38.462 104 63 1 5 108 10 112 2.33e-20 82.8
Msa0269330 MtrunA17_Chr8g0374601 39.423 104 62 1 8 111 25 127 2.70e-20 84.7
Msa0269330 MtrunA17_Chr3g0114061 39.423 104 61 2 10 113 9 110 5.17e-20 81.3
Msa0269330 MtrunA17_Chr1g0200201 41.489 94 54 1 10 103 73 165 5.78e-20 82.8
Msa0269330 MtrunA17_Chr4g0040831 34.862 109 66 2 8 112 14 121 6.03e-20 82.4
Msa0269330 MtrunA17_Chr5g0432451 33.588 131 84 2 10 140 44 171 1.89e-19 81.6
Msa0269330 MtrunA17_Chr3g0129071 36.735 98 61 1 10 107 48 144 2.20e-19 81.6
Msa0269330 MtrunA17_Chr7g0260971 39.806 103 60 2 10 111 15 116 7.25e-18 77.0
Msa0269330 MtrunA17_Chr8g0351721 35.780 109 68 2 4 111 13 120 1.27e-16 73.9
Msa0269330 MtrunA17_Chr7g0245871 36.364 99 61 2 10 107 28 125 8.43e-16 72.0
Msa0269330 MtrunA17_Chr6g0460951 33.028 109 71 2 10 117 41 148 9.04e-16 71.6
Msa0269330 MtrunA17_Chr8g0351701 35.354 99 62 2 10 107 24 121 1.00e-15 71.6
Msa0269330 MtrunA17_Chr1g0184281 36.364 99 61 2 10 107 16 113 4.12e-15 69.7
Msa0269330 MtrunA17_Chr4g0046201 37.500 88 54 1 9 96 6 92 5.33e-15 70.5
Msa0269330 MtrunA17_Chr8g0374581 35.577 104 65 2 8 110 7 109 1.76e-14 68.2
Msa0269330 MtrunA17_Chr6g0460941 36.364 88 54 2 10 96 8 94 2.78e-14 64.7
Msa0269330 MtrunA17_Chr1g0184271 34.000 100 64 2 10 108 13 111 6.27e-14 67.0
Msa0269330 MtrunA17_Chr5g0435641 29.091 110 76 2 8 116 6 114 9.29e-14 65.9
Msa0269330 MtrunA17_Chr7g0261031 33.000 100 65 2 10 108 9 107 3.32e-13 64.7
Msa0269330 MtrunA17_Chr2g0326041 52.083 48 23 0 10 57 34 81 9.21e-13 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0269330 AT3G47870.1 55.660 106 46 1 9 114 36 140 3.03e-36 128
Msa0269330 AT3G13850.1 51.429 105 50 1 8 112 35 138 2.30e-30 111
Msa0269330 AT3G27650.1 43.000 100 56 1 7 106 37 135 3.61e-25 95.1
Msa0269330 AT5G63090.4 42.727 110 62 1 7 116 9 117 1.02e-24 94.7
Msa0269330 AT5G63090.3 42.727 110 62 1 7 116 9 117 1.02e-24 94.7
Msa0269330 AT5G63090.2 42.727 110 62 1 7 116 9 117 1.02e-24 94.7
Msa0269330 AT5G63090.1 42.727 110 62 1 7 116 9 117 1.02e-24 94.7
Msa0269330 AT1G65620.1 48.193 83 42 1 7 89 7 88 5.97e-24 93.2
Msa0269330 AT1G65620.4 48.193 83 42 1 7 89 7 88 5.97e-24 93.2
Msa0269330 AT1G65620.3 48.193 83 42 1 7 89 7 88 5.97e-24 93.2
Msa0269330 AT1G65620.5 48.193 83 42 1 7 89 7 88 5.97e-24 93.2
Msa0269330 AT1G65620.2 48.193 83 42 1 7 89 7 88 5.97e-24 93.2
Msa0269330 AT5G66870.1 42.157 102 58 1 10 111 8 108 1.36e-23 94.4
Msa0269330 AT3G26660.1 38.261 115 68 2 8 120 4 117 8.68e-23 87.8
Msa0269330 AT1G31320.1 45.977 87 46 1 10 96 14 99 1.84e-22 88.6
Msa0269330 AT3G26620.1 35.833 120 74 2 8 127 4 120 3.57e-22 86.3
Msa0269330 AT1G07900.1 38.793 116 67 3 10 124 34 146 3.42e-21 85.5
Msa0269330 AT1G72980.1 40.179 112 65 2 9 119 13 123 3.66e-21 86.3
Msa0269330 AT2G23660.2 41.584 101 58 1 10 110 6 105 2.97e-20 85.5
Msa0269330 AT2G23660.3 41.584 101 58 1 10 110 6 105 2.97e-20 85.5
Msa0269330 AT2G23660.1 41.584 101 58 1 10 110 6 105 2.97e-20 85.5
Msa0269330 AT2G30130.1 40.385 104 60 2 10 113 9 110 5.54e-20 82.4
Msa0269330 AT2G28500.1 38.053 113 67 2 10 122 56 165 7.19e-20 83.2
Msa0269330 AT3G11090.1 36.364 99 62 1 5 103 7 104 1.37e-19 80.9
Msa0269330 AT2G30340.2 38.776 98 59 1 10 107 54 150 2.51e-19 82.4
Msa0269330 AT2G30340.1 38.776 98 59 1 10 107 53 149 3.11e-19 82.0
Msa0269330 AT5G15060.1 47.945 73 37 1 10 81 18 90 3.22e-19 79.3
Msa0269330 AT1G16530.1 36.283 113 63 3 5 109 10 121 7.88e-19 79.0
Msa0269330 AT2G40470.2 37.755 98 60 1 10 107 21 117 8.30e-19 79.7
Msa0269330 AT2G40470.1 37.755 98 60 1 10 107 46 142 1.85e-18 79.3
Msa0269330 AT3G50510.1 38.095 105 63 2 10 113 13 116 4.52e-17 75.1
Msa0269330 AT3G50510.2 38.095 105 63 2 10 113 13 116 4.52e-17 75.1
Msa0269330 AT1G06280.1 38.298 94 53 3 8 101 23 111 7.32e-17 74.7
Msa0269330 AT2G19820.1 34.343 99 62 1 1 96 1 99 1.14e-16 72.0
Msa0269330 AT2G42430.1 29.114 158 105 3 10 161 16 172 2.76e-16 73.9
Msa0269330 AT4G00220.1 35.238 105 66 2 12 115 20 123 1.14e-15 72.0
Msa0269330 AT4G00210.1 36.893 103 63 2 10 111 12 113 2.20e-15 70.9
Msa0269330 AT2G45420.1 34.286 105 67 2 12 115 40 143 1.14e-14 69.7
Msa0269330 AT2G42440.1 34.000 100 64 2 10 108 8 106 1.24e-14 69.3
Msa0269330 AT3G58190.1 36.000 100 62 2 10 108 12 110 1.88e-14 68.6
Msa0269330 AT3G03760.1 35.294 102 64 2 10 110 52 152 4.33e-14 68.2
Msa0269330 AT5G35900.1 29.412 102 71 1 10 111 6 106 1.08e-13 66.2
Msa0269330 AT5G06080.1 31.959 97 64 2 9 104 7 102 8.67e-13 63.2
Msa0269330 AT2G45410.1 35.644 101 63 2 12 111 19 118 8.98e-13 63.5
Msa0269330 AT2G31310.1 34.831 89 56 2 10 97 8 95 1.39e-12 62.8

Find 22 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTTCTTTGATATTTGC+AGG 0.243555 2_3:-78218 None:intergenic
TCACCATTATGATAATAATA+AGG 0.262900 2_3:-78631 None:intergenic
GGTTTATCGGCTGGAAAATA+AGG 0.273342 2_3:-78265 None:intergenic
TGGATGTCTTGGTCTTATTA+TGG 0.281895 2_3:+78432 Msa0269330:CDS
TCACCAACATTGTTAGATAT+TGG 0.284051 2_3:-78604 None:intergenic
CTTCTACATTTCTCTTCATT+TGG 0.300408 2_3:+78544 Msa0269330:CDS
GTTCCTTATTATTATCATAA+TGG 0.313621 2_3:+78628 Msa0269330:CDS
TTGTTAGATATTGGAGGAAT+TGG 0.327674 2_3:-78595 None:intergenic
GCCAATGCTCATCGTTTGTT+TGG 0.347008 2_3:+78298 Msa0269330:CDS
TAAGGAGCTAAAGGGCAATC+TGG 0.416523 2_3:-78247 None:intergenic
GGAATTGGAGAGCTAGTAGA+AGG 0.422957 2_3:-78580 None:intergenic
TTCCCAAGTCATGGATGTCT+TGG 0.482571 2_3:+78421 Msa0269330:CDS
GCTGGAAAATAAGGAGCTAA+AGG 0.488184 2_3:-78256 None:intergenic
CTGGAAAATAAGGAGCTAAA+GGG 0.495690 2_3:-78255 None:intergenic
CTTTAGCGTCTTCACCATGT+TGG 0.497302 2_3:-78326 None:intergenic
CCAACATTGTTAGATATTGG+AGG 0.529834 2_3:-78601 None:intergenic
AGACCAAGACATCCATGACT+TGG 0.541471 2_3:-78424 None:intergenic
CCTCCAATATCTAACAATGT+TGG 0.542797 2_3:+78601 Msa0269330:CDS
ACCAAACAAACGATGAGCAT+TGG 0.553402 2_3:-78299 None:intergenic
CGTGCAAGATTCCCAAGTCA+TGG 0.565788 2_3:+78412 Msa0269330:CDS
GACCAAGACATCCATGACTT+GGG 0.599785 2_3:-78423 None:intergenic
TTTGTTTGGTATTTCCAACA+TGG 0.612102 2_3:+78312 Msa0269330:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTCCTTATTATTATCATAA+TGG + chr2_3:78628-78647 Msa0269330:CDS 20.0%
!! TCACCATTATGATAATAATA+AGG - chr2_3:78634-78653 None:intergenic 20.0%
GGATATTCACAGAAAAAACA+AGG + chr2_3:78186-78205 Msa0269330:CDS 30.0%
CTTTCTTCTTTGATATTTGC+AGG - chr2_3:78221-78240 None:intergenic 30.0%
TTTGTTTGGTATTTCCAACA+TGG + chr2_3:78312-78331 Msa0269330:CDS 30.0%
!!! GAAGTCGATTATTTTTGAGT+CGG + chr2_3:78384-78403 Msa0269330:CDS 30.0%
CTTCTACATTTCTCTTCATT+TGG + chr2_3:78544-78563 Msa0269330:CDS 30.0%
TTGTTAGATATTGGAGGAAT+TGG - chr2_3:78598-78617 None:intergenic 30.0%
TCACCAACATTGTTAGATAT+TGG - chr2_3:78607-78626 None:intergenic 30.0%
CTGGAAAATAAGGAGCTAAA+GGG - chr2_3:78258-78277 None:intergenic 35.0%
!! TGGATGTCTTGGTCTTATTA+TGG + chr2_3:78432-78451 Msa0269330:CDS 35.0%
CCAACATTGTTAGATATTGG+AGG - chr2_3:78604-78623 None:intergenic 35.0%
CCTCCAATATCTAACAATGT+TGG + chr2_3:78601-78620 Msa0269330:CDS 35.0%
GCTGGAAAATAAGGAGCTAA+AGG - chr2_3:78259-78278 None:intergenic 40.0%
! GGTTTATCGGCTGGAAAATA+AGG - chr2_3:78268-78287 None:intergenic 40.0%
ACCAAACAAACGATGAGCAT+TGG - chr2_3:78302-78321 None:intergenic 40.0%
TAAGGAGCTAAAGGGCAATC+TGG - chr2_3:78250-78269 None:intergenic 45.0%
! AGCATTTTCGGTTTATCGGC+TGG - chr2_3:78277-78296 None:intergenic 45.0%
! GGCGAGCATTTTCGGTTTAT+CGG - chr2_3:78281-78300 None:intergenic 45.0%
!!! TGAGCATTGGCGAGCATTTT+CGG - chr2_3:78289-78308 None:intergenic 45.0%
GCCAATGCTCATCGTTTGTT+TGG + chr2_3:78298-78317 Msa0269330:CDS 45.0%
CTTTAGCGTCTTCACCATGT+TGG - chr2_3:78329-78348 None:intergenic 45.0%
TTCCCAAGTCATGGATGTCT+TGG + chr2_3:78421-78440 Msa0269330:CDS 45.0%
GACCAAGACATCCATGACTT+GGG - chr2_3:78426-78445 None:intergenic 45.0%
AGACCAAGACATCCATGACT+TGG - chr2_3:78427-78446 None:intergenic 45.0%
GGAATTGGAGAGCTAGTAGA+AGG - chr2_3:78583-78602 None:intergenic 45.0%
CGTGCAAGATTCCCAAGTCA+TGG + chr2_3:78412-78431 Msa0269330:CDS 50.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 78184 78672 78184 ID=Msa0269330;Name=Msa0269330
chr2_3 mRNA 78184 78672 78184 ID=Msa0269330-mRNA-1;Parent=Msa0269330;Name=Msa0269330-mRNA-1;_AED=0.05;_eAED=0.06;_QI=0|-1|0|1|-1|1|1|0|162
chr2_3 exon 78184 78672 78184 ID=Msa0269330-mRNA-1:exon:2;Parent=Msa0269330-mRNA-1
chr2_3 CDS 78184 78672 78184 ID=Msa0269330-mRNA-1:cds;Parent=Msa0269330-mRNA-1
Gene Sequence

>Msa0269330

ATGGATATTCACAGAAAAAACAAGGCTTGTGCAGCCTGCAAATATCAAAGAAGAAAGTGTACTCCAGATTGCCCTTTAGCTCCTTATTTTCCAGCCGATAAACCGAAAATGCTCGCCAATGCTCATCGTTTGTTTGGTATTTCCAACATGGTGAAGACGCTAAAGTCTATTGATGATGATGATCATAAAGATGAAGCAATGAAGTCGATTATTTTTGAGTCGGAAATGCGTGCAAGATTCCCAAGTCATGGATGTCTTGGTCTTATTATGGAGTATCAAGATATGATAATTGAGTCTATGAAAGAGTTAGATCATGTAAAGCAGTTACTAAGTTTGTGTAAGCTATCACATCAACAAAATCTTCTACATTTCTCTTCATTTGGTCATTCTTCAGTACCTTCTACTAGCTCTCCAATTCCTCCAATATCTAACAATGTTGGTGATGTTCCTTATTATTATCATAATGGTGAAAATAATATGATACTATGA
Protein sequence

>Msa0269330

MDIHRKNKACAACKYQRRKCTPDCPLAPYFPADKPKMLANAHRLFGISNMVKTLKSIDDDDHKDEAMKSIIFESEMRARFPSHGCLGLIMEYQDMIIESMKELDHVKQLLSLCKLSHQQNLLHFSSFGHSSVPSTSSPIPPISNNVGDVPYYYHNGENNMIL*