AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002574

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002574.t1 MTR_2g016030 96.894 161 4 1 1 160 1 161 4.60e-114 320
MS.gene002574.t1 MTR_6g012450 70.370 81 23 1 19 99 110 189 1.62e-36 131
MS.gene002574.t1 MTR_4g082060 67.500 80 26 0 20 99 96 175 1.73e-35 128
MS.gene002574.t1 MTR_7g010950 71.053 76 21 1 24 99 114 188 5.50e-35 127
MS.gene002574.t1 MTR_8g044220 61.628 86 32 1 25 109 96 181 1.26e-34 125
MS.gene002574.t1 MTR_7g086780 71.233 73 20 1 28 99 80 152 6.41e-33 120
MS.gene002574.t1 MTR_5g041380 58.065 93 37 1 18 108 97 189 3.84e-32 117
MS.gene002574.t1 MTR_6g027460 73.239 71 18 1 30 99 79 149 5.75e-32 117
MS.gene002574.t1 MTR_3g435480 57.778 90 29 1 19 99 100 189 6.51e-31 115
MS.gene002574.t1 MTR_5g041530 70.423 71 18 1 32 99 123 193 1.54e-30 114
MS.gene002574.t1 MTR_6g027450 69.014 71 21 1 30 99 72 142 1.60e-30 112
MS.gene002574.t1 MTR_5g041400 62.338 77 29 0 32 108 105 181 4.29e-30 112
MS.gene002574.t1 MTR_5g041420 71.667 60 17 0 40 99 132 191 8.20e-30 110
MS.gene002574.t1 MTR_2g096740 55.263 76 34 0 24 99 40 115 2.09e-27 103
MS.gene002574.t1 MTR_2g096740 55.263 76 34 0 24 99 55 130 2.30e-27 103
MS.gene002574.t1 MTR_8g015840 59.155 71 23 1 34 98 2 72 3.92e-26 99.0
MS.gene002574.t1 MTR_8g068210 47.059 102 48 3 24 123 12 109 4.79e-26 101
MS.gene002574.t1 MTR_8g479350 48.000 100 41 2 48 138 70 167 9.76e-26 100
MS.gene002574.t1 MTR_4g022370 70.175 57 17 0 43 99 79 135 1.30e-25 100
MS.gene002574.t1 MTR_8g027295 56.098 82 32 2 36 113 12 93 3.53e-25 97.8
MS.gene002574.t1 MTR_8g079060 71.154 52 15 0 46 97 29 80 4.16e-25 96.7
MS.gene002574.t1 MTR_4g063780 64.286 70 24 1 43 111 72 141 1.23e-24 97.4
MS.gene002574.t1 MTR_2g093220 55.263 76 34 0 24 99 18 93 1.66e-24 96.3
MS.gene002574.t1 MTR_4g109980 69.811 53 16 0 44 96 38 90 1.70e-24 96.7
MS.gene002574.t1 MTR_3g091820 64.912 57 20 0 43 99 40 96 1.95e-24 96.3
MS.gene002574.t1 MTR_2g059540 73.469 49 13 0 46 94 31 79 2.75e-24 94.0
MS.gene002574.t1 MTR_7g024670 76.000 50 12 0 48 97 79 128 4.21e-24 96.7
MS.gene002574.t1 MTR_7g059400 68.421 57 18 0 43 99 73 129 1.01e-23 95.1
MS.gene002574.t1 MTR_1g077600 54.412 68 31 0 30 97 27 94 1.14e-23 93.6
MS.gene002574.t1 MTR_1g077600 54.412 68 31 0 30 97 27 94 1.36e-23 94.0
MS.gene002574.t1 MTR_4g088580 73.077 52 14 0 48 99 57 108 1.91e-23 94.7
MS.gene002574.t1 MTR_5g031440 68.519 54 17 0 43 96 40 93 1.97e-23 94.4
MS.gene002574.t1 MTR_4g089095 67.308 52 17 0 48 99 52 103 3.48e-23 92.8
MS.gene002574.t1 MTR_4g089095 67.308 52 17 0 48 99 18 69 4.70e-23 92.0
MS.gene002574.t1 MTR_4g461080 54.054 74 34 0 24 97 7 80 9.08e-23 91.7
MS.gene002574.t1 MTR_2g014060 52.632 76 29 1 30 98 2 77 1.11e-22 92.0
MS.gene002574.t1 MTR_1g056810 64.516 62 21 1 39 99 4 65 1.16e-22 91.3
MS.gene002574.t1 MTR_3g090430 65.517 58 20 0 42 99 47 104 1.29e-22 92.0
MS.gene002574.t1 MTR_2g014170 71.429 49 14 0 46 94 45 93 1.51e-22 91.3
MS.gene002574.t1 MTR_2g013370 41.489 94 50 1 6 99 11 99 2.11e-22 90.5
MS.gene002574.t1 MTR_3g077750 66.667 51 17 0 46 96 61 111 1.49e-21 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002574.t1 AT1G29160 62.281 114 23 1 8 101 4 117 3.97e-46 149
MS.gene002574.t1 AT2G34140 63.636 110 24 1 8 101 4 113 6.40e-45 145
MS.gene002574.t1 AT5G62430 58.416 101 28 2 12 99 8 107 1.96e-35 125
MS.gene002574.t1 AT3G47500 58.252 103 43 0 20 122 84 186 4.22e-35 127
MS.gene002574.t1 AT5G39660 82.540 63 11 0 40 102 132 194 1.58e-34 125
MS.gene002574.t1 AT5G39660 82.540 63 11 0 40 102 132 194 1.58e-34 125
MS.gene002574.t1 AT5G39660 82.540 63 11 0 40 102 132 194 1.58e-34 125
MS.gene002574.t1 AT1G26790 56.311 103 38 1 23 125 88 183 3.43e-34 123
MS.gene002574.t1 AT1G69570 60.440 91 29 1 34 124 120 203 5.00e-33 120
MS.gene002574.t1 AT5G60850 57.692 78 33 0 46 123 51 128 2.69e-27 103
MS.gene002574.t1 AT1G51700 71.698 53 15 0 46 98 33 85 3.77e-26 98.6
MS.gene002574.t1 AT3G21270 76.923 52 12 0 46 97 29 80 8.52e-26 97.8
MS.gene002574.t1 AT2G28810 72.727 55 15 0 43 97 74 128 1.63e-25 99.8
MS.gene002574.t1 AT3G50410 71.698 53 15 0 46 98 30 82 2.09e-25 97.8
MS.gene002574.t1 AT4G38000 60.294 68 26 1 43 109 38 105 2.12e-25 97.8
MS.gene002574.t1 AT2G28810 72.727 55 15 0 43 97 91 145 2.63e-25 99.4
MS.gene002574.t1 AT2G37590 68.421 57 18 0 43 99 86 142 7.64e-25 97.8
MS.gene002574.t1 AT3G55370 68.421 57 18 0 43 99 73 129 7.84e-25 97.8
MS.gene002574.t1 AT3G55370 68.421 57 18 0 43 99 73 129 8.04e-25 98.2
MS.gene002574.t1 AT5G65590 68.421 57 18 0 43 99 38 94 1.16e-24 97.4
MS.gene002574.t1 AT3G55370 68.421 57 18 0 43 99 118 174 1.16e-24 98.2
MS.gene002574.t1 AT1G07640 52.500 80 38 0 18 97 49 128 2.69e-24 96.7
MS.gene002574.t1 AT1G07640 76.000 50 12 0 48 97 23 72 3.07e-24 95.5
MS.gene002574.t1 AT1G07640 52.500 80 38 0 18 97 57 136 3.30e-24 96.3
MS.gene002574.t1 AT5G66940 67.925 53 17 0 46 98 32 84 7.88e-24 93.2
MS.gene002574.t1 AT5G60200 66.667 57 19 0 43 99 52 108 1.01e-23 93.6
MS.gene002574.t1 AT5G02460 68.421 57 18 0 43 99 92 148 1.65e-23 95.1
MS.gene002574.t1 AT3G45610 52.778 72 34 0 28 99 22 93 1.93e-23 92.8
MS.gene002574.t1 AT4G24060 63.158 57 21 0 43 99 50 106 2.04e-23 94.4
MS.gene002574.t1 AT1G47655 64.815 54 19 0 41 94 24 77 3.05e-23 91.3
MS.gene002574.t1 AT3G52440 66.102 59 19 1 44 101 22 80 3.55e-23 92.0
MS.gene002574.t1 AT1G28310 68.519 54 17 0 46 99 27 80 3.69e-23 93.2
MS.gene002574.t1 AT3G52440 66.102 59 19 1 44 101 41 99 3.92e-23 92.4
MS.gene002574.t1 AT3G61850 57.812 64 27 0 36 99 52 115 3.98e-23 92.4
MS.gene002574.t1 AT3G61850 57.812 64 27 0 36 99 52 115 3.98e-23 92.4
MS.gene002574.t1 AT3G61850 57.812 64 27 0 36 99 64 127 4.45e-23 92.8
MS.gene002574.t1 AT1G28310 68.519 54 17 0 46 99 51 104 5.88e-23 92.8
MS.gene002574.t1 AT3G61850 57.812 64 27 0 36 99 52 115 6.03e-23 92.4
MS.gene002574.t1 AT3G61850 57.812 64 27 0 36 99 64 127 7.29e-23 92.4
MS.gene002574.t1 AT1G64620 65.385 52 18 0 43 94 46 97 9.91e-23 92.4
MS.gene002574.t1 AT2G28510 71.154 52 15 0 48 99 50 101 1.03e-22 91.7
MS.gene002574.t1 AT4G00940 71.154 52 15 0 48 99 70 121 1.57e-22 91.3
MS.gene002574.t1 AT4G00940 71.154 52 15 0 48 99 70 121 1.57e-22 91.3
MS.gene002574.t1 AT4G00940 71.154 52 15 0 48 99 70 121 1.57e-22 91.3
MS.gene002574.t1 AT1G21340 70.000 50 15 0 48 97 40 89 2.02e-22 90.1
MS.gene002574.t1 AT5G62940 69.388 49 15 0 48 96 75 123 1.15e-21 90.1
MS.gene002574.t1 AT4G21050 58.730 63 26 0 48 110 26 88 1.95e-21 86.7
MS.gene002574.t1 AT2G46590 68.750 48 15 0 46 93 68 115 5.17e-21 87.8
MS.gene002574.t1 AT2G46590 68.750 48 15 0 46 93 80 127 6.02e-21 87.8
MS.gene002574.t1 AT4G21040 60.000 60 20 1 48 103 27 86 2.22e-19 81.6
MS.gene002574.t1 AT4G21080 54.412 68 27 1 48 111 27 94 8.99e-19 80.5
MS.gene002574.t1 AT4G21030 45.588 68 37 0 48 115 23 90 2.10e-14 67.8

Find 45 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATACAAGGGATTAAGCTATT+TGG 0.296201 2.1:+69630341 MS.gene002574:CDS
GGTCTTCCTCCGCCGCTTGC+CGG 0.325640 2.1:-69630741 None:intergenic
GCTTCATAGACACAACTTTC+CGG 0.327262 2.1:-69630638 None:intergenic
GTAAGAGCTGTCAAAGATAC+TGG 0.350596 2.1:+69630531 MS.gene002574:CDS
ATGTCCAAGATGCAAGAGTA+TGG 0.357770 2.1:+69630454 MS.gene002574:CDS
GATGATGGCCATAACTACTT+AGG 0.390058 2.1:+69630671 MS.gene002574:CDS
GTTCTAACCCTAAGTAGTTA+TGG 0.403963 2.1:-69630679 None:intergenic
GTTTCCATACTCTTGCATCT+TGG 0.414049 2.1:-69630458 None:intergenic
TGGGGCCCTCCGTAACGTTC+CGG 0.432988 2.1:+69630562 MS.gene002574:CDS
TTCCGACGACCTGCTCCAAC+CGG 0.436863 2.1:-69630581 None:intergenic
ATCCTCAAGACTTGGCGGCT+TGG 0.465996 2.1:-69630606 None:intergenic
CGTAACGTTCCGGTTGGAGC+AGG 0.491556 2.1:+69630572 MS.gene002574:CDS
CAAAGATACTGGACGGCTGG+TGG 0.496439 2.1:+69630542 MS.gene002574:CDS
ATGATGGCCATAACTACTTA+GGG 0.502994 2.1:+69630672 MS.gene002574:CDS
CTGCTCCAACCGGAACGTTA+CGG 0.518351 2.1:-69630571 None:intergenic
AAAAGAAAGTGAAGATCAAA+CGG 0.525439 2.1:+69630403 MS.gene002574:CDS
GCCCTCCGTAACGTTCCGGT+TGG 0.526190 2.1:+69630566 MS.gene002574:CDS
AAAGATACTGGACGGCTGGT+GGG 0.536772 2.1:+69630543 MS.gene002574:CDS
TTGCATGAGGAATTAAAAGA+AGG 0.537463 2.1:+69630377 MS.gene002574:CDS
TCTTGAGGATAGCGGTTCAC+CGG 0.541063 2.1:+69630619 MS.gene002574:CDS
TGTCAAAGATACTGGACGGC+TGG 0.542444 2.1:+69630539 MS.gene002574:CDS
AGAAAAGGTGAAGAGATACA+AGG 0.544735 2.1:+69630326 MS.gene002574:CDS
ATACTCTTGCATCTTGGACA+TGG 0.546078 2.1:-69630452 None:intergenic
GGCCAAGCCGCCAAGTCTTG+AGG 0.555303 2.1:+69630604 MS.gene002574:CDS
TTCCGGTTGGAGCAGGTCGT+CGG 0.558411 2.1:+69630579 MS.gene002574:CDS
AAGCGGCGGAGGAAGACCTC+AGG 0.572311 2.1:+69630746 MS.gene002574:CDS
AAAATGGCTGAAGTGAGAAA+AGG 0.579551 2.1:+69630311 None:intergenic
AAGATACTGGACGGCTGGTG+GGG 0.581078 2.1:+69630544 MS.gene002574:CDS
CCGCTATCCTCAAGACTTGG+CGG 0.597183 2.1:-69630611 None:intergenic
GAACCGCTATCCTCAAGACT+TGG 0.599554 2.1:-69630614 None:intergenic
GAAAAGGTGAAGAGATACAA+GGG 0.603099 2.1:+69630327 MS.gene002574:CDS
GGTTGGAGCAGGTCGTCGGA+AGG 0.608139 2.1:+69630583 MS.gene002574:CDS
CACAACAATAAAATTGCATG+AGG 0.620119 2.1:+69630364 MS.gene002574:CDS
GAAGCTGCTAGTTCTGATGA+TGG 0.628789 2.1:+69630656 MS.gene002574:CDS
CGGCGGAGGAAGACCTCAGG+TGG 0.630380 2.1:+69630749 MS.gene002574:CDS
TGCTAATGAATAACCACCTG+AGG 0.631649 2.1:-69630762 None:intergenic
GAGCTGTCAAAGATACTGGA+CGG 0.644495 2.1:+69630535 MS.gene002574:CDS
TCCAACCGGAACGTTACGGA+GGG 0.647718 2.1:-69630567 None:intergenic
TCCCGAAAATCACTCTGAGG+AGG 0.648141 2.1:-69630710 None:intergenic
CTCCAACCGGAACGTTACGG+AGG 0.649811 2.1:-69630568 None:intergenic
ACTTCCCGAAAATCACTCTG+AGG 0.686816 2.1:-69630713 None:intergenic
GTAAAGAACAAGAAATCACA+AGG 0.691544 2.1:-69630789 None:intergenic
AGAAAGTGAAGATCAAACGG+TGG 0.696077 2.1:+69630406 MS.gene002574:CDS
CCGCCAAGTCTTGAGGATAG+CGG 0.704408 2.1:+69630611 MS.gene002574:CDS
AAGAACAAGAAATCACAAGG+AGG 0.761754 2.1:-69630786 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAAGAAAGTGAAGATCAAA+CGG + chr2.1:69630403-69630422 MS.gene002574:CDS 25.0%
ATACAAGGGATTAAGCTATT+TGG + chr2.1:69630341-69630360 MS.gene002574:CDS 30.0%
CACAACAATAAAATTGCATG+AGG + chr2.1:69630364-69630383 MS.gene002574:CDS 30.0%
TTGCATGAGGAATTAAAAGA+AGG + chr2.1:69630377-69630396 MS.gene002574:CDS 30.0%
AGAAAAGGTGAAGAGATACA+AGG + chr2.1:69630326-69630345 MS.gene002574:CDS 35.0%
ATGATGGCCATAACTACTTA+GGG + chr2.1:69630672-69630691 MS.gene002574:CDS 35.0%
CAGCTCTTACAAAAATGTCT+TGG - chr2.1:69630521-69630540 None:intergenic 35.0%
GAAAAGGTGAAGAGATACAA+GGG + chr2.1:69630327-69630346 MS.gene002574:CDS 35.0%
GTTCTAACCCTAAGTAGTTA+TGG - chr2.1:69630682-69630701 None:intergenic 35.0%
!!! GATTTTCGGGAAGTATTTTC+CGG + chr2.1:69630722-69630741 MS.gene002574:CDS 35.0%
AGAAAGTGAAGATCAAACGG+TGG + chr2.1:69630406-69630425 MS.gene002574:CDS 40.0%
ATACTCTTGCATCTTGGACA+TGG - chr2.1:69630455-69630474 None:intergenic 40.0%
ATGTCCAAGATGCAAGAGTA+TGG + chr2.1:69630454-69630473 MS.gene002574:CDS 40.0%
GCTTCATAGACACAACTTTC+CGG - chr2.1:69630641-69630660 None:intergenic 40.0%
GTAAGAGCTGTCAAAGATAC+TGG + chr2.1:69630531-69630550 MS.gene002574:CDS 40.0%
GTTTCCATACTCTTGCATCT+TGG - chr2.1:69630461-69630480 None:intergenic 40.0%
TGCTAATGAATAACCACCTG+AGG - chr2.1:69630765-69630784 None:intergenic 40.0%
! GATGATGGCCATAACTACTT+AGG + chr2.1:69630671-69630690 MS.gene002574:CDS 40.0%
ACTTCCCGAAAATCACTCTG+AGG - chr2.1:69630716-69630735 None:intergenic 45.0%
GAGCTGTCAAAGATACTGGA+CGG + chr2.1:69630535-69630554 MS.gene002574:CDS 45.0%
! TGCCTCCTCAGAGTGATTTT+CGG + chr2.1:69630708-69630727 MS.gene002574:CDS 45.0%
!! GAAGCTGCTAGTTCTGATGA+TGG + chr2.1:69630656-69630675 MS.gene002574:CDS 45.0%
AAAGATACTGGACGGCTGGT+GGG + chr2.1:69630543-69630562 MS.gene002574:CDS 50.0%
GAACCGCTATCCTCAAGACT+TGG - chr2.1:69630617-69630636 None:intergenic 50.0%
TGTCAAAGATACTGGACGGC+TGG + chr2.1:69630539-69630558 MS.gene002574:CDS 50.0%
! AAGTATTTTCCGGCAAGCGG+CGG + chr2.1:69630732-69630751 MS.gene002574:CDS 50.0%
! GCCTCCTCAGAGTGATTTTC+GGG + chr2.1:69630709-69630728 MS.gene002574:CDS 50.0%
! TCCCGAAAATCACTCTGAGG+AGG - chr2.1:69630713-69630732 None:intergenic 50.0%
! TCTTGAGGATAGCGGTTCAC+CGG + chr2.1:69630619-69630638 MS.gene002574:CDS 50.0%
!!! GGGAAGTATTTTCCGGCAAG+CGG + chr2.1:69630729-69630748 MS.gene002574:CDS 50.0%
AAGATACTGGACGGCTGGTG+GGG + chr2.1:69630544-69630563 MS.gene002574:CDS 55.0%
ATCCTCAAGACTTGGCGGCT+TGG - chr2.1:69630609-69630628 None:intergenic 55.0%
CAAAGATACTGGACGGCTGG+TGG + chr2.1:69630542-69630561 MS.gene002574:CDS 55.0%
CCGCCAAGTCTTGAGGATAG+CGG + chr2.1:69630611-69630630 MS.gene002574:CDS 55.0%
CCGCTATCCTCAAGACTTGG+CGG - chr2.1:69630614-69630633 None:intergenic 55.0%
CTGCTCCAACCGGAACGTTA+CGG - chr2.1:69630574-69630593 None:intergenic 55.0%
TCCAACCGGAACGTTACGGA+GGG - chr2.1:69630570-69630589 None:intergenic 55.0%
CGTAACGTTCCGGTTGGAGC+AGG + chr2.1:69630572-69630591 MS.gene002574:CDS 60.0%
CTCCAACCGGAACGTTACGG+AGG - chr2.1:69630571-69630590 None:intergenic 60.0%
TTCCGACGACCTGCTCCAAC+CGG - chr2.1:69630584-69630603 None:intergenic 60.0%
TTCCGGTTGGAGCAGGTCGT+CGG + chr2.1:69630579-69630598 MS.gene002574:CDS 60.0%
! TATTTTCCGGCAAGCGGCGG+AGG + chr2.1:69630735-69630754 MS.gene002574:CDS 60.0%
AAGCGGCGGAGGAAGACCTC+AGG + chr2.1:69630746-69630765 MS.gene002574:CDS 65.0%
GCCCTCCGTAACGTTCCGGT+TGG + chr2.1:69630566-69630585 MS.gene002574:CDS 65.0%
GGCCAAGCCGCCAAGTCTTG+AGG + chr2.1:69630604-69630623 MS.gene002574:CDS 65.0%
GGTTGGAGCAGGTCGTCGGA+AGG + chr2.1:69630583-69630602 MS.gene002574:CDS 65.0%
TGGGGCCCTCCGTAACGTTC+CGG + chr2.1:69630562-69630581 MS.gene002574:CDS 65.0%
CGGCGGAGGAAGACCTCAGG+TGG + chr2.1:69630749-69630768 MS.gene002574:CDS 70.0%
GGTCTTCCTCCGCCGCTTGC+CGG - chr2.1:69630744-69630763 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 69630314 69630796 69630314 ID=MS.gene002574
chr2.1 mRNA 69630314 69630796 69630314 ID=MS.gene002574.t1;Parent=MS.gene002574
chr2.1 exon 69630314 69630796 69630314 ID=MS.gene002574.t1.exon1;Parent=MS.gene002574.t1
chr2.1 CDS 69630314 69630796 69630314 ID=cds.MS.gene002574.t1;Parent=MS.gene002574.t1
Gene Sequence

>MS.gene002574

ATGGCTGAAGTGAGAAAAGGTGAAGAGATACAAGGGATTAAGCTATTTGGCACAACAATAAAATTGCATGAGGAATTAAAAGAAGGTGAAAAAGAAAGTGAAGATCAAACGGTGGAGAAGAAGATAGAAAAGATCATACCATGTCCAAGATGCAAGAGTATGGAAACTAAATTTTGTTATTTCAATAATTATAACGTTAATCAACCAAGACATTTTTGTAAGAGCTGTCAAAGATACTGGACGGCTGGTGGGGCCCTCCGTAACGTTCCGGTTGGAGCAGGTCGTCGGAAGGCCAAGCCGCCAAGTCTTGAGGATAGCGGTTCACCGGAAAGTTGTGTCTATGAAGCTGCTAGTTCTGATGATGGCCATAACTACTTAGGGTTAGAACAATTTATGCCTCCTCAGAGTGATTTTCGGGAAGTATTTTCCGGCAAGCGGCGGAGGAAGACCTCAGGTGGTTATTCATTAGCATCCTCCTTGTGA
Protein sequence

>MS.gene002574.t1

MAEVRKGEEIQGIKLFGTTIKLHEELKEGEKESEDQTVEKKIEKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKSCQRYWTAGGALRNVPVGAGRRKAKPPSLEDSGSPESCVYEAASSDDGHNYLGLEQFMPPQSDFREVFSGKRRRKTSGGYSLASSL