AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1413150

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1413150 MtrunA17_Chr2g0283811 96.894 161 4 1 1 160 1 161 3.64e-114 320
Msa1413150 MtrunA17_Chr6g0453321 70.370 81 23 1 19 99 110 189 1.27e-36 131
Msa1413150 MtrunA17_Chr4g0042481 67.500 80 26 0 20 99 96 175 1.36e-35 128
Msa1413150 MtrunA17_Chr7g0217581 69.620 79 23 1 24 102 211 288 7.58e-35 127
Msa1413150 MtrunA17_Chr8g0355261 61.628 86 32 1 25 109 96 181 9.87e-35 125
Msa1413150 MtrunA17_Chr7g0254161 71.233 73 20 1 28 99 82 154 4.71e-33 120
Msa1413150 MtrunA17_Chr5g0417551 58.065 93 37 1 18 108 97 189 3.02e-32 117
Msa1413150 MtrunA17_Chr6g0460731 73.239 71 18 1 30 99 79 149 4.52e-32 117
Msa1413150 MtrunA17_Chr3g0092111 57.778 90 29 1 19 99 100 189 5.12e-31 115
Msa1413150 MtrunA17_Chr5g0417601 70.423 71 18 1 32 99 123 193 1.21e-30 114
Msa1413150 MtrunA17_Chr6g0460721 69.014 71 21 1 30 99 72 142 1.25e-30 112
Msa1413150 MtrunA17_Chr5g0417561 62.338 77 29 0 32 108 105 181 3.37e-30 112
Msa1413150 MtrunA17_Chr5g0417571 71.667 60 17 0 40 99 132 191 6.44e-30 110
Msa1413150 MtrunA17_Chr2g0328021 55.263 76 34 0 24 99 40 115 1.64e-27 103
Msa1413150 MtrunA17_Chr8g0341671 59.155 71 23 1 34 98 2 72 3.08e-26 99.0
Msa1413150 MtrunA17_Chr8g0367161 47.059 102 48 3 24 123 12 109 3.76e-26 101
Msa1413150 MtrunA17_Chr8g0374251 48.000 100 41 2 48 138 70 167 7.66e-26 100
Msa1413150 MtrunA17_Chr4g0010151 70.175 57 17 0 43 99 79 135 1.02e-25 100
Msa1413150 MtrunA17_Chr8g0346551 56.098 82 32 2 36 113 12 93 2.77e-25 97.8
Msa1413150 MtrunA17_Chr8g0374111 71.154 52 15 0 46 97 29 80 3.26e-25 96.7
Msa1413150 MtrunA17_Chr4g0031411 64.286 70 24 1 43 111 72 141 9.63e-25 97.4
Msa1413150 MtrunA17_Chr3g0127201 64.912 57 20 0 43 99 24 80 1.29e-24 96.3
Msa1413150 MtrunA17_Chr2g0326001 55.263 76 34 0 24 99 18 93 1.30e-24 96.3
Msa1413150 MtrunA17_Chr4g0061761 69.811 53 16 0 44 96 38 90 1.33e-24 96.7
Msa1413150 MtrunA17_Chr2g0308011 73.469 49 13 0 46 94 37 85 2.12e-24 94.0
Msa1413150 MtrunA17_Chr7g0223311 76.000 50 12 0 48 97 79 128 3.30e-24 96.7
Msa1413150 MtrunA17_Chr7g0237921 68.421 57 18 0 43 99 73 129 7.90e-24 95.1
Msa1413150 MtrunA17_Chr1g0188851 54.412 68 31 0 30 97 27 94 1.06e-23 94.0
Msa1413150 MtrunA17_Chr4g0047001 73.077 52 14 0 48 99 57 108 1.50e-23 94.7
Msa1413150 MtrunA17_Chr5g0411951 68.519 54 17 0 43 96 40 93 1.54e-23 94.4
Msa1413150 MtrunA17_Chr4g0047761 67.308 52 17 0 48 99 74 125 6.37e-23 92.4
Msa1413150 MtrunA17_Chr4g0030051 54.054 74 34 0 24 97 19 92 8.59e-23 91.7
Msa1413150 MtrunA17_Chr2g0282441 52.632 76 29 1 30 98 2 77 8.70e-23 92.0
Msa1413150 MtrunA17_Chr1g0177251 64.516 62 21 1 39 99 4 65 9.10e-23 91.3
Msa1413150 MtrunA17_Chr3g0126201 65.517 58 20 0 42 99 47 104 1.01e-22 92.0
Msa1413150 MtrunA17_Chr2g0282511 71.429 49 14 0 46 94 45 93 1.18e-22 91.3
Msa1413150 MtrunA17_Chr2g0282051 41.489 94 50 1 6 99 11 99 1.65e-22 90.5
Msa1413150 MtrunA17_Chr3g0117601 66.667 51 17 0 46 96 61 111 1.17e-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
Msa1413150 AT1G29160.1 62.281 114 23 1 8 101 4 117 4.12e-46 149
Msa1413150 AT2G34140.1 63.636 110 24 1 8 101 4 113 6.65e-45 145
Msa1413150 AT5G62430.1 58.416 101 28 2 12 99 8 107 2.03e-35 125
Msa1413150 AT3G47500.1 58.252 103 43 0 20 122 84 186 4.37e-35 127
Msa1413150 AT5G39660.3 82.540 63 11 0 40 102 132 194 1.64e-34 125
Msa1413150 AT5G39660.1 82.540 63 11 0 40 102 132 194 1.64e-34 125
Msa1413150 AT5G39660.2 82.540 63 11 0 40 102 132 194 1.64e-34 125
Msa1413150 AT1G26790.1 56.311 103 38 1 23 125 88 183 3.56e-34 123
Msa1413150 AT1G69570.1 60.440 91 29 1 34 124 120 203 5.18e-33 120
Msa1413150 AT5G60850.1 57.692 78 33 0 46 123 51 128 2.79e-27 103
Msa1413150 AT1G51700.1 71.698 53 15 0 46 98 33 85 3.90e-26 98.6
Msa1413150 AT3G21270.1 76.923 52 12 0 46 97 29 80 8.81e-26 97.8
Msa1413150 AT2G28810.2 72.727 55 15 0 43 97 74 128 1.69e-25 99.8
Msa1413150 AT3G50410.1 71.698 53 15 0 46 98 30 82 2.17e-25 97.8
Msa1413150 AT4G38000.1 60.294 68 26 1 43 109 38 105 2.19e-25 97.8
Msa1413150 AT2G28810.1 72.727 55 15 0 43 97 91 145 2.72e-25 99.4
Msa1413150 AT2G37590.1 68.421 57 18 0 43 99 86 142 7.90e-25 97.8
Msa1413150 AT3G55370.1 68.421 57 18 0 43 99 73 129 8.11e-25 97.8
Msa1413150 AT3G55370.2 68.421 57 18 0 43 99 73 129 8.31e-25 98.2
Msa1413150 AT5G65590.1 68.421 57 18 0 43 99 38 94 1.19e-24 97.4
Msa1413150 AT3G55370.3 68.421 57 18 0 43 99 118 174 1.20e-24 98.2
Msa1413150 AT1G07640.2 52.500 80 38 0 18 97 49 128 2.78e-24 96.7
Msa1413150 AT1G07640.1 76.000 50 12 0 48 97 23 72 3.18e-24 95.5
Msa1413150 AT1G07640.3 52.500 80 38 0 18 97 57 136 3.42e-24 96.3
Msa1413150 AT5G66940.1 67.925 53 17 0 46 98 32 84 8.14e-24 93.2
Msa1413150 AT5G60200.1 66.667 57 19 0 43 99 52 108 1.04e-23 93.6
Msa1413150 AT5G02460.1 68.421 57 18 0 43 99 92 148 1.70e-23 95.1
Msa1413150 AT3G45610.1 52.778 72 34 0 28 99 22 93 1.99e-23 92.8
Msa1413150 AT4G24060.1 63.158 57 21 0 43 99 50 106 2.11e-23 94.4
Msa1413150 AT1G47655.1 64.815 54 19 0 41 94 24 77 3.15e-23 91.3
Msa1413150 AT3G52440.1 66.102 59 19 1 44 101 22 80 3.66e-23 92.0
Msa1413150 AT1G28310.1 68.519 54 17 0 46 99 27 80 3.81e-23 93.2
Msa1413150 AT3G52440.2 66.102 59 19 1 44 101 41 99 4.05e-23 92.4
Msa1413150 AT3G61850.2 57.812 64 27 0 36 99 52 115 4.11e-23 92.4
Msa1413150 AT3G61850.3 57.812 64 27 0 36 99 52 115 4.11e-23 92.4
Msa1413150 AT3G61850.1 57.812 64 27 0 36 99 64 127 4.60e-23 92.8
Msa1413150 AT1G28310.2 68.519 54 17 0 46 99 51 104 6.08e-23 92.8
Msa1413150 AT3G61850.5 57.812 64 27 0 36 99 52 115 6.22e-23 92.4
Msa1413150 AT3G61850.4 57.812 64 27 0 36 99 64 127 7.53e-23 92.4
Msa1413150 AT1G64620.1 65.385 52 18 0 43 94 46 97 1.02e-22 92.4
Msa1413150 AT2G28510.1 71.154 52 15 0 48 99 50 101 1.06e-22 91.7
Msa1413150 AT4G00940.1 71.154 52 15 0 48 99 70 121 1.62e-22 91.3
Msa1413150 AT4G00940.3 71.154 52 15 0 48 99 70 121 1.62e-22 91.3
Msa1413150 AT4G00940.2 71.154 52 15 0 48 99 70 121 1.62e-22 91.3
Msa1413150 AT1G21340.1 70.000 50 15 0 48 97 40 89 2.09e-22 90.1
Msa1413150 AT5G62940.1 69.388 49 15 0 48 96 75 123 1.19e-21 90.1
Msa1413150 AT4G21050.1 58.730 63 26 0 48 110 26 88 2.01e-21 86.7
Msa1413150 AT2G46590.1 68.750 48 15 0 46 93 68 115 5.33e-21 87.8
Msa1413150 AT2G46590.2 68.750 48 15 0 46 93 80 127 6.22e-21 87.8
Msa1413150 AT4G21040.1 60.000 60 20 1 48 103 27 86 2.29e-19 81.6
Msa1413150 AT4G21080.1 54.412 68 27 1 48 111 27 94 9.27e-19 80.5
Msa1413150 AT4G21030.1 45.588 68 37 0 48 115 23 90 2.16e-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 tig0024012:+49341 Msa1413150:CDS
GGTCTTCCTCCGCCGCTTGC+CGG 0.325640 tig0024012:-49741 None:intergenic
GCTTCATAGACACAACTTTC+CGG 0.327262 tig0024012:-49638 None:intergenic
GTAAGAGCTGTCAAAGATAC+TGG 0.350596 tig0024012:+49531 Msa1413150:CDS
ATGTCCAAGATGCAAGAGTA+TGG 0.357770 tig0024012:+49454 Msa1413150:CDS
GATGATGGCCATAACTACTT+AGG 0.390058 tig0024012:+49671 Msa1413150:CDS
GTTCTAACCCTAAGTAGTTA+TGG 0.403963 tig0024012:-49679 None:intergenic
GTTTCCATACTCTTGCATCT+TGG 0.414049 tig0024012:-49458 None:intergenic
TGGGGCCCTCCGTAACGTTC+CGG 0.432988 tig0024012:+49562 Msa1413150:CDS
TTCCGACGACCTGCTCCAAC+CGG 0.436863 tig0024012:-49581 None:intergenic
ATCCTCAAGACTTGGCGGCT+TGG 0.465996 tig0024012:-49606 None:intergenic
CGTAACGTTCCGGTTGGAGC+AGG 0.491556 tig0024012:+49572 Msa1413150:CDS
CAAAGATACTGGACGGCTGG+TGG 0.496439 tig0024012:+49542 Msa1413150:CDS
ATGATGGCCATAACTACTTA+GGG 0.502994 tig0024012:+49672 Msa1413150:CDS
CTGCTCCAACCGGAACGTTA+CGG 0.518351 tig0024012:-49571 None:intergenic
AAAAGAAAGTGAAGATCAAA+CGG 0.525439 tig0024012:+49403 Msa1413150:CDS
GCCCTCCGTAACGTTCCGGT+TGG 0.526190 tig0024012:+49566 Msa1413150:CDS
AAAGATACTGGACGGCTGGT+GGG 0.536772 tig0024012:+49543 Msa1413150:CDS
TTGCATGAGGAATTAAAAGA+AGG 0.537463 tig0024012:+49377 Msa1413150:CDS
TCTTGAGGATAGCGGTTCAC+CGG 0.541063 tig0024012:+49619 Msa1413150:CDS
TGTCAAAGATACTGGACGGC+TGG 0.542444 tig0024012:+49539 Msa1413150:CDS
AGAAAAGGTGAAGAGATACA+AGG 0.544735 tig0024012:+49326 Msa1413150:CDS
ATACTCTTGCATCTTGGACA+TGG 0.546078 tig0024012:-49452 None:intergenic
GGCCAAGCCGCCAAGTCTTG+AGG 0.555303 tig0024012:+49604 Msa1413150:CDS
TTCCGGTTGGAGCAGGTCGT+CGG 0.558411 tig0024012:+49579 Msa1413150:CDS
AAGCGGCGGAGGAAGACCTC+AGG 0.572311 tig0024012:+49746 Msa1413150:CDS
AAAATGGCTGAAGTGAGAAA+AGG 0.579551 tig0024012:+49311 None:intergenic
AAGATACTGGACGGCTGGTG+GGG 0.581078 tig0024012:+49544 Msa1413150:CDS
CCGCTATCCTCAAGACTTGG+CGG 0.597183 tig0024012:-49611 None:intergenic
GAACCGCTATCCTCAAGACT+TGG 0.599554 tig0024012:-49614 None:intergenic
GAAAAGGTGAAGAGATACAA+GGG 0.603099 tig0024012:+49327 Msa1413150:CDS
GGTTGGAGCAGGTCGTCGGA+AGG 0.608139 tig0024012:+49583 Msa1413150:CDS
CACAACAATAAAATTGCATG+AGG 0.620119 tig0024012:+49364 Msa1413150:CDS
GAAGCTGCTAGTTCTGATGA+TGG 0.628789 tig0024012:+49656 Msa1413150:CDS
CGGCGGAGGAAGACCTCAGG+TGG 0.630380 tig0024012:+49749 Msa1413150:CDS
TGCTAATGAATAACCACCTG+AGG 0.631649 tig0024012:-49762 None:intergenic
GAGCTGTCAAAGATACTGGA+CGG 0.644495 tig0024012:+49535 Msa1413150:CDS
TCCAACCGGAACGTTACGGA+GGG 0.647718 tig0024012:-49567 None:intergenic
TCCCGAAAATCACTCTGAGG+AGG 0.648141 tig0024012:-49710 None:intergenic
CTCCAACCGGAACGTTACGG+AGG 0.649811 tig0024012:-49568 None:intergenic
ACTTCCCGAAAATCACTCTG+AGG 0.686816 tig0024012:-49713 None:intergenic
GTAAAGAACAAGAAATCACA+AGG 0.691544 tig0024012:-49789 None:intergenic
AGAAAGTGAAGATCAAACGG+TGG 0.696077 tig0024012:+49406 Msa1413150:CDS
CCGCCAAGTCTTGAGGATAG+CGG 0.704408 tig0024012:+49611 Msa1413150:CDS
AAGAACAAGAAATCACAAGG+AGG 0.761754 tig0024012:-49786 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAAGAAAGTGAAGATCAAA+CGG + tig0024012:49403-49422 Msa1413150:CDS 25.0%
ATACAAGGGATTAAGCTATT+TGG + tig0024012:49341-49360 Msa1413150:CDS 30.0%
CACAACAATAAAATTGCATG+AGG + tig0024012:49364-49383 Msa1413150:CDS 30.0%
TTGCATGAGGAATTAAAAGA+AGG + tig0024012:49377-49396 Msa1413150:CDS 30.0%
AGAAAAGGTGAAGAGATACA+AGG + tig0024012:49326-49345 Msa1413150:CDS 35.0%
GAAAAGGTGAAGAGATACAA+GGG + tig0024012:49327-49346 Msa1413150:CDS 35.0%
CAGCTCTTACAAAAATGTCT+TGG - tig0024012:49521-49540 None:intergenic 35.0%
ATGATGGCCATAACTACTTA+GGG + tig0024012:49672-49691 Msa1413150:CDS 35.0%
GTTCTAACCCTAAGTAGTTA+TGG - tig0024012:49682-49701 None:intergenic 35.0%
!!! GATTTTCGGGAAGTATTTTC+CGG + tig0024012:49722-49741 Msa1413150:CDS 35.0%
AGAAAGTGAAGATCAAACGG+TGG + tig0024012:49406-49425 Msa1413150:CDS 40.0%
ATACTCTTGCATCTTGGACA+TGG - tig0024012:49455-49474 None:intergenic 40.0%
ATGTCCAAGATGCAAGAGTA+TGG + tig0024012:49454-49473 Msa1413150:CDS 40.0%
GTTTCCATACTCTTGCATCT+TGG - tig0024012:49461-49480 None:intergenic 40.0%
GTAAGAGCTGTCAAAGATAC+TGG + tig0024012:49531-49550 Msa1413150:CDS 40.0%
GCTTCATAGACACAACTTTC+CGG - tig0024012:49641-49660 None:intergenic 40.0%
! GATGATGGCCATAACTACTT+AGG + tig0024012:49671-49690 Msa1413150:CDS 40.0%
TGCTAATGAATAACCACCTG+AGG - tig0024012:49765-49784 None:intergenic 40.0%
GAGCTGTCAAAGATACTGGA+CGG + tig0024012:49535-49554 Msa1413150:CDS 45.0%
!! GAAGCTGCTAGTTCTGATGA+TGG + tig0024012:49656-49675 Msa1413150:CDS 45.0%
! TGCCTCCTCAGAGTGATTTT+CGG + tig0024012:49708-49727 Msa1413150:CDS 45.0%
ACTTCCCGAAAATCACTCTG+AGG - tig0024012:49716-49735 None:intergenic 45.0%
TGTCAAAGATACTGGACGGC+TGG + tig0024012:49539-49558 Msa1413150:CDS 50.0%
AAAGATACTGGACGGCTGGT+GGG + tig0024012:49543-49562 Msa1413150:CDS 50.0%
GAACCGCTATCCTCAAGACT+TGG - tig0024012:49617-49636 None:intergenic 50.0%
! TCTTGAGGATAGCGGTTCAC+CGG + tig0024012:49619-49638 Msa1413150:CDS 50.0%
! GCCTCCTCAGAGTGATTTTC+GGG + tig0024012:49709-49728 Msa1413150:CDS 50.0%
! TCCCGAAAATCACTCTGAGG+AGG - tig0024012:49713-49732 None:intergenic 50.0%
!!! GGGAAGTATTTTCCGGCAAG+CGG + tig0024012:49729-49748 Msa1413150:CDS 50.0%
! AAGTATTTTCCGGCAAGCGG+CGG + tig0024012:49732-49751 Msa1413150:CDS 50.0%
CAAAGATACTGGACGGCTGG+TGG + tig0024012:49542-49561 Msa1413150:CDS 55.0%
AAGATACTGGACGGCTGGTG+GGG + tig0024012:49544-49563 Msa1413150:CDS 55.0%
TCCAACCGGAACGTTACGGA+GGG - tig0024012:49570-49589 None:intergenic 55.0%
CTGCTCCAACCGGAACGTTA+CGG - tig0024012:49574-49593 None:intergenic 55.0%
ATCCTCAAGACTTGGCGGCT+TGG - tig0024012:49609-49628 None:intergenic 55.0%
CCGCTATCCTCAAGACTTGG+CGG - tig0024012:49614-49633 None:intergenic 55.0%
CCGCCAAGTCTTGAGGATAG+CGG + tig0024012:49611-49630 Msa1413150:CDS 55.0%
CTCCAACCGGAACGTTACGG+AGG - tig0024012:49571-49590 None:intergenic 60.0%
CGTAACGTTCCGGTTGGAGC+AGG + tig0024012:49572-49591 Msa1413150:CDS 60.0%
TTCCGGTTGGAGCAGGTCGT+CGG + tig0024012:49579-49598 Msa1413150:CDS 60.0%
TTCCGACGACCTGCTCCAAC+CGG - tig0024012:49584-49603 None:intergenic 60.0%
! TATTTTCCGGCAAGCGGCGG+AGG + tig0024012:49735-49754 Msa1413150:CDS 60.0%
TGGGGCCCTCCGTAACGTTC+CGG + tig0024012:49562-49581 Msa1413150:CDS 65.0%
GCCCTCCGTAACGTTCCGGT+TGG + tig0024012:49566-49585 Msa1413150:CDS 65.0%
GGTTGGAGCAGGTCGTCGGA+AGG + tig0024012:49583-49602 Msa1413150:CDS 65.0%
GGCCAAGCCGCCAAGTCTTG+AGG + tig0024012:49604-49623 Msa1413150:CDS 65.0%
AAGCGGCGGAGGAAGACCTC+AGG + tig0024012:49746-49765 Msa1413150:CDS 65.0%
GGTCTTCCTCCGCCGCTTGC+CGG - tig0024012:49744-49763 None:intergenic 70.0%
CGGCGGAGGAAGACCTCAGG+TGG + tig0024012:49749-49768 Msa1413150:CDS 70.0%
Chromosome Type Strat End Strand Name
tig0024012 gene 49314 49796 49314 ID=Msa1413150;Name=Msa1413150
tig0024012 mRNA 49314 49796 49314 ID=Msa1413150-mRNA-1;Parent=Msa1413150;Name=Msa1413150-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|160
tig0024012 exon 49314 49796 49314 ID=Msa1413150-mRNA-1:exon:20984;Parent=Msa1413150-mRNA-1
tig0024012 CDS 49314 49796 49314 ID=Msa1413150-mRNA-1:cds;Parent=Msa1413150-mRNA-1
Gene Sequence

>Msa1413150

ATGGCTGAAGTGAGAAAAGGTGAAGAGATACAAGGGATTAAGCTATTTGGCACAACAATAAAATTGCATGAGGAATTAAAAGAAGGTGAAAAAGAAAGTGAAGATCAAACGGTGGAGAAGAAGATAGAAAAGATCATACCATGTCCAAGATGCAAGAGTATGGAAACTAAATTTTGTTATTTCAATAATTATAACGTTAATCAACCAAGACATTTTTGTAAGAGCTGTCAAAGATACTGGACGGCTGGTGGGGCCCTCCGTAACGTTCCGGTTGGAGCAGGTCGTCGGAAGGCCAAGCCGCCAAGTCTTGAGGATAGCGGTTCACCGGAAAGTTGTGTCTATGAAGCTGCTAGTTCTGATGATGGCCATAACTACTTAGGGTTAGAACAATTTATGCCTCCTCAGAGTGATTTTCGGGAAGTATTTTCCGGCAAGCGGCGGAGGAAGACCTCAGGTGGTTATTCATTAGCATCCTCCTTGTGA
Protein sequence

>Msa1413150

MAEVRKGEEIQGIKLFGTTIKLHEELKEGEKESEDQTVEKKIEKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKSCQRYWTAGGALRNVPVGAGRRKAKPPSLEDSGSPESCVYEAASSDDGHNYLGLEQFMPPQSDFREVFSGKRRRKTSGGYSLASSL*