AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073440.t1 MTR_8g036130 69.730 185 47 3 1 177 1 184 1.28e-84 250
MS.gene073440.t1 MTR_2g035610 94.262 122 7 0 1 122 1 122 5.11e-75 221
MS.gene073440.t1 MTR_4g031910 66.111 180 56 2 1 176 1 179 7.54e-74 222
MS.gene073440.t1 MTR_4g032620 64.815 162 57 0 1 162 1 162 3.09e-71 215
MS.gene073440.t1 MTR_3g466980 62.821 156 57 1 1 156 1 155 8.59e-71 214
MS.gene073440.t1 MTR_3g065100 65.000 160 55 1 1 160 1 159 2.06e-69 211
MS.gene073440.t1 MTR_4g032290 63.333 180 61 2 1 176 1 179 1.16e-64 199
MS.gene073440.t1 MTR_4g032260 69.677 155 47 0 1 155 1 155 2.27e-63 193
MS.gene073440.t1 MTR_3g466830 50.943 159 77 1 3 161 2 159 1.42e-55 173
MS.gene073440.t1 MTR_4g063790 44.872 156 86 0 1 156 1 156 4.91e-49 157
MS.gene073440.t1 MTR_3g466890 45.570 158 85 1 3 160 2 158 2.17e-47 152
MS.gene073440.t1 MTR_3g467080 41.935 155 90 0 1 155 1 155 2.53e-43 142
MS.gene073440.t1 MTR_3g031100 44.516 155 86 0 1 155 1 155 3.00e-43 144
MS.gene073440.t1 MTR_2g016210 43.038 158 90 0 1 158 1 158 7.82e-43 143
MS.gene073440.t1 MTR_5g075380 41.875 160 92 1 1 160 1 159 1.16e-42 140
MS.gene073440.t1 MTR_2g035590 80.412 97 19 0 74 170 1 97 7.29e-41 134
MS.gene073440.t1 MTR_5g047580 43.226 155 86 2 1 155 1 153 1.42e-40 135
MS.gene073440.t1 MTR_1g090697 39.873 158 93 2 1 158 1 156 2.70e-38 129
MS.gene073440.t1 MTR_7g011950 44.156 154 84 2 1 154 1 152 4.84e-36 123
MS.gene073440.t1 MTR_3g466900 41.860 129 74 1 32 160 2 129 1.09e-35 122
MS.gene073440.t1 MTR_3g031240 34.810 158 103 0 1 158 1 158 1.47e-35 123
MS.gene073440.t1 MTR_1g077320 43.506 154 85 2 1 154 1 152 4.18e-35 121
MS.gene073440.t1 MTR_1g090710 36.709 158 99 1 1 158 1 157 4.26e-35 121
MS.gene073440.t1 MTR_1g090783 38.462 156 94 2 3 158 2 155 5.09e-35 120
MS.gene073440.t1 MTR_1g077390 39.610 154 91 2 1 154 1 152 9.93e-35 120
MS.gene073440.t1 MTR_3g466930 42.636 129 73 1 32 160 2 129 1.35e-34 119
MS.gene073440.t1 MTR_3g465410 41.085 129 76 0 29 157 1 129 1.34e-33 117
MS.gene073440.t1 MTR_1g084950 41.290 155 89 2 1 155 1 153 2.43e-33 116
MS.gene073440.t1 MTR_4g028720 41.558 154 88 2 1 154 1 152 2.83e-33 116
MS.gene073440.t1 MTR_7g055800 53.782 119 27 2 1 119 1 91 4.20e-33 114
MS.gene073440.t1 MTR_1g077300 42.857 154 84 2 1 154 1 150 7.63e-33 115
MS.gene073440.t1 MTR_7g055790 58.559 111 28 1 1 111 59 151 2.32e-30 108
MS.gene073440.t1 MTR_4g028800 72.222 72 18 1 1 72 1 70 3.47e-30 105
MS.gene073440.t1 MTR_2g035580 36.774 155 97 1 1 155 1 154 9.52e-27 99.8
MS.gene073440.t1 MTR_7g055940 51.887 106 23 2 1 106 1 78 1.57e-25 94.4
MS.gene073440.t1 MTR_5g047560 33.548 155 85 3 1 155 1 137 1.05e-22 89.0
MS.gene073440.t1 MTR_4g019670 37.879 132 79 1 1 129 1 132 2.20e-21 90.9
MS.gene073440.t1 MTR_7g106510 37.121 132 80 1 1 129 1 132 2.51e-21 90.5
MS.gene073440.t1 MTR_3g093900 34.646 127 83 0 3 129 6 132 2.75e-21 90.5
MS.gene073440.t1 MTR_4g084780 61.538 52 20 0 74 125 1 52 7.57e-15 68.6
MS.gene073440.t1 MTR_6g018920 30.357 112 71 3 1 106 1 111 1.18e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073440.t1 AT5G48670 54.321 162 71 2 1 161 1 160 1.14e-54 176
MS.gene073440.t1 AT5G26630 47.305 167 87 1 1 167 1 166 7.01e-45 148
MS.gene073440.t1 AT1G65330 40.000 180 107 1 3 182 2 180 1.21e-39 136
MS.gene073440.t1 AT1G65300 41.818 165 95 1 3 167 2 165 1.63e-39 136
MS.gene073440.t1 AT5G26650 43.038 158 89 1 4 161 2 158 2.46e-39 137
MS.gene073440.t1 AT5G27960 43.038 158 89 1 4 161 2 158 4.02e-39 136
MS.gene073440.t1 AT1G31630 34.302 172 111 2 3 174 2 171 2.07e-33 121
MS.gene073440.t1 AT3G05860 39.024 164 95 2 1 162 1 161 8.92e-33 116
MS.gene073440.t1 AT3G05860 39.024 164 95 2 1 162 1 161 6.27e-32 115
MS.gene073440.t1 AT3G05860 39.024 164 95 2 1 162 1 161 7.01e-32 115
MS.gene073440.t1 AT5G27810 51.613 93 45 0 29 121 1 93 1.04e-31 111
MS.gene073440.t1 AT1G31640 38.411 151 91 2 3 153 2 150 2.67e-30 115
MS.gene073440.t1 AT5G26580 36.025 161 88 2 1 161 1 146 9.07e-28 107
MS.gene073440.t1 AT2G28700 37.681 138 84 1 1 136 1 138 7.40e-27 104
MS.gene073440.t1 AT1G22590 29.448 163 110 2 1 163 1 158 1.12e-20 84.3
MS.gene073440.t1 AT5G06500 31.818 154 103 1 1 154 1 152 2.98e-20 85.1
MS.gene073440.t1 AT2G40210 37.795 127 79 0 1 127 1 127 3.42e-19 84.0
MS.gene073440.t1 AT5G55690 39.362 94 50 2 1 87 1 94 6.44e-13 65.9
MS.gene073440.t1 AT5G55690 39.362 94 50 2 1 87 1 94 6.44e-13 65.9
MS.gene073440.t1 AT5G58890 40.179 112 58 4 1 105 1 110 2.86e-12 63.9
MS.gene073440.t1 AT2G15660 26.562 128 90 2 38 163 31 156 5.96e-12 62.8

Find 38 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCAATATCCTTCAAATTT+TGG 0.124846 2.4:+53722486 None:intergenic
TTCTTGTTCTTCTCTAATTC+AGG 0.242401 2.4:+53722695 None:intergenic
ATGAACCTCAACCTCATATT+TGG 0.258532 2.4:-53722766 MS.gene073440:CDS
CACAATCATGACTAGGAAAA+AGG 0.298378 2.4:-53722924 None:intergenic
TGAAGCATGTGCTATAGTTC+AGG 0.354873 2.4:-53722795 MS.gene073440:CDS
TTGTTGGTGGTGGTGTCATT+TGG 0.382506 2.4:+53722389 None:intergenic
GTTGATTAACCAAAATTTGA+AGG 0.422385 2.4:-53722495 MS.gene073440:CDS
TTTGCATCATGAATGTCTCT+TGG 0.425971 2.4:+53722663 None:intergenic
GAAGGATATTGATAGAAGAT+TGG 0.427774 2.4:-53722477 MS.gene073440:CDS
TCAAGTCATGACTACTCAAT+TGG 0.431051 2.4:-53722426 MS.gene073440:CDS
ATATTTAATCTATAAATTGT+TGG 0.434030 2.4:+53722373 None:intergenic
ATACGGTGCTCTCAAAATTC+AGG 0.449943 2.4:-53722724 MS.gene073440:CDS
TTGGAAGAAGTGGATAATAA+TGG 0.455688 2.4:-53722458 MS.gene073440:CDS
GATGAATAATTTATTGAAGA+AGG 0.469514 2.4:-53722846 MS.gene073440:CDS
GGAAAGCAACCTATAAGAAA+AGG 0.485933 2.4:-53722868 MS.gene073440:CDS
TTGATTTGAATGACCTTGCT+TGG 0.489187 2.4:-53722517 MS.gene073440:CDS
CTCATATTTGGCCATCACCA+TGG 0.499740 2.4:-53722754 MS.gene073440:CDS
TCATATTTGGCCATCACCAT+GGG 0.503042 2.4:-53722753 MS.gene073440:CDS
GATGAACTAAGCACGCTTTG+TGG 0.506861 2.4:-53722821 MS.gene073440:CDS
GAAGCATGTGCTATAGTTCA+GGG 0.519428 2.4:-53722794 MS.gene073440:CDS
TTTAATCTATAAATTGTTGG+TGG 0.522214 2.4:+53722376 None:intergenic
TGATAGAAGATTGGAAGAAG+TGG 0.523326 2.4:-53722468 MS.gene073440:CDS
AATCTATAAATTGTTGGTGG+TGG 0.528345 2.4:+53722379 None:intergenic
ATCACCATGGGGAGTTCATA+CGG 0.531278 2.4:-53722741 MS.gene073440:CDS
CATGGTGATGGCCAAATATG+AGG 0.531321 2.4:+53722755 None:intergenic
TTTGGTTAATCAACCAAGCA+AGG 0.538786 2.4:+53722504 None:intergenic
AGAGACATTCATGATGCAAA+GGG 0.543276 2.4:-53722660 MS.gene073440:CDS
TCATTGTCAATGACGCTGCT+CGG 0.556837 2.4:-53722889 MS.gene073440:CDS
TGAGTAGTCATGACTTGACT+TGG 0.575659 2.4:+53722431 None:intergenic
AGCAGCGTCATTGACAATGA+AGG 0.575999 2.4:+53722892 None:intergenic
GTATGAACTCCCCATGGTGA+TGG 0.577592 2.4:+53722743 None:intergenic
AAGAGACATTCATGATGCAA+AGG 0.578602 2.4:-53722661 MS.gene073440:CDS
CACAACTCACAATCATGACT+AGG 0.590575 2.4:-53722931 None:intergenic
GATGGCCAAATATGAGGTTG+AGG 0.620009 2.4:+53722761 None:intergenic
AAAACTAAGGAAGGGAAACA+GGG 0.623030 2.4:-53722612 MS.gene073440:CDS
ATATGAGGTTGAGGTTCATG+AGG 0.635051 2.4:+53722770 None:intergenic
AGCACCGTATGAACTCCCCA+TGG 0.692559 2.4:+53722737 None:intergenic
CATATTTGGCCATCACCATG+GGG 0.723900 2.4:-53722752 MS.gene073440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATGAATAATTTATTGAAGA+AGG - chr2.4:53722453-53722472 MS.gene073440:CDS 20.0%
!!! ATTATTCATCCTTTTCTTAT+AGG + chr2.4:53722443-53722462 None:intergenic 20.0%
!!! TATCAATATCCTTCAAATTT+TGG + chr2.4:53722816-53722835 None:intergenic 20.0%
! AAAGTGAAAAAACTAAGGAA+GGG - chr2.4:53722679-53722698 MS.gene073440:CDS 25.0%
! GTTGATTAACCAAAATTTGA+AGG - chr2.4:53722804-53722823 MS.gene073440:CDS 25.0%
AGGAGAAAGTGAAAAAACTA+AGG - chr2.4:53722674-53722693 MS.gene073440:CDS 30.0%
GAAAGTGAAAAAACTAAGGA+AGG - chr2.4:53722678-53722697 MS.gene073440:CDS 30.0%
GAAGGATATTGATAGAAGAT+TGG - chr2.4:53722822-53722841 MS.gene073440:CDS 30.0%
TTCTTGTTCTTCTCTAATTC+AGG + chr2.4:53722607-53722626 None:intergenic 30.0%
TTGGAAGAAGTGGATAATAA+TGG - chr2.4:53722841-53722860 MS.gene073440:CDS 30.0%
AAAAACTAAGGAAGGGAAAC+AGG - chr2.4:53722686-53722705 MS.gene073440:CDS 35.0%
AAAACTAAGGAAGGGAAACA+GGG - chr2.4:53722687-53722706 MS.gene073440:CDS 35.0%
AAGAGACATTCATGATGCAA+AGG - chr2.4:53722638-53722657 MS.gene073440:CDS 35.0%
AGAGACATTCATGATGCAAA+GGG - chr2.4:53722639-53722658 MS.gene073440:CDS 35.0%
ATGAACCTCAACCTCATATT+TGG - chr2.4:53722533-53722552 MS.gene073440:CDS 35.0%
GGAAAGCAACCTATAAGAAA+AGG - chr2.4:53722431-53722450 MS.gene073440:CDS 35.0%
TCAAGTCATGACTACTCAAT+TGG - chr2.4:53722873-53722892 MS.gene073440:CDS 35.0%
TGATAGAAGATTGGAAGAAG+TGG - chr2.4:53722831-53722850 MS.gene073440:CDS 35.0%
TTTGCATCATGAATGTCTCT+TGG + chr2.4:53722639-53722658 None:intergenic 35.0%
TTTGGTTAATCAACCAAGCA+AGG + chr2.4:53722798-53722817 None:intergenic 35.0%
! TTGATTTGAATGACCTTGCT+TGG - chr2.4:53722782-53722801 MS.gene073440:CDS 35.0%
ATACGGTGCTCTCAAAATTC+AGG - chr2.4:53722575-53722594 MS.gene073440:CDS 40.0%
ATATGAGGTTGAGGTTCATG+AGG + chr2.4:53722532-53722551 None:intergenic 40.0%
GAAGCATGTGCTATAGTTCA+GGG - chr2.4:53722505-53722524 MS.gene073440:CDS 40.0%
TCATATTTGGCCATCACCAT+GGG - chr2.4:53722546-53722565 MS.gene073440:CDS 40.0%
TGAAGCATGTGCTATAGTTC+AGG - chr2.4:53722504-53722523 MS.gene073440:CDS 40.0%
TGAGTAGTCATGACTTGACT+TGG + chr2.4:53722871-53722890 None:intergenic 40.0%
!! CATGATGCAAAGGGTTTTGA+AGG - chr2.4:53722648-53722667 MS.gene073440:CDS 40.0%
AGCAGCGTCATTGACAATGA+AGG + chr2.4:53722410-53722429 None:intergenic 45.0%
ATCACCATGGGGAGTTCATA+CGG - chr2.4:53722558-53722577 MS.gene073440:CDS 45.0%
CATATTTGGCCATCACCATG+GGG - chr2.4:53722547-53722566 MS.gene073440:CDS 45.0%
CTCATATTTGGCCATCACCA+TGG - chr2.4:53722545-53722564 MS.gene073440:CDS 45.0%
GATGAACTAAGCACGCTTTG+TGG - chr2.4:53722478-53722497 MS.gene073440:CDS 45.0%
GATGGCCAAATATGAGGTTG+AGG + chr2.4:53722541-53722560 None:intergenic 45.0%
TCATTGTCAATGACGCTGCT+CGG - chr2.4:53722410-53722429 MS.gene073440:CDS 45.0%
!! CATGGTGATGGCCAAATATG+AGG + chr2.4:53722547-53722566 None:intergenic 45.0%
!! TTGTTGGTGGTGGTGTCATT+TGG + chr2.4:53722913-53722932 None:intergenic 45.0%
!!! GCAAAGGGTTTTGAAGGCTA+AGG - chr2.4:53722654-53722673 MS.gene073440:CDS 45.0%
GTATGAACTCCCCATGGTGA+TGG + chr2.4:53722559-53722578 None:intergenic 50.0%
AGCACCGTATGAACTCCCCA+TGG + chr2.4:53722565-53722584 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 53722382 53722939 53722382 ID=MS.gene073440
chr2.4 mRNA 53722382 53722939 53722382 ID=MS.gene073440.t1;Parent=MS.gene073440
chr2.4 exon 53722382 53722939 53722382 ID=MS.gene073440.t1.exon1;Parent=MS.gene073440.t1
chr2.4 CDS 53722382 53722939 53722382 ID=cds.MS.gene073440.t1;Parent=MS.gene073440.t1
Gene Sequence

>MS.gene073440

ATGACTAGGAAAAAGGTGAAACTCGCCTTCATTGTCAATGACGCTGCTCGGAAAGCAACCTATAAGAAAAGGATGAATAATTTATTGAAGAAGGTCGATGAACTAAGCACGCTTTGTGGTATTGAAGCATGTGCTATAGTTCAGGGTCCTCATGAACCTCAACCTCATATTTGGCCATCACCATGGGGAGTTCATACGGTGCTCTCAAAATTCAGGACTATGCCTGAATTAGAGAAGAACAAGAAAATGATGAACCAAGAGACATTCATGATGCAAAGGGTTTTGAAGGCTAAGGAGAAAGTGAAAAAACTAAGGAAGGGAAACAGGGAGCAAGAGATGACAATGATCATGTTTCAATGTCTTAATGCTGAAAAAATTGTGCACGATGATATGTCAATGATTGATTTGAATGACCTTGCTTGGTTGATTAACCAAAATTTGAAGGATATTGATAGAAGATTGGAAGAAGTGGATAATAATGGTCATCCAAGTCAAGTCATGACTACTCAATTGGAGTTAAGTTCAACTCCAAATGACACCACCACCAACAATTTATAG
Protein sequence

>MS.gene073440.t1

MTRKKVKLAFIVNDAARKATYKKRMNNLLKKVDELSTLCGIEACAIVQGPHEPQPHIWPSPWGVHTVLSKFRTMPELEKNKKMMNQETFMMQRVLKAKEKVKKLRKGNREQEMTMIMFQCLNAEKIVHDDMSMIDLNDLAWLINQNLKDIDRRLEEVDNNGHPSQVMTTQLELSSTPNDTTTNNL