AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0934670

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0934670 MtrunA17_Chr6g0452691 89.617 183 19 0 1 183 1 183 2.09e-123 345
Msa0934670 MtrunA17_Chr6g0452661 59.854 137 55 0 1 137 1 137 2.91e-54 172
Msa0934670 MtrunA17_Chr5g0439111 60.284 141 54 1 1 141 1 139 3.58e-50 161
Msa0934670 MtrunA17_Chr4g0055441 50.993 151 73 1 9 159 2 151 3.96e-49 156
Msa0934670 MtrunA17_Chr6g0452671 47.170 159 78 3 1 157 1 155 4.25e-41 137
Msa0934670 MtrunA17_Chr4g0059901 47.706 109 56 1 6 114 7 114 1.36e-28 107
Msa0934670 MtrunA17_Chr5g0444351 33.824 136 87 2 10 145 6 138 9.25e-26 96.7
Msa0934670 MtrunA17_Chr7g0225111 38.532 109 66 1 10 118 6 113 2.19e-25 94.7
Msa0934670 MtrunA17_Chr3g0097221 41.176 119 69 1 3 121 1 118 2.32e-25 99.4
Msa0934670 MtrunA17_Chr2g0311601 38.182 110 67 1 10 119 14 122 8.30e-25 94.4
Msa0934670 MtrunA17_Chr8g0353981 38.462 130 71 2 3 132 1 121 9.03e-25 96.3
Msa0934670 MtrunA17_Chr2g0330201 43.119 109 61 1 6 114 16 123 9.63e-25 97.8
Msa0934670 MtrunA17_Chr5g0437571 37.719 114 70 1 4 117 1 113 1.89e-24 94.0
Msa0934670 MtrunA17_Chr6g0449311 54.023 87 37 1 38 124 2 85 2.95e-24 92.8
Msa0934670 MtrunA17_Chr8g0342351 45.872 109 58 1 6 114 9 116 5.02e-24 95.1
Msa0934670 MtrunA17_Chr4g0030001 34.731 167 91 6 10 163 25 186 6.63e-24 93.2
Msa0934670 MtrunA17_Chr4g0043421 32.692 156 93 4 10 159 16 165 2.87e-23 90.9
Msa0934670 MtrunA17_Chr7g0227511 47.619 84 43 1 6 89 8 90 3.31e-23 90.9
Msa0934670 MtrunA17_Chr5g0438091 30.435 138 95 1 2 139 32 168 6.00e-23 90.9
Msa0934670 MtrunA17_Chr3g0114061 37.838 111 68 1 10 120 9 118 1.24e-22 89.0
Msa0934670 MtrunA17_Chr3g0115431 42.157 102 58 1 10 111 10 110 2.24e-22 89.7
Msa0934670 MtrunA17_Chr6g0449651 40.777 103 60 1 6 108 64 165 2.72e-22 89.0
Msa0934670 MtrunA17_Chr1g0200201 39.130 115 65 2 10 124 73 182 3.29e-22 89.7
Msa0934670 MtrunA17_Chr6g0449641 45.238 84 45 1 6 89 6 88 6.16e-22 86.7
Msa0934670 MtrunA17_Chr4g0058651 45.783 83 44 1 7 89 9 90 8.11e-22 87.4
Msa0934670 MtrunA17_Chr5g0402611 41.121 107 62 1 5 111 4 109 9.17e-22 90.1
Msa0934670 MtrunA17_Chr3g0106101 35.455 110 70 1 10 119 8 116 1.48e-21 86.7
Msa0934670 MtrunA17_Chr5g0432451 36.634 101 63 1 10 110 44 143 3.12e-21 87.0
Msa0934670 MtrunA17_Chr3g0117121 44.578 83 45 1 7 89 8 89 3.45e-21 85.9
Msa0934670 MtrunA17_Chr3g0129071 41.250 80 46 1 10 89 48 126 3.91e-21 87.0
Msa0934670 MtrunA17_Chr4g0040831 44.444 90 45 2 2 87 4 92 4.80e-21 85.9
Msa0934670 MtrunA17_Chr8g0374591 39.216 102 61 1 10 111 9 109 1.43e-20 82.8
Msa0934670 MtrunA17_Chr5g0437401 27.737 137 98 1 5 141 7 142 1.58e-17 75.9
Msa0934670 MtrunA17_Chr3g0113891 38.824 85 51 1 5 89 10 93 3.53e-17 75.5
Msa0934670 MtrunA17_Chr8g0374601 37.255 102 63 1 10 111 27 127 5.57e-17 76.6
Msa0934670 MtrunA17_Chr7g0260971 41.975 81 45 2 10 89 15 94 2.84e-15 70.9
Msa0934670 MtrunA17_Chr4g0046201 37.209 86 53 1 4 89 1 85 6.14e-15 70.9
Msa0934670 MtrunA17_Chr1g0184281 40.741 81 46 2 10 89 16 95 1.22e-14 68.9
Msa0934670 MtrunA17_Chr5g0435641 33.010 103 67 2 10 111 8 109 1.66e-14 68.6
Msa0934670 MtrunA17_Chr8g0351721 36.111 108 67 2 5 111 14 120 5.79e-14 67.4
Msa0934670 MtrunA17_Chr8g0374581 33.333 102 66 2 10 110 9 109 8.24e-14 67.0
Msa0934670 MtrunA17_Chr6g0460951 38.272 81 48 2 10 89 41 120 1.37e-13 66.6
Msa0934670 MtrunA17_Chr1g0184271 37.037 81 49 2 10 89 13 92 1.56e-13 66.6
Msa0934670 MtrunA17_Chr7g0245871 40.741 81 46 2 10 89 28 107 1.94e-13 66.2
Msa0934670 MtrunA17_Chr8g0337271 27.891 147 99 2 9 155 10 149 1.32e-12 63.5
Msa0934670 MtrunA17_Chr2g0326041 47.917 48 25 0 10 57 34 81 2.92e-12 60.1
Msa0934670 MtrunA17_Chr6g0460941 37.037 81 49 2 10 89 8 87 6.84e-12 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0934670 AT3G47870.1 50.459 109 53 1 6 114 33 140 6.42e-32 117
Msa0934670 AT3G26660.1 43.103 116 64 2 8 123 4 117 2.10e-30 108
Msa0934670 AT3G26620.1 43.810 105 58 1 8 112 4 107 1.08e-29 106
Msa0934670 AT3G13850.1 44.828 116 61 2 8 123 35 147 3.79e-25 98.6
Msa0934670 AT1G65620.1 46.067 89 47 1 1 89 1 88 5.12e-24 94.0
Msa0934670 AT1G65620.4 46.067 89 47 1 1 89 1 88 5.12e-24 94.0
Msa0934670 AT1G65620.3 46.067 89 47 1 1 89 1 88 5.12e-24 94.0
Msa0934670 AT1G65620.5 46.067 89 47 1 1 89 1 88 5.12e-24 94.0
Msa0934670 AT1G65620.2 46.067 89 47 1 1 89 1 88 5.12e-24 94.0
Msa0934670 AT3G27650.1 44.000 100 51 2 6 101 36 134 3.04e-23 90.9
Msa0934670 AT2G30130.1 36.975 119 74 1 10 128 9 126 4.09e-23 91.3
Msa0934670 AT2G28500.1 36.364 110 69 1 10 119 56 164 6.46e-22 89.4
Msa0934670 AT5G66870.1 42.529 87 49 1 3 89 1 86 8.45e-22 90.5
Msa0934670 AT2G40470.2 32.283 127 76 2 10 127 21 146 9.24e-22 88.2
Msa0934670 AT1G07900.1 37.755 98 60 1 10 107 34 130 1.13e-21 87.4
Msa0934670 AT2G40470.1 32.283 127 76 2 10 127 46 171 1.34e-21 88.2
Msa0934670 AT1G31320.1 43.750 80 44 1 10 89 14 92 1.81e-21 86.7
Msa0934670 AT5G63090.4 45.783 83 44 1 7 89 9 90 2.81e-21 86.7
Msa0934670 AT5G63090.3 45.783 83 44 1 7 89 9 90 2.81e-21 86.7
Msa0934670 AT5G63090.2 45.783 83 44 1 7 89 9 90 2.81e-21 86.7
Msa0934670 AT5G63090.1 45.783 83 44 1 7 89 9 90 2.81e-21 86.7
Msa0934670 AT1G72980.1 39.474 152 83 5 6 156 10 153 1.25e-20 85.5
Msa0934670 AT1G16530.1 45.679 81 42 2 10 89 15 94 1.57e-20 84.0
Msa0934670 AT2G23660.2 39.583 96 54 2 6 98 2 96 2.81e-20 86.3
Msa0934670 AT2G23660.3 39.583 96 54 2 6 98 2 96 2.81e-20 86.3
Msa0934670 AT2G23660.1 39.583 96 54 2 6 98 2 96 2.81e-20 86.3
Msa0934670 AT3G50510.1 37.383 107 66 1 5 111 8 113 5.15e-20 83.6
Msa0934670 AT3G50510.2 37.383 107 66 1 5 111 8 113 5.15e-20 83.6
Msa0934670 AT2G30340.1 36.170 94 59 1 10 103 53 145 1.47e-19 83.6
Msa0934670 AT2G30340.2 36.170 94 59 1 10 103 54 146 1.57e-19 83.6
Msa0934670 AT1G06280.1 41.975 81 46 1 7 87 22 101 1.38e-18 79.7
Msa0934670 AT3G11090.1 29.747 158 95 4 5 159 7 151 1.04e-16 73.9
Msa0934670 AT2G19820.1 37.805 82 51 0 10 91 13 94 4.79e-16 71.2
Msa0934670 AT2G42430.1 41.975 81 45 2 10 89 16 95 1.64e-15 72.4
Msa0934670 AT5G15060.1 41.096 73 42 1 10 81 18 90 3.72e-15 69.3
Msa0934670 AT4G00210.1 33.333 141 88 4 10 148 12 148 8.32e-15 70.1
Msa0934670 AT3G03760.1 37.255 102 62 2 10 110 52 152 5.70e-14 68.6
Msa0934670 AT5G35900.1 27.273 154 98 4 10 154 6 154 9.36e-14 67.0
Msa0934670 AT2G42440.1 35.227 88 55 2 3 89 1 87 1.38e-13 67.0
Msa0934670 AT5G06080.1 29.801 151 93 4 10 156 8 149 2.89e-13 65.1
Msa0934670 AT3G58190.1 38.272 81 48 2 10 89 12 91 3.52e-13 65.5
Msa0934670 AT2G31310.1 37.037 81 49 2 10 89 8 87 6.23e-13 64.3
Msa0934670 AT4G00220.1 35.238 105 66 2 12 115 20 123 9.83e-13 64.7

Find 37 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCAATCAATAAACCAAAA+AGG 0.299390 6_3:+4565060 Msa0934670:CDS
GGTGTTATTCACCAATATTT+AGG 0.310397 6_3:+4565230 Msa0934670:CDS
AGGAGCTAAAGGACAATCTT+TGG 0.326318 6_3:-4565033 None:intergenic
AAGGATGGAATATTTGTTAC+TGG 0.328353 6_3:-4565371 None:intergenic
CGTGCAGAATTCCCCGTTCA+TGG 0.328980 6_3:+4565200 Msa0934670:CDS
GACAATGTTCATAATTTGTT+TGG 0.346697 6_3:+4565086 Msa0934670:CDS
ACACCAACACATCCATGAAC+GGG 0.408734 6_3:-4565212 None:intergenic
GGTTTATTGATTGGAAAGTA+AGG 0.422123 6_3:-4565053 None:intergenic
CTTTAGTAACTTCACTATGT+TGG 0.429449 6_3:-4565114 None:intergenic
CATTCAATTCTTCGTTATCA+AGG 0.430545 6_3:-4565406 None:intergenic
GGAGCTAAAGGACAATCTTT+GGG 0.439745 6_3:-4565032 None:intergenic
CACGTATCAAACCTAAATAT+TGG 0.439926 6_3:-4565241 None:intergenic
TTCTGGATCAATATCCCAAC+CGG 0.461965 6_3:-4565450 None:intergenic
TGGAGGAGCGGTGGAACGTA+GGG 0.488043 6_3:-4565351 None:intergenic
CTTGATGGTGGTGTTGATGC+CGG 0.496790 6_3:+4565431 Msa0934670:CDS
TGGTGGTGTTGATGCCGGTT+GGG 0.501743 6_3:+4565436 Msa0934670:CDS
CGGTGGAACGTAGGGAGGAG+TGG 0.503129 6_3:-4565343 None:intergenic
ATGGTGGTGTTGATGCCGGT+TGG 0.504635 6_3:+4565435 Msa0934670:CDS
ACATAGAAGAATATGAAGAA+AGG 0.510851 6_3:+4565486 Msa0934670:CDS
ATTGGAAAGTAAGGAGCTAA+AGG 0.516566 6_3:-4565044 None:intergenic
AAATATTCCATCCTTTGCGT+TGG 0.521693 6_3:+4565379 Msa0934670:CDS
GAAGAATTGAATGACCTTGA+TGG 0.523446 6_3:+4565416 Msa0934670:CDS
AATAATTGAATCCATTGCAT+CGG 0.539959 6_3:-4565162 None:intergenic
AACACCAACACATCCATGAA+CGG 0.550657 6_3:-4565213 None:intergenic
AGGTCATCCAACGCAAAGGA+TGG 0.555066 6_3:-4565386 None:intergenic
TGATATAAAAGCCGATGCAA+TGG 0.558406 6_3:+4565151 Msa0934670:CDS
GTGCAGCATGCAAGTATCAA+AGG 0.567109 6_3:+4565000 Msa0934670:CDS
TTCCCCGTTCATGGATGTGT+TGG 0.570456 6_3:+4565209 Msa0934670:CDS
ATTTGTTACTGGAGGAGCGG+TGG 0.577800 6_3:-4565360 None:intergenic
CGGCATCAACACCACCATCA+AGG 0.578433 6_3:-4565430 None:intergenic
CTGGAGGAGCGGTGGAACGT+AGG 0.599834 6_3:-4565352 None:intergenic
AGGAGCGGTGGAACGTAGGG+AGG 0.616041 6_3:-4565348 None:intergenic
ATCAAGGTCATCCAACGCAA+AGG 0.625046 6_3:-4565390 None:intergenic
GATGGAATATTTGTTACTGG+AGG 0.649452 6_3:-4565368 None:intergenic
AATATTTGTTACTGGAGGAG+CGG 0.656478 6_3:-4565363 None:intergenic
CACCAACACATCCATGAACG+GGG 0.662809 6_3:-4565211 None:intergenic
GAATTGAATGACCTTGATGG+TGG 0.712886 6_3:+4565419 Msa0934670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCCAATCAATAAACCAAAA+AGG + chr6_3:4565060-4565079 Msa0934670:CDS 25.0%
!!! AACCTTTTTGGTTTATTGAT+TGG - chr6_3:4565065-4565084 None:intergenic 25.0%
!!! GACAATGTTCATAATTTGTT+TGG + chr6_3:4565086-4565105 Msa0934670:CDS 25.0%
! AATAATTGAATCCATTGCAT+CGG - chr6_3:4565165-4565184 None:intergenic 25.0%
!!! GGATTCAATTATTTTTGAGT+CGG + chr6_3:4565172-4565191 Msa0934670:CDS 25.0%
! ACATAGAAGAATATGAAGAA+AGG + chr6_3:4565486-4565505 Msa0934670:CDS 25.0%
! GGTTTATTGATTGGAAAGTA+AGG - chr6_3:4565056-4565075 None:intergenic 30.0%
! TGAACATTGTCTAACCTTTT+TGG - chr6_3:4565077-4565096 None:intergenic 30.0%
CTTTAGTAACTTCACTATGT+TGG - chr6_3:4565117-4565136 None:intergenic 30.0%
!! GGTGTTATTCACCAATATTT+AGG + chr6_3:4565230-4565249 Msa0934670:CDS 30.0%
CACGTATCAAACCTAAATAT+TGG - chr6_3:4565244-4565263 None:intergenic 30.0%
! AAGGATGGAATATTTGTTAC+TGG - chr6_3:4565374-4565393 None:intergenic 30.0%
CATTCAATTCTTCGTTATCA+AGG - chr6_3:4565409-4565428 None:intergenic 30.0%
! ATGTCTCTAAAAAAGTCTTC+TGG - chr6_3:4565470-4565489 None:intergenic 30.0%
ATTGGAAAGTAAGGAGCTAA+AGG - chr6_3:4565047-4565066 None:intergenic 35.0%
TGATATAAAAGCCGATGCAA+TGG + chr6_3:4565151-4565170 Msa0934670:CDS 35.0%
! AATATTTGTTACTGGAGGAG+CGG - chr6_3:4565366-4565385 None:intergenic 35.0%
! GATGGAATATTTGTTACTGG+AGG - chr6_3:4565371-4565390 None:intergenic 35.0%
AAATATTCCATCCTTTGCGT+TGG + chr6_3:4565379-4565398 Msa0934670:CDS 35.0%
GAAGAATTGAATGACCTTGA+TGG + chr6_3:4565416-4565435 Msa0934670:CDS 35.0%
GGAGCTAAAGGACAATCTTT+GGG - chr6_3:4565035-4565054 None:intergenic 40.0%
AGGAGCTAAAGGACAATCTT+TGG - chr6_3:4565036-4565055 None:intergenic 40.0%
AACACCAACACATCCATGAA+CGG - chr6_3:4565216-4565235 None:intergenic 40.0%
!!! GGAGATTTTGCTGTTGTGAA+CGG - chr6_3:4565325-4565344 None:intergenic 40.0%
GAATTGAATGACCTTGATGG+TGG + chr6_3:4565419-4565438 Msa0934670:CDS 40.0%
TTCTGGATCAATATCCCAAC+CGG - chr6_3:4565453-4565472 None:intergenic 40.0%
GTGCAGCATGCAAGTATCAA+AGG + chr6_3:4565000-4565019 Msa0934670:CDS 45.0%
ACACCAACACATCCATGAAC+GGG - chr6_3:4565215-4565234 None:intergenic 45.0%
ATCAAGGTCATCCAACGCAA+AGG - chr6_3:4565393-4565412 None:intergenic 45.0%
TTCCCCGTTCATGGATGTGT+TGG + chr6_3:4565209-4565228 Msa0934670:CDS 50.0%
CACCAACACATCCATGAACG+GGG - chr6_3:4565214-4565233 None:intergenic 50.0%
! ATTTGTTACTGGAGGAGCGG+TGG - chr6_3:4565363-4565382 None:intergenic 50.0%
AGGTCATCCAACGCAAAGGA+TGG - chr6_3:4565389-4565408 None:intergenic 50.0%
!! CTTGATGGTGGTGTTGATGC+CGG + chr6_3:4565431-4565450 Msa0934670:CDS 50.0%
CGTGCAGAATTCCCCGTTCA+TGG + chr6_3:4565200-4565219 Msa0934670:CDS 55.0%
CGGCATCAACACCACCATCA+AGG - chr6_3:4565433-4565452 None:intergenic 55.0%
!! ATGGTGGTGTTGATGCCGGT+TGG + chr6_3:4565435-4565454 Msa0934670:CDS 55.0%
!! TGGTGGTGTTGATGCCGGTT+GGG + chr6_3:4565436-4565455 Msa0934670:CDS 55.0%
TGGAGGAGCGGTGGAACGTA+GGG - chr6_3:4565354-4565373 None:intergenic 60.0%
CGGTGGAACGTAGGGAGGAG+TGG - chr6_3:4565346-4565365 None:intergenic 65.0%
AGGAGCGGTGGAACGTAGGG+AGG - chr6_3:4565351-4565370 None:intergenic 65.0%
CTGGAGGAGCGGTGGAACGT+AGG - chr6_3:4565355-4565374 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 4564972 4565526 4564972 ID=Msa0934670;Name=Msa0934670
chr6_3 mRNA 4564972 4565526 4564972 ID=Msa0934670-mRNA-1;Parent=Msa0934670;Name=Msa0934670-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|184
chr6_3 exon 4564972 4565526 4564972 ID=Msa0934670-mRNA-1:exon:1448;Parent=Msa0934670-mRNA-1
chr6_3 CDS 4564972 4565526 4564972 ID=Msa0934670-mRNA-1:cds;Parent=Msa0934670-mRNA-1
Gene Sequence

>Msa0934670

ATGAATATCATGAAATCAAACAAAGTTTGTGCAGCATGCAAGTATCAAAGGAAAAAGTGTCCCAAAGATTGTCCTTTAGCTCCTTACTTTCCAATCAATAAACCAAAAAGGTTAGACAATGTTCATAATTTGTTTGGTGTTTCCAACATAGTGAAGTTACTAAAGAATATTAAAGACGATGATATAAAAGCCGATGCAATGGATTCAATTATTTTTGAGTCGGATATTCGTGCAGAATTCCCCGTTCATGGATGTGTTGGTGTTATTCACCAATATTTAGGTTTGATACGTGAGTCTACTGAAGAGTTATATCGCACGCAAAGTTTACTAGCTATGTGTAAGATGAACAACCGTTCACAACAGCAAAATCTCCACTCCTCCCTACGTTCCACCGCTCCTCCAGTAACAAATATTCCATCCTTTGCGTTGGATGACCTTGATAACGAAGAATTGAATGACCTTGATGGTGGTGTTGATGCCGGTTGGGATATTGATCCAGAAGACTTTTTTAGAGACATAGAAGAATATGAAGAAAGGATGCGTATGAATATTTAG
Protein sequence

>Msa0934670

MNIMKSNKVCAACKYQRKKCPKDCPLAPYFPINKPKRLDNVHNLFGVSNIVKLLKNIKDDDIKADAMDSIIFESDIRAEFPVHGCVGVIHQYLGLIRESTEELYRTQSLLAMCKMNNRSQQQNLHSSLRSTAPPVTNIPSFALDDLDNEELNDLDGGVDAGWDIDPEDFFRDIEEYEERMRMNI*