AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1398380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1398380 MtrunA17_Chr3g0115431 92.727 220 11 2 1 219 2 217 1.54e-133 374
Msa1398380 MtrunA17_Chr5g0402611 77.236 123 28 0 1 123 1 123 1.13e-66 208
Msa1398380 MtrunA17_Chr3g0097221 74.576 118 28 2 1 117 1 117 2.08e-56 181
Msa1398380 MtrunA17_Chr4g0058651 65.812 117 40 0 7 123 10 126 5.83e-50 161
Msa1398380 MtrunA17_Chr7g0227511 66.667 111 37 0 2 112 5 115 5.76e-49 158
Msa1398380 MtrunA17_Chr3g0117121 53.503 157 69 2 2 157 4 157 3.03e-48 157
Msa1398380 MtrunA17_Chr6g0449641 67.290 107 35 0 2 108 3 109 1.97e-47 153
Msa1398380 MtrunA17_Chr5g0437571 57.480 127 52 2 6 130 4 130 1.22e-46 152
Msa1398380 MtrunA17_Chr6g0449651 63.636 110 40 0 2 111 61 170 2.84e-46 152
Msa1398380 MtrunA17_Chr3g0114061 61.111 108 42 0 1 108 1 108 3.75e-45 148
Msa1398380 MtrunA17_Chr3g0106101 60.577 104 41 0 5 108 4 107 3.24e-44 146
Msa1398380 MtrunA17_Chr8g0353981 58.394 137 54 2 1 137 1 134 6.79e-44 147
Msa1398380 MtrunA17_Chr2g0311601 61.765 102 39 0 7 108 12 113 7.59e-43 142
Msa1398380 MtrunA17_Chr5g0438091 60.377 106 42 0 6 111 37 142 1.53e-42 142
Msa1398380 MtrunA17_Chr4g0043421 60.784 102 40 0 6 107 13 114 3.22e-42 141
Msa1398380 MtrunA17_Chr3g0129071 60.000 105 42 0 7 111 46 150 3.81e-41 140
Msa1398380 MtrunA17_Chr3g0113891 62.745 102 38 0 5 106 11 112 1.31e-40 137
Msa1398380 MtrunA17_Chr8g0374601 56.364 110 48 0 8 117 26 135 1.92e-40 140
Msa1398380 MtrunA17_Chr5g0437401 60.952 105 41 0 5 109 8 112 9.59e-40 135
Msa1398380 MtrunA17_Chr8g0374591 53.636 110 51 0 8 117 8 117 3.05e-39 132
Msa1398380 MtrunA17_Chr1g0200201 58.000 100 42 0 9 108 73 172 1.02e-38 134
Msa1398380 MtrunA17_Chr4g0030001 56.311 103 44 1 7 108 23 125 1.31e-38 132
Msa1398380 MtrunA17_Chr5g0432451 54.918 122 47 1 7 120 42 163 1.76e-37 130
Msa1398380 MtrunA17_Chr8g0374581 53.153 111 51 1 8 117 8 118 2.16e-35 125
Msa1398380 MtrunA17_Chr7g0225111 47.619 105 55 0 7 111 4 108 3.26e-34 119
Msa1398380 MtrunA17_Chr7g0260971 55.046 109 48 1 2 109 8 116 9.04e-34 120
Msa1398380 MtrunA17_Chr8g0351701 55.660 106 46 1 7 111 22 127 1.70e-33 120
Msa1398380 MtrunA17_Chr8g0351721 41.989 181 98 2 5 184 15 189 1.47e-32 117
Msa1398380 MtrunA17_Chr1g0184271 42.405 158 73 4 8 151 12 165 2.07e-32 117
Msa1398380 MtrunA17_Chr7g0245871 53.922 102 46 1 8 108 27 128 3.79e-32 117
Msa1398380 MtrunA17_Chr5g0444351 46.602 103 55 0 9 111 6 108 4.02e-32 114
Msa1398380 MtrunA17_Chr1g0184281 54.455 101 45 1 8 107 15 115 9.11e-32 115
Msa1398380 MtrunA17_Chr6g0460951 36.000 200 109 4 7 198 39 227 5.45e-31 114
Msa1398380 MtrunA17_Chr7g0261031 49.091 110 55 1 1 109 1 110 4.78e-30 111
Msa1398380 MtrunA17_Chr6g0452661 36.757 185 97 6 9 188 10 179 1.85e-29 110
Msa1398380 MtrunA17_Chr5g0435641 46.226 106 56 1 6 110 5 110 2.44e-29 108
Msa1398380 MtrunA17_Chr6g0452671 46.000 100 54 0 6 105 9 108 1.24e-27 104
Msa1398380 MtrunA17_Chr7g0245861 43.411 129 70 2 5 130 9 137 3.35e-26 99.0
Msa1398380 MtrunA17_Chr6g0452691 46.078 102 54 1 9 109 10 111 3.47e-26 100
Msa1398380 MtrunA17_Chr4g0059901 45.000 100 55 0 9 108 11 110 9.06e-26 101
Msa1398380 MtrunA17_Chr6g0460941 48.352 91 46 1 6 95 5 95 3.30e-25 95.1
Msa1398380 MtrunA17_Chr4g0055441 40.476 126 70 3 9 133 3 124 7.08e-25 96.3
Msa1398380 MtrunA17_Chr8g0342351 38.835 103 63 0 9 111 13 115 5.62e-24 96.7
Msa1398380 MtrunA17_Chr4g0040831 35.878 131 82 1 9 139 16 144 3.45e-23 92.8
Msa1398380 MtrunA17_Chr5g0439111 42.157 102 58 1 9 109 10 111 2.98e-21 88.6
Msa1398380 MtrunA17_Chr2g0330201 35.577 104 67 0 6 109 17 120 6.22e-21 89.0
Msa1398380 MtrunA17_Chr4g0046201 37.778 90 56 0 5 94 3 92 6.14e-20 85.9
Msa1398380 MtrunA17_Chr2g0326041 64.000 50 18 0 7 56 32 81 9.36e-19 78.2
Msa1398380 MtrunA17_Chr2g0326051 57.143 56 24 0 53 108 5 60 2.53e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1398380 AT5G66870.1 78.070 114 25 0 6 119 5 118 5.27e-61 194
Msa1398380 AT2G23660.2 66.379 116 39 0 6 121 3 118 1.04e-54 178
Msa1398380 AT2G23660.3 66.379 116 39 0 6 121 3 118 1.04e-54 178
Msa1398380 AT2G23660.1 66.379 116 39 0 6 121 3 118 1.04e-54 178
Msa1398380 AT5G63090.4 69.643 112 32 1 2 111 3 114 1.17e-49 161
Msa1398380 AT5G63090.3 69.643 112 32 1 2 111 3 114 1.17e-49 161
Msa1398380 AT5G63090.2 69.643 112 32 1 2 111 3 114 1.17e-49 161
Msa1398380 AT5G63090.1 69.643 112 32 1 2 111 3 114 1.17e-49 161
Msa1398380 AT3G27650.1 64.602 113 40 0 1 113 32 144 2.21e-48 157
Msa1398380 AT2G30130.1 62.963 108 40 0 1 108 1 108 4.88e-47 154
Msa1398380 AT1G65620.1 67.227 119 39 0 2 120 3 121 1.51e-46 153
Msa1398380 AT1G65620.4 67.227 119 39 0 2 120 3 121 1.51e-46 153
Msa1398380 AT1G65620.3 67.227 119 39 0 2 120 3 121 1.51e-46 153
Msa1398380 AT1G65620.5 67.227 119 39 0 2 120 3 121 1.51e-46 153
Msa1398380 AT1G65620.2 67.227 119 39 0 2 120 3 121 1.51e-46 153
Msa1398380 AT1G07900.1 60.784 102 40 0 7 108 32 133 8.17e-43 143
Msa1398380 AT2G28500.1 46.452 155 78 2 7 161 54 203 4.75e-42 143
Msa1398380 AT2G30340.2 59.804 102 41 0 7 108 52 153 3.32e-40 139
Msa1398380 AT2G30340.1 59.804 102 41 0 7 108 51 152 3.34e-40 139
Msa1398380 AT1G16530.1 59.223 103 41 1 7 108 13 115 1.27e-39 134
Msa1398380 AT3G11090.1 57.798 109 46 0 5 113 8 116 1.76e-39 134
Msa1398380 AT1G31320.1 62.921 89 33 0 6 94 11 99 2.73e-38 131
Msa1398380 AT2G40470.2 60.000 105 42 0 7 111 19 123 3.29e-37 129
Msa1398380 AT4G00210.1 51.880 133 59 2 6 137 9 137 6.47e-37 129
Msa1398380 AT3G26620.1 50.000 106 53 0 5 110 2 107 8.64e-37 125
Msa1398380 AT2G40470.1 60.000 105 42 0 7 111 44 148 9.72e-37 129
Msa1398380 AT3G26660.1 50.000 106 53 0 5 110 2 107 1.12e-36 125
Msa1398380 AT3G50510.1 49.580 119 59 1 6 123 10 128 1.08e-35 125
Msa1398380 AT3G50510.2 49.580 119 59 1 6 123 10 128 1.08e-35 125
Msa1398380 AT5G35900.1 50.459 109 54 0 5 113 2 110 3.02e-35 124
Msa1398380 AT3G58190.1 44.286 140 73 3 8 145 11 147 1.85e-33 120
Msa1398380 AT3G03760.1 54.369 103 46 1 7 108 50 152 2.46e-33 121
Msa1398380 AT4G00220.1 56.436 101 43 1 11 110 20 120 1.51e-31 115
Msa1398380 AT2G42430.1 52.336 107 50 1 6 111 13 119 8.38e-31 114
Msa1398380 AT2G45420.1 53.465 101 46 1 11 110 40 140 2.03e-29 111
Msa1398380 AT2G45410.1 45.113 133 67 2 11 137 19 151 3.82e-29 108
Msa1398380 AT2G42440.1 47.573 103 53 1 6 107 5 107 5.44e-29 109
Msa1398380 AT2G31310.1 46.602 103 54 1 6 107 5 107 9.22e-28 104
Msa1398380 AT5G06080.1 44.444 108 59 1 5 111 4 111 1.89e-26 101
Msa1398380 AT1G72980.1 43.925 107 60 0 2 108 7 113 2.34e-26 102
Msa1398380 AT3G13850.1 39.806 103 62 0 9 111 37 139 7.55e-26 102
Msa1398380 AT3G47870.1 40.566 106 63 0 6 111 34 139 1.81e-25 102
Msa1398380 AT4G22700.1 37.500 144 79 4 6 139 3 145 5.35e-23 92.4
Msa1398380 AT1G06280.1 45.977 87 47 0 9 95 25 111 2.53e-20 85.9
Msa1398380 AT2G19820.1 36.047 86 54 1 7 91 11 96 6.58e-16 72.0
Msa1398380 AT3G27940.3 30.769 130 88 1 5 132 2 131 7.21e-14 67.4
Msa1398380 AT3G27940.1 30.769 130 88 1 5 132 2 131 7.21e-14 67.4
Msa1398380 AT3G27940.2 30.769 130 88 1 5 132 2 131 7.21e-14 67.4
Msa1398380 AT5G15060.1 41.096 73 41 1 9 79 18 90 2.34e-12 62.8

Find 24 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTTGAGAGATCCTGTTTA+TGG 0.254736 tig0022248:-103525 Msa1398380:CDS
ACCATTAACTGATTCTGAAA+AGG 0.386367 tig0022248:+103267 None:intergenic
ACCTACGTTCACAAAGTGTT+TGG 0.430629 tig0022248:-103636 Msa1398380:CDS
CCATTAACTGATTCTGAAAA+GGG 0.443959 tig0022248:+103268 None:intergenic
AGACCAACACAACCATAAAC+AGG 0.459225 tig0022248:+103513 None:intergenic
AAAGAACTTGCTACTTATGT+TGG 0.467080 tig0022248:-103432 Msa1398380:CDS
TTTGTCAAAGAAGGTGTTCA+AGG 0.477381 tig0022248:-103190 Msa1398380:CDS
GATCCTGTTTATGGTTGTGT+TGG 0.503197 tig0022248:-103516 Msa1398380:CDS
GAAGGTGTTCAAGGCAGAAA+GGG 0.510547 tig0022248:-103181 Msa1398380:CDS
AGAAGGTGTTCAAGGCAGAA+AGG 0.524281 tig0022248:-103182 Msa1398380:CDS
TGAATCTTGCACGCTGCACA+CGG 0.560567 tig0022248:+103726 None:intergenic
GAACTCGACGCCGCCGTCAT+CGG 0.569433 tig0022248:+103387 None:intergenic
AGAAAGGGACAACCTTGGAG+AGG 0.582482 tig0022248:-103166 Msa1398380:CDS
AAGGCAGAAAGGGACAACCT+TGG 0.600174 tig0022248:-103171 Msa1398380:CDS
GAAAGGGACAACCTTGGAGA+GGG 0.609665 tig0022248:-103165 Msa1398380:CDS
GACGCCGCCGTCATCGGTGT+AGG 0.623332 tig0022248:+103393 None:intergenic
CATGCTTCCTACACCGATGA+CGG 0.624741 tig0022248:-103400 Msa1398380:CDS
CAGTGATCATACCCTCTCCA+AGG 0.636121 tig0022248:+103154 None:intergenic
GGTGTAGGAAGCATGATCTG+AGG 0.695632 tig0022248:+103408 None:intergenic
GCTTCCTACACCGATGACGG+CGG 0.697155 tig0022248:-103397 Msa1398380:CDS
CGTGGCAAAGTTACTCAACG+AGG 0.719799 tig0022248:-103604 Msa1398380:CDS
TCAGCGTCGAAAATGCACAA+AGG 0.734134 tig0022248:-103706 Msa1398380:CDS
AGTGTTTGGTGCTAGCAACG+TGG 0.743523 tig0022248:-103622 Msa1398380:CDS
ACCAAACACTTTGTGAACGT+AGG 0.770701 tig0022248:+103635 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTGTTAATTATTCTATT+AGG - tig0022248:103732-103751 Msa1398380:CDS 15.0%
!!! AATTATTCTATTAGGTTTTT+AGG - tig0022248:103740-103759 Msa1398380:CDS 15.0%
!! ACAAAAGTAACAAACAAAAA+AGG + tig0022248:103719-103738 None:intergenic 20.0%
!! GTAAACTTTTGAGGATTTTC+CGG + tig0022248:103161-103180 None:intergenic 30.0%
!! AAAGAACTTGCTACTTATGT+TGG - tig0022248:103383-103402 Msa1398380:CDS 30.0%
! CCATTAACTGATTCTGAAAA+GGG + tig0022248:103550-103569 None:intergenic 30.0%
! ACCATTAACTGATTCTGAAA+AGG + tig0022248:103551-103570 None:intergenic 30.0%
CAAACAAAAAAGGACAAAAG+TGG + tig0022248:103709-103728 None:intergenic 30.0%
! TGAACGTAGGTAAACTTTTG+AGG + tig0022248:103170-103189 None:intergenic 35.0%
!! AAACGAGTTTTCAGCATTGA+AGG + tig0022248:103507-103526 None:intergenic 35.0%
! CCCTTTTCAGAATCAGTTAA+TGG - tig0022248:103547-103566 Msa1398380:CDS 35.0%
ATCATCATCATCATCATCAC+AGG - tig0022248:103574-103593 Msa1398380:CDS 35.0%
! TTTGACAAAAATGCGTCGAT+GGG + tig0022248:103614-103633 None:intergenic 35.0%
!! TTTGTCAAAGAAGGTGTTCA+AGG - tig0022248:103625-103644 Msa1398380:CDS 35.0%
!! AACTTTTGAGGATTTTCCGG+CGG + tig0022248:103158-103177 None:intergenic 40.0%
! ACCTACGTTCACAAAGTGTT+TGG - tig0022248:103179-103198 Msa1398380:CDS 40.0%
ACCAAACACTTTGTGAACGT+AGG + tig0022248:103183-103202 None:intergenic 40.0%
CGTTTGAGAGATCCTGTTTA+TGG - tig0022248:103290-103309 Msa1398380:CDS 40.0%
GATCCTGTTTATGGTTGTGT+TGG - tig0022248:103299-103318 Msa1398380:CDS 40.0%
AGACCAACACAACCATAAAC+AGG + tig0022248:103305-103324 None:intergenic 40.0%
CTTTGACAAAAATGCGTCGA+TGG + tig0022248:103615-103634 None:intergenic 40.0%
! CGACGCATTTTTGTCAAAGA+AGG - tig0022248:103616-103635 Msa1398380:CDS 40.0%
! TCAGCGTCGAAAATGCACAA+AGG - tig0022248:103109-103128 Msa1398380:CDS 45.0%
! TTTTGCACCCTATTTTCCGC+CGG - tig0022248:103139-103158 Msa1398380:CDS 45.0%
! GGATTTTCCGGCGGAAAATA+GGG + tig0022248:103149-103168 None:intergenic 45.0%
! AGGATTTTCCGGCGGAAAAT+AGG + tig0022248:103150-103169 None:intergenic 45.0%
!! AGAAGGTGTTCAAGGCAGAA+AGG - tig0022248:103633-103652 Msa1398380:CDS 45.0%
!! GAAGGTGTTCAAGGCAGAAA+GGG - tig0022248:103634-103653 Msa1398380:CDS 45.0%
TGAATCTTGCACGCTGCACA+CGG + tig0022248:103092-103111 None:intergenic 50.0%
!! AGTGTTTGGTGCTAGCAACG+TGG - tig0022248:103193-103212 Msa1398380:CDS 50.0%
CGTGGCAAAGTTACTCAACG+AGG - tig0022248:103211-103230 Msa1398380:CDS 50.0%
! GGTGTAGGAAGCATGATCTG+AGG + tig0022248:103410-103429 None:intergenic 50.0%
CATGCTTCCTACACCGATGA+CGG - tig0022248:103415-103434 Msa1398380:CDS 50.0%
AAGGCAGAAAGGGACAACCT+TGG - tig0022248:103644-103663 Msa1398380:CDS 50.0%
AGAAAGGGACAACCTTGGAG+AGG - tig0022248:103649-103668 Msa1398380:CDS 50.0%
GAAAGGGACAACCTTGGAGA+GGG - tig0022248:103650-103669 Msa1398380:CDS 50.0%
CAGTGATCATACCCTCTCCA+AGG + tig0022248:103664-103683 None:intergenic 50.0%
! GCTTCCTACACCGATGACGG+CGG - tig0022248:103418-103437 Msa1398380:CDS 60.0%
GAACTCGACGCCGCCGTCAT+CGG + tig0022248:103431-103450 None:intergenic 65.0%
GACGCCGCCGTCATCGGTGT+AGG + tig0022248:103425-103444 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0022248 gene 103068 103769 103068 ID=Msa1398380;Name=Msa1398380
tig0022248 mRNA 103068 103769 103068 ID=Msa1398380-mRNA-1;Parent=Msa1398380;Name=Msa1398380-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|233
tig0022248 exon 103068 103769 103068 ID=Msa1398380-mRNA-1:exon:16573;Parent=Msa1398380-mRNA-1
tig0022248 CDS 103068 103769 103068 ID=Msa1398380-mRNA-1:cds;Parent=Msa1398380-mRNA-1
Gene Sequence

>Msa1398380

ATGTCGTCGTGTAATTCTTCTCCGTGTGCAGCGTGCAAGATTCAGCGTCGAAAATGCACAAAGGAATGCATTTTTGCACCCTATTTTCCGCCGGAAAATCCTCAAAAGTTTACCTACGTTCACAAAGTGTTTGGTGCTAGCAACGTGGCAAAGTTACTCAACGAGGTTGATGCTTCTCAGCGTGAAGATGCTGTTAAGTCTTTAGCTTATGAAGCAGAAGCGCGTTTGAGAGATCCTGTTTATGGTTGTGTTGGTCTTATTTCACATCTTCAGAATAAGCTTAAGAATTTGCAGAATGAACTTAATGTTGCTAAGAAAGAACTTGCTACTTATGTTGGTCCTCAGATCATGCTTCCTACACCGATGACGGCGGCGTCGAGTTCTTATTTTTCTGTGACTACTTCTTCTGTTCATCAACAGCGTCAAGAGTTTTTCACCTTCAATGCTGAAAACTCGTTTTCTAATAACTTTCAGATGAACCCTTTTCAGAATCAGTTAATGGTTTCATCATCATCATCATCATCACAGGCACAGTCATCACAACCCATCGACGCATTTTTGTCAAAGAAGGTGTTCAAGGCAGAAAGGGACAACCTTGGAGAGGGTATGATCACTGTTTCATCTATTTTATTGATTTTCCACTTTTGTCCTTTTTTGTTTGTTACTTTTGTTAATTATTCTATTAGGTTTTTAGGTTTATGA
Protein sequence

>Msa1398380

MSSCNSSPCAACKIQRRKCTKECIFAPYFPPENPQKFTYVHKVFGASNVAKLLNEVDASQREDAVKSLAYEAEARLRDPVYGCVGLISHLQNKLKNLQNELNVAKKELATYVGPQIMLPTPMTAASSSYFSVTTSSVHQQRQEFFTFNAENSFSNNFQMNPFQNQLMVSSSSSSSQAQSSQPIDAFLSKKVFKAERDNLGEGMITVSSILLIFHFCPFLFVTFVNYSIRFLGL*