AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0862840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0862840 MtrunA17_Chr5g0444351 97.931 145 3 0 1 145 1 145 1.91e-106 299
Msa0862840 MtrunA17_Chr7g0225111 82.906 117 20 0 1 117 1 117 1.33e-71 210
Msa0862840 MtrunA17_Chr5g0437571 51.376 109 53 0 6 114 7 115 1.13e-38 129
Msa0862840 MtrunA17_Chr2g0311601 49.524 105 53 0 6 110 14 118 3.09e-38 127
Msa0862840 MtrunA17_Chr3g0106101 45.833 120 62 1 6 125 8 124 2.83e-37 125
Msa0862840 MtrunA17_Chr3g0114061 42.143 140 73 2 6 145 9 140 5.54e-37 124
Msa0862840 MtrunA17_Chr4g0043421 52.525 99 47 0 6 104 16 114 1.43e-35 121
Msa0862840 MtrunA17_Chr5g0438091 45.669 127 66 1 6 129 40 166 6.46e-34 117
Msa0862840 MtrunA17_Chr3g0129071 50.000 106 53 0 6 111 48 153 6.92e-33 115
Msa0862840 MtrunA17_Chr3g0097221 49.074 108 55 0 6 113 8 115 1.17e-32 116
Msa0862840 MtrunA17_Chr4g0030001 42.857 112 63 1 1 111 20 131 6.04e-32 112
Msa0862840 MtrunA17_Chr7g0227511 45.690 116 59 1 6 117 12 127 6.43e-32 111
Msa0862840 MtrunA17_Chr3g0115431 45.631 103 56 0 6 108 10 112 6.50e-32 113
Msa0862840 MtrunA17_Chr4g0058651 47.664 107 56 0 6 112 12 118 6.74e-32 112
Msa0862840 MtrunA17_Chr6g0449641 48.000 100 52 0 6 105 10 109 6.31e-31 108
Msa0862840 MtrunA17_Chr5g0402611 45.631 103 56 0 6 108 9 111 9.28e-31 112
Msa0862840 MtrunA17_Chr3g0117121 49.000 100 51 0 6 105 11 110 1.31e-30 108
Msa0862840 MtrunA17_Chr6g0449651 40.876 137 74 2 6 142 68 197 2.14e-30 108
Msa0862840 MtrunA17_Chr5g0432451 48.077 104 54 0 6 109 44 147 7.62e-29 105
Msa0862840 MtrunA17_Chr1g0200201 43.564 101 57 0 6 106 73 173 8.30e-29 105
Msa0862840 MtrunA17_Chr6g0452691 37.879 132 79 2 6 134 10 141 1.50e-28 103
Msa0862840 MtrunA17_Chr8g0353981 56.250 80 35 0 6 85 8 87 2.11e-28 104
Msa0862840 MtrunA17_Chr3g0113891 44.681 94 52 0 6 99 15 108 2.32e-28 103
Msa0862840 MtrunA17_Chr6g0460951 44.340 106 58 1 6 110 41 146 9.52e-28 102
Msa0862840 MtrunA17_Chr5g0437401 41.584 101 59 0 6 106 12 112 1.00e-27 101
Msa0862840 MtrunA17_Chr7g0260971 45.098 102 55 1 6 106 15 116 2.87e-27 101
Msa0862840 MtrunA17_Chr6g0452671 41.237 97 57 0 6 102 12 108 6.11e-27 99.8
Msa0862840 MtrunA17_Chr1g0184281 43.478 115 60 2 6 119 16 126 8.52e-27 99.8
Msa0862840 MtrunA17_Chr8g0351701 41.667 108 62 1 4 110 22 129 1.13e-25 97.4
Msa0862840 MtrunA17_Chr7g0245871 44.554 101 55 1 6 105 28 128 2.66e-25 96.7
Msa0862840 MtrunA17_Chr7g0261031 41.732 127 67 3 6 125 9 135 7.49e-25 95.1
Msa0862840 MtrunA17_Chr8g0374601 39.604 101 61 0 6 106 27 127 1.03e-24 95.9
Msa0862840 MtrunA17_Chr8g0351721 43.269 104 58 1 4 106 17 120 1.53e-24 94.0
Msa0862840 MtrunA17_Chr1g0184271 37.857 140 78 4 6 144 13 144 3.20e-24 93.6
Msa0862840 MtrunA17_Chr8g0374581 42.574 101 57 1 6 105 9 109 8.39e-24 92.4
Msa0862840 MtrunA17_Chr8g0374591 36.634 101 64 0 6 106 9 109 1.25e-23 89.4
Msa0862840 MtrunA17_Chr5g0435641 41.176 102 59 1 6 106 8 109 1.67e-23 90.9
Msa0862840 MtrunA17_Chr6g0452661 35.294 102 65 1 6 106 10 111 3.03e-22 88.6
Msa0862840 MtrunA17_Chr5g0439111 33.333 144 87 4 6 144 10 149 9.22e-22 87.0
Msa0862840 MtrunA17_Chr6g0460941 42.529 87 49 1 6 91 8 94 6.09e-21 81.3
Msa0862840 MtrunA17_Chr4g0059901 40.000 100 60 0 6 105 11 110 6.18e-21 85.5
Msa0862840 MtrunA17_Chr8g0342351 36.538 104 66 0 6 109 13 116 1.57e-20 84.3
Msa0862840 MtrunA17_Chr4g0055441 34.314 102 66 1 6 106 3 104 3.24e-20 81.3
Msa0862840 MtrunA17_Chr2g0330201 33.663 101 67 0 6 106 20 120 4.21e-19 81.3
Msa0862840 MtrunA17_Chr7g0245861 42.857 91 49 2 4 91 11 101 9.99e-19 77.0
Msa0862840 MtrunA17_Chr4g0040831 34.831 89 58 0 2 90 12 100 1.20e-18 78.2
Msa0862840 MtrunA17_Chr2g0326041 42.105 57 33 0 1 57 29 85 1.30e-14 65.1
Msa0862840 MtrunA17_Chr4g0046201 31.395 86 59 0 6 91 7 92 1.92e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0862840 AT3G26620.1 64.706 102 36 0 5 106 5 106 1.42e-45 145
Msa0862840 AT3G26660.1 64.706 102 36 0 5 106 5 106 1.45e-45 145
Msa0862840 AT2G30130.1 50.926 108 53 0 6 113 9 116 9.43e-38 127
Msa0862840 AT1G31320.1 60.465 86 34 0 6 91 14 99 5.42e-35 120
Msa0862840 AT5G63090.4 42.029 138 80 0 6 143 12 149 1.90e-32 114
Msa0862840 AT5G63090.3 42.029 138 80 0 6 143 12 149 1.90e-32 114
Msa0862840 AT5G63090.2 42.029 138 80 0 6 143 12 149 1.90e-32 114
Msa0862840 AT5G63090.1 42.029 138 80 0 6 143 12 149 1.90e-32 114
Msa0862840 AT3G27650.1 49.000 100 51 0 6 105 40 139 3.17e-32 112
Msa0862840 AT2G28500.1 42.342 111 64 0 1 111 51 161 1.23e-31 113
Msa0862840 AT1G07900.1 42.342 111 64 0 1 111 29 139 1.37e-31 111
Msa0862840 AT1G16530.1 49.505 101 50 1 6 105 15 115 1.64e-31 110
Msa0862840 AT2G30340.1 47.170 106 56 0 6 111 53 158 2.37e-31 113
Msa0862840 AT2G30340.2 47.170 106 56 0 6 111 54 159 2.47e-31 113
Msa0862840 AT2G23660.2 45.631 103 56 0 6 108 6 108 6.78e-31 113
Msa0862840 AT2G23660.3 45.631 103 56 0 6 108 6 108 6.78e-31 113
Msa0862840 AT2G23660.1 45.631 103 56 0 6 108 6 108 6.78e-31 113
Msa0862840 AT5G66870.1 44.660 103 57 0 6 108 8 110 1.02e-30 112
Msa0862840 AT2G40470.2 45.385 130 65 2 6 135 21 144 2.93e-30 108
Msa0862840 AT2G40470.1 45.736 129 64 2 6 134 46 168 4.59e-30 108
Msa0862840 AT3G11090.1 35.294 136 80 1 6 141 12 139 1.11e-28 103
Msa0862840 AT1G65620.1 45.545 101 55 0 6 106 10 110 5.51e-28 102
Msa0862840 AT1G65620.4 45.545 101 55 0 6 106 10 110 5.51e-28 102
Msa0862840 AT1G65620.3 45.545 101 55 0 6 106 10 110 5.51e-28 102
Msa0862840 AT1G65620.5 45.545 101 55 0 6 106 10 110 5.51e-28 102
Msa0862840 AT1G65620.2 45.545 101 55 0 6 106 10 110 5.51e-28 102
Msa0862840 AT4G00210.1 39.416 137 73 3 4 132 10 144 1.15e-27 102
Msa0862840 AT3G03760.1 45.545 101 54 1 6 105 52 152 4.64e-27 102
Msa0862840 AT2G42430.1 43.810 105 58 1 6 109 16 120 1.22e-26 100
Msa0862840 AT3G50510.1 41.905 105 61 0 2 106 9 113 3.89e-26 98.2
Msa0862840 AT3G50510.2 41.905 105 61 0 2 106 9 113 3.89e-26 98.2
Msa0862840 AT5G06080.1 41.322 121 67 2 6 125 8 125 2.06e-25 95.5
Msa0862840 AT2G45410.1 45.000 100 54 1 8 106 19 118 8.10e-25 94.4
Msa0862840 AT3G58190.1 43.137 102 57 1 6 106 12 113 5.64e-24 92.8
Msa0862840 AT4G00220.1 40.385 104 61 1 8 110 20 123 5.93e-24 93.2
Msa0862840 AT2G42440.1 43.000 100 56 1 6 104 8 107 7.48e-24 93.2
Msa0862840 AT3G47870.1 37.736 106 66 0 4 109 35 140 2.65e-23 93.2
Msa0862840 AT2G45420.1 42.308 104 59 1 8 110 40 143 3.62e-23 91.7
Msa0862840 AT3G13850.1 33.766 154 82 2 6 139 37 190 1.11e-22 90.5
Msa0862840 AT5G35900.1 40.777 103 54 1 6 101 6 108 1.29e-20 84.0
Msa0862840 AT2G31310.1 31.206 141 89 3 6 145 8 141 3.06e-20 82.4
Msa0862840 AT1G72980.1 33.077 130 83 2 6 134 14 140 8.87e-18 76.6
Msa0862840 AT1G06280.1 37.209 86 54 0 6 91 25 110 1.09e-17 76.3
Msa0862840 AT2G19820.1 34.021 97 58 2 6 101 13 104 5.87e-15 67.0
Msa0862840 AT4G22700.1 31.579 114 76 2 1 113 1 113 2.64e-13 64.3
Msa0862840 AT5G15060.1 43.243 74 38 2 6 76 18 90 8.32e-13 62.0
Msa0862840 AT1G36000.1 27.957 93 67 0 6 98 10 102 8.13e-12 58.9

Find 33 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTTCATATTGTTGATTT+TGG 0.095309 5_4:+62563085 None:intergenic
AGGATTCAAAATCCTGTTTA+TGG 0.168254 5_4:-62563201 Msa0862840:CDS
AGCAAATCTTTGAGGATTAT+TGG 0.230583 5_4:+62563463 None:intergenic
AGCAATCTGAGTTTGGATTT+TGG 0.249357 5_4:+62563119 None:intergenic
GGATTATTGGCAGGGAAATA+TGG 0.290635 5_4:+62563476 None:intergenic
GGCCCAATCAAACACCTAAT+TGG 0.314557 5_4:-62563008 Msa0862840:CDS
GCTTCTGTCCACCGAATCTA+TGG 0.338967 5_4:-62563443 Msa0862840:CDS
TATGACAAGCAATCTGAGTT+TGG 0.340516 5_4:+62563112 None:intergenic
AAGTCTTAATTGAACCAATT+AGG 0.341976 5_4:+62562994 None:intergenic
GAACCAATTAGGTGTTTGAT+TGG 0.385252 5_4:+62563005 None:intergenic
CCAGCTCAGCTTCTGTATCA+TGG 0.391779 5_4:+62563142 None:intergenic
ATCCCAACACATCCATAAAC+AGG 0.441067 5_4:+62563189 None:intergenic
AATCTTTGAGGATTATTGGC+AGG 0.455276 5_4:+62563467 None:intergenic
TGCTCCATGCTGCTACTTTG+TGG 0.458851 5_4:+62563039 None:intergenic
AACCAATTAGGTGTTTGATT+GGG 0.459934 5_4:+62563006 None:intergenic
CCATGATACAGAAGCTGAGC+TGG 0.490473 5_4:-62563142 Msa0862840:CDS
TGTATTTAGAAGCACAATGT+AGG 0.494601 5_4:-62563221 Msa0862840:CDS
TGGACAGAAGCAAATCTTTG+AGG 0.503992 5_4:+62563455 None:intergenic
CAAAATCAACAATATGAAGC+TGG 0.506425 5_4:-62563084 Msa0862840:CDS
ATCTATGGTGGTGCCAATGT+TGG 0.519520 5_4:-62563428 Msa0862840:CDS
CATTGGCACCACCATAGATT+CGG 0.530883 5_4:+62563432 None:intergenic
TTGACATCATGATTTATGGT+AGG 0.535888 5_4:-62563553 None:intergenic
AATCCTGTTTATGGATGTGT+TGG 0.538555 5_4:-62563192 Msa0862840:CDS
GGAGAGAAAATGCAATCAGA+AGG 0.551169 5_4:+62563497 None:intergenic
CTTGCAAGAGTCAAAGAAGA+AGG 0.555730 5_4:-62563523 Msa0862840:CDS
ATCTTTGAGGATTATTGGCA+GGG 0.557843 5_4:+62563468 None:intergenic
GCCTCCACAAAGTAGCAGCA+TGG 0.580606 5_4:-62563043 Msa0862840:CDS
ATCCTGTTTATGGATGTGTT+GGG 0.594258 5_4:-62563191 Msa0862840:CDS
GCTTGTTCTCTTACATAGTG+AGG 0.601870 5_4:+62563255 None:intergenic
GAGAGAAAATGCAATCAGAA+GGG 0.619697 5_4:+62563498 None:intergenic
TGGCACCACCATAGATTCGG+TGG 0.632816 5_4:+62563435 None:intergenic
TCTGTCCACCGAATCTATGG+TGG 0.637607 5_4:-62563440 Msa0862840:CDS
TCCATGCTGCTACTTTGTGG+AGG 0.665689 5_4:+62563042 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTAATATAATTATAACATA+TGG - chr5_4:62563198-62563217 Msa0862840:CDS 10.0%
!!! TTCTTATCTAGTATTTTTAT+TGG - chr5_4:62563255-62563274 Msa0862840:CDS 15.0%
! AGCAAATCTTTGAGGATTAT+TGG + chr5_4:62563084-62563103 None:intergenic 30.0%
! TGTATTTAGAAGCACAATGT+AGG - chr5_4:62563323-62563342 Msa0862840:intron 30.0%
AGGATTCAAAATCCTGTTTA+TGG - chr5_4:62563343-62563362 Msa0862840:intron 30.0%
!!! CAGCTTCATATTGTTGATTT+TGG + chr5_4:62563462-62563481 None:intergenic 30.0%
CAAAATCAACAATATGAAGC+TGG - chr5_4:62563460-62563479 Msa0862840:CDS 30.0%
AACCAATTAGGTGTTTGATT+GGG + chr5_4:62563541-62563560 None:intergenic 30.0%
GAGAGAAAATGCAATCAGAA+GGG + chr5_4:62563049-62563068 None:intergenic 35.0%
! ATCTTTGAGGATTATTGGCA+GGG + chr5_4:62563079-62563098 None:intergenic 35.0%
! AATCTTTGAGGATTATTGGC+AGG + chr5_4:62563080-62563099 None:intergenic 35.0%
!! CTGAAGCATTTTTCCAACAT+TGG + chr5_4:62563132-62563151 None:intergenic 35.0%
CAATGTTGGAAAAATGCTTC+AGG - chr5_4:62563130-62563149 Msa0862840:CDS 35.0%
AATCCTGTTTATGGATGTGT+TGG - chr5_4:62563352-62563371 Msa0862840:intron 35.0%
ATCCTGTTTATGGATGTGTT+GGG - chr5_4:62563353-62563372 Msa0862840:intron 35.0%
! AGCAATCTGAGTTTGGATTT+TGG + chr5_4:62563428-62563447 None:intergenic 35.0%
TATGACAAGCAATCTGAGTT+TGG + chr5_4:62563435-62563454 None:intergenic 35.0%
GAACCAATTAGGTGTTTGAT+TGG + chr5_4:62563542-62563561 None:intergenic 35.0%
CTTGCAAGAGTCAAAGAAGA+AGG - chr5_4:62563021-62563040 Msa0862840:CDS 40.0%
GGAGAGAAAATGCAATCAGA+AGG + chr5_4:62563050-62563069 None:intergenic 40.0%
GGATTATTGGCAGGGAAATA+TGG + chr5_4:62563071-62563090 None:intergenic 40.0%
TGGACAGAAGCAAATCTTTG+AGG + chr5_4:62563092-62563111 None:intergenic 40.0%
GCTTGTTCTCTTACATAGTG+AGG + chr5_4:62563292-62563311 None:intergenic 40.0%
ATCCCAACACATCCATAAAC+AGG + chr5_4:62563358-62563377 None:intergenic 40.0%
CATTGGCACCACCATAGATT+CGG + chr5_4:62563115-62563134 None:intergenic 45.0%
! ATCTATGGTGGTGCCAATGT+TGG - chr5_4:62563116-62563135 Msa0862840:CDS 45.0%
!! GCAGCATGGAGCATTTTCAA+TGG - chr5_4:62563515-62563534 Msa0862840:CDS 45.0%
GGCCCAATCAAACACCTAAT+TGG - chr5_4:62563536-62563555 Msa0862840:CDS 45.0%
GCTTCTGTCCACCGAATCTA+TGG - chr5_4:62563101-62563120 Msa0862840:CDS 50.0%
TCTGTCCACCGAATCTATGG+TGG - chr5_4:62563104-62563123 Msa0862840:CDS 50.0%
CCAGCTCAGCTTCTGTATCA+TGG + chr5_4:62563405-62563424 None:intergenic 50.0%
CCATGATACAGAAGCTGAGC+TGG - chr5_4:62563402-62563421 Msa0862840:intron 50.0%
!! TCCATGCTGCTACTTTGTGG+AGG + chr5_4:62563505-62563524 None:intergenic 50.0%
!! TGCTCCATGCTGCTACTTTG+TGG + chr5_4:62563508-62563527 None:intergenic 50.0%
TGGCACCACCATAGATTCGG+TGG + chr5_4:62563112-62563131 None:intergenic 55.0%
GCCTCCACAAAGTAGCAGCA+TGG - chr5_4:62563501-62563520 Msa0862840:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 62562999 62563567 62562999 ID=Msa0862840;Name=Msa0862840
chr5_4 mRNA 62562999 62563567 62562999 ID=Msa0862840-mRNA-1;Parent=Msa0862840;Name=Msa0862840-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|2|0|145
chr5_4 exon 62563415 62563567 62563415 ID=Msa0862840-mRNA-1:exon:19532;Parent=Msa0862840-mRNA-1
chr5_4 exon 62562999 62563283 62562999 ID=Msa0862840-mRNA-1:exon:19531;Parent=Msa0862840-mRNA-1
chr5_4 CDS 62563415 62563567 62563415 ID=Msa0862840-mRNA-1:cds;Parent=Msa0862840-mRNA-1
chr5_4 CDS 62562999 62563283 62562999 ID=Msa0862840-mRNA-1:cds;Parent=Msa0862840-mRNA-1
Gene Sequence

>Msa0862840

ATGATTTATGGTAGGTGTGCTGCTTGCAAGAGTCAAAGAAGAAGGTGCCCTTCTGATTGCATTTTCTCTCCATATTTCCCTGCCAATAATCCTCAAAGATTTGCTTCTGTCCACCGAATCTATGGTGGTGCCAATGTTGGAAAAATGCTTCAGCAATTGCCTCACTATGTAAGAGAACAAGCTGCAAATACTTTGTATTTAGAAGCACAATGTAGGATTCAAAATCCTGTTTATGGATGTGTTGGGATCATCTCTAAATTGTATCAACAAATCCATGATACAGAAGCTGAGCTGGCCAAAATCCAAACTCAGATTGCTTGTCATAAGCTCCAAAATCAACAATATGAAGCTGGATCAAACTTCAATCTTTTGCCTCCACAAAGTAGCAGCATGGAGCATTTTCAATGGCCCAATCAAACACCTAATTGGTTCAATTAA
Protein sequence

>Msa0862840

MIYGRCAACKSQRRRCPSDCIFSPYFPANNPQRFASVHRIYGGANVGKMLQQLPHYVREQAANTLYLEAQCRIQNPVYGCVGIISKLYQQIHDTEAELAKIQTQIACHKLQNQQYEAGSNFNLLPPQSSSMEHFQWPNQTPNWFN*