AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene016952

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016952.t1 MTR_5g089170 99.177 243 2 0 1 243 12 254 0.0 500
MS.gene016952.t1 MTR_3g101870 48.632 329 76 11 1 239 11 336 2.66e-90 271
MS.gene016952.t1 MTR_4g011850 75.294 170 3 2 74 243 9 139 2.80e-84 247
MS.gene016952.t1 MTR_5g010680 45.133 226 99 4 4 204 14 239 5.38e-58 188
MS.gene016952.t1 MTR_1g100777 41.129 248 121 5 6 235 10 250 3.18e-55 179
MS.gene016952.t1 MTR_7g091370 45.771 201 99 2 7 207 15 205 1.02e-54 176
MS.gene016952.t1 MTR_0020s0020 39.623 265 127 6 5 238 24 286 3.28e-52 172
MS.gene016952.t1 MTR_5g017470 39.184 245 119 6 7 231 2 236 1.56e-48 161
MS.gene016952.t1 MTR_5g029680 46.597 191 90 2 11 201 29 207 2.45e-45 158
MS.gene016952.t1 MTR_6g043060 69.892 93 28 0 13 105 21 113 3.74e-43 149
MS.gene016952.t1 MTR_1g102860 71.134 97 28 0 12 108 38 134 3.34e-41 144
MS.gene016952.t1 MTR_7g095680 65.957 94 32 0 12 105 47 140 2.90e-40 142
MS.gene016952.t1 MTR_8g087540 56.349 126 53 2 7 132 6 129 1.70e-39 141
MS.gene016952.t1 MTR_1g071360 44.444 171 64 3 12 181 30 170 9.34e-39 137
MS.gene016952.t1 MTR_8g083100 68.132 91 29 0 15 105 23 113 1.29e-38 140
MS.gene016952.t1 MTR_1g071360 44.444 171 64 3 12 181 27 167 1.44e-38 138
MS.gene016952.t1 MTR_1g061170 44.512 164 68 3 8 170 43 184 4.51e-38 138
MS.gene016952.t1 MTR_2g100680 63.830 94 34 0 12 105 29 122 3.05e-37 136
MS.gene016952.t1 MTR_4g088900 40.361 166 87 3 11 172 30 187 1.14e-36 129
MS.gene016952.t1 MTR_2g100670 58.824 102 42 0 4 105 23 124 1.95e-35 128
MS.gene016952.t1 MTR_3g104550 42.138 159 73 1 12 170 44 183 3.95e-35 129
MS.gene016952.t1 MTR_6g086805 59.184 98 40 0 8 105 5 102 4.45e-35 128
MS.gene016952.t1 MTR_4g077970 43.671 158 74 2 14 170 12 155 1.33e-34 129
MS.gene016952.t1 MTR_2g100670 58.824 102 42 0 4 105 131 232 1.59e-34 128
MS.gene016952.t1 MTR_2g017890 57.000 100 42 1 7 106 9 107 9.67e-34 125
MS.gene016952.t1 MTR_8g105780 60.417 96 37 1 13 107 21 116 3.03e-33 124
MS.gene016952.t1 MTR_4g045757 62.069 58 22 0 14 71 14 71 1.96e-19 80.1
MS.gene016952.t1 MTR_5g047190 41.304 92 47 2 22 106 1 92 2.65e-16 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016952.t1 AT1G46264 60.909 220 54 5 9 200 29 244 1.86e-86 260
MS.gene016952.t1 AT5G62020 40.400 250 130 3 7 238 16 264 5.99e-54 176
MS.gene016952.t1 AT4G36990 39.759 249 136 4 1 236 1 248 1.02e-53 175
MS.gene016952.t1 AT4G11660 71.845 103 29 0 6 108 51 153 1.52e-50 169
MS.gene016952.t1 AT1G32330 46.739 184 86 3 11 193 34 206 4.00e-46 160
MS.gene016952.t1 AT1G32330 46.739 184 86 3 11 193 34 206 4.62e-46 160
MS.gene016952.t1 AT2G41690 43.094 181 93 3 12 183 38 217 1.40e-44 150
MS.gene016952.t1 AT4G17750 64.486 107 38 0 4 110 42 148 1.33e-43 154
MS.gene016952.t1 AT3G22830 66.327 98 33 0 9 106 56 153 3.39e-40 143
MS.gene016952.t1 AT5G43840 57.018 114 49 0 12 125 17 130 1.87e-39 138
MS.gene016952.t1 AT3G02990 66.667 96 31 1 10 105 20 114 3.16e-39 141
MS.gene016952.t1 AT5G16820 67.000 100 31 2 10 109 24 121 3.58e-39 141
MS.gene016952.t1 AT5G16820 67.000 100 31 2 10 109 24 121 3.58e-39 141
MS.gene016952.t1 AT5G03720 63.265 98 36 0 14 111 55 152 1.60e-38 139
MS.gene016952.t1 AT5G03720 63.265 98 36 0 14 111 55 152 1.60e-38 139
MS.gene016952.t1 AT2G26150 59.794 97 39 0 9 105 39 135 4.10e-37 133
MS.gene016952.t1 AT2G26150 59.794 97 39 0 9 105 39 135 4.10e-37 133
MS.gene016952.t1 AT3G63350 54.054 111 51 0 8 118 22 132 9.22e-37 131
MS.gene016952.t1 AT3G51910 60.417 96 38 0 9 104 24 119 3.87e-36 129
MS.gene016952.t1 AT4G13980 64.835 91 32 0 15 105 24 114 8.26e-36 132
MS.gene016952.t1 AT5G54070 57.895 95 40 0 10 104 67 161 2.47e-35 128
MS.gene016952.t1 AT3G24520 60.000 95 38 0 11 105 14 108 5.45e-35 127
MS.gene016952.t1 AT1G67970 51.261 119 57 1 13 130 18 136 1.07e-34 127
MS.gene016952.t1 AT4G18880 65.657 99 33 1 7 105 9 106 1.02e-31 120
MS.gene016952.t1 AT5G45710 42.442 172 91 3 14 180 13 181 1.18e-31 119
MS.gene016952.t1 AT5G45710 42.442 172 91 3 14 180 13 181 1.18e-31 119
MS.gene016952.t1 AT4G18870 44.706 85 47 0 14 98 146 230 3.64e-20 87.4
MS.gene016952.t1 AT4G18870 38.596 114 62 3 15 126 14 121 2.91e-18 82.0

Find 36 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATATCAGTGTTTGATTT+AGG 0.203557 5.1:+70548763 None:intergenic
AGCTCTTCTGTGAAGCTATT+TGG 0.233498 5.1:-70548514 MS.gene016952:CDS
CTATTTGGTGTTCCTCTTTG+TGG 0.339191 5.1:-70548499 MS.gene016952:CDS
TCCTTATCATTTGGTAATTG+AGG 0.352875 5.1:+70548544 None:intergenic
ATGAAACTACATTTGTTGTT+TGG 0.362655 5.1:-70549587 MS.gene016952:CDS
CTATTACAATCCTTATCATT+TGG 0.365932 5.1:+70548535 None:intergenic
CTTTGTTCAAAGGGTGAAGC+AGG 0.399996 5.1:+70548619 None:intergenic
ATTGTTGCTTCTTTGTTCAA+AGG 0.403141 5.1:+70548609 None:intergenic
TCTTATTAATCAAGATTACT+AGG 0.404553 5.1:+70548460 None:intergenic
ATAATTTCTCAAGCTTTGTT+AGG 0.408211 5.1:-70549515 MS.gene016952:CDS
TTGTTGCTTCTTTGTTCAAA+GGG 0.445911 5.1:+70548610 None:intergenic
TCAAGAAGGTTGTTGCTGAT+AGG 0.447682 5.1:-70548951 MS.gene016952:CDS
AAACTACATTTGTTGTTTGG+AGG 0.447885 5.1:-70549584 MS.gene016952:CDS
TGGTATGTCTTTGTCAAGAA+AGG 0.453363 5.1:+70549657 None:intergenic
ATTGTTGTTGATAGTGTTGA+GGG 0.457477 5.1:+70548857 None:intergenic
AGATAACATGGTGTTCACTA+TGG 0.459097 5.1:-70549703 None:intergenic
ACCTCAATTACCAAATGATA+AGG 0.460161 5.1:-70548545 MS.gene016952:CDS
CTTCTTGCAGGGTTTCAAGA+AGG 0.465882 5.1:-70548965 MS.gene016952:intron
TTTGATTTAGGAGATGGTAA+TGG 0.467405 5.1:+70548775 None:intergenic
AACAAGATGAAAGTATATGC+TGG 0.489196 5.1:-70548807 MS.gene016952:CDS
TCAGTGTTTGATTTAGGAGA+TGG 0.490616 5.1:+70548769 None:intergenic
TCACTGACCACATTGTATCT+TGG 0.491347 5.1:-70549617 MS.gene016952:CDS
GTCTTTGTCAAGAAAGGAGC+AGG 0.498324 5.1:+70549663 None:intergenic
CTGAGGACAATCAAAGACTA+AGG 0.512782 5.1:-70548729 MS.gene016952:CDS
ATCTATTATGTGAAATCCAC+AGG 0.520532 5.1:-70548888 MS.gene016952:CDS
AGAAGGTTGTTGCTGATAGG+TGG 0.520569 5.1:-70548948 MS.gene016952:CDS
TATCTTAACAGCACTTTCTG+AGG 0.558486 5.1:-70548746 MS.gene016952:CDS
GAAGGTTGTTGCTGATAGGT+GGG 0.581284 5.1:-70548947 MS.gene016952:CDS
TATTGTTGTTGATAGTGTTG+AGG 0.584009 5.1:+70548856 None:intergenic
TGAGAGGATCATCAACAAGT+TGG 0.584975 5.1:+70549637 None:intergenic
AGAAGATCTCTAGCAAACTC+AGG 0.587900 5.1:+70549558 None:intergenic
GATACAATGTGGTCAGTGAG+AGG 0.630246 5.1:+70549621 None:intergenic
TTGTTGTTGATAGTGTTGAG+GGG 0.651120 5.1:+70548858 None:intergenic
AGATCTCTAGCAAACTCAGG+AGG 0.689022 5.1:+70549561 None:intergenic
AGGGTGAAGCAGGACTCACA+TGG 0.700311 5.1:+70548629 None:intergenic
CATCACTCCAAGATACAATG+TGG 0.717706 5.1:+70549610 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTATGCTTGAAAAAAT+TGG + chr5.1:70548631-70548650 None:intergenic 15.0%
!! TTATTATGCTTGAAAAAATT+GGG + chr5.1:70548630-70548649 None:intergenic 15.0%
!!! AGTTATTTAAGTTATTCTTA+TGG + chr5.1:70548807-70548826 None:intergenic 15.0%
!! ACTTACTAAAACAATGAATA+AGG + chr5.1:70548726-70548745 None:intergenic 20.0%
!! TCATTATTATAGTTACATGA+TGG - chr5.1:70548859-70548878 MS.gene016952:CDS 20.0%
!! TTATGAAAATATGCTGAAAA+CGG - chr5.1:70549033-70549052 MS.gene016952:intron 20.0%
! CTATTACAATCCTTATCATT+TGG + chr5.1:70549629-70549648 None:intergenic 25.0%
! CTGACAATAATTTGAGAAAA+TGG - chr5.1:70549120-70549139 MS.gene016952:intron 25.0%
! CTTCTTTAGTTAGTGTAAAA+AGG - chr5.1:70548748-70548767 MS.gene016952:CDS 25.0%
! GCAAATGATTACTTCAAAAA+AGG - chr5.1:70549242-70549261 MS.gene016952:intron 25.0%
! TCATCTTGTTGAAAAATTTG+TGG + chr5.1:70549344-70549363 None:intergenic 25.0%
!! AAGATATCAGTGTTTGATTT+AGG + chr5.1:70549401-70549420 None:intergenic 25.0%
!!! ATAATTTCTCAAGCTTTGTT+AGG - chr5.1:70548646-70548665 MS.gene016952:CDS 25.0%
!!! ATGAAACTACATTTGTTGTT+TGG - chr5.1:70548574-70548593 MS.gene016952:CDS 25.0%
!!! TATTTTGAAGCTTGTTGAAT+TGG - chr5.1:70549583-70549602 MS.gene016952:CDS 25.0%
AATTTGAGAAAATGGAACAG+CGG - chr5.1:70549128-70549147 MS.gene016952:intron 30.0%
ACCTCAATTACCAAATGATA+AGG - chr5.1:70549616-70549635 MS.gene016952:CDS 30.0%
ATAGCGTAAGTGTTTAACAA+AGG - chr5.1:70548945-70548964 MS.gene016952:CDS 30.0%
ATCTATTATGTGAAATCCAC+AGG - chr5.1:70549273-70549292 MS.gene016952:intron 30.0%
! AACAAGATGAAAGTATATGC+TGG - chr5.1:70549354-70549373 MS.gene016952:intron 30.0%
! ATTGTTGCTTCTTTGTTCAA+AGG + chr5.1:70549555-70549574 None:intergenic 30.0%
! TCCTTATCATTTGGTAATTG+AGG + chr5.1:70549620-70549639 None:intergenic 30.0%
! TTGTTGCTTCTTTGTTCAAA+GGG + chr5.1:70549554-70549573 None:intergenic 30.0%
! TTTGATTTAGGAGATGGTAA+TGG + chr5.1:70549389-70549408 None:intergenic 30.0%
!! AAACTACATTTGTTGTTTGG+AGG - chr5.1:70548577-70548596 MS.gene016952:CDS 30.0%
!! ATTGTTGTTGATAGTGTTGA+GGG + chr5.1:70549307-70549326 None:intergenic 30.0%
!! TATTGTTGTTGATAGTGTTG+AGG + chr5.1:70549308-70549327 None:intergenic 30.0%
!! TGGTTCAAGAAGTATCAAAA+AGG + chr5.1:70548787-70548806 None:intergenic 30.0%
CACATGTATCAATGTAGTGT+TGG - chr5.1:70549159-70549178 MS.gene016952:intron 35.0%
CTATATCTGATTGCATTCAG+AGG - chr5.1:70548830-70548849 MS.gene016952:CDS 35.0%
CTCTGAATGCAATCAGATAT+AGG + chr5.1:70548832-70548851 None:intergenic 35.0%
TATCTTAACAGCACTTTCTG+AGG - chr5.1:70549415-70549434 MS.gene016952:intron 35.0%
TCCTCTTTGTGGAAAAAAGA+GGG - chr5.1:70549673-70549692 MS.gene016952:CDS 35.0%
TGGTATGTCTTTGTCAAGAA+AGG + chr5.1:70548507-70548526 None:intergenic 35.0%
TTCCTCTTTGTGGAAAAAAG+AGG - chr5.1:70549672-70549691 MS.gene016952:CDS 35.0%
! TCAGTGTTTGATTTAGGAGA+TGG + chr5.1:70549395-70549414 None:intergenic 35.0%
!! TTGTTGTTGATAGTGTTGAG+GGG + chr5.1:70549306-70549325 None:intergenic 35.0%
AGAAGATCTCTAGCAAACTC+AGG + chr5.1:70548606-70548625 None:intergenic 40.0%
AGCTCTTCTGTGAAGCTATT+TGG - chr5.1:70549647-70549666 MS.gene016952:CDS 40.0%
CATCACTCCAAGATACAATG+TGG + chr5.1:70548554-70548573 None:intergenic 40.0%
CTGAGGACAATCAAAGACTA+AGG - chr5.1:70549432-70549451 MS.gene016952:intron 40.0%
GCTGAAAACGGCTTATGAAA+AGG - chr5.1:70549045-70549064 MS.gene016952:intron 40.0%
TCAAGAAGGTTGTTGCTGAT+AGG - chr5.1:70549210-70549229 MS.gene016952:intron 40.0%
TCACTGACCACATTGTATCT+TGG - chr5.1:70548544-70548563 MS.gene016952:CDS 40.0%
TGAGAGGATCATCAACAAGT+TGG + chr5.1:70548527-70548546 None:intergenic 40.0%
!! CTATTTGGTGTTCCTCTTTG+TGG - chr5.1:70549662-70549681 MS.gene016952:CDS 40.0%
!!! ACCCTCTTTTTTCCACAAAG+AGG + chr5.1:70549677-70549696 None:intergenic 40.0%
AGAAGGTTGTTGCTGATAGG+TGG - chr5.1:70549213-70549232 MS.gene016952:intron 45.0%
AGATCTCTAGCAAACTCAGG+AGG + chr5.1:70548603-70548622 None:intergenic 45.0%
CTTCTTGCAGGGTTTCAAGA+AGG - chr5.1:70549196-70549215 MS.gene016952:intron 45.0%
CTTTGTTCAAAGGGTGAAGC+AGG + chr5.1:70549545-70549564 None:intergenic 45.0%
GAAGGTTGTTGCTGATAGGT+GGG - chr5.1:70549214-70549233 MS.gene016952:intron 45.0%
GATACAATGTGGTCAGTGAG+AGG + chr5.1:70548543-70548562 None:intergenic 45.0%
GTCTTTGTCAAGAAAGGAGC+AGG + chr5.1:70548501-70548520 None:intergenic 45.0%
CTGATGCGTGTCTTCTTGCA+GGG - chr5.1:70549185-70549204 MS.gene016952:intron 50.0%
TCTGATGCGTGTCTTCTTGC+AGG - chr5.1:70549184-70549203 MS.gene016952:intron 50.0%
! GTTGAGGGGTTTTTCTCCTG+TGG + chr5.1:70549292-70549311 None:intergenic 50.0%
AGGGTGAAGCAGGACTCACA+TGG + chr5.1:70549535-70549554 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 70548465 70549718 70548465 ID=MS.gene016952
chr5.1 mRNA 70548465 70549718 70548465 ID=MS.gene016952.t1;Parent=MS.gene016952
chr5.1 exon 70549500 70549718 70549500 ID=MS.gene016952.t1.exon1;Parent=MS.gene016952.t1
chr5.1 CDS 70549500 70549718 70549500 ID=cds.MS.gene016952.t1;Parent=MS.gene016952.t1
chr5.1 exon 70548465 70548977 70548465 ID=MS.gene016952.t1.exon2;Parent=MS.gene016952.t1
chr5.1 CDS 70548465 70548977 70548465 ID=cds.MS.gene016952.t1;Parent=MS.gene016952.t1
Gene Sequence

>MS.gene016952

ATGGTGTTCACTATGGAGTCTCAGAAATCAGTGCCTGCTCCTTTCTTGACAAAGACATACCAACTTGTTGATGATCCTCTCACTGACCACATTGTATCTTGGAGTGATGATGAAACTACATTTGTTGTTTGGAGGCCTCCTGAGTTTGCTAGAGATCTTCTTCCCAATTTTTTCAAGCATAATAATTTCTCAAGCTTTGTTAGGCAACTAAATACATATGTGAGAATCTTCAAATTCTAACTTCTATGTTCTCTATATCCTTATTCATTGTTTTAGTAAGTATCTTCTTTAGTTAGTGTAAAAAGGTCTCATAAATTTTCCTTTTTGATACTTCTTGAACCATAAGAATAACTTAAATAACTTACCTATATCTGATTGCATTCAGAGGTTCAGTTCATTATTATAGTTACATGATGGACTATGATAGTAAAACATCATATATTTAGCAACTGTTTGTATGAACAACTTAAGTAAACGATTATAGCGTAAGTGTTTAACAAAGGAGAAAAGAAAATCAAACTATTTTCATATAATTTCTAAACTGTTTTCAGAAGTTATACTAGAGAACTTATGAAAATATGCTGAAAACGGCTTATGAAAAGGTCATAAGTTATTTATGTAAGCTCTTCAAAACAGTTTTGCAAGCTATGAAGCACTGACAATAATTTGAGAAAATGGAACAGCGGAATAAAGTCACATGTATCAATGTAGTGTTGGTGTCTGATGCGTGTCTTCTTGCAGGGTTTCAAGAAGGTTGTTGCTGATAGGTGGGAGTTTGCAAATGATTACTTCAAAAAAGGAGCTAAGCATCTATTATGTGAAATCCACAGGAGAAAAACCCCTCAACACTATCAACAACAATACTATGAACAATCACCACAAATTTTTCAACAAGATGAAAGTATATGCTGGATTGATTCTCCATTACCATCTCCTAAATCAAACACTGATATCTTAACAGCACTTTCTGAGGACAATCAAAGACTAAGGAGAAAGAATTTCATGCTGTTATCAGAACTCAGTCACATGAAGAATCTTTACAATGATATTATATATTTCATTCAAAACCATGTGAGTCCTGCTTCACCCTTTGAACAAAGAAGCAACAATAGTGCTGCTATTTTGAAGCTTGTTGAATTGGATTCATCATCACCTCAATTACCAAATGATAAGGATTGTAATAGCTCTTCTGTGAAGCTATTTGGTGTTCCTCTTTGTGGAAAAAAGAGGGTTCATCCTAGTAATCTTGATTAA
Protein sequence

>MS.gene016952.t1

MVFTMESQKSVPAPFLTKTYQLVDDPLTDHIVSWSDDETTFVVWRPPEFARDLLPNFFKHNNFSSFVRQLNTYGFKKVVADRWEFANDYFKKGAKHLLCEIHRRKTPQHYQQQYYEQSPQIFQQDESICWIDSPLPSPKSNTDILTALSEDNQRLRRKNFMLLSELSHMKNLYNDIIYFIQNHVSPASPFEQRSNNSAAILKLVELDSSSPQLPNDKDCNSSSVKLFGVPLCGKKRVHPSNLD