AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene001968

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001968.t1 MTR_7g089080 94.737 133 5 1 25 157 170 300 8.65e-81 260
MS.gene001968.t1 MTR_5g088980 64.179 134 43 3 25 157 137 266 1.81e-54 178
MS.gene001968.t1 MTR_8g074000 54.167 120 54 1 37 156 159 277 5.58e-38 135
MS.gene001968.t1 MTR_5g023790 52.500 120 56 1 37 156 155 273 2.78e-36 129
MS.gene001968.t1 MTR_5g023790 52.500 120 56 1 37 156 155 273 2.96e-36 129
MS.gene001968.t1 MTR_5g023790 52.500 120 56 1 37 156 155 273 4.33e-36 130
MS.gene001968.t1 MTR_1g018680 47.619 105 53 2 54 156 91 195 7.12e-29 109
MS.gene001968.t1 MTR_3g102520 44.882 127 66 4 32 156 71 195 5.32e-28 107
MS.gene001968.t1 MTR_1g011470 48.760 121 57 4 37 155 145 262 7.57e-28 107
MS.gene001968.t1 MTR_3g088415 45.238 126 64 4 33 156 220 342 1.59e-27 107
MS.gene001968.t1 MTR_3g088415 45.238 126 64 4 33 156 220 342 1.90e-27 106
MS.gene001968.t1 MTR_3g088415 45.238 126 64 4 33 156 220 342 2.53e-27 107
MS.gene001968.t1 MTR_3g107970 45.082 122 62 4 37 156 197 315 3.78e-27 106
MS.gene001968.t1 MTR_5g044040 93.878 49 3 0 109 157 7 55 2.69e-26 97.4
MS.gene001968.t1 MTR_3g102530 46.667 105 54 2 54 156 84 188 1.24e-25 100
MS.gene001968.t1 MTR_2g102520 40.800 125 73 1 32 156 194 317 1.58e-24 99.4
MS.gene001968.t1 MTR_3g088405 38.760 129 74 4 30 156 220 345 2.35e-23 95.9
MS.gene001968.t1 MTR_3g102510 45.714 105 53 3 54 156 74 176 7.27e-23 93.2
MS.gene001968.t1 MTR_5g011900 36.735 147 87 3 11 157 32 172 1.93e-22 90.5
MS.gene001968.t1 MTR_2g102550 43.511 131 67 5 30 156 142 269 3.37e-22 92.4
MS.gene001968.t1 MTR_3g102560 45.455 99 52 2 59 155 69 167 6.05e-22 90.5
MS.gene001968.t1 MTR_3g102540 41.414 99 56 2 58 154 13 111 1.09e-18 81.3
MS.gene001968.t1 MTR_3g060770 42.268 97 48 2 53 146 31 122 4.50e-18 79.7
MS.gene001968.t1 MTR_2g005960 33.588 131 69 3 33 147 100 228 2.87e-17 76.6
MS.gene001968.t1 MTR_3g061680 36.937 111 62 2 47 154 15 120 5.72e-16 73.9
MS.gene001968.t1 MTR_3g060820 36.735 98 54 2 52 146 20 112 3.27e-15 71.6
MS.gene001968.t1 MTR_3g060400 36.082 97 54 2 53 146 27 118 3.88e-15 71.6
MS.gene001968.t1 MTR_3g460990 36.082 97 54 2 53 146 27 118 3.88e-15 71.6
MS.gene001968.t1 MTR_3g060410 41.176 68 37 1 82 146 130 197 9.15e-12 62.8
MS.gene001968.t1 MTR_6g045270 37.383 107 59 3 53 156 45 146 9.70e-12 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.gene001968.t1 AT2G26760 67.669 133 38 2 25 157 104 231 1.95e-57 184
MS.gene001968.t1 AT5G06150 64.394 132 44 2 25 156 154 282 1.70e-55 178
MS.gene001968.t1 AT4G37490 65.414 133 43 2 25 156 135 265 2.02e-55 181
MS.gene001968.t1 AT5G06150 64.394 132 44 2 25 156 154 282 2.41e-54 178
MS.gene001968.t1 AT3G11520 67.769 121 37 1 36 156 141 259 9.80e-53 172
MS.gene001968.t1 AT3G11520 67.769 121 37 1 36 156 141 259 1.34e-52 173
MS.gene001968.t1 AT1G20610 57.500 120 50 1 37 156 160 278 2.98e-42 146
MS.gene001968.t1 AT1G76310 57.258 124 45 3 37 156 160 279 6.49e-41 140
MS.gene001968.t1 AT1G76310 57.258 124 45 3 37 156 160 279 1.86e-40 140
MS.gene001968.t1 AT1G76310 57.258 124 45 3 37 156 160 279 3.34e-40 140
MS.gene001968.t1 AT1G76310 57.258 124 45 3 37 156 160 279 4.67e-40 141
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 244 348 6.48e-36 130
MS.gene001968.t1 AT1G34460 56.140 114 47 2 19 132 235 345 7.08e-36 130
MS.gene001968.t1 AT1G34460 56.140 114 47 2 19 132 235 345 7.08e-36 130
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 230 334 7.78e-36 130
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 244 348 9.04e-36 130
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 244 348 9.04e-36 130
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 244 348 9.04e-36 130
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 244 348 9.04e-36 130
MS.gene001968.t1 AT1G34460 58.333 108 42 2 25 132 244 348 9.85e-36 130
MS.gene001968.t1 AT1G16330 42.969 128 70 2 29 156 372 496 6.24e-32 120
MS.gene001968.t1 AT1G47210 47.059 119 60 3 39 155 88 205 1.80e-31 117
MS.gene001968.t1 AT1G44110 45.528 123 62 4 36 156 177 296 4.10e-31 117
MS.gene001968.t1 AT4G35620 53.333 120 55 1 37 156 155 273 1.19e-29 112
MS.gene001968.t1 AT4G35620 53.333 120 55 1 37 156 155 273 1.36e-29 112
MS.gene001968.t1 AT1G80370 44.776 134 70 4 24 156 169 299 1.94e-29 112
MS.gene001968.t1 AT2G17620 54.167 120 54 1 37 156 154 272 5.19e-29 111
MS.gene001968.t1 AT1G77390 46.341 123 61 4 36 156 161 280 6.41e-29 110
MS.gene001968.t1 AT1G47220 45.833 120 62 3 39 156 42 160 7.75e-28 106
MS.gene001968.t1 AT1G47230 49.524 105 51 2 54 156 95 199 4.69e-27 105
MS.gene001968.t1 AT5G25380 45.902 122 61 4 36 155 156 274 4.96e-27 105
MS.gene001968.t1 AT5G25380 45.902 122 61 4 36 155 162 280 5.07e-27 105
MS.gene001968.t1 AT5G25380 45.902 122 61 4 36 155 156 274 5.23e-27 105
MS.gene001968.t1 AT5G25380 45.902 122 61 4 36 155 156 274 5.23e-27 105
MS.gene001968.t1 AT5G11300 45.528 123 62 4 36 156 155 274 2.81e-26 103
MS.gene001968.t1 AT5G11300 45.528 123 62 4 36 156 155 274 4.04e-26 103
MS.gene001968.t1 AT5G43080 41.667 120 65 4 39 156 73 189 5.95e-26 101
MS.gene001968.t1 AT5G43080 41.667 120 65 4 39 156 73 189 6.28e-26 101
MS.gene001968.t1 AT1G47230 49.057 106 51 3 54 156 95 200 2.54e-25 100
MS.gene001968.t1 AT1G47210 43.396 106 57 3 39 142 88 192 1.87e-24 94.7
MS.gene001968.t1 AT1G15570 41.803 122 68 3 36 156 171 290 5.55e-24 97.4

Find 45 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGTGAGATAAAGGGTTTC+AGG 0.206490 6.2:+40337835 None:intergenic
CTATGTTGATTGTGAGATAA+AGG 0.290156 6.2:+40337827 None:intergenic
CTCATCCTCTCATTTATCTC+AGG 0.404632 6.2:+40337910 None:intergenic
TCAATGTCAACAATCTCCTT+TGG 0.409201 6.2:+40338277 None:intergenic
TATGTTGATTGTGAGATAAA+GGG 0.409760 6.2:+40337828 None:intergenic
TGGAATCAGTGCCATGCTTA+TGG 0.410047 6.2:-40337752 MS.gene001968:CDS
GCTCCTCCGGTTGTTGCTGA+TGG 0.416872 6.2:-40338600 MS.gene001968:CDS
CATCAAAGTATGAAGAAATC+TGG 0.422694 6.2:-40337729 MS.gene001968:CDS
GGCACCTGGACCTGCTCCTC+CGG 0.428152 6.2:-40338613 MS.gene001968:CDS
GTCAAGAAGGGAACTTCAAT+TGG 0.435390 6.2:-40337776 MS.gene001968:CDS
TCACAATCAACATAGTTGAT+AGG 0.445143 6.2:-40337819 MS.gene001968:CDS
AGAAGGGAACTTCAATTGGT+TGG 0.459265 6.2:-40337772 MS.gene001968:CDS
AGGAATACTCATTGATTGGC+TGG 0.482890 6.2:-40337887 MS.gene001968:CDS
CTGTCAACCTTGTGTCAAGA+AGG 0.491215 6.2:-40337789 MS.gene001968:CDS
TGAGAGGAATACTCATTGAT+TGG 0.498998 6.2:-40337891 MS.gene001968:CDS
ATCATGGAGAAAACCATCCT+AGG 0.509664 6.2:-40337644 None:intergenic
CCACTCAAGCTTCCCTAGGA+TGG 0.512212 6.2:+40337631 None:intergenic
GCAACTCCATCAGCAACAAC+CGG 0.514095 6.2:+40338594 None:intergenic
TCAGCAACAACCGGAGGAGC+AGG 0.519886 6.2:+40338603 None:intergenic
ACAACCGGAGGAGCAGGTCC+AGG 0.525564 6.2:+40338609 None:intergenic
TCATGAACAGATTCTCATCA+TGG 0.547054 6.2:-40337660 MS.gene001968:CDS
TTGACACAAGGTTGACAGCA+AGG 0.554809 6.2:+40337794 None:intergenic
TCATGGAGAAAACCATCCTA+GGG 0.567407 6.2:-40337643 None:intergenic
GCTTGTGTCAATGTGGCACC+TGG 0.568366 6.2:-40338627 None:intergenic
GAGATTGTTGACATTGATGC+TGG 0.574052 6.2:-40338271 MS.gene001968:CDS
CACACAAAGTCATTGACCTC+AGG 0.575877 6.2:+40337703 None:intergenic
AAGCCGTCCACATGATTACA+TGG 0.589639 6.2:-40337941 MS.gene001968:CDS
GAAGTTCCCTTCTTGACACA+AGG 0.595803 6.2:+40337782 None:intergenic
ATACTTTGATGCCATAAGCA+TGG 0.602617 6.2:+40337741 None:intergenic
GAGATAAATGAGAGGATGAG+AGG 0.614173 6.2:-40337907 MS.gene001968:CDS
ACAAAGTCATTGACCTCAGG+TGG 0.615435 6.2:+40337706 None:intergenic
ATGACTGTAAGCTCTATCTG+AGG 0.617761 6.2:+40337679 None:intergenic
TGCTGATGGAGTTGCAGCGG+TGG 0.619658 6.2:-40338586 MS.gene001968:CDS
TGCAGCGGTGGCTAGAAGAG+TGG 0.636261 6.2:-40338574 MS.gene001968:CDS
TGTCAACCTTGTGTCAAGAA+GGG 0.639776 6.2:-40337788 MS.gene001968:CDS
TGACTGTAAGCTCTATCTGA+GGG 0.647144 6.2:+40337680 None:intergenic
TGTTGCTGATGGAGTTGCAG+CGG 0.659533 6.2:-40338589 MS.gene001968:CDS
CACAACCTGAGATAAATGAG+AGG 0.662919 6.2:-40337915 MS.gene001968:CDS
TGAAGAAATCTGGCCACCTG+AGG 0.663492 6.2:-40337719 MS.gene001968:CDS
TGGTTTGACTAACAAACCAA+AGG 0.666669 6.2:-40338293 MS.gene001968:CDS
AGCGGTGGCTAGAAGAGTGG+TGG 0.668282 6.2:-40338571 MS.gene001968:CDS
AGTCCATGTAATCATGTGGA+CGG 0.674217 6.2:+40337938 None:intergenic
TGTGAGTCCATGTAATCATG+TGG 0.686546 6.2:+40337934 None:intergenic
ACTCCATCAGCAACAACCGG+AGG 0.701597 6.2:+40338597 None:intergenic
CAAGTTCTACAAGATAGTTG+AGG 0.706527 6.2:-40338200 MS.gene001968:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTCTTTTATGTTCTTTT+AGG - chr6.2:40337939-40337958 MS.gene001968:CDS 20.0%
!! TATGTTGATTGTGAGATAAA+GGG + chr6.2:40338437-40338456 None:intergenic 25.0%
!!! CTTGTGTATGTGTTTTTTTT+TGG - chr6.2:40338164-40338183 MS.gene001968:intron 25.0%
CATCAAAGTATGAAGAAATC+TGG - chr6.2:40338533-40338552 MS.gene001968:intron 30.0%
TCACAATCAACATAGTTGAT+AGG - chr6.2:40338443-40338462 MS.gene001968:intron 30.0%
! AAAGAAGCATGTTATGTTGT+TGG - chr6.2:40337879-40337898 MS.gene001968:CDS 30.0%
! CTATGTTGATTGTGAGATAA+AGG + chr6.2:40338438-40338457 None:intergenic 30.0%
ATACTTTGATGCCATAAGCA+TGG + chr6.2:40338524-40338543 None:intergenic 35.0%
ATTGTGAGATAAAGGGTTTC+AGG + chr6.2:40338430-40338449 None:intergenic 35.0%
CAAGTTCTACAAGATAGTTG+AGG - chr6.2:40338062-40338081 MS.gene001968:intron 35.0%
GAAATCTGTGCACAAGAAAA+AGG - chr6.2:40337762-40337781 MS.gene001968:CDS 35.0%
TCAATGTCAACAATCTCCTT+TGG + chr6.2:40337988-40338007 None:intergenic 35.0%
TCATGAACAGATTCTCATCA+TGG - chr6.2:40338602-40338621 MS.gene001968:CDS 35.0%
TGAAGTAAGTTCTGCAGAAA+AGG - chr6.2:40337729-40337748 MS.gene001968:CDS 35.0%
TGAGAGGAATACTCATTGAT+TGG - chr6.2:40338371-40338390 MS.gene001968:intron 35.0%
TGGTTTGACTAACAAACCAA+AGG - chr6.2:40337969-40337988 MS.gene001968:intron 35.0%
!!! ATGTTCTTTTAGGTTGCATG+TGG - chr6.2:40337949-40337968 MS.gene001968:CDS 35.0%
ACATGCTTGTGTATGTGTTG+AGG - chr6.2:40338189-40338208 MS.gene001968:intron 40.0%
AGAAGGGAACTTCAATTGGT+TGG - chr6.2:40338490-40338509 MS.gene001968:intron 40.0%
AGTCCATGTAATCATGTGGA+CGG + chr6.2:40338327-40338346 None:intergenic 40.0%
ATGACTGTAAGCTCTATCTG+AGG + chr6.2:40338586-40338605 None:intergenic 40.0%
CACAACCTGAGATAAATGAG+AGG - chr6.2:40338347-40338366 MS.gene001968:intron 40.0%
CTCATCCTCTCATTTATCTC+AGG + chr6.2:40338355-40338374 None:intergenic 40.0%
GAGATAAATGAGAGGATGAG+AGG - chr6.2:40338355-40338374 MS.gene001968:intron 40.0%
GAGATTGTTGACATTGATGC+TGG - chr6.2:40337991-40338010 MS.gene001968:intron 40.0%
GTCAAGAAGGGAACTTCAAT+TGG - chr6.2:40338486-40338505 MS.gene001968:intron 40.0%
TGACTGTAAGCTCTATCTGA+GGG + chr6.2:40338585-40338604 None:intergenic 40.0%
TGTCAACCTTGTGTCAAGAA+GGG - chr6.2:40338474-40338493 MS.gene001968:intron 40.0%
TGTGAGTCCATGTAATCATG+TGG + chr6.2:40338331-40338350 None:intergenic 40.0%
! AGGAATACTCATTGATTGGC+TGG - chr6.2:40338375-40338394 MS.gene001968:intron 40.0%
AAACCTTGCTTCTAGCAGTG+AGG + chr6.2:40337829-40337848 None:intergenic 45.0%
AAGCCGTCCACATGATTACA+TGG - chr6.2:40338321-40338340 MS.gene001968:intron 45.0%
ACAAAGTCATTGACCTCAGG+TGG + chr6.2:40338559-40338578 None:intergenic 45.0%
AGTGCGTGATGGTTTCTTCT+TGG + chr6.2:40337795-40337814 None:intergenic 45.0%
CACACAAAGTCATTGACCTC+AGG + chr6.2:40338562-40338581 None:intergenic 45.0%
CTGTCAACCTTGTGTCAAGA+AGG - chr6.2:40338473-40338492 MS.gene001968:intron 45.0%
GAAGTTCCCTTCTTGACACA+AGG + chr6.2:40338483-40338502 None:intergenic 45.0%
TGGAATCAGTGCCATGCTTA+TGG - chr6.2:40338510-40338529 MS.gene001968:intron 45.0%
TTGACACAAGGTTGACAGCA+AGG + chr6.2:40338471-40338490 None:intergenic 45.0%
! ACAGAAGAAAGAGTGCGTGA+TGG + chr6.2:40337806-40337825 None:intergenic 45.0%
GCAACTCCATCAGCAACAAC+CGG + chr6.2:40337671-40337690 None:intergenic 50.0%
TGAAGAAATCTGGCCACCTG+AGG - chr6.2:40338543-40338562 MS.gene001968:intron 50.0%
TGTCCTCACTGCTAGAAGCA+AGG - chr6.2:40337823-40337842 MS.gene001968:CDS 50.0%
TGTTGCTGATGGAGTTGCAG+CGG - chr6.2:40337673-40337692 MS.gene001968:CDS 50.0%
ACTCCATCAGCAACAACCGG+AGG + chr6.2:40337668-40337687 None:intergenic 55.0%
AGCGGTGGCTAGAAGAGTGG+TGG - chr6.2:40337691-40337710 MS.gene001968:CDS 60.0%
GCTCCTCCGGTTGTTGCTGA+TGG - chr6.2:40337662-40337681 MS.gene001968:CDS 60.0%
TCAGCAACAACCGGAGGAGC+AGG + chr6.2:40337662-40337681 None:intergenic 60.0%
TGCAGCGGTGGCTAGAAGAG+TGG - chr6.2:40337688-40337707 MS.gene001968:CDS 60.0%
TGCTGATGGAGTTGCAGCGG+TGG - chr6.2:40337676-40337695 MS.gene001968:CDS 60.0%
ACAACCGGAGGAGCAGGTCC+AGG + chr6.2:40337656-40337675 None:intergenic 65.0%
GGCACCTGGACCTGCTCCTC+CGG - chr6.2:40337649-40337668 MS.gene001968:CDS 70.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 40337645 40338639 40337645 ID=MS.gene001968
chr6.2 mRNA 40337645 40338639 40337645 ID=MS.gene001968.t1;Parent=MS.gene001968
chr6.2 exon 40338565 40338639 40338565 ID=MS.gene001968.t1.exon1;Parent=MS.gene001968.t1
chr6.2 CDS 40338565 40338639 40338565 ID=cds.MS.gene001968.t1;Parent=MS.gene001968.t1
chr6.2 exon 40338201 40338323 40338201 ID=MS.gene001968.t1.exon2;Parent=MS.gene001968.t1
chr6.2 CDS 40338201 40338323 40338201 ID=cds.MS.gene001968.t1;Parent=MS.gene001968.t1
chr6.2 exon 40337645 40337974 40337645 ID=MS.gene001968.t1.exon3;Parent=MS.gene001968.t1
chr6.2 CDS 40337645 40337974 40337645 ID=cds.MS.gene001968.t1;Parent=MS.gene001968.t1
Gene Sequence

>MS.gene001968

ATGTGGCACCTGGACCTGCTCCTCCGGTTGTTGCTGATGGAGTTGCAGCGGTGGCTAGAAGAGTGGTGGATTGAAGTAAGTTATTGAAGTAAGTTCTGCAGAAAAGGACATTGAAGAGAAATCTGTGCACAAGAAAAAGGAAGAAGTCCAAGAAGAAACCATCACGCACTCTTTCTTCTGTCCTCACTGCTAGAAGCAAGGTTTGTTAGTTATGTTGTTAAGAATAAATTAAACAAAGAAGCATGTTATGTTGTTGGATTGAATTCTCTTTTACGTGTTCTTTTGTTTGTTTACATGTTCTTTTATGTTCTTTTAGGTTGCATGTGGTTTGACTAACAAACCAAAGGAGATTGTTGACATTGATGCTGGTGATGCTAACAATGAGTTAGTTGCTGTTGAATATCTTGAAGACATATACAAGTTCTACAAGATAGTTGAGGTAACAATAACAAACATGACTTTAATTTACTTTTCATTCTATATATTTTTGTTTTGTGTCTGATGTATTGTTCTTTATTGCTTGTGTATGTGTTTTTTTTTGGTTACATGCTTGTGTATGTGTTGAGGCAACAATAACAAACATGACTTTAATTTACTTTTCATTCTATATGTTTTAGTTTTGTGTCTGATGTATTGTTCTTTATTGCTTGTGTATGTGTTGAAAGATTCAGAATGAAAGCCGTCCACATGATTACATGGACTCACAACCTGAGATAAATGAGAGGATGAGAGGAATACTCATTGATTGGCTGGTAGATGTTCACTCAAAATTTAAACTTTCACCTGAAACCCTTTATCTCACAATCAACATAGTTGATAGGTTCCTTGCTGTCAACCTTGTGTCAAGAAGGGAACTTCAATTGGTTGGAATCAGTGCCATGCTTATGGCATCAAAGTATGAAGAAATCTGGCCACCTGAGGTCAATGACTTTGTGTGCCCTCAGATAGAGCTTACAGTCATGAACAGATTCTCATCATGGAGAAAACCATCCTAG
Protein sequence

>MS.gene001968.t1

MWHLDLLLRLLLMELQRWLEEWWIEVACGLTNKPKEIVDIDAGDANNELVAVEYLEDIYKFYKIVEIQNESRPHDYMDSQPEINERMRGILIDWLVDVHSKFKLSPETLYLTINIVDRFLAVNLVSRRELQLVGISAMLMASKYEEIWPPEVNDFVCPQIELTVMNRFSSWRKPS