AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20318

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20318.t1 MTR_5g015090 95.541 157 7 0 1 157 1 157 5.26e-109 307
MS.gene20318.t1 MTR_4g097440 55.747 174 60 6 1 157 1 174 4.83e-54 169
MS.gene20318.t1 MTR_3g103360 38.346 133 70 2 7 136 8 131 1.56e-17 74.7
MS.gene20318.t1 MTR_1g017570 63.636 66 24 0 60 125 59 124 6.28e-16 70.5
MS.gene20318.t1 MTR_7g029400 41.667 96 49 1 58 153 81 169 3.18e-15 69.7
MS.gene20318.t1 MTR_4g070860 44.444 81 45 0 58 138 27 107 8.06e-15 67.8
MS.gene20318.t1 MTR_8g015250 40.625 96 50 1 58 153 71 159 2.98e-14 67.0
MS.gene20318.t1 MTR_8g086020 34.545 110 65 2 28 136 7 110 1.42e-13 64.7
MS.gene20318.t1 MTR_3g117120 38.542 96 51 1 58 145 27 122 8.36e-13 62.8
MS.gene20318.t1 MTR_1g022495 38.095 105 61 1 36 136 1 105 1.98e-12 61.6
MS.gene20318.t1 MTR_1g087040 36.667 90 42 2 36 125 8 82 9.84e-12 59.7
MS.gene20318.t1 MTR_6g016375 46.753 77 41 0 60 136 89 165 3.55e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20318.t1 AT3G49760 41.727 139 80 1 5 142 15 153 8.73e-32 111
MS.gene20318.t1 AT4G37730 41.304 138 73 2 7 136 135 272 2.47e-20 85.5
MS.gene20318.t1 AT2G22850 48.235 85 44 0 59 143 127 211 6.35e-19 80.5
MS.gene20318.t1 AT2G22850 48.235 85 44 0 59 143 127 211 6.35e-19 80.5
MS.gene20318.t1 AT3G30530 38.255 149 86 3 1 146 18 163 8.14e-16 70.9
MS.gene20318.t1 AT1G75390 38.333 120 73 1 31 149 10 129 2.34e-15 69.7
MS.gene20318.t1 AT1G75390 42.708 96 54 1 31 125 10 105 1.21e-14 66.6
MS.gene20318.t1 AT2G18160 39.130 92 49 1 52 136 15 106 1.91e-13 64.7
MS.gene20318.t1 AT4G34590 41.176 85 50 0 58 142 24 108 7.67e-13 62.8
MS.gene20318.t1 AT1G13600 49.367 79 40 0 58 136 83 161 2.27e-12 62.4
MS.gene20318.t1 AT5G38800 41.818 110 54 3 38 146 56 156 2.52e-12 61.6
MS.gene20318.t1 AT4G36730 34.513 113 55 2 48 141 192 304 3.14e-12 63.2
MS.gene20318.t1 AT4G36730 34.513 113 55 2 48 141 194 306 3.24e-12 63.2
MS.gene20318.t1 AT2G04038 43.750 96 49 1 36 131 54 144 5.17e-12 60.8
MS.gene20318.t1 AT5G15830 45.570 79 43 0 58 136 71 149 1.84e-11 59.7

Find 53 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGACATCTAGAGAATTTA+CGG 0.286559 5.1:-7765358 MS.gene20318:CDS
GTCAAACATAGGTCAAAATA+TGG 0.308208 5.1:-7765201 MS.gene20318:CDS
GGATGGCTCGAACCGGAATA+TGG 0.309967 5.1:-7765447 MS.gene20318:CDS
ATATCATTCTCCTCCGCTTT+CGG 0.329484 5.1:+7765420 None:intergenic
GCAACCCGTTGTTCAATTCC+CGG 0.358900 5.1:+7765306 None:intergenic
CCTCTATGCCTCTGATTTCA+CGG 0.361395 5.1:-7765588 MS.gene20318:CDS
GTGACCTCCGTGCCGATTCC+CGG 0.363167 5.1:+7765393 None:intergenic
GCTTTCGGTCCTCCATATTC+CGG 0.399400 5.1:+7765435 None:intergenic
CTTAGGGCTGGTGGATTGGA+AGG 0.405550 5.1:+7765517 None:intergenic
ACCGGTTTAGAGTTGAAAAC+CGG 0.409929 5.1:-7765325 MS.gene20318:CDS
CCGGTTGGAACGAACCATGC+TGG 0.411515 5.1:-7765234 MS.gene20318:CDS
CCAGAGCTTGAAGTGAGCTT+AGG 0.420132 5.1:+7765500 None:intergenic
CTCACTTCAAGCTCTGGTTC+AGG 0.435261 5.1:-7765494 MS.gene20318:CDS
TGAGCTTAGGGCTGGTGGAT+TGG 0.452930 5.1:+7765513 None:intergenic
AAAACCGGGAATTGAACAAC+GGG 0.452979 5.1:-7765310 MS.gene20318:CDS
ATTTACGGAACCAGGTGAAC+CGG 0.455271 5.1:-7765343 MS.gene20318:CDS
CCAGCATGGTTCGTTCCAAC+CGG 0.461195 5.1:+7765234 None:intergenic
CAACTCTAAACCGGTTCACC+TGG 0.478647 5.1:+7765333 None:intergenic
CAGAGCTTGAAGTGAGCTTA+GGG 0.481961 5.1:+7765501 None:intergenic
CCTAAGCTCACTTCAAGCTC+TGG 0.485944 5.1:-7765500 MS.gene20318:CDS
CGGTCATGGATGGCTCGAAC+CGG 0.489104 5.1:-7765454 MS.gene20318:CDS
CGGTTCGAGCCATCCATGAC+CGG 0.490515 5.1:+7765455 None:intergenic
TTCAACCTTTCTCATCTGCA+TGG 0.491200 5.1:-7765175 MS.gene20318:CDS
GGAGGAGAATGATATCAAAC+CGG 0.491685 5.1:-7765412 MS.gene20318:CDS
AATGATATCAAACCGGGAAT+CGG 0.493933 5.1:-7765405 MS.gene20318:CDS
GGCATAGAGGGAAGAGAGCA+TGG 0.513902 5.1:+7765601 None:intergenic
TGAAGTGAGCTTAGGGCTGG+TGG 0.522392 5.1:+7765508 None:intergenic
CGGTTGGAACGAACCATGCT+GGG 0.526524 5.1:-7765233 MS.gene20318:CDS
GAACCGAAAATGAGTGGCTC+CGG 0.546667 5.1:-7765253 MS.gene20318:CDS
CCGTGAAATCAGAGGCATAG+AGG 0.553569 5.1:+7765588 None:intergenic
CGTGAAATCAGAGGCATAGA+GGG 0.563127 5.1:+7765589 None:intergenic
CGAAAATGAGTGGCTCCGGT+TGG 0.563412 5.1:-7765249 MS.gene20318:CDS
GCTTGAAGTGAGCTTAGGGC+TGG 0.566940 5.1:+7765505 None:intergenic
CATGGCCATGCAGATGAGAA+AGG 0.571565 5.1:+7765170 None:intergenic
CCGGTTTAGAGTTGAAAACC+GGG 0.582456 5.1:-7765324 MS.gene20318:CDS
TCTAGAGAATTTACGGAACC+AGG 0.588686 5.1:-7765351 MS.gene20318:CDS
GTCTAACGCCGTGAAATCAG+AGG 0.590668 5.1:+7765580 None:intergenic
TATCAAACCGGGAATCGGCA+CGG 0.599707 5.1:-7765400 MS.gene20318:CDS
GGTCAAAAGTTGTCAAACAT+AGG 0.610074 5.1:-7765212 MS.gene20318:CDS
GGAATATGGAGGACCGAAAG+CGG 0.611264 5.1:-7765433 MS.gene20318:CDS
GAATGTTAGAAATATCCCAC+GGG 0.613842 5.1:+7765546 None:intergenic
GAGGAGAATGATATCAAACC+GGG 0.616694 5.1:-7765411 MS.gene20318:CDS
AGACGAAAGTTTAACCCCGT+GGG 0.627155 5.1:-7765561 MS.gene20318:CDS
TTAGGGCTGGTGGATTGGAA+GGG 0.629980 5.1:+7765518 None:intergenic
TCAGCTGTGACAATATTGCA+TGG 0.636378 5.1:+7765152 None:intergenic
TAGACGAAAGTTTAACCCCG+TGG 0.639794 5.1:-7765562 MS.gene20318:CDS
AGAATGTTAGAAATATCCCA+CGG 0.649981 5.1:+7765545 None:intergenic
GAAAACCGGGAATTGAACAA+CGG 0.656607 5.1:-7765311 MS.gene20318:CDS
GCCTACGAACCGAAAATGAG+TGG 0.658730 5.1:-7765259 MS.gene20318:CDS
ATATGGAGGACCGAAAGCGG+AGG 0.670255 5.1:-7765430 MS.gene20318:CDS
TGGCTCGAACCGGAATATGG+AGG 0.676236 5.1:-7765444 MS.gene20318:CDS
CAAACCGGGAATCGGCACGG+AGG 0.765542 5.1:-7765397 MS.gene20318:CDS
AATGTTAGAAATATCCCACG+GGG 0.803619 5.1:+7765547 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGACATCTAGAGAATTTA+CGG - chr5.1:7765389-7765408 MS.gene20318:CDS 25.0%
AGAATGTTAGAAATATCCCA+CGG + chr5.1:7765205-7765224 None:intergenic 30.0%
GTCAAACATAGGTCAAAATA+TGG - chr5.1:7765546-7765565 MS.gene20318:CDS 30.0%
AATGATATCAAACCGGGAAT+CGG - chr5.1:7765342-7765361 MS.gene20318:CDS 35.0%
AATGTTAGAAATATCCCACG+GGG + chr5.1:7765203-7765222 None:intergenic 35.0%
GAATGTTAGAAATATCCCAC+GGG + chr5.1:7765204-7765223 None:intergenic 35.0%
GGTCAAAAGTTGTCAAACAT+AGG - chr5.1:7765535-7765554 MS.gene20318:CDS 35.0%
AAAACCGGGAATTGAACAAC+GGG - chr5.1:7765437-7765456 MS.gene20318:CDS 40.0%
ATATCATTCTCCTCCGCTTT+CGG + chr5.1:7765330-7765349 None:intergenic 40.0%
GAAAACCGGGAATTGAACAA+CGG - chr5.1:7765436-7765455 MS.gene20318:CDS 40.0%
GAGGAGAATGATATCAAACC+GGG - chr5.1:7765336-7765355 MS.gene20318:CDS 40.0%
GGAGGAGAATGATATCAAAC+CGG - chr5.1:7765335-7765354 MS.gene20318:CDS 40.0%
TCAGCTGTGACAATATTGCA+TGG + chr5.1:7765598-7765617 None:intergenic 40.0%
TCTAGAGAATTTACGGAACC+AGG - chr5.1:7765396-7765415 MS.gene20318:CDS 40.0%
TTCAACCTTTCTCATCTGCA+TGG - chr5.1:7765572-7765591 MS.gene20318:CDS 40.0%
! ACCGGTTTAGAGTTGAAAAC+CGG - chr5.1:7765422-7765441 MS.gene20318:CDS 40.0%
AACGAAAAACCGGTCATGGA+TGG - chr5.1:7765283-7765302 MS.gene20318:CDS 45.0%
ACCAAACGAAAAACCGGTCA+TGG - chr5.1:7765279-7765298 MS.gene20318:CDS 45.0%
AGACGAAAGTTTAACCCCGT+GGG - chr5.1:7765186-7765205 MS.gene20318:CDS 45.0%
AGGCGAACCAAACGAAAAAC+CGG - chr5.1:7765273-7765292 MS.gene20318:CDS 45.0%
ATTTACGGAACCAGGTGAAC+CGG - chr5.1:7765404-7765423 MS.gene20318:CDS 45.0%
CAGAGCTTGAAGTGAGCTTA+GGG + chr5.1:7765249-7765268 None:intergenic 45.0%
CCTCTATGCCTCTGATTTCA+CGG - chr5.1:7765159-7765178 MS.gene20318:CDS 45.0%
TAGACGAAAGTTTAACCCCG+TGG - chr5.1:7765185-7765204 MS.gene20318:CDS 45.0%
! CCCGGTTTTCAACTCTAAAC+CGG + chr5.1:7765426-7765445 None:intergenic 45.0%
! CCGGTTTAGAGTTGAAAACC+GGG - chr5.1:7765423-7765442 MS.gene20318:CDS 45.0%
! CGTGAAATCAGAGGCATAGA+GGG + chr5.1:7765161-7765180 None:intergenic 45.0%
! TGACAACTTTTGACCCAGCA+TGG + chr5.1:7765530-7765549 None:intergenic 45.0%
!! TCCATGACCGGTTTTTCGTT+TGG + chr5.1:7765283-7765302 None:intergenic 45.0%
CATGGCCATGCAGATGAGAA+AGG + chr5.1:7765580-7765599 None:intergenic 50.0%
CCAGAGCTTGAAGTGAGCTT+AGG + chr5.1:7765250-7765269 None:intergenic 50.0%
CCTAAGCTCACTTCAAGCTC+TGG - chr5.1:7765247-7765266 MS.gene20318:CDS 50.0%
GAACCGAAAATGAGTGGCTC+CGG - chr5.1:7765494-7765513 MS.gene20318:CDS 50.0%
GCAACCCGTTGTTCAATTCC+CGG + chr5.1:7765444-7765463 None:intergenic 50.0%
GCCTACGAACCGAAAATGAG+TGG - chr5.1:7765488-7765507 MS.gene20318:CDS 50.0%
GCTTTCGGTCCTCCATATTC+CGG + chr5.1:7765315-7765334 None:intergenic 50.0%
GGAATATGGAGGACCGAAAG+CGG - chr5.1:7765314-7765333 MS.gene20318:CDS 50.0%
GTCTAACGCCGTGAAATCAG+AGG + chr5.1:7765170-7765189 None:intergenic 50.0%
TATCAAACCGGGAATCGGCA+CGG - chr5.1:7765347-7765366 MS.gene20318:CDS 50.0%
! CAACCGGAGCCACTCATTTT+CGG + chr5.1:7765500-7765519 None:intergenic 50.0%
! CAACTCTAAACCGGTTCACC+TGG + chr5.1:7765417-7765436 None:intergenic 50.0%
! CCGTGAAATCAGAGGCATAG+AGG + chr5.1:7765162-7765181 None:intergenic 50.0%
! CTCACTTCAAGCTCTGGTTC+AGG - chr5.1:7765253-7765272 MS.gene20318:CDS 50.0%
!! GCCACTCATTTTCGGTTCGT+AGG + chr5.1:7765492-7765511 None:intergenic 50.0%
!! TTAGGGCTGGTGGATTGGAA+GGG + chr5.1:7765232-7765251 None:intergenic 50.0%
ATATGGAGGACCGAAAGCGG+AGG - chr5.1:7765317-7765336 MS.gene20318:CDS 55.0%
CCAGCATGGTTCGTTCCAAC+CGG + chr5.1:7765516-7765535 None:intergenic 55.0%
CGAAAATGAGTGGCTCCGGT+TGG - chr5.1:7765498-7765517 MS.gene20318:CDS 55.0%
CGGTTGGAACGAACCATGCT+GGG - chr5.1:7765514-7765533 MS.gene20318:CDS 55.0%
GCTTGAAGTGAGCTTAGGGC+TGG + chr5.1:7765245-7765264 None:intergenic 55.0%
GGATGGCTCGAACCGGAATA+TGG - chr5.1:7765300-7765319 MS.gene20318:CDS 55.0%
TGAAGTGAGCTTAGGGCTGG+TGG + chr5.1:7765242-7765261 None:intergenic 55.0%
TGGCTCGAACCGGAATATGG+AGG - chr5.1:7765303-7765322 MS.gene20318:CDS 55.0%
! TGAGCTTAGGGCTGGTGGAT+TGG + chr5.1:7765237-7765256 None:intergenic 55.0%
!! CTTAGGGCTGGTGGATTGGA+AGG + chr5.1:7765233-7765252 None:intergenic 55.0%
CCGGTTGGAACGAACCATGC+TGG - chr5.1:7765513-7765532 MS.gene20318:CDS 60.0%
CGGTCATGGATGGCTCGAAC+CGG - chr5.1:7765293-7765312 MS.gene20318:CDS 60.0%
CGGTTCGAGCCATCCATGAC+CGG + chr5.1:7765295-7765314 None:intergenic 60.0%
CAAACCGGGAATCGGCACGG+AGG - chr5.1:7765350-7765369 MS.gene20318:CDS 65.0%
!! GTGACCTCCGTGCCGATTCC+CGG + chr5.1:7765357-7765376 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 7765148 7765621 7765148 ID=MS.gene20318
chr5.1 mRNA 7765148 7765621 7765148 ID=MS.gene20318.t1;Parent=MS.gene20318
chr5.1 exon 7765148 7765621 7765148 ID=MS.gene20318.t1.exon1;Parent=MS.gene20318.t1
chr5.1 CDS 7765148 7765621 7765148 ID=cds.MS.gene20318.t1;Parent=MS.gene20318.t1
Gene Sequence

>MS.gene20318

ATGCTCTCTTCCCTCTATGCCTCTGATTTCACGGCGTTAGACGAAAGTTTAACCCCGTGGGATATTTCTAACATTCTCTCACCCTTCCAATCCACCAGCCCTAAGCTCACTTCAAGCTCTGGTTCAGGCGAACCAAACGAAAAACCGGTCATGGATGGCTCGAACCGGAATATGGAGGACCGAAAGCGGAGGAGAATGATATCAAACCGGGAATCGGCACGGAGGTCACGTATGAGAAAACAAAGACATCTAGAGAATTTACGGAACCAGGTGAACCGGTTTAGAGTTGAAAACCGGGAATTGAACAACGGGTTGCAGTTTTTGCTGTATCAATGCAATCGCCTACGAACCGAAAATGAGTGGCTCCGGTTGGAACGAACCATGCTGGGTCAAAAGTTGTCAAACATAGGTCAAAATATGGTTTTTCAACCTTTCTCATCTGCATGGCCATGCAATATTGTCACAGCTGAATAA
Protein sequence

>MS.gene20318.t1

MLSSLYASDFTALDESLTPWDISNILSPFQSTSPKLTSSSGSGEPNEKPVMDGSNRNMEDRKRRRMISNRESARRSRMRKQRHLENLRNQVNRFRVENRELNNGLQFLLYQCNRLRTENEWLRLERTMLGQKLSNIGQNMVFQPFSSAWPCNIVTAE