AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004664

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004664.t1 MTR_1g072110 95.417 240 8 2 1 240 1 237 2.57e-165 456
MS.gene004664.t1 MTR_7g095150 51.452 241 58 10 6 238 12 201 3.51e-60 189
MS.gene004664.t1 MTR_1g103640 47.101 138 50 3 102 237 63 179 1.17e-34 124
MS.gene004664.t1 MTR_2g102140 38.636 132 69 3 118 237 142 273 1.55e-17 80.5
MS.gene004664.t1 MTR_7g105780 40.157 127 52 5 111 237 97 199 1.99e-17 79.7
MS.gene004664.t1 MTR_4g012060 50.649 77 35 2 159 234 175 249 1.04e-15 75.1
MS.gene004664.t1 MTR_1g111640 51.429 70 29 2 166 235 135 199 8.33e-15 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004664.t1 AT1G05420 37.220 223 87 7 49 239 19 220 1.01e-27 105
MS.gene004664.t1 AT1G05420 37.220 223 87 7 49 239 35 236 1.51e-27 105
MS.gene004664.t1 AT2G32100 37.423 163 72 5 95 239 88 238 7.51e-24 96.3
MS.gene004664.t1 AT4G14860 57.143 77 31 1 165 239 96 172 3.46e-22 90.5
MS.gene004664.t1 AT1G79960 45.946 74 40 0 164 237 187 260 3.39e-17 79.3
MS.gene004664.t1 AT5G04820 32.895 152 89 4 86 237 74 212 2.18e-15 73.6
MS.gene004664.t1 AT2G36050 33.600 125 55 2 113 237 77 173 8.72e-13 66.6
MS.gene004664.t1 AT3G52540 31.200 125 58 3 113 237 104 200 1.44e-11 63.2

Find 59 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACTGATAGTTGTAGAAAT+TGG 0.240910 1.1:-54321104 None:intergenic
TTCCTCAGATTTCTTGTGTT+TGG 0.289544 1.1:-54321026 None:intergenic
AACACTCACAAGTTCATTCT+TGG 0.302219 1.1:+54321683 MS.gene004664:CDS
CTACTCACCTGATCCTTATA+TGG 0.303517 1.1:+54321544 MS.gene004664:CDS
CTTCTCACGCTCAATACTAT+TGG 0.339069 1.1:-54321465 None:intergenic
AAATCTGCTGGCTCAGGTTC+GGG 0.339475 1.1:-54321323 None:intergenic
TAAAGTGTGGTCTGAGGTTA+AGG 0.350644 1.1:-54321240 None:intergenic
ATGAACTTGTGAGTGTTCTT+TGG 0.354503 1.1:-54321677 None:intergenic
GATCTTCTAAAATCCATATA+AGG 0.364006 1.1:-54321557 None:intergenic
TGATGGATGTGAAATCAAAT+TGG 0.370791 1.1:+54321612 MS.gene004664:CDS
GAAATCTGCTGGCTCAGGTT+CGG 0.383556 1.1:-54321324 None:intergenic
AAGGCTGCTGCGAAATCTGC+TGG 0.394882 1.1:-54321335 None:intergenic
TGAACTTGTGAGTGTTCTTT+GGG 0.402029 1.1:-54321676 None:intergenic
TGTATATTCAATTAATGAGT+TGG 0.404911 1.1:-54321396 None:intergenic
GTTGTAGAAATTGGACTTGT+GGG 0.416852 1.1:-54321095 None:intergenic
CGCTTCTTCTTCTCCTCCCC+CGG 0.419956 1.1:+54321368 MS.gene004664:CDS
GAAACAGGAGAAAGAGAAAG+AGG 0.423520 1.1:+54321487 MS.gene004664:CDS
TATTGAGCGTGAGAAGAAAC+AGG 0.440175 1.1:+54321472 MS.gene004664:CDS
AATTCTTGATCATAATTGAC+GGG 0.444957 1.1:-54321196 None:intergenic
GCTGCGAAATCTGCTGGCTC+AGG 0.454177 1.1:-54321329 None:intergenic
AGAGATGGTGGAGGCGCGAC+CGG 0.455026 1.1:+54321586 MS.gene004664:CDS
CTAAAATCCATATAAGGATC+AGG 0.462583 1.1:-54321551 None:intergenic
AATTAATGAGTTGGAGCTAC+CGG 0.467305 1.1:-54321387 None:intergenic
ATACTATTGGACTTATCCAT+TGG 0.483511 1.1:-54321452 None:intergenic
GGAGGCGCGACCGGAGTTGA+TGG 0.488669 1.1:+54321595 MS.gene004664:CDS
AGATTGCATTCAGCATTCTT+CGG 0.492875 1.1:+54321424 MS.gene004664:CDS
TGTTCTTTGGGTTGAGAGCA+AGG 0.508816 1.1:-54321664 None:intergenic
GAAGAAGCGTTGAGAGGCGA+AGG 0.509416 1.1:-54321354 None:intergenic
ATTAATGAGTTGGAGCTACC+GGG 0.511814 1.1:-54321386 None:intergenic
CTATTGGACTTATCCATTGG+TGG 0.513854 1.1:-54321449 None:intergenic
AGAGGTTGATGTAGTGAAGG+TGG 0.515313 1.1:-54321282 None:intergenic
TTCAACTTCGAGTTCAAAAG+AGG 0.515870 1.1:-54321300 None:intergenic
AACAAAGAAGCAACTCATGC+AGG 0.516734 1.1:-54321640 None:intergenic
GCATTCTTCGGTACCACCAA+TGG 0.516823 1.1:+54321436 MS.gene004664:CDS
AAATTCTTGATCATAATTGA+CGG 0.524121 1.1:-54321197 None:intergenic
GATGCAGATGTAGATGAAGA+AGG 0.533865 1.1:-54321170 None:intergenic
ACCATGACTAAAATGACATG+AGG 0.563547 1.1:-54321730 None:intergenic
CATATAAGGATCAGGTGAGT+AGG 0.566346 1.1:-54321543 None:intergenic
GTGTGGTCTGAGGTTAAGGA+AGG 0.576057 1.1:-54321236 None:intergenic
TAGAAGATCGATGCAAGAGA+TGG 0.580424 1.1:+54321571 MS.gene004664:CDS
GATTTCACATCCATCAACTC+CGG 0.581756 1.1:-54321605 None:intergenic
AAAAGAGGTTGATGTAGTGA+AGG 0.582071 1.1:-54321285 None:intergenic
AAGATCGATGCAAGAGATGG+TGG 0.583074 1.1:+54321574 MS.gene004664:CDS
ACAGGAGAAAGAGAAAGAGG+AGG 0.589206 1.1:+54321490 MS.gene004664:CDS
AGTTGTAGAAATTGGACTTG+TGG 0.600672 1.1:-54321096 None:intergenic
ATCGATGCAAGAGATGGTGG+AGG 0.602628 1.1:+54321577 MS.gene004664:CDS
GGAGAAGAAGAAGCGTTGAG+AGG 0.620274 1.1:-54321360 None:intergenic
CATGAGGGTTACGAGAAGAT+CGG 0.623248 1.1:-54321714 None:intergenic
TTAATGAGTTGGAGCTACCG+GGG 0.639288 1.1:-54321385 None:intergenic
GTAGAAATTGGACTTGTGGG+TGG 0.648560 1.1:-54321092 None:intergenic
AGAGCATAAAGTGTGGTCTG+AGG 0.656840 1.1:-54321246 None:intergenic
TAAGGATCAGGTGAGTAGGT+CGG 0.659190 1.1:-54321539 None:intergenic
ATTCTTGATCATAATTGACG+GGG 0.668719 1.1:-54321195 None:intergenic
GTGAAGAAGAGCATAAAGTG+TGG 0.669604 1.1:-54321253 None:intergenic
CCATGACTAAAATGACATGA+GGG 0.681032 1.1:-54321729 None:intergenic
TGTGGTCTGAGGTTAAGGAA+GGG 0.682154 1.1:-54321235 None:intergenic
TTGATGATGATGTTGATGTG+AGG 0.685082 1.1:-54321135 None:intergenic
TAATGAGTTGGAGCTACCGG+GGG 0.686460 1.1:-54321384 None:intergenic
TGCCAAACACAAGAAATCTG+AGG 0.686722 1.1:+54321024 MS.gene004664:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTCTTGATCATAATTGA+CGG - chr1.1:54321200-54321219 None:intergenic 20.0%
!! TGTATATTCAATTAATGAGT+TGG - chr1.1:54321399-54321418 None:intergenic 20.0%
! AATTCTTGATCATAATTGAC+GGG - chr1.1:54321199-54321218 None:intergenic 25.0%
! AATTTGAAAAACATAGGTTG+AGG - chr1.1:54321052-54321071 None:intergenic 25.0%
! GAGTTGAATTTGAAAAACAT+AGG - chr1.1:54321058-54321077 None:intergenic 25.0%
!!! GATCTTCTAAAATCCATATA+AGG - chr1.1:54321560-54321579 None:intergenic 25.0%
ATACTATTGGACTTATCCAT+TGG - chr1.1:54321455-54321474 None:intergenic 30.0%
ATTCTTGATCATAATTGACG+GGG - chr1.1:54321198-54321217 None:intergenic 30.0%
CTAAAATCCATATAAGGATC+AGG - chr1.1:54321554-54321573 None:intergenic 30.0%
TCACTGATAGTTGTAGAAAT+TGG - chr1.1:54321107-54321126 None:intergenic 30.0%
! TGATGGATGTGAAATCAAAT+TGG + chr1.1:54321612-54321631 MS.gene004664:CDS 30.0%
AACACTCACAAGTTCATTCT+TGG + chr1.1:54321683-54321702 MS.gene004664:CDS 35.0%
AGATTGCATTCAGCATTCTT+CGG + chr1.1:54321424-54321443 MS.gene004664:CDS 35.0%
AGTTGTAGAAATTGGACTTG+TGG - chr1.1:54321099-54321118 None:intergenic 35.0%
ATGAACTTGTGAGTGTTCTT+TGG - chr1.1:54321680-54321699 None:intergenic 35.0%
GTTGTAGAAATTGGACTTGT+GGG - chr1.1:54321098-54321117 None:intergenic 35.0%
TGAACTTGTGAGTGTTCTTT+GGG - chr1.1:54321679-54321698 None:intergenic 35.0%
TTCCTCAGATTTCTTGTGTT+TGG - chr1.1:54321029-54321048 None:intergenic 35.0%
! AATTAATGAGTTGGAGCTAC+CGG - chr1.1:54321390-54321409 None:intergenic 35.0%
! TTCAACTTCGAGTTCAAAAG+AGG - chr1.1:54321303-54321322 None:intergenic 35.0%
!! AAAAGAGGTTGATGTAGTGA+AGG - chr1.1:54321288-54321307 None:intergenic 35.0%
!! TTGATGATGATGTTGATGTG+AGG - chr1.1:54321138-54321157 None:intergenic 35.0%
!!! AAAGAGGAGGTTTTGTTCAA+CGG + chr1.1:54321503-54321522 MS.gene004664:CDS 35.0%
AACAAAGAAGCAACTCATGC+AGG - chr1.1:54321643-54321662 None:intergenic 40.0%
CATATAAGGATCAGGTGAGT+AGG - chr1.1:54321546-54321565 None:intergenic 40.0%
CTACTCACCTGATCCTTATA+TGG + chr1.1:54321544-54321563 MS.gene004664:CDS 40.0%
CTATTGGACTTATCCATTGG+TGG - chr1.1:54321452-54321471 None:intergenic 40.0%
CTTCTCACGCTCAATACTAT+TGG - chr1.1:54321468-54321487 None:intergenic 40.0%
GAAACAGGAGAAAGAGAAAG+AGG + chr1.1:54321487-54321506 MS.gene004664:CDS 40.0%
GATGCAGATGTAGATGAAGA+AGG - chr1.1:54321173-54321192 None:intergenic 40.0%
GATTTCACATCCATCAACTC+CGG - chr1.1:54321608-54321627 None:intergenic 40.0%
TAGAAGATCGATGCAAGAGA+TGG + chr1.1:54321571-54321590 MS.gene004664:CDS 40.0%
TATTGAGCGTGAGAAGAAAC+AGG + chr1.1:54321472-54321491 MS.gene004664:CDS 40.0%
TGCCAAACACAAGAAATCTG+AGG + chr1.1:54321024-54321043 MS.gene004664:CDS 40.0%
! ATTAATGAGTTGGAGCTACC+GGG - chr1.1:54321389-54321408 None:intergenic 40.0%
! GTGAAGAAGAGCATAAAGTG+TGG - chr1.1:54321256-54321275 None:intergenic 40.0%
! TAAAGTGTGGTCTGAGGTTA+AGG - chr1.1:54321243-54321262 None:intergenic 40.0%
AAGATCGATGCAAGAGATGG+TGG + chr1.1:54321574-54321593 MS.gene004664:CDS 45.0%
ACAGGAGAAAGAGAAAGAGG+AGG + chr1.1:54321490-54321509 MS.gene004664:CDS 45.0%
AGAGCATAAAGTGTGGTCTG+AGG - chr1.1:54321249-54321268 None:intergenic 45.0%
CATGAGGGTTACGAGAAGAT+CGG - chr1.1:54321717-54321736 None:intergenic 45.0%
GTAGAAATTGGACTTGTGGG+TGG - chr1.1:54321095-54321114 None:intergenic 45.0%
TAAGGATCAGGTGAGTAGGT+CGG - chr1.1:54321542-54321561 None:intergenic 45.0%
! TGTGGTCTGAGGTTAAGGAA+GGG - chr1.1:54321238-54321257 None:intergenic 45.0%
! TTAATGAGTTGGAGCTACCG+GGG - chr1.1:54321388-54321407 None:intergenic 45.0%
!! AGAGGTTGATGTAGTGAAGG+TGG - chr1.1:54321285-54321304 None:intergenic 45.0%
!! TGTTCTTTGGGTTGAGAGCA+AGG - chr1.1:54321667-54321686 None:intergenic 45.0%
!!! GGTTTTGTTCAACGGAAGTG+TGG + chr1.1:54321511-54321530 MS.gene004664:CDS 45.0%
GCATTCTTCGGTACCACCAA+TGG + chr1.1:54321436-54321455 MS.gene004664:CDS 50.0%
! ATCGATGCAAGAGATGGTGG+AGG + chr1.1:54321577-54321596 MS.gene004664:CDS 50.0%
! GTGTGGTCTGAGGTTAAGGA+AGG - chr1.1:54321239-54321258 None:intergenic 50.0%
! TAATGAGTTGGAGCTACCGG+GGG - chr1.1:54321387-54321406 None:intergenic 50.0%
!! AAATCTGCTGGCTCAGGTTC+GGG - chr1.1:54321326-54321345 None:intergenic 50.0%
!! GAAATCTGCTGGCTCAGGTT+CGG - chr1.1:54321327-54321346 None:intergenic 50.0%
!! GGAGAAGAAGAAGCGTTGAG+AGG - chr1.1:54321363-54321382 None:intergenic 50.0%
AAGGCTGCTGCGAAATCTGC+TGG - chr1.1:54321338-54321357 None:intergenic 55.0%
!! GAAGAAGCGTTGAGAGGCGA+AGG - chr1.1:54321357-54321376 None:intergenic 55.0%
CGCTTCTTCTTCTCCTCCCC+CGG + chr1.1:54321368-54321387 MS.gene004664:CDS 60.0%
!! GCTGCGAAATCTGCTGGCTC+AGG - chr1.1:54321332-54321351 None:intergenic 60.0%
! TGAGTTGGAGCTACCGGGGG+AGG - chr1.1:54321384-54321403 None:intergenic 65.0%
!! AGAGATGGTGGAGGCGCGAC+CGG + chr1.1:54321586-54321605 MS.gene004664:CDS 65.0%
! GGAGGCGCGACCGGAGTTGA+TGG + chr1.1:54321595-54321614 MS.gene004664:CDS 70.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 54321023 54321745 54321023 ID=MS.gene004664
chr1.1 mRNA 54321023 54321745 54321023 ID=MS.gene004664.t1;Parent=MS.gene004664
chr1.1 exon 54321023 54321745 54321023 ID=MS.gene004664.t1.exon1;Parent=MS.gene004664.t1
chr1.1 CDS 54321023 54321745 54321023 ID=cds.MS.gene004664.t1;Parent=MS.gene004664.t1
Gene Sequence

>MS.gene004664

ATGCCAAACACAAGAAATCTGAGGAACCTCAACCTATGTTTTTCAAATTCAACTCTTGAATCAAAATCTCCACCCACAAGTCCAATTTCTACAACTATCAGTGAAGCAGCTTCCTCACATCAACATCATCATCAAATTCATCACAAACCTTCTTCATCTACATCTGCATCTTCCCCGTCAATTATGATCAAGAATTTCAACTCTCTCTATGACCCTTCCTTAACCTCAGACCACACTTTATGCTCTTCTTCACTCTCTACCACCTTCACTACATCAACCTCTTTTGAACTCGAAGTTGAACCCGAACCTGAGCCAGCAGATTTCGCAGCAGCCTTCGCCTCTCAACGCTTCTTCTTCTCCTCCCCCGGTAGCTCCAACTCATTAATTGAATATACAAACACAGATTGCATTCAGCATTCTTCGGTACCACCAATGGATAAGTCCAATAGTATTGAGCGTGAGAAGAAACAGGAGAAAGAGAAAGAGGAGGTTTTGTTCAACGGAAGTGTGGCAGTACCGACCTACTCACCTGATCCTTATATGGATTTTAGAAGATCGATGCAAGAGATGGTGGAGGCGCGACCGGAGTTGATGGATGTGAAATCAAATTGGAACATCCTGCATGAGTTGCTTCTTTGTTACCTTGCTCTCAACCCAAAGAACACTCACAAGTTCATTCTTGGTGCTTTTGCCGATCTTCTCGTAACCCTCATGTCATTTTAG
Protein sequence

>MS.gene004664.t1

MPNTRNLRNLNLCFSNSTLESKSPPTSPISTTISEAASSHQHHHQIHHKPSSSTSASSPSIMIKNFNSLYDPSLTSDHTLCSSSLSTTFTTSTSFELEVEPEPEPADFAAAFASQRFFFSSPGSSNSLIEYTNTDCIQHSSVPPMDKSNSIEREKKQEKEKEEVLFNGSVAVPTYSPDPYMDFRRSMQEMVEARPELMDVKSNWNILHELLLCYLALNPKNTHKFILGAFADLLVTLMSF