AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20286

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20286.t1 MTR_7g117590 71.605 162 31 2 2 149 12 172 2.71e-78 229
MS.gene20286.t1 MTR_1g054470 52.778 144 42 4 2 145 23 140 1.48e-43 140
MS.gene20286.t1 MTR_2g012700 37.273 110 68 1 40 148 10 119 2.42e-28 101
MS.gene20286.t1 MTR_2g062330 39.655 116 65 3 34 148 27 138 8.81e-27 98.2
MS.gene20286.t1 MTR_5g071400 69.811 53 14 2 3 55 9 59 3.40e-18 74.7
MS.gene20286.t1 MTR_0010s0310 35.556 90 55 1 53 139 151 240 1.10e-15 71.6
MS.gene20286.t1 MTR_5g078270 34.831 89 55 1 54 139 210 298 3.33e-14 68.6
MS.gene20286.t1 MTR_6g477950 36.275 102 61 3 48 148 46 144 8.40e-14 67.4
MS.gene20286.t1 MTR_5g071400 76.316 38 7 2 18 55 1 36 6.96e-12 57.8
MS.gene20286.t1 MTR_3g008190 29.167 96 67 1 54 148 6 101 1.43e-11 57.8
MS.gene20286.t1 MTR_7g117585 35.714 84 51 2 68 149 64 146 2.33e-11 58.5
MS.gene20286.t1 MTR_6g087720 33.735 83 54 1 55 136 216 298 4.22e-11 59.7
MS.gene20286.t1 MTR_0010s0290 31.373 102 63 3 54 149 223 323 4.31e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATCAACTATTCGAATTT+TGG 0.090848 5.1:-8172566 None:intergenic
TACAGGTAATGGGTGAAAAT+TGG 0.209416 5.1:-8172278 None:intergenic
CCATCGACTTCTTCTTCATT+TGG 0.245009 5.1:-8172310 None:intergenic
GTGGATGGTTTGAGTTTGTT+AGG 0.256057 5.1:+8172656 MS.gene20286:CDS
GGCTGTTGGACGGAGTGTTC+TGG 0.356206 5.1:+8172408 MS.gene20286:CDS
CGAATAGTTGATGATGAAAC+TGG 0.373610 5.1:+8172574 MS.gene20286:CDS
GAATGTGAAGTTCGTGATAA+AGG 0.381874 5.1:+8172607 MS.gene20286:CDS
AAGTTCGTGATAAAGGAAAT+TGG 0.388847 5.1:+8172614 MS.gene20286:CDS
ACAGGTAATGGGTGAAAATT+GGG 0.407202 5.1:-8172277 None:intergenic
ATTAGTTCTGCTACGGCTGT+TGG 0.467637 5.1:+8172394 MS.gene20286:CDS
TGGATGGTTTGAGTTTGTTA+GGG 0.477462 5.1:+8172657 MS.gene20286:CDS
AAATGTCTTCTTCTAGTAGC+AGG 0.479507 5.1:+8172147 None:intergenic
TTTGAAATTGTGCAGATACT+GGG 0.501474 5.1:-8172333 None:intergenic
CTGCAGCCATGTAATTGATC+CGG 0.509939 5.1:+8172237 MS.gene20286:intron
ATGGAGAAATACGTTGGTAG+TGG 0.538951 5.1:+8172637 MS.gene20286:CDS
CCATGTAATTGATCCGGAGT+TGG 0.545499 5.1:+8172243 MS.gene20286:CDS
GGCATCAATTCGTCCAACTC+CGG 0.549037 5.1:-8172256 None:intergenic
CCAACTCCGGATCAATTACA+TGG 0.550497 5.1:-8172243 None:intergenic
AGAAATACGTTGGTAGTGGA+TGG 0.551017 5.1:+8172641 MS.gene20286:CDS
CTTTGAATTGCAATCTTCCG+AGG 0.557056 5.1:-8172526 None:intergenic
TCGTGATAAAGGAAATTGGA+TGG 0.565929 5.1:+8172618 MS.gene20286:CDS
TGAATGTGTAGCATATTCCT+CGG 0.575111 5.1:+8172509 MS.gene20286:intron
GCATAGTATTAGTTCTGCTA+CGG 0.580120 5.1:+8172387 MS.gene20286:CDS
GATACAAATAATTTGTGTGG+AGG 0.593345 5.1:-8172727 None:intergenic
GTTCTGCTACGGCTGTTGGA+CGG 0.598239 5.1:+8172398 MS.gene20286:CDS
AATTGGATGGAGAAATACGT+TGG 0.604235 5.1:+8172631 MS.gene20286:CDS
ACTGATACAAATAATTTGTG+TGG 0.607437 5.1:-8172730 None:intergenic
CCAAATGAAGAAGAAGTCGA+TGG 0.658231 5.1:+8172310 MS.gene20286:CDS
AGGGCAAAAGAACTCAACGA+AGG 0.725140 5.1:+8172676 MS.gene20286:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTAATTTTATTTTTGC+AGG + chr5.1:8172433-8172452 MS.gene20286:intron 15.0%
!!! CAATTTCAAAATTTTCAAAA+CGG + chr5.1:8172346-8172365 MS.gene20286:CDS 15.0%
!!! TTTTTGTTTTTTTAATCTTC+TGG + chr5.1:8172191-8172210 MS.gene20286:intron 15.0%
!! ACTGATACAAATAATTTGTG+TGG - chr5.1:8172733-8172752 None:intergenic 25.0%
!! ATCATCAACTATTCGAATTT+TGG - chr5.1:8172569-8172588 None:intergenic 25.0%
AAGTTCGTGATAAAGGAAAT+TGG + chr5.1:8172614-8172633 MS.gene20286:CDS 30.0%
! AAAACGGTGATCATACTTTT+TGG + chr5.1:8172362-8172381 MS.gene20286:CDS 30.0%
! GATACAAATAATTTGTGTGG+AGG - chr5.1:8172730-8172749 None:intergenic 30.0%
! TTTGAAATTGTGCAGATACT+GGG - chr5.1:8172336-8172355 None:intergenic 30.0%
!!! TTTTGAAATTGTGCAGATAC+TGG - chr5.1:8172337-8172356 None:intergenic 30.0%
AATTGGATGGAGAAATACGT+TGG + chr5.1:8172631-8172650 MS.gene20286:CDS 35.0%
GAATGTGAAGTTCGTGATAA+AGG + chr5.1:8172607-8172626 MS.gene20286:CDS 35.0%
TCGTGATAAAGGAAATTGGA+TGG + chr5.1:8172618-8172637 MS.gene20286:CDS 35.0%
TGAATGTGTAGCATATTCCT+CGG + chr5.1:8172509-8172528 MS.gene20286:intron 35.0%
! GATTTTCGTCTACAGGTAAT+GGG - chr5.1:8172291-8172310 None:intergenic 35.0%
! TCATTTGGATTTTCGTCTAC+AGG - chr5.1:8172298-8172317 None:intergenic 35.0%
!! ACAGGTAATGGGTGAAAATT+GGG - chr5.1:8172280-8172299 None:intergenic 35.0%
!! CGAATAGTTGATGATGAAAC+TGG + chr5.1:8172574-8172593 MS.gene20286:CDS 35.0%
!! GCATAGTATTAGTTCTGCTA+CGG + chr5.1:8172387-8172406 MS.gene20286:CDS 35.0%
!! TACAGGTAATGGGTGAAAAT+TGG - chr5.1:8172281-8172300 None:intergenic 35.0%
!! TGGATGGTTTGAGTTTGTTA+GGG + chr5.1:8172657-8172676 MS.gene20286:CDS 35.0%
CCAAATGAAGAAGAAGTCGA+TGG + chr5.1:8172310-8172329 MS.gene20286:CDS 40.0%
CTTTGAATTGCAATCTTCCG+AGG - chr5.1:8172529-8172548 None:intergenic 40.0%
TTGCAGGATTATTTGCGCAT+GGG + chr5.1:8172449-8172468 MS.gene20286:intron 40.0%
TTTGCAGGATTATTTGCGCA+TGG + chr5.1:8172448-8172467 MS.gene20286:intron 40.0%
! ATGGAGAAATACGTTGGTAG+TGG + chr5.1:8172637-8172656 MS.gene20286:CDS 40.0%
! GGATTTTCGTCTACAGGTAA+TGG - chr5.1:8172292-8172311 None:intergenic 40.0%
! GTGGATGGTTTGAGTTTGTT+AGG + chr5.1:8172656-8172675 MS.gene20286:CDS 40.0%
!! AGAAATACGTTGGTAGTGGA+TGG + chr5.1:8172641-8172660 MS.gene20286:CDS 40.0%
!! CCATCGACTTCTTCTTCATT+TGG - chr5.1:8172313-8172332 None:intergenic 40.0%
AGGGCAAAAGAACTCAACGA+AGG + chr5.1:8172676-8172695 MS.gene20286:CDS 45.0%
CCAACTCCGGATCAATTACA+TGG - chr5.1:8172246-8172265 None:intergenic 45.0%
CCATGTAATTGATCCGGAGT+TGG + chr5.1:8172243-8172262 MS.gene20286:CDS 45.0%
CTGCAGCCATGTAATTGATC+CGG + chr5.1:8172237-8172256 MS.gene20286:intron 45.0%
!! ATTAGTTCTGCTACGGCTGT+TGG + chr5.1:8172394-8172413 MS.gene20286:CDS 45.0%
CAGGATTATTTGCGCATGGG+TGG + chr5.1:8172452-8172471 MS.gene20286:intron 50.0%
GATTATTTGCGCATGGGTGG+TGG + chr5.1:8172455-8172474 MS.gene20286:intron 50.0%
GGCATCAATTCGTCCAACTC+CGG - chr5.1:8172259-8172278 None:intergenic 50.0%
GTTCTGCTACGGCTGTTGGA+CGG + chr5.1:8172398-8172417 MS.gene20286:CDS 55.0%
! GGCTGTTGGACGGAGTGTTC+TGG + chr5.1:8172408-8172427 MS.gene20286:CDS 60.0%
! GCGCATGGGTGGTGGCTTTC+TGG + chr5.1:8172463-8172482 MS.gene20286:intron 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 8172149 8172762 8172149 ID=MS.gene20286
chr5.1 mRNA 8172149 8172762 8172149 ID=MS.gene20286.t1;Parent=MS.gene20286
chr5.1 exon 8172149 8172168 8172149 ID=MS.gene20286.t1.exon1;Parent=MS.gene20286.t1
chr5.1 CDS 8172149 8172168 8172149 ID=cds.MS.gene20286.t1;Parent=MS.gene20286.t1
chr5.1 exon 8172243 8172429 8172243 ID=MS.gene20286.t1.exon2;Parent=MS.gene20286.t1
chr5.1 CDS 8172243 8172429 8172243 ID=cds.MS.gene20286.t1;Parent=MS.gene20286.t1
chr5.1 exon 8172520 8172762 8172520 ID=MS.gene20286.t1.exon3;Parent=MS.gene20286.t1
chr5.1 CDS 8172520 8172762 8172520 ID=cds.MS.gene20286.t1;Parent=MS.gene20286.t1
Gene Sequence

>MS.gene20286

ATGTCTTCTTCTAGTAGCAGGTAACTTCAATGTTTGAGTTGTTTTTTGTTTTTTTAATCTTCTGGTTATTTATTAGATTTTGTTGAAACTGCAGCCATGTAATTGATCCGGAGTTGGACGAATTGATGCCCAATTTTCACCCATTACCTGTAGACGAAAATCCAAATGAAGAAGAAGTCGATGGCCCAGTATCTGCACAATTTCAAAATTTTCAAAACGGTGATCATACTTTTTGGATGCATAGTATTAGTTCTGCTACGGCTGTTGGACGGAGTGTTCTGGTTAGTTTTAATTTTATTTTTGCAGGATTATTTGCGCATGGGTGGTGGCTTTCTGGTTGAAAAGTAATATTATTTGTTTTGAATGTGTAGCATATTCCTCGGAAGATTGCAATTCAAAGTATGTATGTGAATCAATCCAAAATTCGAATAGTTGATGATGAAACTGGAGAAGAATATGAATGTGAAGTTCGTGATAAAGGAAATTGGATGGAGAAATACGTTGGTAGTGGATGGTTTGAGTTTGTTAGGGCAAAAGAACTCAACGAAGGAGATTCGTTGTTCTTCACTATTGATAATCCTCCACACAAATTATTTGTATCAGTGATTAGATAG
Protein sequence

>MS.gene20286.t1

MSSSSSSHVIDPELDELMPNFHPLPVDENPNEEEVDGPVSAQFQNFQNGDHTFWMHSISSATAVGRSVLHIPRKIAIQSMYVNQSKIRIVDDETGEEYECEVRDKGNWMEKYVGSGWFEFVRAKELNEGDSLFFTIDNPPHKLFVSVIR