AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42848

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42848.t1 MTR_7g072120 82.381 210 29 4 1 202 1 210 7.89e-128 358
MS.gene42848.t1 MTR_7g072170 80.000 210 34 2 1 202 1 210 1.32e-124 351
MS.gene42848.t1 MTR_7g072270 79.227 207 37 1 1 201 1 207 2.67e-124 350
MS.gene42848.t1 MTR_7g072140 78.571 210 37 2 1 202 1 210 1.36e-122 345
MS.gene42848.t1 MTR_7g072250 67.281 217 50 3 1 200 25 237 1.73e-100 291
MS.gene42848.t1 MTR_7g072270 78.182 165 30 1 1 159 1 165 2.56e-96 277
MS.gene42848.t1 MTR_7g071710 95.763 118 5 0 86 203 1 118 1.15e-81 238
MS.gene42848.t1 MTR_4g029430 56.345 197 81 2 6 201 5 197 1.21e-79 236
MS.gene42848.t1 MTR_1g014180 51.613 186 80 5 16 196 5 185 1.11e-58 182
MS.gene42848.t1 MTR_1g014150 46.196 184 91 4 14 195 11 188 5.14e-47 153
MS.gene42848.t1 MTR_1g014160 39.894 188 88 6 26 195 59 239 4.99e-30 111
MS.gene42848.t1 MTR_2g103840 30.539 167 108 5 39 201 42 204 6.57e-23 92.0
MS.gene42848.t1 MTR_5g074550 30.556 180 110 6 26 195 17 191 4.22e-21 86.7
MS.gene42848.t1 MTR_4g010180 27.273 187 129 6 20 202 11 194 1.21e-20 85.9
MS.gene42848.t1 MTR_2g103850 29.167 168 111 5 39 202 43 206 1.52e-19 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42848.t1 AT5G01750 57.000 200 85 1 4 202 15 214 6.78e-92 268
MS.gene42848.t1 AT3G11740 58.421 190 77 2 15 202 2 191 1.47e-82 243
MS.gene42848.t1 AT2G14560 51.295 193 92 2 9 200 1 192 2.62e-71 215
MS.gene42848.t1 AT2G14560 50.510 196 95 2 6 200 58 252 2.53e-70 215
MS.gene42848.t1 AT1G33840 46.445 211 101 2 1 199 1 211 6.83e-68 207
MS.gene42848.t1 AT5G01750 55.063 158 70 1 4 160 15 172 6.33e-67 203
MS.gene42848.t1 AT2G14560 48.171 164 83 2 9 171 1 163 2.60e-55 174
MS.gene42848.t1 AT2G14560 49.045 157 78 2 6 161 58 213 2.21e-54 173
MS.gene42848.t1 AT3G16900 43.243 185 85 4 16 199 15 180 6.46e-50 160
MS.gene42848.t1 AT1G33840 42.775 173 87 2 1 161 1 173 6.87e-50 160
MS.gene42848.t1 AT3G56180 35.052 194 119 4 12 201 14 204 1.40e-36 127
MS.gene42848.t1 AT3G56180 34.536 194 118 5 12 201 14 202 3.18e-34 120
MS.gene42848.t1 AT3G10986 32.632 190 121 4 15 197 3 192 6.85e-30 109
MS.gene42848.t1 AT3G15810 32.143 168 104 6 39 202 44 205 2.11e-24 95.9
MS.gene42848.t1 AT1G80120 32.738 168 106 4 39 202 30 194 1.38e-19 83.2
MS.gene42848.t1 AT2G38640 32.544 169 105 5 33 198 30 192 4.15e-17 76.3
MS.gene42848.t1 AT5G20640 28.729 181 112 5 36 201 33 211 1.87e-15 72.4
MS.gene42848.t1 AT2G30270 28.902 173 108 7 26 195 19 179 4.87e-15 70.5
MS.gene42848.t1 AT2G05910 28.402 169 100 7 39 198 28 184 7.06e-14 67.4
MS.gene42848.t1 AT5G41590 24.432 176 123 4 33 198 44 219 2.95e-11 60.8

Find 51 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATCACAAACATCTTCTT+TGG 0.257604 7.2:+32017753 None:intergenic
GGATTTGGCGGTCGTGAAAA+AGG 0.290385 7.2:-32018664 MS.gene42848:CDS
TGCTCCCTATCCGGTGGATT+TGG 0.306791 7.2:-32018679 MS.gene42848:CDS
GCACCCACCACCACCATATT+CGG 0.362096 7.2:-32018714 MS.gene42848:CDS
ACAATATTGAGAGCCGAATA+TGG 0.363340 7.2:+32018701 None:intergenic
ATTGCCATTGACATCTTTAA+CGG 0.374139 7.2:+32018617 None:intergenic
TAGGGTGGTGATGGGGTTAC+CGG 0.377318 7.2:+32018530 None:intergenic
GTGGTGGTGGGTGCCGGCAT+CGG 0.380802 7.2:+32018723 None:intergenic
CCTCCGTGACCGCCGTGTCT+TGG 0.425443 7.2:-32018562 MS.gene42848:CDS
TCAATATTGTGCTCCCTATC+CGG 0.428008 7.2:-32018688 MS.gene42848:CDS
CTTGCGACGTAGGGTGGTGA+TGG 0.430403 7.2:+32018521 None:intergenic
GCCGGCATCGGTGGTTGATA+AGG 0.437331 7.2:+32018735 None:intergenic
AATATGGTGGTGGTGGGTGC+CGG 0.438186 7.2:+32018717 None:intergenic
GTGGTGGGTGCCGGCATCGG+TGG 0.452113 7.2:+32018726 None:intergenic
GATAAACAGTGACCGCAAAA+TGG 0.467602 7.2:+32017497 None:intergenic
TTCACGACCGCCAAATCCAC+CGG 0.471320 7.2:+32018669 None:intergenic
TTGCGACGTAGGGTGGTGAT+GGG 0.485246 7.2:+32018522 None:intergenic
ACCGCCAAATCCACCGGATA+GGG 0.489401 7.2:+32018675 None:intergenic
TCCTTATCAACCACCGATGC+CGG 0.493777 7.2:-32018736 MS.gene42848:CDS
CGTGTCTTGGTTGATGCCTC+CGG 0.494853 7.2:-32018549 MS.gene42848:CDS
ATGAAAGCGTAATCAACATT+GGG 0.498374 7.2:+32017475 None:intergenic
TAAAGTCAAAGGTAGTTGGT+TGG 0.499063 7.2:-32017731 MS.gene42848:CDS
TCCCTATCCGGTGGATTTGG+CGG 0.505154 7.2:-32018676 MS.gene42848:CDS
TATGAAAGCGTAATCAACAT+TGG 0.519673 7.2:+32017474 None:intergenic
CAACCAAGACACGGCGGTCA+CGG 0.526860 7.2:+32018559 None:intergenic
AACGGTGAAGTTGTCTGCCA+TGG 0.529412 7.2:+32018635 None:intergenic
TTGTACGTACCTTGCGACGT+AGG 0.529527 7.2:+32018511 None:intergenic
TACTAACAACATTGTTGCAC+AGG 0.530405 7.2:-32017680 MS.gene42848:intron
TGTTGATTACGCTTTCATAG+TGG 0.534696 7.2:-32017470 MS.gene42848:CDS
TGTACGTACCTTGCGACGTA+GGG 0.547525 7.2:+32018512 None:intergenic
AGAGCCGAATATGGTGGTGG+TGG 0.571753 7.2:+32018710 None:intergenic
AATGTCGTGTTTAAAGTGAA+AGG 0.575214 7.2:-32018597 MS.gene42848:CDS
CGATCTTGTATTATTTACGC+TGG 0.576867 7.2:-32017706 MS.gene42848:CDS
AGTGACTATGCATGATCGGT+GGG 0.580863 7.2:-32017884 MS.gene42848:CDS
GACCGCCAAATCCACCGGAT+AGG 0.585193 7.2:+32018674 None:intergenic
CATCACCACCCTACGTCGCA+AGG 0.590882 7.2:-32018520 MS.gene42848:intron
TTCACCGTTAAAGATGTCAA+TGG 0.593126 7.2:-32018621 MS.gene42848:CDS
CCAAGACACGGCGGTCACGG+AGG 0.598529 7.2:+32018562 None:intergenic
CAAGACACGGCGGTCACGGA+GGG 0.598937 7.2:+32018563 None:intergenic
TAGTGACTATGCATGATCGG+TGG 0.614019 7.2:-32017885 MS.gene42848:CDS
GGTGGTGATGGGGTTACCGG+AGG 0.620164 7.2:+32018533 None:intergenic
ATATTGTGCTCCCTATCCGG+TGG 0.628631 7.2:-32018685 MS.gene42848:CDS
AGATAGTGACTATGCATGAT+CGG 0.644746 7.2:-32017888 MS.gene42848:CDS
TGCGACGTAGGGTGGTGATG+GGG 0.652061 7.2:+32018523 None:intergenic
CGGAGGCATCAACCAAGACA+CGG 0.654823 7.2:+32018550 None:intergenic
TTGAGAGCCGAATATGGTGG+TGG 0.662726 7.2:+32018707 None:intergenic
ACGTACCTTGCGACGTAGGG+TGG 0.669594 7.2:+32018515 None:intergenic
GAGCCGAATATGGTGGTGGT+GGG 0.669874 7.2:+32018711 None:intergenic
GATCGGTGGGAAGCTTACAG+AGG 0.712766 7.2:-32017871 MS.gene42848:CDS
ATATTGAGAGCCGAATATGG+TGG 0.741009 7.2:+32018704 None:intergenic
AGGCATCAACCAAGACACGG+CGG 0.796971 7.2:+32018553 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAGTTTTTACTTTATTTTT+GGG + chr7.2:32018157-32018176 None:intergenic 10.0%
!!! TATTTTTTAAAATAAAGAGT+AGG - chr7.2:32017769-32017788 MS.gene42848:CDS 10.0%
!!! TTAAGTTTTTACTTTATTTT+TGG + chr7.2:32018158-32018177 None:intergenic 10.0%
!!! TGTATATACAAAAGTATATT+AGG - chr7.2:32018529-32018548 MS.gene42848:CDS 15.0%
!!! AAAAAAATAGTTTTGCTCAA+TGG - chr7.2:32018093-32018112 MS.gene42848:intron 20.0%
!!! ATATTAGGTTTTACTTTGAT+TGG - chr7.2:32018544-32018563 MS.gene42848:CDS 20.0%
! AAAATCACAAACATCTTCTT+TGG + chr7.2:32018420-32018439 None:intergenic 25.0%
! ACACTTTATTGAGTTATATG+AGG + chr7.2:32018228-32018247 None:intergenic 25.0%
! AGTGTGTGAATTTCAATAAT+TGG - chr7.2:32018122-32018141 MS.gene42848:intron 25.0%
! TTGAGTTATATGAGGTATAA+TGG + chr7.2:32018220-32018239 None:intergenic 25.0%
! TTTGATTGGATTATCACTTA+AGG - chr7.2:32018558-32018577 MS.gene42848:CDS 25.0%
!! AATTGATAAAGACCATTTTG+CGG - chr7.2:32018661-32018680 MS.gene42848:CDS 25.0%
!!! ATTTTAAAGTCAAAGGTAGT+TGG - chr7.2:32018435-32018454 MS.gene42848:intron 25.0%
!!! GTTTGTGATTTTAAAGTCAA+AGG - chr7.2:32018428-32018447 MS.gene42848:intron 25.0%
ATTGCCATTGACATCTTTAA+CGG + chr7.2:32017556-32017575 None:intergenic 30.0%
! AATGTCGTGTTTAAAGTGAA+AGG - chr7.2:32017573-32017592 MS.gene42848:intron 30.0%
! ATGAAAGCGTAATCAACATT+GGG + chr7.2:32018698-32018717 None:intergenic 30.0%
! CAAACTAGATGTTTTTCTAG+CGG - chr7.2:32018388-32018407 MS.gene42848:intron 30.0%
! GATTCATCAAGTTGTACTAT+TGG - chr7.2:32018256-32018275 MS.gene42848:intron 30.0%
! TATGAAAGCGTAATCAACAT+TGG + chr7.2:32018699-32018718 None:intergenic 30.0%
!! AAACTAGATGTTTTTCTAGC+GGG - chr7.2:32018389-32018408 MS.gene42848:intron 30.0%
ACAATATTGAGAGCCGAATA+TGG + chr7.2:32017472-32017491 None:intergenic 35.0%
AGATAGTGACTATGCATGAT+CGG - chr7.2:32018282-32018301 MS.gene42848:intron 35.0%
CGATCTTGTATTATTTACGC+TGG - chr7.2:32018464-32018483 MS.gene42848:intron 35.0%
CGCTAGAAAAACATCTAGTT+TGG + chr7.2:32018390-32018409 None:intergenic 35.0%
TAAAGTCAAAGGTAGTTGGT+TGG - chr7.2:32018439-32018458 MS.gene42848:intron 35.0%
TACTAACAACATTGTTGCAC+AGG - chr7.2:32018490-32018509 MS.gene42848:intron 35.0%
TTCACCGTTAAAGATGTCAA+TGG - chr7.2:32017549-32017568 MS.gene42848:intron 35.0%
! TGTTGATTACGCTTTCATAG+TGG - chr7.2:32018700-32018719 MS.gene42848:CDS 35.0%
ATATTGAGAGCCGAATATGG+TGG + chr7.2:32017469-32017488 None:intergenic 40.0%
CGTGAAAAAGGTAATGACCA+TGG - chr7.2:32017518-32017537 MS.gene42848:CDS 40.0%
GATAAACAGTGACCGCAAAA+TGG + chr7.2:32018676-32018695 None:intergenic 40.0%
TCAATATTGTGCTCCCTATC+CGG - chr7.2:32017482-32017501 MS.gene42848:CDS 40.0%
AAGAGTAGGACATCCAAGTG+TGG - chr7.2:32017783-32017802 MS.gene42848:CDS 45.0%
AGTGACTATGCATGATCGGT+GGG - chr7.2:32018286-32018305 MS.gene42848:intron 45.0%
TAGTGACTATGCATGATCGG+TGG - chr7.2:32018285-32018304 MS.gene42848:intron 45.0%
AACGGTGAAGTTGTCTGCCA+TGG + chr7.2:32017538-32017557 None:intergenic 50.0%
ATATTGTGCTCCCTATCCGG+TGG - chr7.2:32017485-32017504 MS.gene42848:CDS 50.0%
GGATTTGGCGGTCGTGAAAA+AGG - chr7.2:32017506-32017525 MS.gene42848:CDS 50.0%
TCCTTATCAACCACCGATGC+CGG - chr7.2:32017434-32017453 MS.gene42848:CDS 50.0%
TGTACGTACCTTGCGACGTA+GGG + chr7.2:32017661-32017680 None:intergenic 50.0%
TTGAGAGCCGAATATGGTGG+TGG + chr7.2:32017466-32017485 None:intergenic 50.0%
TTGTACGTACCTTGCGACGT+AGG + chr7.2:32017662-32017681 None:intergenic 50.0%
ACCGCCAAATCCACCGGATA+GGG + chr7.2:32017498-32017517 None:intergenic 55.0%
AGGCATCAACCAAGACACGG+CGG + chr7.2:32017620-32017639 None:intergenic 55.0%
CAACCACGTGAGTCCACACT+TGG + chr7.2:32017799-32017818 None:intergenic 55.0%
CATCCAAGTGTGGACTCACG+TGG - chr7.2:32017793-32017812 MS.gene42848:CDS 55.0%
GATCGGTGGGAAGCTTACAG+AGG - chr7.2:32018299-32018318 MS.gene42848:intron 55.0%
GCACCCACCACCACCATATT+CGG - chr7.2:32017456-32017475 MS.gene42848:CDS 55.0%
TTCACGACCGCCAAATCCAC+CGG + chr7.2:32017504-32017523 None:intergenic 55.0%
TTGCGACGTAGGGTGGTGAT+GGG + chr7.2:32017651-32017670 None:intergenic 55.0%
! CGTGTCTTGGTTGATGCCTC+CGG - chr7.2:32017621-32017640 MS.gene42848:intron 55.0%
! TCCCTATCCGGTGGATTTGG+CGG - chr7.2:32017494-32017513 MS.gene42848:CDS 55.0%
! TGCTCCCTATCCGGTGGATT+TGG - chr7.2:32017491-32017510 MS.gene42848:CDS 55.0%
!! AATATGGTGGTGGTGGGTGC+CGG + chr7.2:32017456-32017475 None:intergenic 55.0%
!! AGAGCCGAATATGGTGGTGG+TGG + chr7.2:32017463-32017482 None:intergenic 55.0%
!! CGGAGGCATCAACCAAGACA+CGG + chr7.2:32017623-32017642 None:intergenic 55.0%
!! GAGCCGAATATGGTGGTGGT+GGG + chr7.2:32017462-32017481 None:intergenic 55.0%
!! TAGGGTGGTGATGGGGTTAC+CGG + chr7.2:32017643-32017662 None:intergenic 55.0%
ACGTACCTTGCGACGTAGGG+TGG + chr7.2:32017658-32017677 None:intergenic 60.0%
CAACCAAGACACGGCGGTCA+CGG + chr7.2:32017614-32017633 None:intergenic 60.0%
CATCACCACCCTACGTCGCA+AGG - chr7.2:32017650-32017669 MS.gene42848:intron 60.0%
CTTGCGACGTAGGGTGGTGA+TGG + chr7.2:32017652-32017671 None:intergenic 60.0%
GACCGCCAAATCCACCGGAT+AGG + chr7.2:32017499-32017518 None:intergenic 60.0%
! TGCGACGTAGGGTGGTGATG+GGG + chr7.2:32017650-32017669 None:intergenic 60.0%
!! GCCGGCATCGGTGGTTGATA+AGG + chr7.2:32017438-32017457 None:intergenic 60.0%
CAAGACACGGCGGTCACGGA+GGG + chr7.2:32017610-32017629 None:intergenic 65.0%
!! GGTGGTGATGGGGTTACCGG+AGG + chr7.2:32017640-32017659 None:intergenic 65.0%
CCAAGACACGGCGGTCACGG+AGG + chr7.2:32017611-32017630 None:intergenic 70.0%
CCTCCGTGACCGCCGTGTCT+TGG - chr7.2:32017608-32017627 MS.gene42848:intron 70.0%
!! GTGGTGGTGGGTGCCGGCAT+CGG + chr7.2:32017450-32017469 None:intergenic 70.0%
!! GTGGTGGGTGCCGGCATCGG+TGG + chr7.2:32017447-32017466 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 32017426 32018766 32017426 ID=MS.gene42848
chr7.2 mRNA 32017426 32018766 32017426 ID=MS.gene42848.t1;Parent=MS.gene42848
chr7.2 exon 32018521 32018766 32018521 ID=MS.gene42848.t1.exon1;Parent=MS.gene42848.t1
chr7.2 CDS 32018521 32018766 32018521 ID=cds.MS.gene42848.t1;Parent=MS.gene42848.t1
chr7.2 exon 32017681 32017908 32017681 ID=MS.gene42848.t1.exon2;Parent=MS.gene42848.t1
chr7.2 CDS 32017681 32017908 32017681 ID=cds.MS.gene42848.t1;Parent=MS.gene42848.t1
chr7.2 exon 32017426 32017563 32017426 ID=MS.gene42848.t1.exon3;Parent=MS.gene42848.t1
chr7.2 CDS 32017426 32017563 32017426 ID=cds.MS.gene42848.t1;Parent=MS.gene42848.t1
Gene Sequence

>MS.gene42848

ATGGCTTATCCTTATCAACCACCGATGCCGGCACCCACCACCACCATATTCGGCTCTCAATATTGTGCTCCCTATCCGGTGGATTTGGCGGTCGTGAAAAAGGTAATGACCATGGCAGACAACTTCACCGTTAAAGATGTCAATGGCAATGTCGTGTTTAAAGTGAAAGGTTCTCTCTTAACCCTCCGTGACCGCCGTGTCTTGGTTGATGCCTCCGGTAACCCCATCACCACCCTACGTCGCAAGGTACGTACAACTTTATTAAGAAACTTTGCTTTCATATTTTTATTTTAATGCTCAATATTTTAATTTTGTGATGATTTTTTCTACATATATGATATTTTATTTTTTAAAATAAAGAGTAGGACATCCAAGTGTGGACTCACGTGGTTGCACGTTGAGCATTATCTTTAGATAAGACGTAATTTTATTACATTTAATAATATTTAATATGAAAAATTGTATGTGTTGTAAAATTATATATTTTGTAACTTGAAACACTTTATATCAAAGTTTGTAAGTTAAAAATTATGCAATTTAAATTTAGCTGATGATTAATTTTAGTAATCTTTTCAAAGAGAAATATGATCTATTTTACTCATCATACGAGCTCATATATAAGTTATTCACTTTCTGCAGAAAAAAAATAGTTATTCACTATCAACTAAAAAAAATAGTTTTGCTCAATGGAGTCTTAGTGTGTGAATTTCAATAATTGGTTGATGAAACCCAAAAATAAAGTAAAAACTTAAATGTTAGAGTAATGTTTATTGTTAAAAAATTCATATTATCCATTATACCTCATATAACTCAATAAAGTGTTGTTTAATGATTCATCAAGTTGTACTATTGGTGCAGATAGTGACTATGCATGATCGGTGGGAAGCTTACAGAGGAGAAAGCACAAATTCGAAAGATCTTATATTTACATTGAGAAAATCATCGCTATTGCAGTTGAAGACCAAACTAGATGTTTTTCTAGCGGGTAATACCAAAGAAGATGTTTGTGATTTTAAAGTCAAAGGTAGTTGGTTGGAACGATCTTGTATTATTTACGCTGGTGATACTAACAACATTGTTGCACAGGTAATTAAAAAGCATCTTGTATATACAAAAGTATATTAGGTTTTACTTTGATTGGATTATCACTTAAGGAAATATACTAATCATAAATCAATTTTTGTGATATTGTTGTTACTGCAGATGCACAAAAAGCACACTATTCAAAGTATTTTAATTGATAAAGACCATTTTGCGGTCACTGTTTATCCCAATGTTGATTACGCTTTCATAGTGGCATTAATCGCGATTCTTAATGAGATTAACGAAGATGATGATTGA
Protein sequence

>MS.gene42848.t1

MAYPYQPPMPAPTTTIFGSQYCAPYPVDLAVVKKVMTMADNFTVKDVNGNVVFKVKGSLLTLRDRRVLVDASGNPITTLRRKIVTMHDRWEAYRGESTNSKDLIFTLRKSSLLQLKTKLDVFLAGNTKEDVCDFKVKGSWLERSCIIYAGDTNNIVAQMHKKHTIQSILIDKDHFAVTVYPNVDYAFIVALIAILNEINEDDD