AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG028162

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028162 MtrunA17_Chr5g0436051 94.246 504 7 3 1 482 113 616 0.0 983
MsaG028162 MtrunA17_Chr3g0112601 71.401 514 114 6 1 482 1 513 0.0 736
MsaG028162 MtrunA17_Chr1g0154501 50.939 479 195 9 32 481 1 468 1.53e-163 470
MsaG028162 MtrunA17_Chr8g0373781 58.637 411 136 5 105 481 121 531 1.43e-162 470
MsaG028162 MtrunA17_Chr5g0403301 54.485 301 91 4 206 481 27 306 5.68e-103 310
MsaG028162 MtrunA17_Chr5g0403261 36.585 369 129 9 32 298 1 366 5.49e-69 224
MsaG028162 MtrunA17_Chr5g0403271 64.706 153 49 1 334 481 1 153 1.16e-59 193
MsaG028162 MtrunA17_Chr5g0403291 48.315 89 46 0 137 225 382 470 9.31e-23 101
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028162 AT2G39830.1 64.833 509 144 9 8 482 21 528 0.0 634
MsaG028162 AT2G39830.2 64.453 512 144 10 8 482 21 531 0.0 629
MsaG028162 AT2G39830.3 64.427 506 142 9 8 482 21 519 0.0 625
MsaG028162 AT2G39830.4 62.830 417 124 8 8 394 21 436 7.54e-177 503
MsaG028162 AT4G36860.1 59.233 417 141 5 92 481 139 553 6.56e-165 477
MsaG028162 AT4G36860.3 59.233 417 141 5 92 481 163 577 1.32e-164 478
MsaG028162 AT1G19270.1 45.693 534 205 8 32 482 1 532 3.27e-155 452
MsaG028162 AT1G19270.2 45.693 534 205 8 32 482 1 532 3.27e-155 452
MsaG028162 AT4G36860.2 58.176 318 106 4 92 384 139 454 1.89e-123 368
MsaG028162 AT5G66610.3 48.189 359 158 6 138 475 73 424 7.56e-105 320
MsaG028162 AT5G66610.1 48.189 359 158 6 138 475 200 551 3.54e-104 322
MsaG028162 AT5G66620.1 46.175 366 158 6 138 474 285 640 6.06e-102 319
MsaG028162 AT5G66620.3 46.175 366 158 6 138 474 276 631 1.01e-101 318
MsaG028162 AT5G66620.4 46.175 366 158 6 138 474 276 631 1.01e-101 318
MsaG028162 AT5G66610.2 44.819 386 158 7 138 475 200 578 2.73e-98 308
MsaG028162 AT5G17890.1 46.849 365 162 8 139 474 1240 1601 1.70e-90 302
MsaG028162 AT5G66640.1 44.444 351 160 6 157 474 90 438 1.07e-89 281
MsaG028162 AT5G66640.7 44.444 351 160 6 157 474 90 438 1.07e-89 281
MsaG028162 AT5G66630.1 42.466 365 170 8 138 474 346 698 3.96e-89 287
MsaG028162 AT5G66640.5 44.444 351 160 6 157 474 122 470 4.23e-89 281
MsaG028162 AT5G66640.4 44.444 351 160 6 157 474 121 469 4.43e-89 280
MsaG028162 AT5G66640.3 45.231 325 145 5 183 474 7 331 1.16e-85 267
MsaG028162 AT5G66640.6 39.886 351 172 7 157 474 122 466 1.14e-72 238
MsaG028162 AT5G66640.2 39.886 351 172 7 157 474 121 465 1.18e-72 238
MsaG028162 AT5G66620.2 39.738 229 106 5 138 344 276 494 3.17e-50 179

Find 105 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAAGCAAACTTCACATTT+TGG 0.126071 5:-58302353 None:intergenic
AGGCATAAACCTCTTGTTTC+TGG 0.186251 5:-58303459 None:intergenic
AATATGTGTATATACCTTTA+AGG 0.205624 5:-58303958 None:intergenic
GTCTCATGTTGAAAACAAAT+TGG 0.214527 5:+58304204 MsaT028162.1:CDS
TTAAAACAAGATTTGTGATA+TGG 0.216060 5:-58302317 None:intergenic
CTGTATTCATTGGGATAAAA+TGG 0.256062 5:-58301971 None:intergenic
AATGAAGCTGTTAATAAATA+TGG 0.258522 5:+58304295 MsaT028162.1:CDS
ACAGCAATTCTTGTTCTATA+TGG 0.261118 5:+58303707 MsaT028162.1:CDS
CATGAGATGGACAATACTTT+TGG 0.265205 5:-58302972 None:intergenic
CATGCATGGTTACGCCTTAA+AGG 0.286050 5:+58303944 MsaT028162.1:CDS
AGTATAGATGCCACCCCTTT+TGG 0.293022 5:+58302947 MsaT028162.1:CDS
AATGATTCTTCTCCAGCTTA+TGG 0.306927 5:+58304253 MsaT028162.1:CDS
CTTTCTCATCCATGTATATA+TGG 0.313577 5:+58300343 MsaT028162.1:CDS
ATTGGAGGCCATAGACTTAT+AGG 0.316467 5:+58303641 MsaT028162.1:CDS
AAGATTTCACCTGTATTCAT+TGG 0.335163 5:-58301981 None:intergenic
AACTACCTCGCGCTCGGTAA+TGG 0.338884 5:-58302187 None:intergenic
ATCAAACCAGCAGCATTTAT+AGG 0.343784 5:-58302922 None:intergenic
GAAAGTCTGGTTTCATGAAA+TGG 0.348540 5:+58300904 MsaT028162.1:CDS
AACAAGAGGTTTATGCCTTT+CGG 0.351720 5:+58303464 MsaT028162.1:CDS
ACGACCACTCCTTCCTCTAT+TGG 0.353168 5:-58300952 None:intergenic
GTGCATGGAATCTGCTATAA+TGG 0.356084 5:+58303203 MsaT028162.1:intron
ACTACCTCGCGCTCGGTAAT+GGG 0.362527 5:-58302186 None:intergenic
ATAATCTATGGAAATTGTTT+AGG 0.366827 5:+58302108 MsaT028162.1:CDS
AGTCTATGGCCTCCAATTCT+TGG 0.369796 5:-58303635 None:intergenic
CAGAAGGAGAAAGAGGATTT+AGG 0.374040 5:+58301706 MsaT028162.1:CDS
GCACTTAATGATGCTATTGT+TGG 0.375277 5:+58303330 MsaT028162.1:CDS
ATGAAACCAGACTTTCTCTC+TGG 0.376624 5:-58300897 None:intergenic
TTCTCATGCCTATAAGTCTA+TGG 0.380772 5:-58303649 None:intergenic
AACCTCTTGTTTCTGGCAAA+TGG 0.381781 5:-58303452 None:intergenic
CATTAGCCCATCAAGGATAT+AGG 0.386946 5:+58301867 MsaT028162.1:intron
ATGGCATGCAGGTTACTAAC+AGG 0.396063 5:+58303896 MsaT028162.1:intron
CTCGAACATATTCGTTTGAC+TGG 0.400738 5:+58304331 MsaT028162.1:CDS
CATAATAATCTCTGATTGAA+TGG 0.404836 5:-58303251 None:intergenic
CTGTAGTTGTGAAAGATTAG+AGG 0.408619 5:+58303017 MsaT028162.1:CDS
TGCAATCAGGAGATAATCTA+TGG 0.410658 5:+58302096 MsaT028162.1:CDS
TGTTGTTTCAGATTCATAGA+AGG 0.415721 5:+58303612 MsaT028162.1:intron
TTGTTTACCAAAGCTCTAGA+TGG 0.420805 5:-58301017 None:intergenic
GAATCTGCTATAATGGATAC+TGG 0.421279 5:+58303210 MsaT028162.1:CDS
ATTCATAGAAGGCCAAGAAT+TGG 0.426756 5:+58303623 MsaT028162.1:CDS
AGATTTCACCTGTATTCATT+GGG 0.428419 5:-58301980 None:intergenic
CATATGCCTTCCTCTACTTC+AGG 0.435073 5:-58304070 None:intergenic
TTCAAAGGTGGGTCCAATAG+AGG 0.438064 5:+58300939 MsaT028162.1:CDS
TCAATCAGAGATTATTATGA+AGG 0.445893 5:+58303255 MsaT028162.1:CDS
CAAGACATGCCTTCCTCTGC+AGG 0.450171 5:-58300987 None:intergenic
TCTTCTCCAGCTTATGGTGG+TGG 0.452845 5:+58304259 MsaT028162.1:CDS
TCTCATGTTGAAAACAAATT+GGG 0.452858 5:+58304205 MsaT028162.1:CDS
GCGTGCTCCATCTAGAGCTT+TGG 0.454192 5:+58301010 MsaT028162.1:CDS
TAAAATGGTGCAGGAGCATA+AGG 0.458370 5:-58301956 None:intergenic
TCACACCCAGAGAGAAAGTC+TGG 0.460029 5:+58300891 MsaT028162.1:CDS
CAGATTCCTATAAATGCTGC+TGG 0.468618 5:+58302916 MsaT028162.1:intron
AGACTTTGCACCTTTCTTTG+AGG 0.470152 5:-58304185 None:intergenic
GAGTGGCATCGAAAGCAGTC+TGG 0.476246 5:-58302153 None:intergenic
ATGCAATGAGAGTTTGTTGC+TGG 0.480588 5:-58304133 None:intergenic
TGGAAATTGTTTAGGCTGCA+TGG 0.497463 5:+58302116 MsaT028162.1:CDS
GAAGATATGAAGAGACCAAA+TGG 0.499622 5:+58301754 MsaT028162.1:CDS
TTCTCTTTCAACAAGAAGCA+TGG 0.501914 5:-58303307 None:intergenic
CTAAAACCACCACCATAAGC+TGG 0.509878 5:-58304265 None:intergenic
CTGCAGAGGAAGGCATGTCT+TGG 0.516391 5:+58300988 MsaT028162.1:CDS
TAGAGCTCAGAAGGAGAAAG+AGG 0.516816 5:+58301699 MsaT028162.1:CDS
ACCATGCATGCATCAACTCA+TGG 0.520688 5:-58303931 None:intergenic
TGATCGTGCTAGAGCTCAGA+AGG 0.527771 5:+58301690 MsaT028162.1:CDS
TCTCTGATTGAATGGTATAG+AGG 0.533543 5:-58303243 None:intergenic
GGATCAAACTACCTCGCGCT+CGG 0.536169 5:-58302193 None:intergenic
GCTGCTTCTTCCTCAAAGAA+AGG 0.536522 5:+58304175 MsaT028162.1:CDS
CATAGAAGGCCAAGAATTGG+AGG 0.541624 5:+58303626 MsaT028162.1:CDS
GTCAGGTTCTGTCATATATG+TGG 0.544593 5:+58304092 MsaT028162.1:CDS
TCTCTTTCAACAAGAAGCAT+GGG 0.545613 5:-58303306 None:intergenic
CCCATCAAGGATATAGGTGG+GGG 0.548766 5:+58301873 MsaT028162.1:intron
CACCATTTGCCAGAAACAAG+AGG 0.548780 5:+58303450 MsaT028162.1:CDS
TCATTGGGATAAAATGGTGC+AGG 0.553987 5:-58301965 None:intergenic
TGAAACCAGACTTTCTCTCT+GGG 0.553994 5:-58300896 None:intergenic
CATTATGATCCTGCAGAGGA+AGG 0.555932 5:+58300978 MsaT028162.1:CDS
AACATGTGTTCTTATTACAC+AGG 0.561919 5:-58304361 None:intergenic
GATTCTTCTCCAGCTTATGG+TGG 0.562395 5:+58304256 MsaT028162.1:CDS
AGTAGAGGAAGGCATATGTC+AGG 0.562990 5:+58304075 MsaT028162.1:CDS
CCATGCATGCATCAACTCAT+GGG 0.575521 5:-58303930 None:intergenic
AGCCCATCAAGGATATAGGT+GGG 0.576893 5:+58301871 MsaT028162.1:intron
CCCATGAGTTGATGCATGCA+TGG 0.580940 5:+58303930 MsaT028162.1:CDS
AGCAACAAACTCTCATTGCA+TGG 0.581985 5:+58304135 MsaT028162.1:CDS
TCACAGTTTGCTCTTCCGAA+AGG 0.583186 5:-58303479 None:intergenic
CTGAAGAAAGTGACATTGCA+TGG 0.583861 5:-58301729 None:intergenic
GTATTGTCATATTCATGAGA+TGG 0.585321 5:-58302985 None:intergenic
GCCCATCAAGGATATAGGTG+GGG 0.591148 5:+58301872 MsaT028162.1:intron
CAATCTCAGTCCTGAAGTAG+AGG 0.592599 5:+58304060 MsaT028162.1:CDS
TGAGGAAGAAGCAGCAGCTG+TGG 0.594186 5:-58304167 None:intergenic
TAGCCCATCAAGGATATAGG+TGG 0.597899 5:+58301870 MsaT028162.1:intron
TGATTGATATGATCAGAAGA+AGG 0.604305 5:-58300319 None:intergenic
CATCAAGGATATAGGTGGGG+GGG 0.609524 5:+58301875 MsaT028162.1:intron
CATTGAACAGAAGACTATGT+GGG 0.609543 5:+58302070 MsaT028162.1:intron
AGAAAATGAAGATTATGGAA+AGG 0.614335 5:+58301898 MsaT028162.1:CDS
CTCAGTCCTGAAGTAGAGGA+AGG 0.619865 5:+58304064 MsaT028162.1:CDS
AATGGTGCAGGAGCATAAGG+AGG 0.625823 5:-58301953 None:intergenic
AGTAAAGTACCATATATACA+TGG 0.626223 5:-58300352 None:intergenic
TTCTCCCATTACCGAGCGCG+AGG 0.628667 5:+58302182 MsaT028162.1:CDS
AAGGTGGGTCCAATAGAGGA+AGG 0.645391 5:+58300943 MsaT028162.1:CDS
ATTGAACAGAAGACTATGTG+GGG 0.648467 5:+58302071 MsaT028162.1:intron
GCATTGAACAGAAGACTATG+TGG 0.658253 5:+58302069 MsaT028162.1:intron
TTGTTCTATATGGTCTACCA+AGG 0.659611 5:+58303717 MsaT028162.1:CDS
ACATGTGTTCTTATTACACA+GGG 0.664721 5:-58304360 None:intergenic
GGGTCCAATAGAGGAAGGAG+TGG 0.672837 5:+58300948 MsaT028162.1:CDS
ATGGTGCAGGAGCATAAGGA+GGG 0.678829 5:-58301952 None:intergenic
CCATCAAGGATATAGGTGGG+GGG 0.680331 5:+58301874 MsaT028162.1:intron
TAATGGGAGAATGACAAGAG+TGG 0.685159 5:-58302170 None:intergenic
TCATCATTATGATCCTGCAG+AGG 0.695986 5:+58300974 MsaT028162.1:CDS
TTGAACAGAAGACTATGTGG+GGG 0.724066 5:+58302072 MsaT028162.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 58300313 58304369 58300313 ID=MsaG028162
Chr5 mRNA 58300313 58304369 58300313 ID=MsaT028162.1;Parent=MsaG028162
Chr5 exon 58300313 58300364 58300313 ID=MsaT028162.1.exon1;Parent=MsaT028162.1
Chr5 CDS 58300313 58300364 58300313 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58300877 58301031 58300877 ID=MsaT028162.1.exon2;Parent=MsaT028162.1
Chr5 CDS 58300877 58301031 58300877 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58301688 58301775 58301688 ID=MsaT028162.1.exon3;Parent=MsaT028162.1
Chr5 CDS 58301688 58301775 58301688 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58301882 58301993 58301882 ID=MsaT028162.1.exon4;Parent=MsaT028162.1
Chr5 CDS 58301882 58301993 58301882 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58302080 58302203 58302080 ID=MsaT028162.1.exon5;Parent=MsaT028162.1
Chr5 CDS 58302080 58302203 58302080 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58302296 58302379 58302296 ID=MsaT028162.1.exon6;Parent=MsaT028162.1
Chr5 CDS 58302296 58302379 58302296 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58302919 58303038 58302919 ID=MsaT028162.1.exon7;Parent=MsaT028162.1
Chr5 CDS 58302919 58303038 58302919 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58303204 58303362 58303204 ID=MsaT028162.1.exon8;Parent=MsaT028162.1
Chr5 CDS 58303204 58303362 58303204 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58303444 58303506 58303444 ID=MsaT028162.1.exon9;Parent=MsaT028162.1
Chr5 CDS 58303444 58303506 58303444 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58303623 58303738 58303623 ID=MsaT028162.1.exon10;Parent=MsaT028162.1
Chr5 CDS 58303623 58303738 58303623 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58303907 58303965 58303907 ID=MsaT028162.1.exon11;Parent=MsaT028162.1
Chr5 CDS 58303907 58303965 58303907 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Chr5 exon 58304053 58304369 58304053 ID=MsaT028162.1.exon12;Parent=MsaT028162.1
Chr5 CDS 58304053 58304369 58304053 ID=cds.MsaT028162.1;Parent=MsaT028162.1
Gene Sequence

>MsaT028162.1

ATGGCTCCTTCTTCTGATCATATCAATCATCTTTCTCATCCATGTATATATGGGGATTATGTGTCTTCACACCCAGAGAGAAAGTCTGGTTTCATGAAATGGCTTAGTAAGCTTTTCAAAGGTGGGTCCAATAGAGGAAGGAGTGGTCGTCATCATTATGATCCTGCAGAGGAAGGCATGTCTTGGCGTGCTCCATCTAGAGCTTTGGATGATCGTGCTAGAGCTCAGAAGGAGAAAGAGGATTTAGGCCATGCAATGTCACTTTCTTCAGCAGAAGATATGAAGAGACCAAATGGATATAGGTGGGGGGGAGAAAATGAAGATTATGGAAAGGCACTTCATGATAACTTTAACTCATCTGCACACCCTCCTTATGCTCCTGCACCATTTTATCCCAATGAATACAGAAGACTATGTGGGGGCTGCAATCAGGAGATAATCTATGGAAATTGTTTAGGCTGCATGGATACTTATTTTCATCCAGACTGCTTTCGATGCCACTCTTGTCATTCTCCCATTACCGAGCGCGAGTTTTCTTTGTCAGGGAAGCATCCATATCACAAATCTTGTTTTAAAGAGTTGACTCACCCAAAATGTGAAGTTTGCTTCCAATTTATTCCTATAAATGCTGCTGGTTTGATTGAGTATAGATGCCACCCCTTTTGGTCCCAAAAGTATTGTCCATCTCATGAATATGACAATACAGCTCGCTGCTGTAGTTGTGAAAGATTAGAGTGCATGGAATCTGCTATAATGGATACTGGTGACTGTCAGCCTCTATACCATTCAATCAGAGATTATTATGAAGGAATGCATATGAAAATTGATCAGCAAGTTCCCATGCTTCTTGTTGAAAGAGAAGCACTTAATGATGCTATTGTTGGAGAGAAGACTGGATTTCACCATTTGCCAGAAACAAGAGGTTTATGCCTTTCGGAAGAGCAAACTGTGACCAGTATTCATAGAAGGCCAAGAATTGGAGGCCATAGACTTATAGGCATGAGAACTCAACCTCAAAAGCTAATAAGAAAATGTGAAGTTACAGCAATTCTTGTTCTATATGGTCTACCAAGGTTACTAACAGGTGCTATACTTGCCCATGAGTTGATGCATGCATGGTTACGCCTTAAAGGTTATCGCAATCTCAGTCCTGAAGTAGAGGAAGGCATATGTCAGGTTCTGTCATATATGTGGCTTGAGTCAGAAGTTATGCCAGCAACAAACTCTCATTGCATGGCATCAACATCCACAGCTGCTGCTTCTTCCTCAAAGAAAGGTGCAAAGTCTCATGTTGAAAACAAATTGGGTGAATTCTTCAAGAATCAAATTGTCAATGATTCTTCTCCAGCTTATGGTGGTGGTTTTAGAGCTGCAAATGAAGCTGTTAATAAATATGGTCTACGTAGTACTCTCGAACATATTCGTTTGACTGGTTTTATCCCTGTGTAA
Protein sequence

>MsaT028162.1

MAPSSDHINHLSHPCIYGDYVSSHPERKSGFMKWLSKLFKGGSNRGRSGRHHYDPAEEGMSWRAPSRALDDRARAQKEKEDLGHAMSLSSAEDMKRPNGYRWGGENEDYGKALHDNFNSSAHPPYAPAPFYPNEYRRLCGGCNQEIIYGNCLGCMDTYFHPDCFRCHSCHSPITEREFSLSGKHPYHKSCFKELTHPKCEVCFQFIPINAAGLIEYRCHPFWSQKYCPSHEYDNTARCCSCERLECMESAIMDTGDCQPLYHSIRDYYEGMHMKIDQQVPMLLVEREALNDAIVGEKTGFHHLPETRGLCLSEEQTVTSIHRRPRIGGHRLIGMRTQPQKLIRKCEVTAILVLYGLPRLLTGAILAHELMHAWLRLKGYRNLSPEVEEGICQVLSYMWLESEVMPATNSHCMASTSTAAASSSKKGAKSHVENKLGEFFKNQIVNDSSPAYGGGFRAANEAVNKYGLRSTLEHIRLTGFIPV*