AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG008415

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG008415 MtrunA17_Chr3g0088371 81.675 191 32 1 423 610 1 191 4.11e-106 318
MsaG008415 MtrunA17_Chr1g0172971 76.515 132 16 1 1 132 1 117 2.54e-58 204
MsaG008415 MtrunA17_Chr2g0324011 26.337 243 134 4 228 470 374 571 1.16e-21 99.4
MsaG008415 MtrunA17_Chr1g0203721 24.308 325 187 8 231 548 433 705 2.46e-18 89.4
MsaG008415 MtrunA17_Chr1g0202341 27.755 245 122 9 228 467 415 609 1.52e-17 86.7
MsaG008415 MtrunA17_Chr1g0207551 24.324 296 168 7 231 523 399 641 3.46e-17 85.5
MsaG008415 MtrunA17_Chr5g0448761 22.188 320 199 8 228 546 431 701 4.06e-17 85.5
MsaG008415 MtrunA17_Chr3g0082121 38.235 102 63 0 226 327 398 499 9.51e-17 84.0
MsaG008415 MtrunA17_Chr3g0082121 28.889 135 87 3 399 532 529 655 1.48e-12 70.9
MsaG008415 MtrunA17_Chr3g0118611 24.746 295 172 8 231 524 312 557 2.58e-16 82.8
MsaG008415 MtrunA17_Chr8g0363841 25.926 243 137 5 228 470 381 580 2.64e-16 82.8
MsaG008415 MtrunA17_Chr3g0080351 26.027 292 158 8 236 523 438 675 7.60e-16 81.3
MsaG008415 MtrunA17_Chr2g0329031 23.762 303 176 9 228 528 369 618 2.80e-14 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG008415 AT4G15090.1 25.634 355 203 9 231 578 419 719 2.01e-23 105
MsaG008415 AT4G15090.5 25.634 355 203 9 231 578 419 719 2.01e-23 105
MsaG008415 AT4G15090.3 25.634 355 203 9 231 578 419 719 2.01e-23 105
MsaG008415 AT4G15090.2 25.634 355 203 9 231 578 419 719 2.01e-23 105
MsaG008415 AT4G15090.4 25.634 355 203 9 231 578 419 719 2.01e-23 105
MsaG008415 AT3G22170.2 26.000 250 137 6 219 467 416 618 3.93e-18 89.0
MsaG008415 AT3G22170.1 26.000 250 137 6 219 467 416 618 3.93e-18 89.0
MsaG008415 AT2G27110.2 21.867 375 240 11 231 602 390 714 4.37e-13 73.2
MsaG008415 AT2G27110.1 21.867 375 240 11 231 602 390 714 4.37e-13 73.2
MsaG008415 AT2G27110.3 21.867 375 240 11 231 602 245 569 5.24e-13 72.8
MsaG008415 AT4G19990.1 37.113 97 51 3 398 494 440 526 2.48e-11 67.4
MsaG008415 AT4G19990.3 37.113 97 51 3 398 494 497 583 2.51e-11 67.4
MsaG008415 AT4G19990.4 37.113 97 51 3 398 494 497 583 2.51e-11 67.4
MsaG008415 AT4G19990.6 35.052 97 53 2 398 494 497 583 2.57e-11 67.4
MsaG008415 AT4G19990.2 35.052 97 53 2 398 494 497 583 2.57e-11 67.4
MsaG008415 AT4G19990.5 37.113 97 51 3 398 494 497 583 2.62e-11 67.4
MsaG008415 AT4G19990.7 37.113 97 51 3 398 494 511 597 2.67e-11 67.0

Find 102 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATGCTGAGTTGGACTTTA+AGG 0.133287 2:+34400634 MsaT008415.1:CDS
AGTCGCTTCTTTGACTTAAT+TGG 0.149305 2:-34401454 None:intergenic
CTTTAGTCATTTCAACATTA+TGG 0.194287 2:+34400592 MsaT008415.1:CDS
TTCTTTGACTTAATTGGATT+TGG 0.266522 2:-34401448 None:intergenic
TCTGTTGTTGGCCTGTTGTT+AGG 0.292589 2:-34398984 None:intergenic
CGATCATGATCTTCAAAACT+TGG 0.305304 2:-34400932 None:intergenic
TTACTTCTCGAAATGATCTA+AGG 0.311482 2:-34399175 None:intergenic
GCCTTCGAATGTTGATGTTT+TGG 0.322848 2:+34400883 MsaT008415.1:CDS
TTGAAGATCTTGGAGTTCTT+AGG 0.331625 2:+34401052 MsaT008415.1:CDS
GCATACGATTTGCGTAAGTT+TGG 0.338878 2:-34400448 None:intergenic
CTCGACGGTGTTCTTGAAGC+TGG 0.383392 2:+34401292 MsaT008415.1:CDS
TTTGTTTCTTCCGATTGATA+AGG 0.384635 2:-34401516 None:intergenic
GAGAACGTCTTATGAAGTTA+TGG 0.394356 2:+34399250 MsaT008415.1:CDS
TTTGGTCTTTCTTTGAACTT+TGG 0.398856 2:-34401430 None:intergenic
TTCCTTCAAATACTATTATG+AGG 0.399583 2:+34400766 MsaT008415.1:CDS
GAAGGCCTACCTCAGACTTT+AGG 0.402909 2:+34400417 MsaT008415.1:intron
CATGTCGTATGTTTGAGAAC+AGG 0.415108 2:+34401008 MsaT008415.1:CDS
GTCTTATGAAGTTATGGGTC+AGG 0.415385 2:+34399256 MsaT008415.1:CDS
GAAGTTATGGGTCAGGGAGT+TGG 0.426260 2:+34399263 MsaT008415.1:CDS
CGTTATGTTTGTAACAAAGA+AGG 0.427485 2:+34398936 MsaT008415.1:CDS
GCTGTTGGTGAAACATCTGC+TGG 0.428855 2:+34401391 MsaT008415.1:CDS
CGAGAAGTAAATGAAGTTCA+AGG 0.430014 2:+34399188 MsaT008415.1:CDS
TTGATATCGTTGTGCTTGAC+TGG 0.433430 2:-34401200 None:intergenic
GAGGAGTTGCTTCTTTCTAA+AGG 0.437852 2:+34401325 MsaT008415.1:CDS
TCCATGATTCTTTATTGCTA+GGG 0.444266 2:-34398773 None:intergenic
TTCCATGATTCTTTATTGCT+AGG 0.445442 2:-34398774 None:intergenic
TTCTTTGAACTTTGGTGCGG+TGG 0.447203 2:-34401422 None:intergenic
GAAAGGGTTGGTTGTAAAGC+TGG 0.447509 2:+34399053 MsaT008415.1:CDS
TATGCATTGGTCTTCAGCTT+GGG 0.450920 2:+34400466 MsaT008415.1:CDS
ATGTGTATAAGATATATAGA+TGG 0.452819 2:+34399105 MsaT008415.1:CDS
ACATCAACTTCATCTGATAG+TGG 0.459514 2:+34398648 MsaT008415.1:CDS
CTTGCTTTGCATTTATTCAC+AGG 0.460007 2:+34400732 MsaT008415.1:CDS
GACCGCATCAGCTGACTGTT+GGG 0.463150 2:-34400686 None:intergenic
ACCTGTGGACTGTCTGTTGT+TGG 0.465317 2:-34398996 None:intergenic
AGAACGTCTTATGAAGTTAT+GGG 0.466325 2:+34399251 MsaT008415.1:CDS
GTTTACTTAATCCTAACAAC+AGG 0.470860 2:+34398973 MsaT008415.1:CDS
CGCTTTAAAACATATTGTCC+AGG 0.471916 2:-34401109 None:intergenic
GGCAGAAATTCCTTATCAAT+CGG 0.471938 2:+34401506 MsaT008415.1:CDS
ATCATGATCGATTTGATGAA+AGG 0.476999 2:+34400945 MsaT008415.1:CDS
GTATGCATTGGTCTTCAGCT+TGG 0.479582 2:+34400465 MsaT008415.1:CDS
TTTAAGTCTGAAAACCGAAA+AGG 0.483010 2:-34399302 None:intergenic
CTCCTCATAATAGTATTTGA+AGG 0.485089 2:-34400768 None:intergenic
CTTTCTAAAGGTATTCGTAC+AGG 0.486879 2:+34401337 MsaT008415.1:CDS
GATCATGATCTTCAAAACTT+GGG 0.487945 2:-34400931 None:intergenic
CATTCTTTGAAGACAATACC+TGG 0.489494 2:+34401091 MsaT008415.1:CDS
TATGAGGAGGACACAACAAA+AGG 0.490908 2:+34400782 MsaT008415.1:CDS
GTCTTCAGTGCCAACATTGA+CGG 0.491796 2:-34401176 None:intergenic
TTGAAGACTTAGATGGCGTC+GGG 0.493598 2:-34401360 None:intergenic
CTGTTGGTGAAACATCTGCT+GGG 0.493682 2:+34401392 MsaT008415.1:CDS
ACATTATGGTTCAGAGAATG+AGG 0.494022 2:+34400606 MsaT008415.1:CDS
CCCCTAGCAATAAAGAATCA+TGG 0.497001 2:+34398772 MsaT008415.1:CDS
TGAATAAATGCAAAGCAAGA+AGG 0.503349 2:-34400728 None:intergenic
TCTTTGAACTTTGGTGCGGT+GGG 0.503874 2:-34401421 None:intergenic
TTACAACCAACCCTTTCCTC+AGG 0.505082 2:-34399047 None:intergenic
AGCTGGAATATATTTGAAGC+TGG 0.507410 2:+34399070 MsaT008415.1:CDS
GAGGGATAATCATGCTGAGT+TGG 0.508852 2:+34400625 MsaT008415.1:CDS
ACAAAACAAGAAATCTGATA+AGG 0.511435 2:+34398902 MsaT008415.1:CDS
CTAAGGTAACACGAATGCTC+TGG 0.517941 2:-34399158 None:intergenic
GAATAAATGCAAAGCAAGAA+GGG 0.521406 2:-34400727 None:intergenic
GTCAGCATGAATCATTGCTA+GGG 0.522802 2:-34398733 None:intergenic
GGTAATTATGCATATAACAC+TGG 0.523547 2:+34398840 MsaT008415.1:CDS
TAACAAAGAAGGTTTCAAGA+AGG 0.525236 2:+34398947 MsaT008415.1:CDS
TAAGATATATAGATGGGATG+TGG 0.528498 2:+34399112 MsaT008415.1:CDS
CATAATAGTATTTGAAGGAA+AGG 0.529686 2:-34400763 None:intergenic
GAATGCTCTGGTTTATGTAA+TGG 0.534744 2:-34399146 None:intergenic
CCATGATTCTTTATTGCTAG+GGG 0.537011 2:-34398772 None:intergenic
TGTCAGCATGAATCATTGCT+AGG 0.540740 2:-34398734 None:intergenic
ATGAGGAGGACACAACAAAA+GGG 0.542065 2:+34400783 MsaT008415.1:CDS
AATCGAACAAGTGAGTGGTC+TGG 0.543268 2:-34400569 None:intergenic
AACAAAGAAGGTTTCAAGAA+GGG 0.545537 2:+34398948 MsaT008415.1:CDS
GTTATGGGTCAGGGAGTTGG+AGG 0.547221 2:+34399266 MsaT008415.1:CDS
AAGATCTTGGAGTTCTTAGG+TGG 0.553166 2:+34401055 MsaT008415.1:CDS
ATGTCGTATGTTTGAGAACA+GGG 0.560861 2:+34401009 MsaT008415.1:CDS
GGCCTACCTCAGACTTTAGG+TGG 0.565384 2:+34400420 MsaT008415.1:intron
TCTTCAAAAGTAGCTGCTGT+TGG 0.568528 2:+34401376 MsaT008415.1:CDS
GGACCGCATCAGCTGACTGT+TGG 0.570066 2:-34400687 None:intergenic
TTTGAAGACTTAGATGGCGT+CGG 0.575863 2:-34401361 None:intergenic
ATCATGATCTTCAAAACTTG+GGG 0.577988 2:-34400930 None:intergenic
ATGAAATCGACCGTCAATGT+TGG 0.583819 2:+34401166 MsaT008415.1:CDS
ATCCCAACAGTCAGCTGATG+CGG 0.597403 2:+34400684 MsaT008415.1:CDS
CTTACGCAAATCGTATGCAT+TGG 0.597846 2:+34400453 MsaT008415.1:CDS
TATGATGATGCTGATAATGA+CGG 0.599988 2:+34400860 MsaT008415.1:CDS
TGTGTATAAGATATATAGAT+GGG 0.601002 2:+34399106 MsaT008415.1:CDS
TCACTGATTCATGCTGAGAG+TGG 0.606950 2:+34398693 MsaT008415.1:CDS
TCCAAAACATCAACATTCGA+AGG 0.607058 2:-34400884 None:intergenic
CTTCAAATACTATTATGAGG+AGG 0.607664 2:+34400769 MsaT008415.1:CDS
TCTTATGAAGTTATGGGTCA+GGG 0.609153 2:+34399257 MsaT008415.1:CDS
GCCAACAACAGACAGTCCAC+AGG 0.619933 2:+34398995 MsaT008415.1:CDS
ATGATGATGCTGATAATGAC+GGG 0.620534 2:+34400861 MsaT008415.1:CDS
TTCACAAACTCAATAACCTG+TGG 0.626760 2:-34399011 None:intergenic
TGAAGCTTTATCAGTGATTG+TGG 0.633753 2:+34401549 MsaT008415.1:CDS
TGTTGGTGAAACATCTGCTG+GGG 0.639082 2:+34401393 MsaT008415.1:CDS
CATTATGGTTCAGAGAATGA+GGG 0.643278 2:+34400607 MsaT008415.1:CDS
GATTTCATCTTATCGACAGA+CGG 0.652942 2:-34401151 None:intergenic
GACAAGCCACCTAAAGTCTG+AGG 0.653221 2:-34400426 None:intergenic
TGTCGTATGTTTGAGAACAG+GGG 0.653807 2:+34401010 MsaT008415.1:CDS
TAAAGAATCGAACAAGTGAG+TGG 0.654901 2:-34400574 None:intergenic
TCTTTCTTTGAACTTTGGTG+CGG 0.659854 2:-34401425 None:intergenic
AATAAATGCAAAGCAAGAAG+GGG 0.664515 2:-34400726 None:intergenic
TCAGCATGAATCATTGCTAG+GGG 0.681156 2:-34398732 None:intergenic
AGCCACCTAAAGTCTGAGGT+AGG 0.684957 2:-34400422 None:intergenic
AGGGGTGTACGTGTTTACAA+CGG 0.709933 2:-34400708 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 34398639 34401582 34398639 ID=MsaG008415
Chr2 mRNA 34398639 34401582 34398639 ID=MsaT008415.1;Parent=MsaG008415
Chr2 exon 34398639 34399309 34398639 ID=MsaT008415.1.exon1;Parent=MsaT008415.1
Chr2 CDS 34398639 34399309 34398639 ID=cds.MsaT008415.1;Parent=MsaT008415.1
Chr2 exon 34400421 34401582 34400421 ID=MsaT008415.1.exon2;Parent=MsaT008415.1
Chr2 CDS 34400421 34401582 34400421 ID=cds.MsaT008415.1;Parent=MsaT008415.1
Gene Sequence

>MsaT008415.1

ATGGATTTGACATCAACTTCATCTGATAGTGGACAACTGAGTGTTGAAACTTCATCACTGATTCATGCTGAGAGTGGACAATTGAGTGTTACTCCCCTAGCAATGATTCATGCTGACAGTTCTCAATGTTACTCCCCTAGCAATAAAGAATCATGGAAGTCTTTAGTCTTTCAATCTATTAAAGAGATTGAAGATTTTTATGGTAATTATGCATATAACACTGGATTTTCTATTAGGACTATGTTGAAGTCGAAGAATAATTCACAAAACAAGAAATCTGATAAGGTACATTATTTGCGTTATGTTTGTAACAAAGAAGGTTTCAAGAAGGGAAGTTTACTTAATCCTAACAACAGGCCAACAACAGACAGTCCACAGGTTATTGAGTTTGTGAAAGTGAAAGAAAAACCTGAGGAAAGGGTTGGTTGTAAAGCTGGAATATATTTGAAGCTGGATGAAGTTTTGAATGTGTATAAGATATATAGATGGGATGTGGATCACTGTCATCCATTACATAAACCAGAGCATTCGTGTTACCTTAGATCATTTCGAGAAGTAAATGAAGTTCAAGGACAACTAGCTCTTAAAAATTCTAAAGCTGGAATGTCGATGAGAACGTCTTATGAAGTTATGGGTCAGGGAGTTGGAGGCATAGAGAATCTTCCTTTTCGGCCTACCTCAGACTTTAGGTGGCTTGTCCAAACTTACGCAAATCGTATGCATTGGTCTTCAGCTTGGGTCAAGTCACATTTTACAGCTGGTCTGAAAACGACTCAGTTAAGTGAGTCTTTCAATGCTTTTCTTCGTGGATTTCTACAGCCAGACCACTCACTTGTTCGATTCTTTAGTCATTTCAACATTATGGTTCAGAGAATGAGGGATAATCATGCTGAGTTGGACTTTAAGGCTGCAAACACTAGAACAAAAAATAATTATCCCAACAGTCAGCTGATGCGGTCCGTTGTAAACACGTACACCCCTTCTTGCTTTGCATTTATTCACAGGCAGTATGACCTTTCCTTCAAATACTATTATGAGGAGGACACAACAAAAGGGTCTGCCTTTGAGAAGTTTTTCAAAGTTTTCACAATTGATAAGGTTGATGATAATTATGATGATGCTGATAATGACGGGCCTTCGAATGTTGATGTTTTGGATGCAGAACTTCAAGAAAACGTTTCCCCAAGTTTTGAAGATCATGATCGATTTGATGAAAGGCTTGTCACAGTTGACATTAGAAGCAAAAGTTTTAGTTGTTCATGTCGTATGTTTGAGAACAGGGGCTTCTTATGTCGACATGTTTTGAAGATCTTGGAGTTCTTAGGTGGACATGTGCAATATCATTCTTTGAAGACAATACCTGGACAATATGTTTTAAAGCGTTGGACTAGAGATGTGCGTCCGTCTGTCGATAAGATGAAATCGACCGTCAATGTTGGCACTGAAGACACCAGTCAAGCACAACGATATCAACAAATTTGTGCTGTTACAGTTCAGCTTTCTACACGTTTTTGTGCAGATCCAGAGTCATCTAAAATTTTTCTCGACGGTGTTCTTGAAGCTGGAAAAAAGGCAGAGGAGTTGCTTCTTTCTAAAGGTATTCGTACAGGCCCGACGCCATCTAAGTCTTCAAAAGTAGCTGCTGTTGGTGAAACATCTGCTGGGGTGAAGCCCACCGCACCAAAGTTCAAAGAAAGACCAAATCCAATTAAGTCAAAGAAGCGACTTAAAAGTGATTATGAAAAAGCTAGAGAAAGGCAGAAATTCCTTATCAATCGGAAGAAACAAAAGAGAGATGATGAAGCTTTATCAGTGATTGTGGTCCCTGATTGA
Protein sequence

>MsaT008415.1

MDLTSTSSDSGQLSVETSSLIHAESGQLSVTPLAMIHADSSQCYSPSNKESWKSLVFQSIKEIEDFYGNYAYNTGFSIRTMLKSKNNSQNKKSDKVHYLRYVCNKEGFKKGSLLNPNNRPTTDSPQVIEFVKVKEKPEERVGCKAGIYLKLDEVLNVYKIYRWDVDHCHPLHKPEHSCYLRSFREVNEVQGQLALKNSKAGMSMRTSYEVMGQGVGGIENLPFRPTSDFRWLVQTYANRMHWSSAWVKSHFTAGLKTTQLSESFNAFLRGFLQPDHSLVRFFSHFNIMVQRMRDNHAELDFKAANTRTKNNYPNSQLMRSVVNTYTPSCFAFIHRQYDLSFKYYYEEDTTKGSAFEKFFKVFTIDKVDDNYDDADNDGPSNVDVLDAELQENVSPSFEDHDRFDERLVTVDIRSKSFSCSCRMFENRGFLCRHVLKILEFLGGHVQYHSLKTIPGQYVLKRWTRDVRPSVDKMKSTVNVGTEDTSQAQRYQQICAVTVQLSTRFCADPESSKIFLDGVLEAGKKAEELLLSKGIRTGPTPSKSSKVAAVGETSAGVKPTAPKFKERPNPIKSKKRLKSDYEKARERQKFLINRKKQKRDDEALSVIVVPD*