AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0014080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0014080 MtrunA17_Chr1g0164131 70.349 172 33 3 15 168 285 456 2.06e-63 203
Msa0014080 MtrunA17_Chr1g0163811 62.112 161 39 4 26 168 90 246 4.08e-57 180
Msa0014080 MtrunA17_Chr1g0164031 60.625 160 45 3 1 142 54 213 2.73e-51 166
Msa0014080 MtrunA17_Chr1g0164951 67.769 121 29 2 47 158 1 120 3.29e-49 154
Msa0014080 MtrunA17_Chr6g0478011 27.841 176 101 4 11 164 99 270 1.51e-14 69.7
Msa0014080 MtrunA17_Chr8g0391651 29.379 177 99 5 11 165 395 567 2.30e-14 69.7
Msa0014080 MtrunA17_Chr8g0391651 27.168 173 106 4 11 164 325 496 1.89e-11 61.6
Msa0014080 MtrunA17_Chr6g0478291 26.816 179 105 4 11 167 287 461 2.35e-13 67.0
Msa0014080 MtrunA17_Chr4g0059641 26.744 172 108 4 11 164 58 229 2.45e-13 66.2
Msa0014080 MtrunA17_Chr2g0296901 27.612 134 83 2 45 164 156 289 4.29e-13 66.2
Msa0014080 MtrunA17_Chr6g0482901 27.933 179 103 5 11 167 291 465 7.52e-13 65.5
Msa0014080 MtrunA17_Chr6g0473241 27.273 132 86 2 46 167 393 524 1.13e-12 65.1
Msa0014080 MtrunA17_Chr6g0482791 27.273 176 102 5 11 164 279 450 2.51e-12 63.9
Msa0014080 MtrunA17_Chr6g0482561 25.466 161 102 3 20 162 204 364 2.54e-12 63.9
Msa0014080 MtrunA17_Chr6g0482601 25.466 161 102 3 20 162 277 437 2.96e-12 63.5
Msa0014080 MtrunA17_Chr6g0473341 27.273 132 86 2 46 167 393 524 2.98e-12 63.5
Msa0014080 MtrunA17_Chr2g0296811 28.462 130 83 2 45 164 65 194 4.60e-12 62.0
Msa0014080 MtrunA17_Chr6g0481751 25.455 165 105 3 12 158 276 440 4.61e-12 63.2
Msa0014080 MtrunA17_Chr6g0482821 25.466 161 102 3 20 162 368 528 4.92e-12 63.2
Msa0014080 MtrunA17_Chr6g0473461 26.316 133 88 2 46 168 63 195 5.72e-12 61.2
Msa0014080 MtrunA17_Chr6g0482771 25.967 181 106 5 11 167 280 456 5.88e-12 62.8
Msa0014080 MtrunA17_Chr6g0473431 26.515 132 87 2 46 167 393 524 6.59e-12 62.8
Msa0014080 MtrunA17_Chr5g0395201 31.061 132 81 2 46 167 411 542 6.87e-12 62.8
Msa0014080 MtrunA17_Chr6g0473261 26.515 132 87 2 46 167 441 572 8.61e-12 62.4
Msa0014080 MtrunA17_Chr6g0473351 26.515 132 87 2 46 167 390 521 9.56e-12 62.4
Msa0014080 MtrunA17_Chr6g0473481 26.515 132 87 2 46 167 393 524 1.35e-11 62.0
Msa0014080 MtrunA17_Chr6g0473511 26.515 132 87 2 46 167 393 524 1.35e-11 62.0
Msa0014080 MtrunA17_Chr2g0282801 26.404 178 112 3 10 168 132 309 1.54e-11 61.6
Msa0014080 MtrunA17_Chr6g0481981 26.087 161 101 3 20 162 269 429 1.58e-11 61.6
Msa0014080 MtrunA17_Chr6g0473251 26.515 132 87 2 46 167 390 521 1.75e-11 61.6
Msa0014080 MtrunA17_Chr6g0481621 28.485 165 96 5 18 162 385 547 1.89e-11 61.2
Msa0014080 MtrunA17_Chr6g0468041 24.806 129 87 2 46 164 39 167 2.25e-11 59.7
Msa0014080 MtrunA17_Chr6g0473491 26.515 132 87 2 46 167 393 524 2.33e-11 61.2
Msa0014080 MtrunA17_Chr3g0091741 29.412 136 86 2 42 167 251 386 2.94e-11 60.8
Msa0014080 MtrunA17_Chr7g0218641 29.730 111 69 1 64 165 204 314 3.30e-11 60.8
Msa0014080 MtrunA17_Chr6g0482971 26.257 179 106 5 11 167 277 451 4.59e-11 60.5
Msa0014080 MtrunA17_Chr3g0116201 24.242 165 107 3 18 164 272 436 4.61e-11 60.1
Msa0014080 MtrunA17_Chr4g0060641 27.381 168 102 4 20 168 203 369 5.42e-11 60.1
Msa0014080 MtrunA17_Chr6g0482571 25.153 163 104 3 18 162 220 382 5.95e-11 59.7
Msa0014080 MtrunA17_Chr4g0033981 33.929 112 65 1 65 167 293 404 6.19e-11 60.1
Msa0014080 MtrunA17_Chr6g0483431 27.746 173 111 5 6 164 183 355 7.27e-11 59.7
Msa0014080 MtrunA17_Chr6g0481991 25.767 163 103 3 18 162 393 555 7.52e-11 59.7
Msa0014080 MtrunA17_Chr4g0039041 27.007 137 82 3 46 168 450 582 8.57e-11 59.7
Msa0014080 MtrunA17_Chr1g0162281 28.488 172 105 3 11 164 312 483 8.59e-11 59.7
Msa0014080 MtrunA17_Chr6g0482661 26.207 145 88 4 35 164 19 159 8.78e-11 58.5
Msa0014080 MtrunA17_Chr8g0378041 31.776 107 64 1 68 165 241 347 9.84e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0014080 AT1G66345.1 33.714 175 98 3 10 166 281 455 1.25e-24 99.8
Msa0014080 AT4G28010.1 28.994 169 98 4 16 164 160 326 8.66e-14 68.6
Msa0014080 AT3G07290.1 30.702 114 70 1 64 168 271 384 5.28e-13 66.2
Msa0014080 AT1G09900.1 22.905 179 116 4 10 168 216 392 2.34e-12 64.3
Msa0014080 AT3G04760.1 25.698 179 107 4 12 168 207 381 6.10e-12 63.2
Msa0014080 AT1G06710.15 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.18 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.17 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.14 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.16 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.10 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.11 30.303 132 82 2 46 167 434 565 9.77e-12 62.8
Msa0014080 AT1G06710.7 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.1 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.9 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.4 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.13 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.3 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.8 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.2 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.19 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.5 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.6 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT1G06710.12 30.303 132 82 2 46 167 434 565 1.08e-11 62.8
Msa0014080 AT5G39710.1 28.369 141 83 3 43 169 328 464 3.91e-11 60.8

Find 40 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGACTCTGTTGTTAGATAA+AGG 0.253923 1_1:+22142913 Msa0014080:CDS
GAAGAATTTGATTGGTGATT+TGG 0.317260 1_1:+22142478 Msa0014080:CDS
AATAGTTGGATGCACGGATT+TGG 0.326104 1_1:+22142764 Msa0014080:CDS
AAATGGAAGGGAAAGGGTTA+AGG 0.355266 1_1:+22142715 Msa0014080:CDS
GGGAAAGGGTTAAGGGCTTA+TGG 0.355443 1_1:+22142723 Msa0014080:CDS
TGGGATGGTTGGAGGAGTGC+TGG 0.368813 1_1:+22142784 Msa0014080:CDS
TTTGAGGAAATGCTGATTGC+TGG 0.390211 1_1:+22142813 Msa0014080:CDS
TGACTCTGTTGTTAGATAAA+GGG 0.404920 1_1:+22142914 Msa0014080:CDS
TGGAGAAGCTTTGTGAGAAC+GGG 0.417550 1_1:+22142866 Msa0014080:CDS
AATGGAAGGGAAAGGGTTAA+GGG 0.455130 1_1:+22142716 Msa0014080:CDS
GATATAGAGAATGTTGGAAA+AGG 0.470378 1_1:+22142391 None:intergenic
GAGAATGTTGGAAAAGGAAG+AGG 0.471068 1_1:+22142397 None:intergenic
ACTTATTCTCATTTGATACA+TGG 0.474528 1_1:+22142955 Msa0014080:CDS
TATACGAGCGCTTTGTAAGA+AGG 0.474842 1_1:+22142659 Msa0014080:CDS
ATAGTTGGATGCACGGATTT+GGG 0.478308 1_1:+22142765 Msa0014080:CDS
TGAGGGAAATGGAAGGGAAA+GGG 0.483007 1_1:+22142709 Msa0014080:CDS
ATGCACGGATTTGGGATGGT+TGG 0.483572 1_1:+22142773 Msa0014080:CDS
CACGGATTTGGGATGGTTGG+AGG 0.485935 1_1:+22142776 Msa0014080:CDS
GGTTGGATTGATGAGGGAAA+TGG 0.509075 1_1:+22142698 Msa0014080:CDS
TTGTTGCAGAAGAATTTGAT+TGG 0.523742 1_1:+22142470 Msa0014080:CDS
GTGGAGAAGCTTTGTGAGAA+CGG 0.525411 1_1:+22142865 Msa0014080:CDS
GGACGGATTGAAGAAGCGGT+TGG 0.529830 1_1:+22142681 Msa0014080:CDS
TGAGAACGGGGAAGTTGAGA+AGG 0.531528 1_1:+22142879 Msa0014080:CDS
AAGAAGCGGTTGGATTGATG+AGG 0.531949 1_1:+22142691 Msa0014080:CDS
ATACGAGCGCTTTGTAAGAA+GGG 0.549619 1_1:+22142660 Msa0014080:CDS
GAGCGCTTTGTAAGAAGGGA+CGG 0.552286 1_1:+22142664 Msa0014080:CDS
ACTTATGAATGTGTAATAGT+TGG 0.554265 1_1:+22142750 Msa0014080:CDS
AGAAGCGGTTGGATTGATGA+GGG 0.555368 1_1:+22142692 Msa0014080:CDS
ATGAGGGAAATGGAAGGGAA+AGG 0.570228 1_1:+22142708 Msa0014080:CDS
TATAATGAGATGTTGAGAAG+AGG 0.570705 1_1:+22142599 Msa0014080:CDS
GAAGGGACGGATTGAAGAAG+CGG 0.610527 1_1:+22142677 Msa0014080:CDS
ATTTGATACATGGCTATGTG+AGG 0.612048 1_1:+22142965 Msa0014080:CDS
TTGGATGCACGGATTTGGGA+TGG 0.614923 1_1:+22142769 Msa0014080:CDS
TGAGAATAAGTAACATCACT+CGG 0.615983 1_1:-22142943 None:intergenic
TTTGATACATGGCTATGTGA+GGG 0.622718 1_1:+22142966 Msa0014080:CDS
GGATTGATGAGGGAAATGGA+AGG 0.626810 1_1:+22142702 Msa0014080:CDS
GATTGATGAGGGAAATGGAA+GGG 0.637041 1_1:+22142703 Msa0014080:CDS
ATGTGTAATAGTTGGATGCA+CGG 0.673047 1_1:+22142758 Msa0014080:CDS
GGAGAAGCTTTGTGAGAACG+GGG 0.711603 1_1:+22142867 Msa0014080:CDS
AGCGCTCGTATAAATAAACG+AGG 0.759336 1_1:-22142648 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGATGTATACATTTTTTTTT+TGG + chr1_1:22142561-22142580 Msa0014080:intron 15.0%
!!! ATTTTTTTTTTGGTAGAAAT+TGG + chr1_1:22142571-22142590 Msa0014080:intron 15.0%
! TGATTGTTCATGTTAAAGTT+AGG + chr1_1:22142513-22142532 Msa0014080:intron 25.0%
! TTCATGTTAAAGTTAGGTTA+GGG + chr1_1:22142519-22142538 Msa0014080:intron 25.0%
! ACTTATGAATGTGTAATAGT+TGG + chr1_1:22142750-22142769 Msa0014080:CDS 25.0%
! ACTTATTCTCATTTGATACA+TGG + chr1_1:22142955-22142974 Msa0014080:CDS 25.0%
TTGTTGCAGAAGAATTTGAT+TGG + chr1_1:22142470-22142489 Msa0014080:CDS 30.0%
! GAAGAATTTGATTGGTGATT+TGG + chr1_1:22142478-22142497 Msa0014080:CDS 30.0%
GTTCATGTTAAAGTTAGGTT+AGG + chr1_1:22142518-22142537 Msa0014080:intron 30.0%
TCATGTTAAAGTTAGGTTAG+GGG + chr1_1:22142520-22142539 Msa0014080:intron 30.0%
TATAATGAGATGTTGAGAAG+AGG + chr1_1:22142599-22142618 Msa0014080:CDS 30.0%
TTGACTCTGTTGTTAGATAA+AGG + chr1_1:22142913-22142932 Msa0014080:CDS 30.0%
TGACTCTGTTGTTAGATAAA+GGG + chr1_1:22142914-22142933 Msa0014080:CDS 30.0%
TGAGAATAAGTAACATCACT+CGG - chr1_1:22142946-22142965 None:intergenic 30.0%
TAAAGTTAGGTTAGGGGATT+TGG + chr1_1:22142526-22142545 Msa0014080:intron 35.0%
! AGGGGATTTGGATTTTTCTT+TGG + chr1_1:22142538-22142557 Msa0014080:intron 35.0%
! AGATGTTGAGAAGAGGTTTT+AGG + chr1_1:22142606-22142625 Msa0014080:intron 35.0%
! GATGTTGAGAAGAGGTTTTA+GGG + chr1_1:22142607-22142626 Msa0014080:intron 35.0%
ATGTGTAATAGTTGGATGCA+CGG + chr1_1:22142758-22142777 Msa0014080:CDS 35.0%
ATTTGATACATGGCTATGTG+AGG + chr1_1:22142965-22142984 Msa0014080:CDS 35.0%
TTTGATACATGGCTATGTGA+GGG + chr1_1:22142966-22142985 Msa0014080:CDS 35.0%
GAAGAGGAAAAAGACGATGA+AGG + chr1_1:22142413-22142432 Msa0014080:CDS 40.0%
AGCGCTCGTATAAATAAACG+AGG - chr1_1:22142651-22142670 None:intergenic 40.0%
TATACGAGCGCTTTGTAAGA+AGG + chr1_1:22142659-22142678 Msa0014080:CDS 40.0%
ATACGAGCGCTTTGTAAGAA+GGG + chr1_1:22142660-22142679 Msa0014080:CDS 40.0%
GATTGATGAGGGAAATGGAA+GGG + chr1_1:22142703-22142722 Msa0014080:CDS 40.0%
AAATGGAAGGGAAAGGGTTA+AGG + chr1_1:22142715-22142734 Msa0014080:CDS 40.0%
AATGGAAGGGAAAGGGTTAA+GGG + chr1_1:22142716-22142735 Msa0014080:CDS 40.0%
AATAGTTGGATGCACGGATT+TGG + chr1_1:22142764-22142783 Msa0014080:CDS 40.0%
ATAGTTGGATGCACGGATTT+GGG + chr1_1:22142765-22142784 Msa0014080:CDS 40.0%
! TTTGAGGAAATGCTGATTGC+TGG + chr1_1:22142813-22142832 Msa0014080:CDS 40.0%
!! GTTCCTTGTTGTTCATCGTA+AGG + chr1_1:22142840-22142859 Msa0014080:intron 40.0%
AAGAAGCGGTTGGATTGATG+AGG + chr1_1:22142691-22142710 Msa0014080:CDS 45.0%
AGAAGCGGTTGGATTGATGA+GGG + chr1_1:22142692-22142711 Msa0014080:CDS 45.0%
GGTTGGATTGATGAGGGAAA+TGG + chr1_1:22142698-22142717 Msa0014080:CDS 45.0%
GGATTGATGAGGGAAATGGA+AGG + chr1_1:22142702-22142721 Msa0014080:CDS 45.0%
ATGAGGGAAATGGAAGGGAA+AGG + chr1_1:22142708-22142727 Msa0014080:CDS 45.0%
TGAGGGAAATGGAAGGGAAA+GGG + chr1_1:22142709-22142728 Msa0014080:CDS 45.0%
!!! GGAGTGCTGGTTTGTTTTTG+AGG + chr1_1:22142797-22142816 Msa0014080:CDS 45.0%
CCACCTTACGATGAACAACA+AGG - chr1_1:22142846-22142865 None:intergenic 45.0%
!! CCTTGTTGTTCATCGTAAGG+TGG + chr1_1:22142843-22142862 Msa0014080:intron 45.0%
TGTTGTTCATCGTAAGGTGG+TGG + chr1_1:22142846-22142865 Msa0014080:intron 45.0%
! GTGGAGAAGCTTTGTGAGAA+CGG + chr1_1:22142865-22142884 Msa0014080:CDS 45.0%
! TGGAGAAGCTTTGTGAGAAC+GGG + chr1_1:22142866-22142885 Msa0014080:CDS 45.0%
GAGCGCTTTGTAAGAAGGGA+CGG + chr1_1:22142664-22142683 Msa0014080:CDS 50.0%
!! GAAGGGACGGATTGAAGAAG+CGG + chr1_1:22142677-22142696 Msa0014080:CDS 50.0%
GGGAAAGGGTTAAGGGCTTA+TGG + chr1_1:22142723-22142742 Msa0014080:CDS 50.0%
TTGGATGCACGGATTTGGGA+TGG + chr1_1:22142769-22142788 Msa0014080:CDS 50.0%
! ATGCACGGATTTGGGATGGT+TGG + chr1_1:22142773-22142792 Msa0014080:CDS 50.0%
! GGAGAAGCTTTGTGAGAACG+GGG + chr1_1:22142867-22142886 Msa0014080:CDS 50.0%
TGAGAACGGGGAAGTTGAGA+AGG + chr1_1:22142879-22142898 Msa0014080:CDS 50.0%
!! GGACGGATTGAAGAAGCGGT+TGG + chr1_1:22142681-22142700 Msa0014080:CDS 55.0%
! CACGGATTTGGGATGGTTGG+AGG + chr1_1:22142776-22142795 Msa0014080:CDS 55.0%
! TGGGATGGTTGGAGGAGTGC+TGG + chr1_1:22142784-22142803 Msa0014080:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 22142401 22142996 22142401 ID=Msa0014080;Name=Msa0014080
chr1_1 mRNA 22142401 22142996 22142401 ID=Msa0014080-mRNA-1;Parent=Msa0014080;Name=Msa0014080-mRNA-1;_AED=0.42;_eAED=0.43;_QI=0|0|0|1|0.33|0.5|4|0|169
chr1_1 exon 22142401 22142529 22142401 ID=Msa0014080-mRNA-1:exon:7771;Parent=Msa0014080-mRNA-1
chr1_1 exon 22142587 22142620 22142587 ID=Msa0014080-mRNA-1:exon:7772;Parent=Msa0014080-mRNA-1
chr1_1 exon 22142628 22142839 22142628 ID=Msa0014080-mRNA-1:exon:7773;Parent=Msa0014080-mRNA-1
chr1_1 exon 22142862 22142996 22142862 ID=Msa0014080-mRNA-1:exon:7774;Parent=Msa0014080-mRNA-1
chr1_1 CDS 22142401 22142529 22142401 ID=Msa0014080-mRNA-1:cds;Parent=Msa0014080-mRNA-1
chr1_1 CDS 22142587 22142620 22142587 ID=Msa0014080-mRNA-1:cds;Parent=Msa0014080-mRNA-1
chr1_1 CDS 22142628 22142839 22142628 ID=Msa0014080-mRNA-1:cds;Parent=Msa0014080-mRNA-1
chr1_1 CDS 22142862 22142996 22142862 ID=Msa0014080-mRNA-1:cds;Parent=Msa0014080-mRNA-1
Gene Sequence

>Msa0014080

ATGTTGGAAAAGGAAGAGGAAAAAGACGATGAAGGTGAGTTAGTTAAGTTAGTTACATTGTTGAAGAGATTGTTGCAGAAGAATTTGATTGGTGATTTGGTTGCTTATTTGTTGATTGTTCATGTTAAAAAATTGGAGATGTATAATGAGATGTTGAGAAGAGGGAGAATTTGTTTGTTAACACCTCGTTTATTTATACGAGCGCTTTGTAAGAAGGGACGGATTGAAGAAGCGGTTGGATTGATGAGGGAAATGGAAGGGAAAGGGTTAAGGGCTTATGGTGACACTTATGAATGTGTAATAGTTGGATGCACGGATTTGGGATGGTTGGAGGAGTGCTGGTTTGTTTTTGAGGAAATGCTGATTGCTGGATTTGTGGTGGAGAAGCTTTGTGAGAACGGGGAAGTTGAGAAGGTGAATGATATGTTGACTCTGTTGTTAGATAAAGGGTTTTTGCCGAGTGATGTTACTTATTCTCATTTGATACATGGCTATGTGAGGGAGTTCTGA
Protein sequence

>Msa0014080

MLEKEEEKDDEGELVKLVTLLKRLLQKNLIGDLVAYLLIVHVKKLEMYNEMLRRGRICLLTPRLFIRALCKKGRIEEAVGLMREMEGKGLRAYGDTYECVIVGCTDLGWLEECWFVFEEMLIAGFVVEKLCENGEVEKVNDMLTLLLDKGFLPSDVTYSHLIHGYVREF*