AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1392940

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1392940 MtrunA17_Chr8g0390821 83.333 114 19 0 1 114 542 655 2.48e-56 184
Msa1392940 MtrunA17_Chr5g0427901 72.807 114 31 0 1 114 515 628 4.96e-49 164
Msa1392940 MtrunA17_Chr7g0223801 71.171 111 32 0 4 114 505 615 4.78e-47 159
Msa1392940 MtrunA17_Chr7g0217971 75.676 111 27 0 2 112 480 590 1.27e-42 147
Msa1392940 MtrunA17_Chr1g0166551 66.372 113 36 1 2 112 389 501 8.45e-41 140
Msa1392940 MtrunA17_Chr7g0223761 62.500 112 41 1 2 112 226 337 1.59e-39 134
Msa1392940 MtrunA17_Chr6g0481381 67.647 102 32 1 9 109 72 173 1.67e-37 125
Msa1392940 MtrunA17_Chr2g0298861 63.393 112 40 1 2 112 517 628 7.79e-37 131
Msa1392940 MtrunA17_Chr7g0223721 61.607 112 42 1 2 112 505 616 5.87e-36 129
Msa1392940 MtrunA17_Chr7g0245531 56.757 111 48 0 2 112 202 312 3.41e-35 122
Msa1392940 MtrunA17_Chr7g0221661 60.909 110 43 0 1 110 504 613 6.55e-35 125
Msa1392940 MtrunA17_Chr7g0233311 57.143 112 47 1 2 112 506 617 1.28e-34 125
Msa1392940 MtrunA17_Chr2g0298851 62.500 112 40 2 2 112 506 616 4.83e-34 123
Msa1392940 MtrunA17_Chr7g0228281 60.177 113 44 1 1 112 520 632 6.57e-34 123
Msa1392940 MtrunA17_Chr7g0225671 59.292 113 45 1 1 112 510 622 1.58e-33 122
Msa1392940 MtrunA17_Chr7g0233301 55.357 112 49 1 2 112 475 586 1.60e-33 122
Msa1392940 MtrunA17_Chr7g0223871 55.752 113 49 1 1 112 20 132 1.96e-33 113
Msa1392940 MtrunA17_Chr2g0293581 58.036 112 46 1 2 112 507 618 1.01e-32 119
Msa1392940 MtrunA17_Chr2g0287631 55.357 112 49 1 2 112 506 617 1.38e-32 119
Msa1392940 MtrunA17_Chr1g0152001 56.881 109 46 1 2 109 189 297 2.57e-32 115
Msa1392940 MtrunA17_Chr7g0245541 53.153 111 52 0 2 112 89 199 9.10e-32 110
Msa1392940 MtrunA17_Chr4g0040931 58.182 110 45 1 1 109 504 613 2.02e-31 116
Msa1392940 MtrunA17_Chr4g0012541 55.752 113 49 1 1 112 495 607 3.09e-31 115
Msa1392940 MtrunA17_Chr7g0223851 56.637 113 48 1 1 112 513 625 1.92e-30 113
Msa1392940 MtrunA17_Chr1g0188611 57.143 112 40 3 2 112 184 288 2.99e-30 109
Msa1392940 MtrunA17_Chr7g0223831 54.955 111 49 1 1 110 476 586 8.75e-29 108
Msa1392940 MtrunA17_Chr7g0215261 54.054 111 49 1 2 110 471 581 2.52e-28 107
Msa1392940 MtrunA17_Chr7g0223791 67.692 65 21 0 4 68 115 179 2.14e-25 94.0
Msa1392940 MtrunA17_Chr7g0223681 47.748 111 58 0 2 112 415 525 4.77e-24 95.1
Msa1392940 MtrunA17_Chr7g0223821 54.867 113 48 1 1 110 505 617 2.45e-23 93.2
Msa1392940 MtrunA17_Chr7g0223821 52.381 84 37 1 30 110 620 703 1.13e-17 77.0
Msa1392940 MtrunA17_Chr7g0223711 45.455 110 60 0 3 112 506 615 4.44e-21 87.0
Msa1392940 MtrunA17_Chr7g0223781 44.860 107 59 0 4 110 505 611 6.79e-21 86.3
Msa1392940 MtrunA17_Chr7g0223181 42.857 112 64 0 2 113 505 616 7.47e-21 86.3
Msa1392940 MtrunA17_Chr7g0248151 45.045 111 59 1 4 112 507 617 7.96e-21 86.3
Msa1392940 MtrunA17_Chr7g0223731 42.727 110 63 0 4 113 506 615 9.37e-21 85.9
Msa1392940 MtrunA17_Chr7g0223701 44.762 105 58 0 3 107 514 618 2.77e-20 84.7
Msa1392940 MtrunA17_Chr4g0031321 41.071 112 66 0 2 113 505 616 1.10e-19 82.8
Msa1392940 MtrunA17_Chr7g0248131 45.946 111 58 1 4 112 509 619 1.35e-19 82.8
Msa1392940 MtrunA17_Chr4g0031301 41.071 112 66 0 2 113 505 616 1.43e-19 82.4
Msa1392940 MtrunA17_Chr7g0223541 42.202 109 63 0 4 112 464 572 2.34e-19 82.0
Msa1392940 MtrunA17_Chr7g0223751 42.202 109 63 0 4 112 506 614 1.17e-18 80.1
Msa1392940 MtrunA17_Chr7g0223291 40.179 112 67 0 2 113 505 616 1.59e-18 79.7
Msa1392940 MtrunA17_Chr4g0073741 37.500 112 70 0 2 113 504 615 3.85e-18 78.6
Msa1392940 MtrunA17_Chr8g0350731 43.119 109 62 0 4 112 534 642 6.32e-18 77.8
Msa1392940 MtrunA17_Chr7g0262821 39.286 112 68 0 2 113 505 616 6.57e-18 77.8
Msa1392940 MtrunA17_Chr7g0223621 42.593 108 62 0 4 111 506 613 9.82e-18 77.4
Msa1392940 MtrunA17_Chr7g0223631 42.342 111 64 0 2 112 490 600 1.88e-17 76.6
Msa1392940 MtrunA17_Chr7g0223031 42.574 101 58 0 4 104 506 606 4.56e-17 75.5
Msa1392940 MtrunA17_Chr7g0223741 46.591 88 47 0 4 91 507 594 9.05e-16 71.6
Msa1392940 MtrunA17_Chr6g0462681 35.135 111 72 0 2 112 504 614 5.16e-14 66.6
Msa1392940 MtrunA17_Chr6g0462601 35.780 109 70 0 4 112 506 614 8.07e-13 63.2
Msa1392940 MtrunA17_Chr6g0462711 36.697 109 69 0 6 114 515 623 2.03e-12 62.0
Msa1392940 MtrunA17_Chr6g0462611 32.110 109 74 0 4 112 454 562 9.69e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1392940 AT3G12580.1 40.179 112 67 0 2 113 505 616 3.50e-19 82.0
Msa1392940 AT5G02490.1 39.286 112 68 0 2 113 505 616 6.22e-19 81.3
Msa1392940 AT3G09440.1 40.179 112 67 0 2 113 505 616 4.68e-18 78.6
Msa1392940 AT3G09440.4 40.179 112 67 0 2 113 505 616 4.68e-18 78.6
Msa1392940 AT3G09440.2 40.179 112 67 0 2 113 505 616 4.68e-18 78.6
Msa1392940 AT3G09440.3 40.179 112 67 0 2 113 505 616 4.68e-18 78.6
Msa1392940 AT5G02500.1 40.179 112 67 0 2 113 505 616 5.31e-18 78.6
Msa1392940 AT1G16030.1 38.393 112 69 0 2 113 504 615 2.96e-17 76.3
Msa1392940 AT1G56410.1 37.838 111 67 1 2 112 505 613 1.11e-14 68.9
Msa1392940 AT5G28540.1 40.000 110 63 2 4 111 532 640 2.30e-13 65.1
Msa1392940 AT5G42020.1 39.091 110 64 2 4 111 532 640 1.28e-12 63.2
Msa1392940 AT5G42020.3 39.091 110 64 2 4 111 537 645 1.29e-12 63.2
Msa1392940 AT5G02500.2 34.653 101 66 0 13 113 386 486 1.75e-11 59.7

Find 17 sgRNAs with CRISPR-Local

Find 15 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACATCTATTTCGCCCTGC+TGG 0.366838 tig0021537:-100347 None:intergenic
TTAAAGATGAGAAATTTCTA+AGG 0.424154 tig0021537:+100175 Msa1392940:CDS
TGTTCTTGAAAATCATTTGA+AGG 0.440813 tig0021537:+100365 Msa1392940:CDS
GAAATTTGCTTATAATGTGC+TGG 0.458514 tig0021537:-100404 None:intergenic
ATATCCACTGGTAGTATGAA+TGG 0.473390 tig0021537:+100072 None:intergenic
AACATCTATTTCGCCCTGCT+GGG 0.486798 tig0021537:-100346 None:intergenic
TATCCACTGGTAGTATGAAT+GGG 0.501165 tig0021537:+100073 None:intergenic
ATGACTGTGTTTACAAGTTG+TGG 0.501382 tig0021537:+100223 Msa1392940:CDS
ATCTAATGCATTCATTACAT+TGG 0.517217 tig0021537:-100202 None:intergenic
TTTGCTTGACAGTACCCAGC+AGG 0.525967 tig0021537:+100332 Msa1392940:CDS
AGATGAGAAATTTCTAAGGA+AGG 0.534008 tig0021537:+100179 Msa1392940:CDS
GAAATGATTAGAGAAGCTGA+AGG 0.611330 tig0021537:+100144 Msa1392940:CDS
GGTACTGTCAAGCAAACTTG+TGG 0.622834 tig0021537:-100325 None:intergenic
GAAATTTCTCATCTTTAACA+CGG 0.622873 tig0021537:-100170 None:intergenic
TTGCTTGACAGTACCCAGCA+GGG 0.645277 tig0021537:+100333 Msa1392940:CDS
GATCAACTCTGCAATTACAA+AGG 0.652327 tig0021537:+100302 Msa1392940:CDS
GTGGATTGCTCTGAATAATG+AGG 0.666371 tig0021537:+100242 Msa1392940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAGATGAGAAATTTCTA+AGG + tig0021537:100175-100194 Msa1392940:CDS 20.0%
! GAAATTTCTCATCTTTAACA+CGG - tig0021537:100173-100192 None:intergenic 25.0%
! ATCTAATGCATTCATTACAT+TGG - tig0021537:100205-100224 None:intergenic 25.0%
! TGTTCTTGAAAATCATTTGA+AGG + tig0021537:100365-100384 Msa1392940:CDS 25.0%
! AGATGAGAAATTTCTAAGGA+AGG + tig0021537:100179-100198 Msa1392940:CDS 30.0%
! GAAATTTGCTTATAATGTGC+TGG - tig0021537:100407-100426 None:intergenic 30.0%
GAAATGATTAGAGAAGCTGA+AGG + tig0021537:100144-100163 Msa1392940:CDS 35.0%
ATGACTGTGTTTACAAGTTG+TGG + tig0021537:100223-100242 Msa1392940:CDS 35.0%
GATCAACTCTGCAATTACAA+AGG + tig0021537:100302-100321 Msa1392940:CDS 35.0%
! GTGGATTGCTCTGAATAATG+AGG + tig0021537:100242-100261 Msa1392940:CDS 40.0%
GGTACTGTCAAGCAAACTTG+TGG - tig0021537:100328-100347 None:intergenic 45.0%
AACATCTATTTCGCCCTGCT+GGG - tig0021537:100349-100368 None:intergenic 45.0%
TTTGCTTGACAGTACCCAGC+AGG + tig0021537:100332-100351 Msa1392940:CDS 50.0%
TTGCTTGACAGTACCCAGCA+GGG + tig0021537:100333-100352 Msa1392940:CDS 50.0%
GAACATCTATTTCGCCCTGC+TGG - tig0021537:100350-100369 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0021537 gene 100087 100431 100087 ID=Msa1392940;Name=Msa1392940
tig0021537 mRNA 100087 100431 100087 ID=Msa1392940-mRNA-1;Parent=Msa1392940;Name=Msa1392940-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|114
tig0021537 exon 100087 100431 100087 ID=Msa1392940-mRNA-1:exon:13506;Parent=Msa1392940-mRNA-1
tig0021537 CDS 100087 100431 100087 ID=Msa1392940-mRNA-1:cds;Parent=Msa1392940-mRNA-1
Gene Sequence

>Msa1392940

ATGAATGGGATTACAATAACTAATAACAAAGAAAGATTGTCATCTCAAGAAATTGAAGAAATGATTAGAGAAGCTGAAGGTTTCCGTGTTAAAGATGAGAAATTTCTAAGGAAGGCCAATGTAATGAATGCATTAGATGACTGTGTTTACAAGTTGTGGATTGCTCTGAATAATGAGGATGTTAAATTAAAGCTCTCTTCTCAAGTAACTGACAAGATCAACTCTGCAATTACAAAGGCCACAAGTTTGCTTGACAGTACCCAGCAGGGCGAAATAGATGTTCTTGAAAATCATTTGAAGGAGCTTGAGAGTATATTCCAGCACATTATAAGCAAATTTCTCTAG
Protein sequence

>Msa1392940

MNGITITNNKERLSSQEIEEMIREAEGFRVKDEKFLRKANVMNALDDCVYKLWIALNNEDVKLKLSSQVTDKINSAITKATSLLDSTQQGEIDVLENHLKELESIFQHIISKFL*