AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1455540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1455540 MtrunA17_Chr5g0446601 86.486 185 20 3 2 184 10 191 2.22e-92 267
Msa1455540 MtrunA17_Chr5g0446561 80.392 102 14 2 84 184 1 97 9.74e-30 105
Msa1455540 MtrunA17_Chr4g0076321 45.946 111 51 3 3 107 7 114 3.77e-25 94.7
Msa1455540 MtrunA17_Chr4g0076381 46.296 108 54 1 4 107 46 153 6.01e-25 97.1
Msa1455540 MtrunA17_Chr1g0165041 44.144 111 55 1 16 119 6 116 3.89e-24 93.6
Msa1455540 MtrunA17_Chr4g0067091 47.312 93 49 0 13 105 19 111 4.80e-23 91.7
Msa1455540 MtrunA17_Chr1g0191981 47.826 92 48 0 13 104 1 92 5.76e-23 89.0
Msa1455540 MtrunA17_Chr3g0102351 47.778 90 47 0 16 105 27 116 7.05e-23 90.5
Msa1455540 MtrunA17_Chr5g0446491 47.778 90 47 0 16 105 23 112 7.12e-23 90.1
Msa1455540 MtrunA17_Chr2g0296321 46.154 91 49 0 15 105 65 155 4.64e-22 89.7
Msa1455540 MtrunA17_Chr2g0290491 46.667 90 48 0 16 105 17 106 6.97e-22 87.0
Msa1455540 MtrunA17_Chr1g0185911 42.268 97 56 0 9 105 22 118 1.03e-21 87.0
Msa1455540 MtrunA17_Chr8g0382931 43.956 91 51 0 15 105 27 117 1.02e-20 85.1
Msa1455540 MtrunA17_Chr1g0195851 43.434 99 56 0 7 105 27 125 1.13e-20 84.7
Msa1455540 MtrunA17_Chr7g0263601 39.806 103 61 1 3 105 14 115 2.90e-20 83.2
Msa1455540 MtrunA17_Chr8g0384451 41.758 91 53 0 15 105 39 129 1.16e-19 82.4
Msa1455540 MtrunA17_Chr1g0159291 36.986 73 46 0 21 93 7 79 7.96e-12 58.9
Msa1455540 MtrunA17_Chr4g0062271 23.232 99 71 1 20 113 15 113 2.77e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1455540 AT1G21970.1 44.737 114 59 1 6 115 49 162 6.38e-25 97.4
Msa1455540 AT5G47670.2 50.000 90 45 0 16 105 29 118 1.80e-24 95.1
Msa1455540 AT5G47670.1 50.000 90 45 0 16 105 58 147 2.48e-24 95.5
Msa1455540 AT5G47670.3 50.000 90 45 0 16 105 58 147 2.48e-24 95.5
Msa1455540 AT5G47640.1 50.000 90 45 0 16 105 27 116 4.67e-23 91.3
Msa1455540 AT2G47810.1 44.231 104 57 1 1 104 37 139 1.57e-22 89.0
Msa1455540 AT4G14540.1 46.392 97 49 1 9 105 17 110 2.13e-22 88.6
Msa1455540 AT2G37060.2 43.137 102 53 2 8 105 23 123 3.19e-21 85.9
Msa1455540 AT2G37060.3 43.137 102 53 2 8 105 23 123 3.19e-21 85.9
Msa1455540 AT2G37060.1 43.137 102 53 2 8 105 23 123 3.19e-21 85.9
Msa1455540 AT2G38880.2 43.000 100 53 1 16 111 21 120 4.94e-21 84.7
Msa1455540 AT2G38880.1 43.000 100 53 1 16 111 21 120 4.94e-21 84.7
Msa1455540 AT2G38880.5 43.000 100 53 1 16 111 21 120 4.94e-21 84.7
Msa1455540 AT2G38880.3 43.000 100 53 1 16 111 21 120 5.42e-21 84.3
Msa1455540 AT1G09030.1 44.444 90 50 0 19 108 6 95 6.01e-21 84.3
Msa1455540 AT3G53340.5 40.741 108 59 2 8 111 22 128 1.24e-20 84.3
Msa1455540 AT3G53340.1 40.741 108 59 2 8 111 22 128 1.24e-20 84.3
Msa1455540 AT2G38880.7 42.105 95 55 0 16 110 21 115 1.91e-20 83.2
Msa1455540 AT2G38880.11 43.750 96 50 1 16 107 21 116 1.91e-20 83.6
Msa1455540 AT2G38880.8 43.750 96 50 1 16 107 21 116 1.91e-20 83.6
Msa1455540 AT3G53340.4 43.750 96 49 2 8 99 22 116 7.04e-20 81.3
Msa1455540 AT2G38880.4 43.478 92 48 1 16 103 21 112 8.15e-20 80.5
Msa1455540 AT3G53340.3 43.750 96 49 2 8 99 22 116 2.41e-19 80.5
Msa1455540 AT3G53340.2 43.750 96 49 2 8 99 22 116 2.41e-19 80.5
Msa1455540 AT2G38880.9 43.333 90 51 0 16 105 21 110 1.40e-18 78.6
Msa1455540 AT2G38880.10 43.333 90 51 0 16 105 21 110 1.40e-18 78.6
Msa1455540 AT2G38880.6 43.333 90 51 0 16 105 21 110 1.40e-18 78.6
Msa1455540 AT2G13570.1 40.659 91 54 0 15 105 35 125 9.06e-18 77.8

Find 48 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTAATTACTATGCACAAAT+TGG 0.166101 tig0036297:+6424 Msa1455540:CDS
GGGTCAGCAAACACGAAATT+TGG 0.207485 tig0036297:-6596 Msa1455540:intergenic
ATTATTGCAAGTTAGATTAT+AGG 0.238725 tig0036297:+6378 Msa1455540:CDS
GGAGGTGGAGGTGGAGGTGG+GGG 0.276683 tig0036297:-6524 Msa1455540:intergenic
GGTGGAGGTGGAGGTGGAGG+TGG 0.283304 tig0036297:-6527 Msa1455540:intergenic
TATAATCTAACTTGCAATAA+TGG 0.324070 tig0036297:-6376 Msa1455540:intergenic
CGATGAAAGCAAGGAAATTA+TGG 0.324481 tig0036297:+6307 Msa1455540:CDS
GTGGAGGTGGAGGTGGAGGT+GGG 0.327374 tig0036297:-6526 Msa1455540:intergenic
TGGAGGTGGAGGTGGAGGTG+GGG 0.345065 tig0036297:-6525 Msa1455540:intergenic
GCTGGTGGAGGTGGAGGTGG+AGG 0.387641 tig0036297:-6530 Msa1455540:intergenic
GGCAGCGGCGCTGGTGGAGG+TGG 0.393543 tig0036297:-6539 Msa1455540:intergenic
TGAATTCATTAGCTTTGTTA+CGG 0.429430 tig0036297:+6343 Msa1455540:CDS
AGCGGCGCTGGTGGAGGTGG+AGG 0.431125 tig0036297:-6536 Msa1455540:intergenic
TGTGGCAGCGGCGCTGGTGG+AGG 0.432008 tig0036297:-6542 Msa1455540:intergenic
TTAATTACTATGCACAAATT+GGG 0.437018 tig0036297:+6425 Msa1455540:CDS
CATAATTTCCTTGCTTTCAT+CGG 0.441388 tig0036297:-6306 Msa1455540:intergenic
GGCGCTGGTGGAGGTGGAGG+TGG 0.447225 tig0036297:-6533 Msa1455540:intergenic
GTTTGCTGACCCAACAGAAA+TGG 0.455645 tig0036297:+6607 Msa1455540:CDS
TCCTGTGGCAGCGGCGCTGG+TGG 0.456100 tig0036297:-6545 None:intergenic
AAATCCTGTGGCAGCGGCGC+TGG 0.458062 tig0036297:-6548 None:intergenic
TACTATTGTGGTGATGTTAG+AGG 0.472434 tig0036297:+6172 None:intergenic
ACACGAAATTTGGATCCAAC+GGG 0.476879 tig0036297:-6586 Msa1455540:intergenic
CATTAGCTTTGTTACGGCTG+AGG 0.482313 tig0036297:+6349 Msa1455540:CDS
AAAATTGCACCCATTTCTGT+TGG 0.484335 tig0036297:-6617 Msa1455540:intergenic
AAATTGCACCCATTTCTGTT+GGG 0.486823 tig0036297:-6616 Msa1455540:intergenic
TCTTGCACCCTCGAACTAGC+TGG 0.492382 tig0036297:-6206 Msa1455540:intergenic
ATCTAACTTGCAATAATGGT+TGG 0.494716 tig0036297:-6372 Msa1455540:intergenic
AGCCTATGCACATTGGCAAT+GGG 0.499486 tig0036297:-6248 Msa1455540:intergenic
CAGCCTATGCACATTGGCAA+TGG 0.504717 tig0036297:-6249 Msa1455540:intergenic
TCCACCAGCGCCGCTGCCAC+AGG 0.505082 tig0036297:+6544 Msa1455540:CDS
TTTCGTGATCGTTCTCGTGT+AGG 0.522771 tig0036297:+6491 Msa1455540:CDS
AACACGAAATTTGGATCCAA+CGG 0.532134 tig0036297:-6587 Msa1455540:intergenic
TTTGCTGACCCAACAGAAAT+GGG 0.535965 tig0036297:+6608 Msa1455540:CDS
GATAGAGAACTTGGTGGTGG+TGG 0.540606 tig0036297:+6656 Msa1455540:CDS
TTCCCATTGCCAATGTGCAT+AGG 0.544086 tig0036297:+6246 Msa1455540:CDS
GATGATGATGATAGAGAACT+TGG 0.547404 tig0036297:+6647 Msa1455540:CDS
GAGTGCAACCAGCTAGTTCG+AGG 0.550758 tig0036297:+6198 Msa1455540:CDS
ATGCACATTGGCAATGGGAA+AGG 0.554205 tig0036297:-6243 Msa1455540:intergenic
TCAAGCTCATAATTTCCCGT+TGG 0.560346 tig0036297:+6571 Msa1455540:CDS
GCTTGAAAATCCTGTGGCAG+CGG 0.563556 tig0036297:-6554 Msa1455540:intergenic
GAACTTGGTGGTGGTGGTGA+TGG 0.569523 tig0036297:+6662 Msa1455540:CDS
TTTCATCAGCCTATGCACAT+TGG 0.570566 tig0036297:-6255 Msa1455540:intergenic
GATGATGATAGAGAACTTGG+TGG 0.615654 tig0036297:+6650 Msa1455540:CDS
GGTGATGGCAACTCAAGTGA+TGG 0.623580 tig0036297:+6677 Msa1455540:CDS
ATTGTGGTGATGTTAGAGGA+TGG 0.634454 tig0036297:+6176 None:intergenic
GATGATAGAGAACTTGGTGG+TGG 0.661700 tig0036297:+6653 Msa1455540:CDS
TTATGAGCTTGAAAATCCTG+TGG 0.676989 tig0036297:-6560 Msa1455540:intergenic
AGTGCAACCAGCTAGTTCGA+GGG 0.693334 tig0036297:+6199 Msa1455540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAATCTAACTTGCAATAA+TGG - tig0036297:6379-6398 Msa1455540:intergenic 20.0%
!! ATTATTGCAAGTTAGATTAT+AGG + tig0036297:6378-6397 Msa1455540:CDS 20.0%
!! TTAATTACTATGCACAAATT+GGG + tig0036297:6425-6444 Msa1455540:CDS 20.0%
!!! TGAATTCATTAGCTTTGTTA+CGG + tig0036297:6343-6362 Msa1455540:CDS 25.0%
! GTTAATTACTATGCACAAAT+TGG + tig0036297:6424-6443 Msa1455540:CDS 25.0%
AAAAATAACCGATGAAAGCA+AGG + tig0036297:6298-6317 Msa1455540:CDS 30.0%
CATAATTTCCTTGCTTTCAT+CGG - tig0036297:6309-6328 Msa1455540:intergenic 30.0%
! ATCTAACTTGCAATAATGGT+TGG - tig0036297:6375-6394 Msa1455540:intergenic 30.0%
!!! TCGGTTATTTTTGCATGTCT+AGG - tig0036297:6290-6309 Msa1455540:intergenic 35.0%
CGATGAAAGCAAGGAAATTA+TGG + tig0036297:6307-6326 Msa1455540:CDS 35.0%
TTATGAGCTTGAAAATCCTG+TGG - tig0036297:6563-6582 Msa1455540:intergenic 35.0%
AACACGAAATTTGGATCCAA+CGG - tig0036297:6590-6609 Msa1455540:intergenic 35.0%
AAATTGCACCCATTTCTGTT+GGG - tig0036297:6619-6638 Msa1455540:intergenic 35.0%
AAAATTGCACCCATTTCTGT+TGG - tig0036297:6620-6639 Msa1455540:intergenic 35.0%
! ACAGAAATGGGTGCAATTTT+AGG + tig0036297:6620-6639 Msa1455540:CDS 35.0%
! GATGATGATGATAGAGAACT+TGG + tig0036297:6647-6666 Msa1455540:CDS 35.0%
TTTCATCAGCCTATGCACAT+TGG - tig0036297:6258-6277 Msa1455540:intergenic 40.0%
! AAAAAGTTGGATGTAGCGGA+GGG - tig0036297:6474-6493 Msa1455540:intergenic 40.0%
CACGAAAAAGTTGGATGTAG+CGG - tig0036297:6478-6497 Msa1455540:intergenic 40.0%
GAGAACGATCACGAAAAAGT+TGG - tig0036297:6487-6506 Msa1455540:intergenic 40.0%
TCAAGCTCATAATTTCCCGT+TGG + tig0036297:6571-6590 Msa1455540:CDS 40.0%
ACACGAAATTTGGATCCAAC+GGG - tig0036297:6589-6608 Msa1455540:intergenic 40.0%
TTTGCTGACCCAACAGAAAT+GGG + tig0036297:6608-6627 Msa1455540:CDS 40.0%
GATGATGATAGAGAACTTGG+TGG + tig0036297:6650-6669 Msa1455540:CDS 40.0%
ATGCACATTGGCAATGGGAA+AGG - tig0036297:6246-6265 Msa1455540:intergenic 45.0%
TTCCCATTGCCAATGTGCAT+AGG + tig0036297:6246-6265 Msa1455540:CDS 45.0%
AGCCTATGCACATTGGCAAT+GGG - tig0036297:6251-6270 Msa1455540:intergenic 45.0%
!! CATTAGCTTTGTTACGGCTG+AGG + tig0036297:6349-6368 Msa1455540:CDS 45.0%
GAAAAAGTTGGATGTAGCGG+AGG - tig0036297:6475-6494 Msa1455540:intergenic 45.0%
TTTCGTGATCGTTCTCGTGT+AGG + tig0036297:6491-6510 Msa1455540:CDS 45.0%
GGGTCAGCAAACACGAAATT+TGG - tig0036297:6599-6618 Msa1455540:intergenic 45.0%
! GTTTGCTGACCCAACAGAAA+TGG + tig0036297:6607-6626 Msa1455540:CDS 45.0%
! GATGATAGAGAACTTGGTGG+TGG + tig0036297:6653-6672 Msa1455540:CDS 45.0%
AGTGCAACCAGCTAGTTCGA+GGG + tig0036297:6199-6218 Msa1455540:CDS 50.0%
CAGCCTATGCACATTGGCAA+TGG - tig0036297:6252-6271 Msa1455540:intergenic 50.0%
GCTTGAAAATCCTGTGGCAG+CGG - tig0036297:6557-6576 Msa1455540:intergenic 50.0%
!! GATAGAGAACTTGGTGGTGG+TGG + tig0036297:6656-6675 Msa1455540:CDS 50.0%
! GGTGATGGCAACTCAAGTGA+TGG + tig0036297:6677-6696 Msa1455540:CDS 50.0%
GAGTGCAACCAGCTAGTTCG+AGG + tig0036297:6198-6217 Msa1455540:CDS 55.0%
TCTTGCACCCTCGAACTAGC+TGG - tig0036297:6209-6228 Msa1455540:intergenic 55.0%
!! GAACTTGGTGGTGGTGGTGA+TGG + tig0036297:6662-6681 Msa1455540:CDS 55.0%
TGGAGGTGGAGGTGGAGGTG+GGG - tig0036297:6528-6547 Msa1455540:intergenic 65.0%
GTGGAGGTGGAGGTGGAGGT+GGG - tig0036297:6529-6548 Msa1455540:intergenic 65.0%
AAATCCTGTGGCAGCGGCGC+TGG - tig0036297:6551-6570 Msa1455540:intergenic 65.0%
GGAGGTGGAGGTGGAGGTGG+GGG - tig0036297:6527-6546 Msa1455540:intergenic 70.0%
GGTGGAGGTGGAGGTGGAGG+TGG - tig0036297:6530-6549 Msa1455540:intergenic 70.0%
GCTGGTGGAGGTGGAGGTGG+AGG - tig0036297:6533-6552 Msa1455540:intergenic 70.0%
!! GGCGCTGGTGGAGGTGGAGG+TGG - tig0036297:6536-6555 Msa1455540:intergenic 75.0%
!! AGCGGCGCTGGTGGAGGTGG+AGG - tig0036297:6539-6558 Msa1455540:intergenic 75.0%
!! TGTGGCAGCGGCGCTGGTGG+AGG - tig0036297:6545-6564 Msa1455540:intergenic 75.0%
TCCACCAGCGCCGCTGCCAC+AGG + tig0036297:6544-6563 Msa1455540:CDS 75.0%
! TCCTGTGGCAGCGGCGCTGG+TGG - tig0036297:6548-6567 Msa1455540:intergenic 75.0%
!!! GGCAGCGGCGCTGGTGGAGG+TGG - tig0036297:6542-6561 Msa1455540:intergenic 80.0%
Chromosome Type Strat End Strand Name
tig0036297 gene 6185 6739 6185 ID=Msa1455540;Name=Msa1455540
tig0036297 mRNA 6185 6739 6185 ID=Msa1455540-mRNA-1;Parent=Msa1455540;Name=Msa1455540-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|184
tig0036297 exon 6185 6739 6185 ID=Msa1455540-mRNA-1:exon:20311;Parent=Msa1455540-mRNA-1
tig0036297 CDS 6185 6739 6185 ID=Msa1455540-mRNA-1:cds;Parent=Msa1455540-mRNA-1
Gene Sequence

>Msa1455540

ATGTTAGAGGATGGAGTGCAACCAGCTAGTTCGAGGGTGCAAGAAGAATCTGCAAGAGCCTTTCCCATTGCCAATGTGCATAGGCTGATGAAAAAAGCTCTTCCTAGACATGCAAAAATAACCGATGAAAGCAAGGAAATTATGGTGAAATATGCAGCTGAATTCATTAGCTTTGTTACGGCTGAGGCCAACCATTATTGCAAGTTAGATTATAGGACAACAGTTACTGCTGAAGATTTGTTAATTACTATGCACAAATTGGGTTTTGACGTCTATGCTGAGTATTCCCTCCGCTACATCCAACTTTTTCGTGATCGTTCTCGTGTAGGTCAATATGCTCCCCCACCTCCACCTCCACCTCCACCAGCGCCGCTGCCACAGGATTTTCAAGCTCATAATTTCCCGTTGGATCCAAATTTCGTGTTTGCTGACCCAACAGAAATGGGTGCAATTTTAGGAGATGATGATGATGATAGAGAACTTGGTGGTGGTGGTGATGGCAACTCAAGTGATGGAAGCTTTGATGTTATGACTTTTCTTAATAGTGATGACTAA

Protein sequence

>Msa1455540

MLEDGVQPASSRVQEESARAFPIANVHRLMKKALPRHAKITDESKEIMVKYAAEFISFVTAEANHYCKLDYRTTVTAEDLLITMHKLGFDVYAEYSLRYIQLFRDRSRVGQYAPPPPPPPPPAPLPQDFQAHNFPLDPNFVFADPTEMGAILGDDDDDRELGGGGDGNSSDGSFDVMTFLNSDD*