AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20078

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20078.t1 MTR_7g101740 94.059 101 6 0 2 102 15 115 4.48e-68 199
MS.gene20078.t1 MTR_1g063950 70.330 91 27 0 12 102 33 123 4.58e-43 137
MS.gene20078.t1 MTR_1g094750 66.154 65 22 0 23 87 46 110 1.56e-25 92.4
MS.gene20078.t1 MTR_5g021820 49.296 71 36 0 18 88 31 101 7.67e-20 77.4
MS.gene20078.t1 MTR_3g117610 52.239 67 32 0 22 88 40 106 1.55e-19 77.0
MS.gene20078.t1 MTR_4g072910 53.165 79 36 1 14 91 22 100 2.99e-19 75.9
MS.gene20078.t1 MTR_4g072190 53.030 66 31 0 24 89 33 98 5.24e-19 75.1
MS.gene20078.t1 MTR_8g076040 51.515 66 32 0 18 83 32 97 5.96e-19 75.1
MS.gene20078.t1 MTR_1g024085 46.575 73 39 0 17 89 27 99 3.58e-18 74.3
MS.gene20078.t1 MTR_3g113310 53.125 64 30 0 26 89 41 104 4.11e-18 73.2
MS.gene20078.t1 MTR_1g061570 50.769 65 32 0 23 87 15 79 5.21e-18 73.6
MS.gene20078.t1 MTR_3g084210 50.000 68 33 1 26 92 24 91 3.52e-16 67.8
MS.gene20078.t1 MTR_3g084230 50.746 67 32 1 26 91 24 90 4.10e-16 67.8
MS.gene20078.t1 MTR_3g084250 48.529 68 34 1 26 92 24 91 5.93e-16 67.4
MS.gene20078.t1 MTR_4g072830 48.438 64 32 1 26 88 22 85 9.10e-16 66.6
MS.gene20078.t1 MTR_4g072540 49.254 67 33 1 26 91 20 86 1.19e-15 66.2
MS.gene20078.t1 MTR_4g072580 50.000 64 31 1 26 88 19 82 1.32e-15 66.2
MS.gene20078.t1 MTR_3g084160 47.761 67 34 1 26 91 24 90 1.74e-15 66.2
MS.gene20078.t1 MTR_4g072600 51.562 64 30 1 26 88 19 82 1.75e-15 65.9
MS.gene20078.t1 MTR_4g072670 50.746 67 32 1 26 91 20 86 1.80e-15 65.9
MS.gene20078.t1 MTR_4g072820 50.769 65 31 1 25 88 18 82 1.86e-15 65.9
MS.gene20078.t1 MTR_6g077850 36.458 96 53 2 1 88 1 96 2.13e-15 66.2
MS.gene20078.t1 MTR_8g461420 49.254 67 33 1 26 91 24 90 2.87e-15 65.5
MS.gene20078.t1 MTR_4g072570 47.059 68 35 1 26 92 24 91 3.49e-15 65.5
MS.gene20078.t1 MTR_4g072160 50.000 62 31 0 26 87 36 97 3.68e-15 66.6
MS.gene20078.t1 MTR_4g072740 47.761 67 34 1 26 91 19 85 3.97e-15 65.1
MS.gene20078.t1 MTR_4g072770 50.746 67 32 1 27 92 15 81 4.82e-15 64.7
MS.gene20078.t1 MTR_3g084190 46.269 67 35 1 26 91 24 90 1.07e-14 63.9
MS.gene20078.t1 MTR_4g072330 46.269 67 35 1 26 91 22 88 1.20e-14 63.9
MS.gene20078.t1 MTR_3g110045 50.746 67 32 1 26 91 83 149 1.74e-14 65.1
MS.gene20078.t1 MTR_4g072530 50.000 64 31 1 26 88 24 87 1.85e-14 63.5
MS.gene20078.t1 MTR_4g072630 46.269 67 35 1 26 91 20 86 1.87e-14 63.2
MS.gene20078.t1 MTR_4g072490 46.269 67 35 1 26 91 19 85 1.88e-14 63.2
MS.gene20078.t1 MTR_4g072500 47.059 68 35 1 26 92 24 91 2.78e-14 63.2
MS.gene20078.t1 MTR_4g072370 49.254 67 33 1 26 91 22 88 2.89e-14 62.8
MS.gene20078.t1 MTR_2g043960 44.595 74 41 0 24 97 73 146 3.17e-14 64.7
MS.gene20078.t1 MTR_4g072510 47.761 67 34 1 26 91 20 86 3.95e-14 62.4
MS.gene20078.t1 MTR_4g072720 46.269 67 35 1 26 91 20 86 5.13e-14 62.0
MS.gene20078.t1 MTR_4g072465 47.761 67 34 1 26 91 20 86 5.30e-14 62.0
MS.gene20078.t1 MTR_4g072860 50.000 68 33 1 26 92 25 92 5.53e-14 62.4
MS.gene20078.t1 MTR_4g072230 48.529 68 32 2 26 92 25 90 6.40e-14 62.0
MS.gene20078.t1 MTR_4g072880 45.588 68 36 1 26 92 25 92 7.25e-14 62.0
MS.gene20078.t1 MTR_3g084150 45.588 68 36 1 26 92 24 91 8.06e-14 62.0
MS.gene20078.t1 MTR_4g124750 46.479 71 38 0 24 94 66 136 8.15e-14 63.5
MS.gene20078.t1 MTR_4g072380 51.613 62 27 2 25 84 19 79 8.74e-14 61.6
MS.gene20078.t1 MTR_3g084180 45.588 68 36 1 26 92 24 91 1.01e-13 61.6
MS.gene20078.t1 MTR_7g405740 41.667 84 47 1 4 87 46 127 1.11e-13 63.2
MS.gene20078.t1 MTR_8g096470 48.333 60 31 0 28 87 47 106 1.19e-13 62.0
MS.gene20078.t1 MTR_4g072300 44.776 67 36 1 26 91 25 91 1.40e-13 61.2
MS.gene20078.t1 MTR_4g072640 49.206 63 31 1 27 88 25 87 1.58e-13 61.2
MS.gene20078.t1 MTR_4g072450 46.970 66 34 1 27 91 20 85 1.71e-13 60.8
MS.gene20078.t1 MTR_8g461410 44.118 68 37 1 26 92 24 91 1.84e-13 60.8
MS.gene20078.t1 MTR_3g084220 45.588 68 36 1 26 92 24 91 1.88e-13 60.8
MS.gene20078.t1 MTR_3g084240 47.059 68 35 1 26 92 24 91 2.23e-13 60.8
MS.gene20078.t1 MTR_3g084170 47.059 68 35 1 26 92 24 91 2.23e-13 60.8
MS.gene20078.t1 MTR_5g008370 49.275 69 34 1 26 93 24 92 2.28e-13 62.0
MS.gene20078.t1 MTR_4g072470 46.970 66 34 1 27 91 20 85 2.31e-13 60.5
MS.gene20078.t1 MTR_8g461210 42.667 75 43 0 25 99 33 107 2.32e-13 61.2
MS.gene20078.t1 MTR_4g072870 44.776 67 36 1 26 91 25 91 2.35e-13 60.5
MS.gene20078.t1 MTR_4g072590 47.761 67 34 1 26 91 19 85 3.17e-13 60.1
MS.gene20078.t1 MTR_4g072250 48.529 68 33 2 26 92 25 91 3.34e-13 60.1
MS.gene20078.t1 MTR_4g072310 47.059 68 35 1 26 92 25 92 3.38e-13 60.1
MS.gene20078.t1 MTR_4g072890 44.776 67 36 1 26 91 25 91 3.67e-13 60.1
MS.gene20078.t1 MTR_4g072690 46.970 66 34 1 27 91 20 85 4.30e-13 59.7
MS.gene20078.t1 MTR_8g096500 50.820 61 30 0 27 87 49 109 4.37e-13 61.6
MS.gene20078.t1 MTR_4g072260 45.312 64 34 1 26 88 25 88 4.43e-13 60.1
MS.gene20078.t1 MTR_4g072610 48.438 64 32 1 26 88 18 81 4.91e-13 59.7
MS.gene20078.t1 MTR_8g096440 51.667 60 29 0 28 87 46 105 7.21e-13 60.8
MS.gene20078.t1 MTR_4g072280 55.319 47 21 0 26 72 25 71 7.62e-13 58.9
MS.gene20078.t1 MTR_4g072240 43.284 67 37 1 26 91 25 91 8.01e-13 59.3
MS.gene20078.t1 MTR_4g072220 45.312 64 34 1 26 88 25 88 8.32e-13 59.3
MS.gene20078.t1 MTR_4g050700 47.059 68 35 1 26 92 25 92 1.18e-12 58.9
MS.gene20078.t1 MTR_2g012410 47.059 68 35 1 26 92 25 92 1.18e-12 58.9
MS.gene20078.t1 MTR_3g117630 46.269 67 35 1 26 91 24 90 1.44e-12 58.5
MS.gene20078.t1 MTR_4g072850 46.269 67 35 1 26 91 26 92 1.51e-12 58.5
MS.gene20078.t1 MTR_3g098970 42.424 66 38 0 27 92 53 118 2.36e-12 59.3
MS.gene20078.t1 MTR_4g072270 43.750 64 35 1 26 88 25 88 2.38e-12 58.2
MS.gene20078.t1 MTR_3g117640 49.231 65 31 2 26 88 33 97 3.14e-12 58.2
MS.gene20078.t1 MTR_3g110032 40.000 75 44 1 19 92 18 92 3.22e-12 57.8
MS.gene20078.t1 MTR_3g084260 44.928 69 37 1 25 92 24 92 5.36e-12 57.4
MS.gene20078.t1 MTR_3g110042 46.875 64 33 1 26 88 24 87 6.82e-12 57.0
MS.gene20078.t1 MTR_3g110038 44.776 67 36 1 26 91 24 90 7.08e-12 57.0
MS.gene20078.t1 MTR_4g072650 46.875 64 33 1 26 88 18 81 1.09e-11 56.2
MS.gene20078.t1 MTR_4g072980 45.455 66 34 2 25 88 25 90 1.24e-11 56.2
MS.gene20078.t1 MTR_5g008360 42.647 68 38 1 26 92 15 82 1.45e-11 55.8
MS.gene20078.t1 MTR_4g072940 49.153 59 29 1 26 83 56 114 1.48e-11 57.0
MS.gene20078.t1 MTR_4g072550 44.118 68 37 1 26 92 35 102 2.26e-11 55.8
MS.gene20078.t1 MTR_4g072480 41.176 68 39 1 26 92 24 91 3.75e-11 55.1
MS.gene20078.t1 MTR_4g072660 42.188 64 36 1 26 88 19 82 4.72e-11 54.7
MS.gene20078.t1 MTR_4g072620 41.176 68 39 1 26 92 24 91 8.34e-11 54.3
MS.gene20078.t1 MTR_4g072680 39.706 68 40 1 26 92 24 91 9.29e-11 53.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20078.t1 AT2G37030 58.333 84 35 0 19 102 41 124 2.44e-30 104
MS.gene20078.t1 AT3G53250 51.899 79 35 1 19 97 44 119 8.27e-25 90.9
MS.gene20078.t1 AT5G03310 60.759 79 25 3 23 95 35 113 1.41e-24 89.7
MS.gene20078.t1 AT3G53250 51.899 79 35 1 19 97 75 150 1.55e-24 90.9
MS.gene20078.t1 AT2G21220 50.000 72 36 0 18 89 31 102 2.37e-20 79.0
MS.gene20078.t1 AT5G66260 46.914 81 43 0 11 91 18 98 2.58e-20 78.6
MS.gene20078.t1 AT4G34760 47.222 72 38 0 18 89 34 105 2.31e-19 76.3
MS.gene20078.t1 AT2G18010 48.571 70 36 0 19 88 40 109 3.11e-18 73.6
MS.gene20078.t1 AT1G75580 53.030 66 31 0 24 89 41 106 1.60e-17 71.6
MS.gene20078.t1 AT1G19830 51.471 68 33 0 21 88 42 109 1.63e-17 72.0
MS.gene20078.t1 AT4G38860 47.945 73 37 1 18 89 31 103 3.10e-17 70.9
MS.gene20078.t1 AT1G75590 44.776 67 37 0 23 89 38 104 7.55e-17 71.2
MS.gene20078.t1 AT4G34750 46.154 65 35 0 25 89 35 99 1.16e-16 70.9
MS.gene20078.t1 AT4G34750 46.154 65 35 0 25 89 35 99 1.16e-16 70.9
MS.gene20078.t1 AT4G34770 49.333 75 35 2 22 93 30 104 4.14e-16 68.2
MS.gene20078.t1 AT5G10990 39.506 81 46 1 22 102 36 113 3.77e-15 66.6
MS.gene20078.t1 AT3G43120 51.562 64 31 0 24 87 76 139 5.04e-15 66.6
MS.gene20078.t1 AT1G19840 43.284 67 38 0 23 89 37 103 6.64e-15 66.2
MS.gene20078.t1 AT4G36110 48.438 64 33 0 25 88 38 101 7.51e-15 64.7
MS.gene20078.t1 AT5G20810 51.667 60 29 0 24 83 76 135 8.89e-15 66.2
MS.gene20078.t1 AT5G20810 51.667 60 29 0 24 83 76 135 1.89e-14 65.9
MS.gene20078.t1 AT3G51200 45.070 71 38 1 18 87 30 100 4.56e-14 62.8
MS.gene20078.t1 AT2G16580 43.662 71 40 0 18 88 35 105 8.77e-14 62.4
MS.gene20078.t1 AT4G34800 47.059 68 32 2 25 88 19 86 1.85e-13 60.8
MS.gene20078.t1 AT4G34810 47.761 67 30 2 27 88 48 114 5.17e-13 60.5
MS.gene20078.t1 AT2G28085 40.278 72 39 1 21 88 49 120 9.17e-13 60.1
MS.gene20078.t1 AT1G79130 39.394 66 40 0 22 87 43 108 2.73e-12 58.9
MS.gene20078.t1 AT3G09870 38.824 85 45 2 16 93 29 113 4.95e-12 57.8
MS.gene20078.t1 AT4G34790 49.231 65 30 2 27 88 39 103 5.32e-12 57.8
MS.gene20078.t1 AT1G56150 44.262 61 34 0 27 87 38 98 5.87e-12 57.8
MS.gene20078.t1 AT4G34780 47.826 69 28 3 26 88 27 93 7.42e-12 57.4
MS.gene20078.t1 AT3G20220 40.625 64 37 1 25 87 45 108 1.02e-11 57.0
MS.gene20078.t1 AT1G16510 41.270 63 37 0 25 87 52 114 1.14e-11 57.8
MS.gene20078.t1 AT4G38850 41.176 68 36 2 25 88 19 86 1.19e-11 56.2
MS.gene20078.t1 AT5G50760 42.373 59 34 0 30 88 58 116 7.38e-11 56.2
MS.gene20078.t1 AT3G12830 38.095 63 39 0 25 87 48 110 8.77e-11 55.1

Find 15 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACAAGACCTTGTGATTAT+TGG 0.292286 7.2:+10825328 MS.gene20078:CDS
TGACCCTTTGGAACATCATT+TGG 0.307933 7.2:-10825390 None:intergenic
AAGAGATTTGTCATCAAGAT+TGG 0.323912 7.2:+10825441 MS.gene20078:CDS
GTTGTCTTGTGTGTTTGAAA+TGG 0.397531 7.2:+10825359 MS.gene20078:CDS
TACACAACCAAGTGACCCTT+TGG 0.425312 7.2:-10825402 None:intergenic
CAACTCCACACATAATGAAA+AGG 0.510469 7.2:+10825590 MS.gene20078:CDS
TGATGTTCCAAAGGGTCACT+TGG 0.513916 7.2:+10825395 MS.gene20078:CDS
ATTCCAAATGATGTTCCAAA+GGG 0.528407 7.2:+10825387 MS.gene20078:CDS
TTCTCGAGCTTGTTCCAACA+AGG 0.548481 7.2:-10825490 None:intergenic
TATTCCAAATGATGTTCCAA+AGG 0.550997 7.2:+10825386 MS.gene20078:CDS
AGGAAAAGATGTTCATTACA+TGG 0.560384 7.2:-10825549 None:intergenic
AGACCTTGTGATTATTGGTG+TGG 0.567971 7.2:+10825333 MS.gene20078:CDS
GGTCACTTGGTTGTGTATGT+AGG 0.581397 7.2:+10825408 MS.gene20078:CDS
TGGCAAAACTAAGAACACTA+AGG 0.605481 7.2:-10825569 None:intergenic
AATCCACACCAATAATCACA+AGG 0.693686 7.2:-10825336 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAGATTTGTCATCAAGAT+TGG + chr7.2:10825441-10825460 MS.gene20078:CDS 30.0%
AGGAAAAGATGTTCATTACA+TGG - chr7.2:10825552-10825571 None:intergenic 30.0%
ATTCCAAATGATGTTCCAAA+GGG + chr7.2:10825387-10825406 MS.gene20078:CDS 30.0%
TATTCCAAATGATGTTCCAA+AGG + chr7.2:10825386-10825405 MS.gene20078:CDS 30.0%
! AAACACCTTTTCATTATGTG+TGG - chr7.2:10825598-10825617 None:intergenic 30.0%
AATCCACACCAATAATCACA+AGG - chr7.2:10825339-10825358 None:intergenic 35.0%
CAACTCCACACATAATGAAA+AGG + chr7.2:10825590-10825609 MS.gene20078:CDS 35.0%
GTTGTCTTGTGTGTTTGAAA+TGG + chr7.2:10825359-10825378 MS.gene20078:CDS 35.0%
TGACAAGACCTTGTGATTAT+TGG + chr7.2:10825328-10825347 MS.gene20078:CDS 35.0%
TGGCAAAACTAAGAACACTA+AGG - chr7.2:10825572-10825591 None:intergenic 35.0%
! CTTTTCATTATGTGTGGAGT+TGG - chr7.2:10825592-10825611 None:intergenic 35.0%
!!! ACTCCATCATCCACTTTTTA+AGG + chr7.2:10825467-10825486 MS.gene20078:CDS 35.0%
AGACCTTGTGATTATTGGTG+TGG + chr7.2:10825333-10825352 MS.gene20078:CDS 40.0%
AGGCCTTAAAAAGTGGATGA+TGG - chr7.2:10825473-10825492 None:intergenic 40.0%
TCCAACAAGGCCTTAAAAAG+TGG - chr7.2:10825480-10825499 None:intergenic 40.0%
!! TGACCCTTTGGAACATCATT+TGG - chr7.2:10825393-10825412 None:intergenic 40.0%
!!! TCCACTTTTTAAGGCCTTGT+TGG + chr7.2:10825476-10825495 MS.gene20078:CDS 40.0%
GGTCACTTGGTTGTGTATGT+AGG + chr7.2:10825408-10825427 MS.gene20078:CDS 45.0%
TACACAACCAAGTGACCCTT+TGG - chr7.2:10825405-10825424 None:intergenic 45.0%
TGATGTTCCAAAGGGTCACT+TGG + chr7.2:10825395-10825414 MS.gene20078:CDS 45.0%
! TTCTCGAGCTTGTTCCAACA+AGG - chr7.2:10825493-10825512 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 10825321 10825629 10825321 ID=MS.gene20078
chr7.2 mRNA 10825321 10825629 10825321 ID=MS.gene20078.t1;Parent=MS.gene20078
chr7.2 exon 10825321 10825629 10825321 ID=MS.gene20078.t1.exon1;Parent=MS.gene20078.t1
chr7.2 CDS 10825321 10825629 10825321 ID=cds.MS.gene20078.t1;Parent=MS.gene20078.t1
Gene Sequence

>MS.gene20078

ATGAGATTGACAAGACCTTGTGATTATTGGTGTGGATTGTTGTCTTGTGTGTTTGAAATGGATTCTATTCCAAATGATGTTCCAAAGGGTCACTTGGTTGTGTATGTAGGTGAGAATTATAAGAGATTTGTCATCAAGATTGGAATACTCCATCATCCACTTTTTAAGGCCTTGTTGGAACAAGCTCGAGAAGAATATGATTTCATTGCAGATTCTAAACTTTGTATTCCATGTAATGAACATCTTTTCCTTAGTGTTCTTAGTTTTGCCAACTCCACACATAATGAAAAGGTGTTTGTTTGTGTCTGA
Protein sequence

>MS.gene20078.t1

MRLTRPCDYWCGLLSCVFEMDSIPNDVPKGHLVVYVGENYKRFVIKIGILHHPLFKALLEQAREEYDFIADSKLCIPCNEHLFLSVLSFANSTHNEKVFVCV