AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene016735

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016735.t1 MTR_5g085390 95.238 105 5 0 1 105 1 105 1.30e-61 187
MS.gene016735.t1 MTR_6g011200 74.286 105 27 0 1 105 1 105 1.08e-54 170
MS.gene016735.t1 MTR_6g011250 67.308 104 34 0 1 104 1 104 3.74e-48 152
MS.gene016735.t1 MTR_4g099230 68.750 96 30 0 10 105 3 98 6.30e-45 142
MS.gene016735.t1 MTR_6g011230 65.094 106 34 2 1 104 1 105 4.84e-43 139
MS.gene016735.t1 MTR_4g107450 65.385 78 26 1 8 85 9 85 4.10e-31 111
MS.gene016735.t1 MTR_8g017090 54.082 98 44 1 7 104 10 106 1.35e-29 107
MS.gene016735.t1 MTR_3g073690 45.263 95 51 1 10 104 10 103 1.59e-28 102
MS.gene016735.t1 MTR_8g040900 47.126 87 45 1 3 89 1 86 1.40e-27 100
MS.gene016735.t1 MTR_3g452660 45.361 97 52 1 7 103 5 100 3.62e-27 101
MS.gene016735.t1 MTR_6g004550 62.319 69 26 0 37 105 1 69 7.25e-27 96.7
MS.gene016735.t1 MTR_5g017950 43.434 99 55 1 7 105 6 103 1.31e-26 100
MS.gene016735.t1 MTR_6g005080 43.878 98 54 1 7 104 8 104 1.48e-26 95.9
MS.gene016735.t1 MTR_6g005070 43.878 98 54 1 7 104 7 103 2.02e-26 95.5
MS.gene016735.t1 MTR_7g033800 42.857 98 55 1 7 104 9 105 3.88e-26 95.5
MS.gene016735.t1 MTR_3g077240 42.857 98 55 1 7 104 8 104 7.49e-26 95.5
MS.gene016735.t1 MTR_4g105170 41.837 98 56 1 7 104 9 105 8.55e-26 95.1
MS.gene016735.t1 MTR_4g083680 46.250 80 42 1 10 89 16 94 1.49e-25 94.4
MS.gene016735.t1 MTR_5g083960 37.500 104 61 2 1 104 34 133 1.68e-25 94.7
MS.gene016735.t1 MTR_2g100020 54.878 82 36 1 8 89 18 98 3.12e-25 95.9
MS.gene016735.t1 MTR_2g068760 42.553 94 49 2 10 103 14 102 3.98e-25 92.8
MS.gene016735.t1 MTR_3g031660 46.250 80 42 1 10 89 8 86 2.56e-24 91.3
MS.gene016735.t1 MTR_2g093310 48.750 80 40 1 10 89 34 112 2.56e-24 91.7
MS.gene016735.t1 MTR_5g075020 41.573 89 48 2 1 89 38 122 3.09e-24 92.0
MS.gene016735.t1 MTR_5g075020 41.573 89 48 2 1 89 42 126 3.31e-24 92.0
MS.gene016735.t1 MTR_3g094690 37.500 104 61 2 1 104 42 141 1.26e-23 90.9
MS.gene016735.t1 MTR_5g083230 42.169 83 47 1 7 89 4 85 1.52e-23 89.0
MS.gene016735.t1 MTR_5g083010 38.614 101 57 2 5 105 7 102 5.26e-23 87.8
MS.gene016735.t1 MTR_4g060950 49.383 81 39 2 10 89 25 104 7.00e-23 87.8
MS.gene016735.t1 MTR_3g071590 45.000 80 43 1 10 89 9 87 1.08e-22 86.7
MS.gene016735.t1 MTR_3g094690 36.538 104 61 2 1 104 42 140 3.15e-22 87.0
MS.gene016735.t1 MTR_3g071420 38.614 101 57 2 5 105 10 105 4.25e-22 85.5
MS.gene016735.t1 MTR_1g095850 48.750 80 40 1 10 89 73 151 5.18e-22 86.3
MS.gene016735.t1 MTR_5g093010 35.106 94 60 1 10 103 6 98 2.84e-21 82.4
MS.gene016735.t1 MTR_7g028905 37.234 94 58 1 10 103 6 98 2.87e-21 81.6
MS.gene016735.t1 MTR_8g079620 39.604 101 57 2 3 103 5 101 1.23e-20 83.2
MS.gene016735.t1 MTR_8g079660 39.604 101 57 2 3 103 5 101 8.88e-20 81.3
MS.gene016735.t1 MTR_5g080470 34.694 98 62 2 8 104 6 102 6.77e-17 72.4
MS.gene016735.t1 MTR_8g079580 37.255 102 59 3 3 103 5 102 1.69e-16 72.0
MS.gene016735.t1 MTR_1g070220 40.244 82 47 2 10 90 16 96 1.00e-15 69.7
MS.gene016735.t1 MTR_6g027710 38.202 89 50 3 3 90 37 121 1.97e-15 68.9
MS.gene016735.t1 MTR_7g096530 37.805 82 49 2 10 90 15 95 8.44e-15 67.4
MS.gene016735.t1 MTR_7g074990 34.021 97 62 2 10 105 21 116 1.56e-14 67.0
MS.gene016735.t1 MTR_8g036105 35.052 97 61 2 10 105 19 114 2.71e-14 65.9
MS.gene016735.t1 MTR_6g027700 35.802 81 50 2 10 89 8 87 1.20e-13 63.9
MS.gene016735.t1 MTR_8g036085 31.959 97 64 2 10 105 24 119 1.27e-13 64.3
MS.gene016735.t1 MTR_1g070205 36.585 82 50 2 10 90 13 93 1.60e-13 63.9
MS.gene016735.t1 MTR_4g088035 32.099 81 54 1 9 89 6 85 3.37e-13 63.5
MS.gene016735.t1 MTR_7g096610 35.366 82 51 2 10 90 9 89 1.31e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016735.t1 AT3G47870 58.947 95 38 1 9 103 36 129 2.77e-35 123
MS.gene016735.t1 AT3G13850 51.546 97 46 1 8 104 35 130 1.71e-29 106
MS.gene016735.t1 AT1G65620 50.602 83 40 1 7 89 7 88 4.99e-28 101
MS.gene016735.t1 AT1G65620 50.602 83 40 1 7 89 7 88 4.99e-28 101
MS.gene016735.t1 AT1G65620 50.602 83 40 1 7 89 7 88 4.99e-28 101
MS.gene016735.t1 AT1G65620 50.602 83 40 1 7 89 7 88 4.99e-28 101
MS.gene016735.t1 AT1G65620 50.602 83 40 1 7 89 7 88 4.99e-28 101
MS.gene016735.t1 AT3G27650 50.602 83 40 1 7 89 37 118 7.04e-28 99.8
MS.gene016735.t1 AT5G66870 41.667 96 51 2 10 105 8 98 2.48e-26 99.4
MS.gene016735.t1 AT1G31320 47.500 80 41 1 10 89 14 92 1.95e-25 94.0
MS.gene016735.t1 AT5G63090 41.837 98 56 1 7 104 9 105 2.86e-25 94.0
MS.gene016735.t1 AT5G63090 41.837 98 56 1 7 104 9 105 2.86e-25 94.0
MS.gene016735.t1 AT5G63090 41.837 98 56 1 7 104 9 105 2.86e-25 94.0
MS.gene016735.t1 AT5G63090 41.837 98 56 1 7 104 9 105 2.86e-25 94.0
MS.gene016735.t1 AT2G40470 42.697 89 47 2 1 89 15 99 1.27e-24 92.4
MS.gene016735.t1 AT2G40470 42.697 89 47 2 1 89 40 124 2.42e-24 92.4
MS.gene016735.t1 AT2G30340 36.893 103 61 2 1 103 48 146 9.26e-24 91.7
MS.gene016735.t1 AT2G30340 36.893 103 61 2 1 103 47 145 9.49e-24 91.7
MS.gene016735.t1 AT1G07900 48.750 80 40 1 10 89 34 112 1.24e-23 89.7
MS.gene016735.t1 AT2G23660 42.553 94 53 1 10 103 6 98 2.30e-23 91.7
MS.gene016735.t1 AT2G23660 42.553 94 53 1 10 103 6 98 2.30e-23 91.7
MS.gene016735.t1 AT2G23660 42.553 94 53 1 10 103 6 98 2.30e-23 91.7
MS.gene016735.t1 AT2G28500 48.750 80 40 1 10 89 56 134 3.76e-23 89.4
MS.gene016735.t1 AT3G26660 36.458 96 60 1 8 103 4 98 8.93e-23 85.5
MS.gene016735.t1 AT3G26620 36.458 96 60 1 8 103 4 98 9.63e-23 85.5
MS.gene016735.t1 AT2G30130 39.362 94 56 1 10 103 9 101 1.43e-22 87.0
MS.gene016735.t1 AT1G72980 51.852 81 38 1 9 89 13 92 2.94e-22 86.7
MS.gene016735.t1 AT1G06280 45.000 80 43 1 8 87 23 101 1.77e-21 84.7
MS.gene016735.t1 AT3G11090 35.644 101 60 2 5 105 7 102 3.43e-21 82.8
MS.gene016735.t1 AT1G16530 38.947 95 56 2 10 103 15 108 6.85e-21 82.0
MS.gene016735.t1 AT3G50510 37.374 99 61 1 5 103 8 105 4.23e-20 80.9
MS.gene016735.t1 AT3G50510 37.374 99 61 1 5 103 8 105 4.23e-20 80.9
MS.gene016735.t1 AT2G19820 40.000 80 48 0 10 89 13 92 1.15e-18 75.1
MS.gene016735.t1 AT5G15060 45.205 73 39 1 10 81 18 90 3.33e-18 74.7
MS.gene016735.t1 AT3G03760 35.417 96 60 2 10 104 52 146 1.79e-15 69.7
MS.gene016735.t1 AT5G35900 30.526 95 65 1 10 104 6 99 2.59e-15 68.6
MS.gene016735.t1 AT2G42430 37.805 82 49 2 10 90 16 96 1.03e-14 67.4
MS.gene016735.t1 AT4G00220 32.632 95 62 2 12 105 20 113 1.95e-14 66.6
MS.gene016735.t1 AT4G00210 37.805 82 49 2 10 90 12 92 2.51e-14 66.2
MS.gene016735.t1 AT2G31310 36.145 83 51 2 10 91 8 89 6.10e-14 64.7
MS.gene016735.t1 AT5G06080 31.633 98 65 2 8 104 6 102 1.54e-13 63.2
MS.gene016735.t1 AT2G42440 33.735 83 53 2 10 91 8 89 6.55e-13 62.8
MS.gene016735.t1 AT3G58190 35.366 82 51 2 10 90 12 92 1.09e-12 61.6
MS.gene016735.t1 AT2G45420 36.250 80 49 2 12 90 40 118 1.40e-12 62.0
MS.gene016735.t1 AT2G45410 32.632 95 62 2 12 105 19 112 1.95e-11 58.2

Find 20 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGGTGTTATTATGAATTA+TGG 0.198268 5.3:+69171516 MS.gene016735:CDS
CATGCTGCACAAGCCTTGTT+TGG 0.269582 5.3:-69171276 None:intergenic
TCCTTTAGCTCCTTATTTCC+CGG 0.285923 5.3:+69171332 MS.gene016735:CDS
AATATCCGACTCAATAATTA+TGG 0.288561 5.3:-69171466 None:intergenic
GGTTTATCGGCCGGGAAATA+AGG 0.295833 5.3:-69171342 None:intergenic
AGCAACGCTCATCGTTTGTT+TGG 0.383470 5.3:+69171375 MS.gene016735:CDS
AGATATGTTAAAGCAGTCTA+TGG 0.416875 5.3:+69171539 MS.gene016735:CDS
CTTTAGTATCCTTTGTATGT+TGG 0.435097 5.3:-69171403 None:intergenic
CGTGCAAAATCTCCCGTTCA+TGG 0.444453 5.3:+69171489 MS.gene016735:CDS
ACACCAAGACATCCATGAAC+GGG 0.497015 5.3:-69171501 None:intergenic
TTTGGTTTGATGATATTCAT+TGG 0.504277 5.3:-69171258 None:intergenic
TCTCCCGTTCATGGATGTCT+TGG 0.510462 5.3:+69171498 MS.gene016735:CDS
AAAGCAGTCTATGGAAGAGT+TGG 0.512156 5.3:+69171548 MS.gene016735:CDS
AAGGATACTAAAGGAAATCA+AGG 0.515917 5.3:+69171413 MS.gene016735:CDS
GCCGGGAAATAAGGAGCTAA+AGG 0.524058 5.3:-69171333 None:intergenic
CAACATACAAAGGATACTAA+AGG 0.551295 5.3:+69171404 MS.gene016735:CDS
GAGATCCATAATTATTGAGT+CGG 0.580015 5.3:+69171461 MS.gene016735:CDS
GAATATCATCAAACCAAACA+AGG 0.597163 5.3:+69171263 MS.gene016735:CDS
TTGGTGTTTCCAACATACAA+AGG 0.602738 5.3:+69171394 MS.gene016735:CDS
AACACCAAGACATCCATGAA+CGG 0.603796 5.3:-69171502 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATATCCGACTCAATAATTA+TGG - chr5.3:69171469-69171488 None:intergenic 25.0%
!!! CTTGGTGTTATTATGAATTA+TGG + chr5.3:69171516-69171535 MS.gene016735:CDS 25.0%
!!! GCTAAACATTTTTGGTTTAT+CGG - chr5.3:69171358-69171377 None:intergenic 25.0%
AAGGATACTAAAGGAAATCA+AGG + chr5.3:69171413-69171432 MS.gene016735:CDS 30.0%
AGATATGTTAAAGCAGTCTA+TGG + chr5.3:69171539-69171558 MS.gene016735:CDS 30.0%
CAACATACAAAGGATACTAA+AGG + chr5.3:69171404-69171423 MS.gene016735:CDS 30.0%
CTTTAGTATCCTTTGTATGT+TGG - chr5.3:69171406-69171425 None:intergenic 30.0%
GAATATCATCAAACCAAACA+AGG + chr5.3:69171263-69171282 MS.gene016735:CDS 30.0%
GAGATCCATAATTATTGAGT+CGG + chr5.3:69171461-69171480 MS.gene016735:CDS 30.0%
! TTGGTGTTTCCAACATACAA+AGG + chr5.3:69171394-69171413 MS.gene016735:CDS 35.0%
!! TGAGCGTTGCTAAACATTTT+TGG - chr5.3:69171366-69171385 None:intergenic 35.0%
!!! AACATTTTTGGTTTATCGGC+CGG - chr5.3:69171354-69171373 None:intergenic 35.0%
AAAGCAGTCTATGGAAGAGT+TGG + chr5.3:69171548-69171567 MS.gene016735:CDS 40.0%
AACACCAAGACATCCATGAA+CGG - chr5.3:69171505-69171524 None:intergenic 40.0%
! TCCTTTAGCTCCTTATTTCC+CGG + chr5.3:69171332-69171351 MS.gene016735:CDS 40.0%
!!! ACATTTTTGGTTTATCGGCC+GGG - chr5.3:69171353-69171372 None:intergenic 40.0%
ACACCAAGACATCCATGAAC+GGG - chr5.3:69171504-69171523 None:intergenic 45.0%
AGCAACGCTCATCGTTTGTT+TGG + chr5.3:69171375-69171394 MS.gene016735:CDS 45.0%
CGTGCAAAATCTCCCGTTCA+TGG + chr5.3:69171489-69171508 MS.gene016735:CDS 50.0%
GCCGGGAAATAAGGAGCTAA+AGG - chr5.3:69171336-69171355 None:intergenic 50.0%
GGTTTATCGGCCGGGAAATA+AGG - chr5.3:69171345-69171364 None:intergenic 50.0%
TCTCCCGTTCATGGATGTCT+TGG + chr5.3:69171498-69171517 MS.gene016735:CDS 50.0%
!! CATGCTGCACAAGCCTTGTT+TGG - chr5.3:69171279-69171298 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 69171261 69171575 69171261 ID=MS.gene016735
chr5.3 mRNA 69171261 69171575 69171261 ID=MS.gene016735.t1;Parent=MS.gene016735
chr5.3 exon 69171261 69171575 69171261 ID=MS.gene016735.t1.exon1;Parent=MS.gene016735.t1
chr5.3 CDS 69171261 69171575 69171261 ID=cds.MS.gene016735.t1;Parent=MS.gene016735.t1
Gene Sequence

>MS.gene016735

ATGAATATCATCAAACCAAACAAGGCTTGTGCAGCATGCAAGTATCAAAGAAGAAAGTGTTCAAGTGAGTGTCCTTTAGCTCCTTATTTCCCGGCCGATAAACCAAAAATGTTTAGCAACGCTCATCGTTTGTTTGGTGTTTCCAACATACAAAGGATACTAAAGGAAATCAAGGACGACGATCAAAAAGATGATGCGATGAGATCCATAATTATTGAGTCGGATATTCGTGCAAAATCTCCCGTTCATGGATGTCTTGGTGTTATTATGAATTATGGAGATATGTTAAAGCAGTCTATGGAAGAGTTGGATCAT
Protein sequence

>MS.gene016735.t1

MNIIKPNKACAACKYQRRKCSSECPLAPYFPADKPKMFSNAHRLFGVSNIQRILKEIKDDDQKDDAMRSIIIESDIRAKSPVHGCLGVIMNYGDMLKQSMEELDH