AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006648

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006648.t1 MTR_4g088035 47.191 89 47 0 14 102 6 94 1.46e-26 102
MS.gene006648.t1 MTR_3g073690 41.346 104 61 0 15 118 10 113 1.31e-23 93.2
MS.gene006648.t1 MTR_2g093310 41.935 93 54 0 15 107 34 126 3.47e-23 92.0
MS.gene006648.t1 MTR_2g100020 35.461 141 89 1 10 148 15 155 3.81e-23 93.6
MS.gene006648.t1 MTR_3g031660 42.105 95 55 0 15 109 8 102 7.70e-23 90.5
MS.gene006648.t1 MTR_1g095850 34.884 129 77 1 15 136 73 201 2.19e-22 90.9
MS.gene006648.t1 MTR_4g107450 41.837 98 57 0 10 107 6 103 2.21e-22 92.0
MS.gene006648.t1 MTR_5g083230 35.714 126 76 2 10 134 2 123 3.70e-22 88.6
MS.gene006648.t1 MTR_8g017090 41.667 108 52 2 13 111 11 116 4.13e-22 91.3
MS.gene006648.t1 MTR_4g105170 43.011 93 53 0 15 107 12 104 6.96e-22 88.6
MS.gene006648.t1 MTR_7g033800 41.935 93 54 0 15 107 12 104 1.43e-21 87.0
MS.gene006648.t1 MTR_3g077240 38.835 103 63 0 5 107 1 103 1.65e-21 87.4
MS.gene006648.t1 MTR_6g011250 45.679 81 43 1 12 91 7 87 1.67e-21 87.4
MS.gene006648.t1 MTR_4g083680 41.379 87 51 0 10 96 11 97 2.04e-21 86.7
MS.gene006648.t1 MTR_3g071590 41.053 95 52 1 15 109 9 99 2.65e-21 86.3
MS.gene006648.t1 MTR_2g068760 37.838 111 59 2 10 120 9 109 6.07e-21 85.1
MS.gene006648.t1 MTR_6g011200 39.806 103 58 2 12 110 7 109 6.09e-21 87.4
MS.gene006648.t1 MTR_5g083960 35.185 108 68 1 15 120 40 147 8.98e-21 85.5
MS.gene006648.t1 MTR_6g005070 39.785 93 56 0 15 107 10 102 9.35e-21 84.3
MS.gene006648.t1 MTR_6g005080 39.785 93 56 0 15 107 11 103 2.31e-20 83.2
MS.gene006648.t1 MTR_5g083010 47.436 78 41 0 14 91 11 88 2.65e-20 84.0
MS.gene006648.t1 MTR_6g011230 38.053 113 67 1 7 116 4 116 3.12e-20 84.3
MS.gene006648.t1 MTR_7g074990 41.000 100 58 1 15 113 21 120 3.63e-20 85.1
MS.gene006648.t1 MTR_4g060950 39.362 94 56 1 15 107 25 118 3.76e-20 84.0
MS.gene006648.t1 MTR_5g017950 40.860 93 55 0 15 107 9 101 5.80e-20 85.9
MS.gene006648.t1 MTR_5g075020 45.455 77 42 0 15 91 44 120 7.06e-20 84.0
MS.gene006648.t1 MTR_5g075020 45.455 77 42 0 15 91 48 124 7.28e-20 84.0
MS.gene006648.t1 MTR_3g094690 37.113 97 61 0 15 111 48 144 8.98e-20 84.0
MS.gene006648.t1 MTR_3g071420 44.872 78 43 0 14 91 14 91 1.17e-19 82.4
MS.gene006648.t1 MTR_8g079580 40.404 99 58 1 15 112 9 107 1.34e-19 83.2
MS.gene006648.t1 MTR_8g040900 45.455 77 42 0 15 91 8 84 4.27e-19 82.0
MS.gene006648.t1 MTR_4g099230 40.404 99 58 1 15 112 3 101 4.68e-19 80.1
MS.gene006648.t1 MTR_8g079620 35.577 104 67 0 13 116 7 110 9.39e-19 81.3
MS.gene006648.t1 MTR_6g027700 35.644 101 64 1 15 114 8 108 9.98e-19 80.5
MS.gene006648.t1 MTR_3g452660 38.144 97 60 0 15 111 8 104 1.70e-18 81.6
MS.gene006648.t1 MTR_3g094690 38.144 97 59 1 15 111 48 143 1.82e-18 80.5
MS.gene006648.t1 MTR_5g080470 30.827 133 90 2 10 140 3 135 2.56e-18 79.0
MS.gene006648.t1 MTR_8g079660 34.314 102 67 0 15 116 9 110 6.32e-18 79.3
MS.gene006648.t1 MTR_8g036085 39.000 100 60 1 15 113 24 123 6.42e-18 79.0
MS.gene006648.t1 MTR_5g093010 35.484 93 60 0 15 107 6 98 6.79e-18 76.6
MS.gene006648.t1 MTR_7g028905 32.673 101 68 0 11 111 2 102 1.30e-17 75.5
MS.gene006648.t1 MTR_8g036105 36.111 108 68 1 15 121 19 126 3.43e-17 76.6
MS.gene006648.t1 MTR_5g085390 37.963 108 62 2 12 118 7 110 3.69e-17 77.0
MS.gene006648.t1 MTR_7g096530 34.677 124 70 3 1 123 1 114 4.90e-17 76.3
MS.gene006648.t1 MTR_6g027710 36.190 105 63 2 15 118 41 142 6.87e-17 76.3
MS.gene006648.t1 MTR_1g070220 29.936 157 92 5 15 169 16 156 9.17e-16 72.8
MS.gene006648.t1 MTR_7g096610 33.333 108 71 1 10 116 4 111 1.25e-15 72.8
MS.gene006648.t1 MTR_7g075230 48.052 77 37 2 15 88 13 89 6.99e-15 70.1
MS.gene006648.t1 MTR_1g070205 26.437 174 112 4 15 172 13 186 9.26e-15 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006648.t1 AT1G06280 59.406 101 34 1 12 112 22 115 1.76e-40 137
MS.gene006648.t1 AT3G13850 43.363 113 53 2 13 116 35 145 6.59e-28 106
MS.gene006648.t1 AT3G50510 37.383 107 67 0 15 121 13 119 2.13e-25 97.8
MS.gene006648.t1 AT3G50510 37.383 107 67 0 15 121 13 119 2.13e-25 97.8
MS.gene006648.t1 AT1G72980 45.098 102 56 0 10 111 9 110 2.40e-24 95.5
MS.gene006648.t1 AT5G63090 41.176 102 60 0 6 107 3 104 1.59e-22 90.1
MS.gene006648.t1 AT5G63090 41.176 102 60 0 6 107 3 104 1.59e-22 90.1
MS.gene006648.t1 AT5G63090 41.176 102 60 0 6 107 3 104 1.59e-22 90.1
MS.gene006648.t1 AT5G63090 41.176 102 60 0 6 107 3 104 1.59e-22 90.1
MS.gene006648.t1 AT1G07900 48.052 77 40 0 15 91 34 110 2.90e-22 89.4
MS.gene006648.t1 AT5G66870 33.571 140 78 2 15 140 8 146 3.26e-22 92.0
MS.gene006648.t1 AT2G28500 39.423 104 60 1 15 118 56 156 4.34e-22 90.1
MS.gene006648.t1 AT2G23660 41.935 93 54 0 15 107 6 98 3.01e-21 89.4
MS.gene006648.t1 AT2G23660 41.935 93 54 0 15 107 6 98 3.01e-21 89.4
MS.gene006648.t1 AT2G23660 41.935 93 54 0 15 107 6 98 3.01e-21 89.4
MS.gene006648.t1 AT1G16530 31.967 122 79 2 15 135 15 133 6.40e-21 85.5
MS.gene006648.t1 AT3G27650 35.849 106 68 0 3 108 28 133 8.56e-21 84.7
MS.gene006648.t1 AT2G30130 38.947 95 58 0 15 109 9 103 9.10e-21 85.5
MS.gene006648.t1 AT1G65620 48.052 77 40 0 15 91 10 86 1.97e-20 84.7
MS.gene006648.t1 AT1G65620 48.052 77 40 0 15 91 10 86 1.97e-20 84.7
MS.gene006648.t1 AT1G65620 48.052 77 40 0 15 91 10 86 1.97e-20 84.7
MS.gene006648.t1 AT1G65620 48.052 77 40 0 15 91 10 86 1.97e-20 84.7
MS.gene006648.t1 AT1G65620 48.052 77 40 0 15 91 10 86 1.97e-20 84.7
MS.gene006648.t1 AT4G00210 36.752 117 73 1 7 122 4 120 5.53e-20 84.3
MS.gene006648.t1 AT2G30340 40.206 97 58 0 15 111 54 150 7.07e-20 84.7
MS.gene006648.t1 AT2G30340 40.206 97 58 0 15 111 53 149 8.74e-20 84.7
MS.gene006648.t1 AT3G47870 35.780 109 63 2 10 111 32 140 1.09e-19 85.1
MS.gene006648.t1 AT1G31320 37.363 91 57 0 6 96 5 95 1.50e-19 82.0
MS.gene006648.t1 AT3G11090 38.776 98 60 0 14 111 11 108 1.99e-19 81.3
MS.gene006648.t1 AT3G26660 32.110 109 67 1 15 116 6 114 1.46e-18 77.8
MS.gene006648.t1 AT3G26620 32.110 109 67 1 15 116 6 114 1.59e-18 77.8
MS.gene006648.t1 AT2G40470 36.735 98 62 0 15 112 21 118 2.64e-18 79.3
MS.gene006648.t1 AT2G40470 36.735 98 62 0 15 112 46 143 8.89e-18 78.6
MS.gene006648.t1 AT2G42430 43.750 80 44 1 10 88 11 90 1.81e-17 78.2
MS.gene006648.t1 AT4G00220 39.216 102 61 1 17 117 20 121 2.11e-17 77.4
MS.gene006648.t1 AT5G35900 36.170 94 56 1 14 107 5 94 3.55e-17 76.6
MS.gene006648.t1 AT2G45410 33.613 119 78 1 17 134 19 137 7.04e-17 75.5
MS.gene006648.t1 AT5G06080 34.694 98 63 1 14 110 7 104 9.17e-17 74.7
MS.gene006648.t1 AT2G31310 33.945 109 71 1 9 116 2 110 1.02e-16 74.7
MS.gene006648.t1 AT3G58190 30.303 132 88 2 15 142 12 143 3.79e-16 73.9
MS.gene006648.t1 AT2G19820 35.106 94 60 1 4 96 2 95 5.64e-16 71.2
MS.gene006648.t1 AT2G42440 30.275 109 75 1 9 116 2 110 1.55e-15 72.8
MS.gene006648.t1 AT3G03760 36.190 105 63 2 15 118 52 153 5.79e-15 71.6
MS.gene006648.t1 AT2G45420 37.255 102 63 1 17 117 40 141 6.80e-15 71.2
MS.gene006648.t1 AT5G15060 30.508 118 70 4 7 122 10 117 1.33e-12 62.8

Find 33 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGACTGCTGCTGAATATT+TGG 0.145265 4.1:-26816601 None:intergenic
TGAACAATATGTATTATAAA+TGG 0.237268 4.1:-26816533 None:intergenic
AGAAATATTAGTAATAATAA+TGG 0.289856 4.1:+26816076 MS.gene006648:CDS
TCTCCATAAGAACCATTTAT+AGG 0.292857 4.1:-26816322 None:intergenic
AATTCTCTACTTCTGCTTGA+TGG 0.303337 4.1:-26816175 None:intergenic
AAGTTGTGGATTCATTGATA+TGG 0.307263 4.1:+26816275 MS.gene006648:CDS
AGGCAAAGGGATCCTATAAA+TGG 0.334383 4.1:+26816310 MS.gene006648:CDS
GATCCTATAAATGGTTCTTA+TGG 0.354301 4.1:+26816319 MS.gene006648:CDS
TACAAGATCTTGATAGTTTG+AGG 0.357044 4.1:+26816563 MS.gene006648:CDS
GTGACTGCTGCTGAATATTT+GGG 0.405388 4.1:-26816600 None:intergenic
AGTTGTGGATTCATTGATAT+GGG 0.416674 4.1:+26816276 MS.gene006648:CDS
GAAATATTAGTAATAATAAT+GGG 0.417105 4.1:+26816077 MS.gene006648:CDS
AAAGCAGTGCACAAAGTGTT+TGG 0.418599 4.1:+26816199 MS.gene006648:CDS
GCACTTGTACCAATTGGCTT+TGG 0.432491 4.1:-26816408 None:intergenic
GAGGTGGCACTTGTACCAAT+TGG 0.442273 4.1:-26816414 None:intergenic
GATTATCATCATCTTCATCA+TGG 0.452314 4.1:+26816478 MS.gene006648:CDS
TCACAGTCATACTATATTGC+AGG 0.457053 4.1:+26816619 MS.gene006648:CDS
CTTCTGCTTGATGGAAAGTA+AGG 0.478129 4.1:-26816166 None:intergenic
CAGAGATCACCAAAGCCAAT+TGG 0.487224 4.1:+26816399 MS.gene006648:CDS
TAATCAACTGCATTATGATC+AGG 0.493064 4.1:-26816460 None:intergenic
ATTATCATCATCTTCATCAT+GGG 0.522912 4.1:+26816479 MS.gene006648:CDS
GCTCTAACTTTCCCTTGAGG+TGG 0.530192 4.1:-26816430 None:intergenic
CATCATGGGAATCATAAGAA+TGG 0.531608 4.1:+26816493 MS.gene006648:CDS
GGGAGATAGAAGAAAAGTTG+TGG 0.539608 4.1:+26816261 MS.gene006648:CDS
TGATATGGGAAGCACTCTCT+AGG 0.540083 4.1:+26816290 MS.gene006648:CDS
GCGCAGCATGCAAGCATCAA+AGG 0.554577 4.1:+26816113 MS.gene006648:CDS
GGAAGCACTCTCTAGGCAAA+GGG 0.561200 4.1:+26816297 MS.gene006648:CDS
GGGAAGCACTCTCTAGGCAA+AGG 0.562224 4.1:+26816296 MS.gene006648:CDS
TTGGTACAAGTGCCACCTCA+AGG 0.567329 4.1:+26816418 MS.gene006648:CDS
TCTGCTCTAACTTTCCCTTG+AGG 0.597530 4.1:-26816433 None:intergenic
GTTTGTAAGAAATGCTCAAG+AGG 0.598939 4.1:+26816240 MS.gene006648:CDS
TGGTACAAGTGCCACCTCAA+GGG 0.602942 4.1:+26816419 MS.gene006648:CDS
TTTGTAAGAAATGCTCAAGA+GGG 0.635754 4.1:+26816241 MS.gene006648:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAATATTAGTAATAATAA+TGG + chr4.1:26816076-26816095 MS.gene006648:CDS 10.0%
!! GAAATATTAGTAATAATAAT+GGG + chr4.1:26816077-26816096 MS.gene006648:CDS 10.0%
!! CACTAAATTAGTAATTAATT+TGG + chr4.1:26816939-26816958 MS.gene006648:intron 15.0%
!! TGAACAATATGTATTATAAA+TGG - chr4.1:26816536-26816555 None:intergenic 15.0%
!! TTTAACAAAAAACATGAGAT+TGG - chr4.1:26816650-26816669 None:intergenic 20.0%
!!! TTTTCCTGTTTCAATATTTT+AGG + chr4.1:26817007-26817026 MS.gene006648:intron 20.0%
! AATTTGGTCAAACTATACTA+AGG + chr4.1:26816955-26816974 MS.gene006648:intron 25.0%
! AGTTGTGACATTATCAAATA+TGG + chr4.1:26816797-26816816 MS.gene006648:intron 25.0%
! ATTATCATCATCTTCATCAT+GGG + chr4.1:26816479-26816498 MS.gene006648:CDS 25.0%
AACAAAAAACATGAGATTGG+TGG - chr4.1:26816647-26816666 None:intergenic 30.0%
AAGTTGTGGATTCATTGATA+TGG + chr4.1:26816275-26816294 MS.gene006648:CDS 30.0%
AGTTGTGGATTCATTGATAT+GGG + chr4.1:26816276-26816295 MS.gene006648:CDS 30.0%
GATCCTATAAATGGTTCTTA+TGG + chr4.1:26816319-26816338 MS.gene006648:CDS 30.0%
GATTATCATCATCTTCATCA+TGG + chr4.1:26816478-26816497 MS.gene006648:CDS 30.0%
GTCACCTAAAATATTGAAAC+AGG - chr4.1:26817014-26817033 None:intergenic 30.0%
TAATCAACTGCATTATGATC+AGG - chr4.1:26816463-26816482 None:intergenic 30.0%
TCTCCATAAGAACCATTTAT+AGG - chr4.1:26816325-26816344 None:intergenic 30.0%
TTTGTAAGAAATGCTCAAGA+GGG + chr4.1:26816241-26816260 MS.gene006648:CDS 30.0%
! TACAAGATCTTGATAGTTTG+AGG + chr4.1:26816563-26816582 MS.gene006648:CDS 30.0%
!! ACTACAAAAGAGCACTATAT+GGG - chr4.1:26816865-26816884 None:intergenic 30.0%
AATTCTCTACTTCTGCTTGA+TGG - chr4.1:26816178-26816197 None:intergenic 35.0%
CATCATGGGAATCATAAGAA+TGG + chr4.1:26816493-26816512 MS.gene006648:CDS 35.0%
GTTTGTAAGAAATGCTCAAG+AGG + chr4.1:26816240-26816259 MS.gene006648:CDS 35.0%
TCACAGTCATACTATATTGC+AGG + chr4.1:26816619-26816638 MS.gene006648:CDS 35.0%
! CATATAGTGCTCTTTTGTAG+TGG + chr4.1:26816864-26816883 MS.gene006648:intron 35.0%
!! CACTACAAAAGAGCACTATA+TGG - chr4.1:26816866-26816885 None:intergenic 35.0%
AGGCAAAGGGATCCTATAAA+TGG + chr4.1:26816310-26816329 MS.gene006648:CDS 40.0%
CTTCTGCTTGATGGAAAGTA+AGG - chr4.1:26816169-26816188 None:intergenic 40.0%
GAGCATACTTGTGACTAGTA+AGG - chr4.1:26816843-26816862 None:intergenic 40.0%
GGGAGATAGAAGAAAAGTTG+TGG + chr4.1:26816261-26816280 MS.gene006648:CDS 40.0%
GTGACTGCTGCTGAATATTT+GGG - chr4.1:26816603-26816622 None:intergenic 40.0%
TGTGACTGCTGCTGAATATT+TGG - chr4.1:26816604-26816623 None:intergenic 40.0%
! AAAGCAGTGCACAAAGTGTT+TGG + chr4.1:26816199-26816218 MS.gene006648:CDS 40.0%
CAGAGATCACCAAAGCCAAT+TGG + chr4.1:26816399-26816418 MS.gene006648:CDS 45.0%
TCTGCTCTAACTTTCCCTTG+AGG - chr4.1:26816436-26816455 None:intergenic 45.0%
! GCACTTGTACCAATTGGCTT+TGG - chr4.1:26816411-26816430 None:intergenic 45.0%
!! TGATATGGGAAGCACTCTCT+AGG + chr4.1:26816290-26816309 MS.gene006648:CDS 45.0%
GAGGTGGCACTTGTACCAAT+TGG - chr4.1:26816417-26816436 None:intergenic 50.0%
GCTCTAACTTTCCCTTGAGG+TGG - chr4.1:26816433-26816452 None:intergenic 50.0%
TGGTACAAGTGCCACCTCAA+GGG + chr4.1:26816419-26816438 MS.gene006648:CDS 50.0%
TTGGTACAAGTGCCACCTCA+AGG + chr4.1:26816418-26816437 MS.gene006648:CDS 50.0%
!! GGAAGCACTCTCTAGGCAAA+GGG + chr4.1:26816297-26816316 MS.gene006648:CDS 50.0%
GCGCAGCATGCAAGCATCAA+AGG + chr4.1:26816113-26816132 MS.gene006648:CDS 55.0%
!! GGGAAGCACTCTCTAGGCAA+AGG + chr4.1:26816296-26816315 MS.gene006648:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 26816070 26817048 26816070 ID=MS.gene006648
chr4.1 mRNA 26816070 26817048 26816070 ID=MS.gene006648.t1;Parent=MS.gene006648
chr4.1 exon 26816070 26816640 26816070 ID=MS.gene006648.t1.exon1;Parent=MS.gene006648.t1
chr4.1 CDS 26816070 26816640 26816070 ID=cds.MS.gene006648.t1;Parent=MS.gene006648.t1
chr4.1 exon 26817029 26817048 26817029 ID=MS.gene006648.t1.exon2;Parent=MS.gene006648.t1
chr4.1 CDS 26817029 26817048 26817029 ID=cds.MS.gene006648.t1;Parent=MS.gene006648.t1
Gene Sequence

>MS.gene006648

ATGCAGAGAAATATTAGTAATAATAATGGGATGCATCAAGCATGCGCAGCATGCAAGCATCAAAGGAAAAAATGCAGTGAAAATTGCATATTAGCACCTTACTTTCCATCAAGCAGAAGTAGAGAATTCAAAGCAGTGCACAAAGTGTTTGGTGTTAGCAACATAACAAAGTTTGTAAGAAATGCTCAAGAGGGAGATAGAAGAAAAGTTGTGGATTCATTGATATGGGAAGCACTCTCTAGGCAAAGGGATCCTATAAATGGTTCTTATGGAGAGTATACAAAAGTTTACAATGAGTATAAAAGAGTATTTGATGAACTTAAGATGTTCAGAGATCACCAAAGCCAATTGGTACAAGTGCCACCTCAAGGGAAAGTTAGAGCAGAAACACCTGATCATAATGCAGTTGATTATCATCATCTTCATCATGGGAATCATAAGAATGGTATTGTTGATTCTACTACCATTTATAATACATATTGTTCAAATTATTTACAAGATCTTGATAGTTTGAGGACTGAAGTTGTCATCCCAAATATTCAGCAGCAGTCACAGTCATACTATATTGCAGGTACCACCAATCTCATGTTTTTTGTTAAAATTAATTGATTATGCATGAGTTAAATTATGTTGTTTGTTATTTAATTAATGAGTTAAATTATGTTGCTTGTTATTTAGCATTTTTCTAGTTGATACTATTGTTACACTATTGTGTAAAACTTCAAACAGTTGTGACATTATCAAATATGGTAAAGAGTGCACAAAAAAGTCCTTACTAGTCACAAGTATGCTCCCATATAGTGCTCTTTTGTAGTGGTTGATCTGTACTCTTGATCAAATATATATATTTTACTAAATATTTTTTACTACACTAAATTAGTAATTAATTTGGTCAAACTATACTAAGGTAAAATAACTCAAATCTAACTATGTATCATTTTCCTGTTTCAATATTTTAGGTGACGAATTCAACCAATGA
Protein sequence

>MS.gene006648.t1

MQRNISNNNGMHQACAACKHQRKKCSENCILAPYFPSSRSREFKAVHKVFGVSNITKFVRNAQEGDRRKVVDSLIWEALSRQRDPINGSYGEYTKVYNEYKRVFDELKMFRDHQSQLVQVPPQGKVRAETPDHNAVDYHHLHHGNHKNGIVDSTTIYNTYCSNYLQDLDSLRTEVVIPNIQQQSQSYYIAGDEFNQ