AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49609

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49609.t1 MTR_5g037930 98.438 128 2 0 1 128 1 128 1.19e-92 263
MS.gene49609.t1 MTR_5g037950 73.228 127 33 1 1 127 1 126 1.07e-54 167
MS.gene49609.t1 MTR_5g037890 68.750 128 38 1 1 128 1 126 6.07e-54 165
MS.gene49609.t1 MTR_7g009070 59.615 104 42 0 24 127 30 133 1.95e-44 142
MS.gene49609.t1 MTR_3g112410 47.664 107 56 0 20 126 6 112 8.35e-37 122
MS.gene49609.t1 MTR_1g023140 46.296 108 58 0 21 128 7 114 3.04e-36 120
MS.gene49609.t1 MTR_5g021180 42.478 113 65 0 14 126 2 114 9.17e-35 117
MS.gene49609.t1 MTR_8g107460 41.509 106 62 0 21 126 255 360 6.38e-28 105
MS.gene49609.t1 MTR_2g010750 38.095 105 65 0 20 124 9 113 2.04e-23 88.2
MS.gene49609.t1 MTR_7g073680 40.659 91 54 0 31 121 35 125 5.22e-22 85.1
MS.gene49609.t1 MTR_8g005320 35.238 105 68 0 19 123 25 129 7.88e-22 84.7
MS.gene49609.t1 MTR_8g006685 38.710 93 57 0 31 123 106 198 2.85e-21 85.1
MS.gene49609.t1 MTR_8g006560 38.710 93 57 0 31 123 106 198 2.85e-21 85.1
MS.gene49609.t1 MTR_2g082590 32.381 105 71 0 20 124 10 114 5.88e-21 82.0
MS.gene49609.t1 MTR_4g081380 37.273 110 67 2 20 128 10 118 1.36e-20 80.9
MS.gene49609.t1 MTR_2g082590 37.209 86 54 0 39 124 42 127 6.80e-19 77.0
MS.gene49609.t1 MTR_4g094690 36.585 82 50 1 46 125 85 166 2.26e-16 71.2
MS.gene49609.t1 MTR_1g098660 31.250 96 63 2 31 125 67 160 2.39e-16 71.2
MS.gene49609.t1 MTR_2g079420 37.500 88 53 2 40 125 84 171 2.31e-14 66.2
MS.gene49609.t1 MTR_8g059015 35.227 88 55 2 40 125 87 174 6.32e-14 65.1
MS.gene49609.t1 MTR_3g089065 32.143 84 55 2 45 126 89 172 3.05e-13 63.2
MS.gene49609.t1 MTR_7g080250 35.443 79 50 1 42 119 94 172 3.94e-13 63.2
MS.gene49609.t1 MTR_1g114290 32.911 79 49 2 40 117 84 159 5.56e-12 60.1
MS.gene49609.t1 MTR_4g085880 34.211 76 49 1 45 119 84 159 7.63e-12 59.3
MS.gene49609.t1 MTR_3g112400 30.928 97 47 3 20 116 5 81 2.87e-11 55.8
MS.gene49609.t1 MTR_2g079340 38.028 71 43 1 44 113 54 124 9.16e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49609.t1 AT5G39950 46.923 130 64 1 1 125 1 130 1.32e-42 137
MS.gene49609.t1 AT1G59730 42.969 128 72 1 1 127 1 128 4.13e-38 125
MS.gene49609.t1 AT1G69880 49.074 108 55 0 19 126 36 143 1.86e-35 119
MS.gene49609.t1 AT5G42980 47.222 108 57 0 21 128 6 113 1.42e-34 116
MS.gene49609.t1 AT1G19730 49.533 107 53 1 21 126 7 113 1.78e-34 116
MS.gene49609.t1 AT3G51030 44.340 106 59 0 21 126 7 112 6.08e-34 114
MS.gene49609.t1 AT1G45145 44.860 107 59 0 20 126 5 111 7.70e-34 114
MS.gene49609.t1 AT3G17880 40.000 105 63 0 22 126 265 369 3.12e-25 98.2
MS.gene49609.t1 AT3G17880 39.623 106 64 0 21 126 271 376 3.96e-25 98.2
MS.gene49609.t1 AT3G56420 39.130 92 56 0 30 121 50 141 1.36e-23 89.7
MS.gene49609.t1 AT3G56420 39.130 92 56 0 30 121 50 141 1.36e-23 89.7
MS.gene49609.t1 AT3G56420 39.130 92 56 0 30 121 50 141 1.36e-23 89.7
MS.gene49609.t1 AT1G11530 34.286 105 69 0 20 124 2 106 8.93e-21 81.3
MS.gene49609.t1 AT2G40790 39.130 92 56 0 30 121 50 141 1.18e-19 79.3
MS.gene49609.t1 AT2G40790 39.130 92 56 0 30 121 50 141 1.18e-19 79.3
MS.gene49609.t1 AT3G08710 34.951 103 65 1 21 123 26 126 1.23e-19 79.0
MS.gene49609.t1 AT3G08710 34.951 103 65 1 21 123 26 126 1.23e-19 79.0
MS.gene49609.t1 AT3G08710 34.951 103 65 1 21 123 26 126 1.23e-19 79.0
MS.gene49609.t1 AT3G15360 37.363 91 49 3 40 125 102 189 4.36e-16 71.2
MS.gene49609.t1 AT1G43560 30.159 126 79 5 9 128 39 161 9.50e-16 69.7
MS.gene49609.t1 AT2G35010 38.554 83 47 2 46 125 110 191 1.64e-14 67.0
MS.gene49609.t1 AT2G35010 38.554 83 47 2 46 125 110 191 1.64e-14 67.0
MS.gene49609.t1 AT1G76760 33.333 75 49 1 41 114 80 154 2.20e-14 66.2
MS.gene49609.t1 AT4G03520 34.940 83 52 2 45 125 101 183 8.21e-14 65.1
MS.gene49609.t1 AT1G31020 30.556 108 73 1 20 125 49 156 9.70e-14 64.3
MS.gene49609.t1 AT1G03680 35.802 81 50 2 47 125 97 177 2.34e-13 63.5
MS.gene49609.t1 AT3G02730 35.632 87 55 1 43 128 88 174 2.87e-13 63.5
MS.gene49609.t1 AT5G16400 34.091 88 57 1 42 128 97 184 3.94e-13 63.2
MS.gene49609.t1 AT1G52990 31.522 92 61 2 36 126 222 312 7.63e-12 61.2
MS.gene49609.t1 AT4G04950 29.787 94 66 0 32 125 11 104 2.51e-11 60.1
MS.gene49609.t1 AT4G32580 27.660 94 68 0 32 125 11 104 7.73e-11 56.6
MS.gene49609.t1 AT2G15570 25.843 89 65 1 32 119 74 162 8.66e-11 56.6
MS.gene49609.t1 AT2G15570 25.843 89 65 1 32 119 75 163 9.36e-11 56.6

Find 25 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCAGCTTGTTAGTTTCTT+TGG 0.210380 5.1:+28582008 None:intergenic
CCTTCCATTCCACTGCTAAA+TGG 0.240816 5.1:-28582050 MS.gene49609:CDS
TAAGATGGTAATTGAATTTA+CGG 0.284078 5.1:-28581893 MS.gene49609:intron
GATTGACGTGGATGAATTAA+TGG 0.293121 5.1:-28581788 MS.gene49609:intron
GCAGCAAAGTCTTGAATGAT+TGG 0.331944 5.1:+28581838 None:intergenic
AAAGTTGTTGACAAGGTTGT+AGG 0.405303 5.1:-28581195 MS.gene49609:CDS
CAGCTTGTTAGTTTCTTTGG+AGG 0.429788 5.1:+28582011 None:intergenic
TTCTTCATCAGTATGAATGT+TGG 0.495900 5.1:+28581222 None:intergenic
AAGTTGTTGACAAGGTTGTA+GGG 0.506438 5.1:-28581194 MS.gene49609:CDS
CCTTCCATTTAGCAGTGGAA+TGG 0.530623 5.1:+28582046 None:intergenic
CTCCAAAGAAACTAACAAGC+TGG 0.546462 5.1:-28582010 MS.gene49609:intron
GTGTGGACCTTGCAAATACA+TGG 0.552168 5.1:-28581863 MS.gene49609:CDS
CCATTTAGCAGTGGAATGGA+AGG 0.552428 5.1:+28582050 None:intergenic
CCATTCCACTGCTAAATGGA+AGG 0.553763 5.1:-28582046 MS.gene49609:CDS
ACATTCATACTGATGAAGAA+AGG 0.574346 5.1:-28581219 MS.gene49609:CDS
ATTGGATCCATGTATTTGCA+AGG 0.586486 5.1:+28581856 None:intergenic
GGGAGGCAATTTATCCAACA+TGG 0.596510 5.1:-28582118 MS.gene49609:CDS
GAATTTACGGCTGCATGGTG+TGG 0.600755 5.1:-28581880 MS.gene49609:CDS
GAAAGGAAAAGTTGTTGACA+AGG 0.605147 5.1:-28581202 MS.gene49609:CDS
AATTTATCCAACATGGAGCA+TGG 0.613422 5.1:-28582111 MS.gene49609:CDS
ATAAGCCTTCCATTTAGCAG+TGG 0.613671 5.1:+28582041 None:intergenic
TGTATGACCATGCTCCATGT+TGG 0.627275 5.1:+28582104 None:intergenic
AGTTGTTGACAAGGTTGTAG+GGG 0.631631 5.1:-28581193 MS.gene49609:CDS
AGATTTCATCAAGATTGACG+TGG 0.662014 5.1:-28581800 MS.gene49609:CDS
TAATTGAATTTACGGCTGCA+TGG 0.665704 5.1:-28581885 MS.gene49609:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTTTATATAATGTATAGA+TGG + chr5.1:28581576-28581595 None:intergenic 15.0%
!! ATGTTATATATCCTAATATA+AGG - chr5.1:28581542-28581561 MS.gene49609:intron 15.0%
!! TGTTATATATCCTAATATAA+GGG - chr5.1:28581543-28581562 MS.gene49609:intron 15.0%
!!! AAGATGAACTTTTTTTTTAA+AGG - chr5.1:28581887-28581906 MS.gene49609:CDS 15.0%
!!! AGATGAACTTTTTTTTTAAA+GGG - chr5.1:28581888-28581907 MS.gene49609:CDS 15.0%
!!! ATTATTTTTCAATTGTAAAC+AGG - chr5.1:28581989-28582008 MS.gene49609:intron 15.0%
!!! TATACTCAAATGATTATTTT+AGG + chr5.1:28581748-28581767 None:intergenic 15.0%
!!! TTATTTTTCAATTGTAAACA+GGG - chr5.1:28581990-28582009 MS.gene49609:intron 15.0%
!! ATAATTAATGTATCAAACTC+CGG - chr5.1:28581765-28581784 MS.gene49609:intron 20.0%
!! TAAGATGGTAATTGAATTTA+CGG - chr5.1:28581373-28581392 MS.gene49609:intron 20.0%
!!! AATACTGTTAAGTTGAATTA+AGG + chr5.1:28581801-28581820 None:intergenic 20.0%
!!! ATACTGTTAAGTTGAATTAA+GGG + chr5.1:28581800-28581819 None:intergenic 20.0%
!!! GATGAACTTTTTTTTTAAAG+GGG - chr5.1:28581889-28581908 MS.gene49609:CDS 20.0%
!!! TTTGTTTTTTTAACTCTCAT+GGG - chr5.1:28581331-28581350 MS.gene49609:intron 20.0%
!!! TTTTGTTTTTTTAACTCTCA+TGG - chr5.1:28581330-28581349 MS.gene49609:intron 20.0%
! TTACTTATAAGCTCTTACTT+TGG - chr5.1:28581666-28581685 MS.gene49609:intron 25.0%
!!! TGTATTTTTTTGGCTTAAGA+TGG - chr5.1:28581358-28581377 MS.gene49609:intron 25.0%
ACATTCATACTGATGAAGAA+AGG - chr5.1:28582047-28582066 MS.gene49609:CDS 30.0%
GAATTAAGGGATATAAAAGC+CGG + chr5.1:28581787-28581806 None:intergenic 30.0%
GTTATGACTAGACACAAAAT+TGG - chr5.1:28581913-28581932 MS.gene49609:intron 30.0%
TTCTTCATCAGTATGAATGT+TGG + chr5.1:28582047-28582066 None:intergenic 30.0%
!! ATTTGAAACGAGACTTTTTG+AGG - chr5.1:28581951-28581970 MS.gene49609:intron 30.0%
AAAGTTGTTGACAAGGTTGT+AGG - chr5.1:28582071-28582090 MS.gene49609:CDS 35.0%
AAGTTGTTGACAAGGTTGTA+GGG - chr5.1:28582072-28582091 MS.gene49609:CDS 35.0%
AATTTATCCAACATGGAGCA+TGG - chr5.1:28581155-28581174 MS.gene49609:CDS 35.0%
AGATTTCATCAAGATTGACG+TGG - chr5.1:28581466-28581485 MS.gene49609:intron 35.0%
ATTGGATCCATGTATTTGCA+AGG + chr5.1:28581413-28581432 None:intergenic 35.0%
GAAAGGAAAAGTTGTTGACA+AGG - chr5.1:28582064-28582083 MS.gene49609:CDS 35.0%
GATTGACGTGGATGAATTAA+TGG - chr5.1:28581478-28581497 MS.gene49609:intron 35.0%
TAATTGAATTTACGGCTGCA+TGG - chr5.1:28581381-28581400 MS.gene49609:intron 35.0%
!!! CATGGGATCGTGTATTTTTT+TGG - chr5.1:28581348-28581367 MS.gene49609:intron 35.0%
AGTTGTTGACAAGGTTGTAG+GGG - chr5.1:28582073-28582092 MS.gene49609:CDS 40.0%
ATAAGCCTTCCATTTAGCAG+TGG + chr5.1:28581228-28581247 None:intergenic 40.0%
CTCCAAAGAAACTAACAAGC+TGG - chr5.1:28581256-28581275 MS.gene49609:CDS 40.0%
GCAGCAAAGTCTTGAATGAT+TGG + chr5.1:28581431-28581450 None:intergenic 40.0%
! TGGTCTTTTTCCATACGAAC+AGG - chr5.1:28581686-28581705 MS.gene49609:intron 40.0%
!! CACCAGCTTGTTAGTTTCTT+TGG + chr5.1:28581261-28581280 None:intergenic 40.0%
!! CAGCTTGTTAGTTTCTTTGG+AGG + chr5.1:28581258-28581277 None:intergenic 40.0%
CAAGGTTGTAGGGGCAAAAA+AGG - chr5.1:28582082-28582101 MS.gene49609:CDS 45.0%
CCATACGAACAGGATGACTA+AGG - chr5.1:28581696-28581715 MS.gene49609:intron 45.0%
CCATTCCACTGCTAAATGGA+AGG - chr5.1:28581220-28581239 MS.gene49609:CDS 45.0%
CCATTTAGCAGTGGAATGGA+AGG + chr5.1:28581219-28581238 None:intergenic 45.0%
CCTTAGTCATCCTGTTCGTA+TGG + chr5.1:28581699-28581718 None:intergenic 45.0%
CCTTCCATTCCACTGCTAAA+TGG - chr5.1:28581216-28581235 MS.gene49609:CDS 45.0%
CCTTCCATTTAGCAGTGGAA+TGG + chr5.1:28581223-28581242 None:intergenic 45.0%
GGGAGGCAATTTATCCAACA+TGG - chr5.1:28581148-28581167 MS.gene49609:CDS 45.0%
GTGTGGACCTTGCAAATACA+TGG - chr5.1:28581403-28581422 MS.gene49609:intron 45.0%
TGGTGTGCTGCCCTTATATT+AGG + chr5.1:28581556-28581575 None:intergenic 45.0%
TGTATGACCATGCTCCATGT+TGG + chr5.1:28581165-28581184 None:intergenic 45.0%
GAATTTACGGCTGCATGGTG+TGG - chr5.1:28581386-28581405 MS.gene49609:intron 50.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 28581146 28582142 28581146 ID=MS.gene49609
chr5.1 mRNA 28581146 28582142 28581146 ID=MS.gene49609.t1;Parent=MS.gene49609
chr5.1 exon 28582011 28582142 28582011 ID=MS.gene49609.t1.exon1;Parent=MS.gene49609.t1
chr5.1 CDS 28582011 28582142 28582011 ID=cds.MS.gene49609.t1;Parent=MS.gene49609.t1
chr5.1 exon 28581789 28581911 28581789 ID=MS.gene49609.t1.exon2;Parent=MS.gene49609.t1
chr5.1 CDS 28581789 28581911 28581789 ID=cds.MS.gene49609.t1;Parent=MS.gene49609.t1
chr5.1 exon 28581146 28581277 28581146 ID=MS.gene49609.t1.exon3;Parent=MS.gene49609.t1
chr5.1 CDS 28581146 28581277 28581146 ID=cds.MS.gene49609.t1;Parent=MS.gene49609.t1
Gene Sequence

>MS.gene49609

ATGGGAGGCAATTTATCCAACATGGAGCATGGTCATACATCTGCAAAGTCATTATCATCTCACATTCTTACCTTCCATTCCACTGCTAAATGGAAGGCTTATTTTGATGCCTCCAAAGAAACTAACAAGCTGGTGCGTTATTATTAATTTAATTTAAAGCTATACTAATTATTTTGTATTTTCATTTTGTTTTTTTAACTCTCATGGGATCGTGTATTTTTTTGGCTTAAGATGGTAATTGAATTTACGGCTGCATGGTGTGGACCTTGCAAATACATGGATCCAATCATTCAAGACTTTGCTGCAAAATACATAAAAGTAGATTTCATCAAGATTGACGTGGATGAATTAATGGTATTATTACATTTTTATTTCATTTTACTATTATTATTACTCATGTTATATATCCTAATATAAGGGCAGCACACCATCTATACATTATATAAAGATGAATGACATATTACTTATAAGCTCTTTTTATTAATTTTACAAATATTATGTAAAACAAAAATAGTGTATTTTACTTATAAGCTCTTACTTTGGTCTTTTTCCATACGAACAGGATGACTAAGGCAAAAAAAAAAAAAAGTACGAATATTCCTAAAATAATCATTTGAGTATAATTAATGTATCAAACTCCGGCTTTTATATCCCTTAATTCAACTTAACAGTATTAATAAAGAGTATATTTGATAGAAAATAATAAATATATTTCATAACTTGAAATGAGATTTATATTTAAAGATGAACTTTTTTTTTAAAGGGGAGTTATGACTAGACACAAAATTGGTAATTTTTTAGCTACATTTGAAACGAGACTTTTTGAGGAATTGACTTGTGCACATTATTTTTCAATTGTAAACAGGGTGTCTCTCAAGAGTTTCAAGTGCAAGCAATGCCAACATTCATACTGATGAAGAAAGGAAAAGTTGTTGACAAGGTTGTAGGGGCAAAAAAGGAAGAGCTTGAAAAGTTGATTGAGAAGCATCAAAACTAA
Protein sequence

>MS.gene49609.t1

MGGNLSNMEHGHTSAKSLSSHILTFHSTAKWKAYFDASKETNKLMVIEFTAAWCGPCKYMDPIIQDFAAKYIKVDFIKIDVDELMGVSQEFQVQAMPTFILMKKGKVVDKVVGAKKEELEKLIEKHQN