AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49344


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49344.t1 MTR_1g070480 89.637 193 20 0 1 193 1 193 5.29e-113 320
MS.gene49344.t1 MTR_7g096220 54.945 182 81 1 11 191 18 199 2.42e-64 197
MS.gene49344.t1 MTR_2g100260 48.252 143 68 2 33 170 38 179 8.67e-37 126
MS.gene49344.t1 MTR_3g012070 81.053 95 17 1 97 191 34 127 1.90e-36 125
MS.gene49344.t1 MTR_1g080760 49.068 161 77 2 34 193 37 193 6.79e-34 119
MS.gene49344.t1 MTR_6g092690 39.634 164 93 2 11 168 11 174 2.88e-33 118
MS.gene49344.t1 MTR_4g014060 40.288 139 81 1 33 169 61 199 5.78e-31 112
MS.gene49344.t1 MTR_0562s0010 40.288 139 81 1 33 169 61 199 5.78e-31 112
MS.gene49344.t1 MTR_5g083490 34.184 196 109 2 6 181 8 203 4.08e-29 107
MS.gene49344.t1 MTR_2g100270 46.784 171 81 2 9 169 3 173 1.20e-27 103
MS.gene49344.t1 MTR_8g016150 38.788 165 93 1 7 163 2 166 6.70e-26 98.6
MS.gene49344.t1 MTR_1g093090 46.914 81 41 1 33 111 24 104 1.31e-17 77.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49344.t1 AT1G04260 42.045 176 102 0 18 193 7 182 4.07e-47 152
MS.gene49344.t1 AT1G55190 52.448 143 68 0 26 168 31 173 6.99e-42 139
MS.gene49344.t1 AT3G13710 43.373 166 80 1 17 168 8 173 1.10e-39 134
MS.gene49344.t1 AT1G08770 41.808 177 99 2 17 191 33 207 4.71e-35 122
MS.gene49344.t1 AT3G13720 46.528 144 77 0 25 168 30 173 5.39e-35 122
MS.gene49344.t1 AT5G01640 39.333 150 89 1 33 180 56 205 9.21e-31 112
MS.gene49344.t1 AT2G38360 35.099 151 96 1 33 181 56 206 6.45e-29 107
MS.gene49344.t1 AT2G40380 42.000 150 85 1 33 180 48 197 1.08e-28 106
MS.gene49344.t1 AT5G56230 35.196 179 107 4 6 177 6 182 1.84e-26 100
MS.gene49344.t1 AT3G56110 39.456 147 87 1 33 177 46 192 8.71e-26 99.0
MS.gene49344.t1 AT3G56110 39.456 147 87 1 33 177 46 192 8.71e-26 99.0
MS.gene49344.t1 AT3G56110 39.456 147 87 1 33 177 46 192 8.71e-26 99.0
MS.gene49344.t1 AT3G56110 39.456 147 87 1 33 177 46 192 8.71e-26 99.0
MS.gene49344.t1 AT1G17700 40.278 144 86 0 26 169 31 174 3.14e-25 96.7
MS.gene49344.t1 AT5G07110 36.552 145 90 1 33 175 46 190 3.09e-24 95.1
MS.gene49344.t1 AT5G05380 41.497 147 84 1 33 177 49 195 1.61e-23 93.2
MS.gene49344.t1 AT5G05380 41.497 147 84 1 33 177 92 238 3.22e-23 93.6
MS.gene49344.t1 AT5G05380 41.497 147 84 1 33 177 100 246 3.42e-23 93.6
MS.gene49344.t1 AT5G05380 41.497 147 84 1 33 177 116 262 5.51e-23 93.2
MS.gene49344.t1 AT1G55640 31.387 137 94 0 34 170 41 177 3.31e-18 78.6
MS.gene49344.t1 AT4G29658 33.803 142 90 1 33 170 36 177 1.87e-15 71.6

Find 71 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAAGAAGAGATCTTTGA+TGG 0.279860 1.1:+53063939 MS.gene49344:CDS
TTGGAAGGTGGGGTGGCGCG+TGG 0.324938 1.1:-53063501 None:intergenic
GTGAGGGAGAGTGAAGGATT+GGG 0.331674 1.1:-53063562 None:intergenic
GGTAGAGGAGGCTGAGGAAG+AGG 0.352812 1.1:-53063665 None:intergenic
GAAGGGAGAGAGTTGTAAGT+TGG 0.355663 1.1:-53063465 None:intergenic
TCCTCGCCGTCTTCGCCGCT+TGG 0.362575 1.1:+53063709 MS.gene49344:CDS
GGAAGGTGGGGTGGCGCGTG+GGG 0.374482 1.1:-53063499 None:intergenic
CACGTGGGGTAGTTGGAAGG+TGG 0.378025 1.1:-53063513 None:intergenic
TGAGGGAGAGAGGGTGGTAG+AGG 0.379952 1.1:-53063680 None:intergenic
GGTGATTTACTTTCAGTTGT+TGG 0.381427 1.1:+53063960 MS.gene49344:CDS
GTAAGTTGGAGTGGGATAGA+TGG 0.383602 1.1:-53063451 None:intergenic
AGTGAGGGAGAGTGAAGGAT+TGG 0.391419 1.1:-53063563 None:intergenic
CGCTCGTCTTCACCGGCGTC+TGG 0.396795 1.1:+53063832 MS.gene49344:CDS
GTGGTTTCGGAGAGGGAGTG+AGG 0.418352 1.1:-53063579 None:intergenic
GGAGGCTGAGGAAGAGGATG+AGG 0.423523 1.1:-53063659 None:intergenic
GAAGAACCAAGCGGCGAAGA+CGG 0.427174 1.1:-53063715 None:intergenic
GAGGGTGGTAGAGGAGGCTG+AGG 0.433438 1.1:-53063671 None:intergenic
TGGGAGGCACGTGGGGTAGT+TGG 0.435134 1.1:-53063520 None:intergenic
GGGGTAGTTGGAAGGTGGGG+TGG 0.436768 1.1:-53063508 None:intergenic
TGGTTTCGGAGAGGGAGTGA+GGG 0.443935 1.1:-53063578 None:intergenic
GGGAGAGAGGGTGGTAGAGG+AGG 0.457006 1.1:-53063677 None:intergenic
AGGAAGACGATGAGGGAGAG+AGG 0.457920 1.1:-53063690 None:intergenic
TGGAAGGTGGGGTGGCGCGT+GGG 0.467570 1.1:-53063500 None:intergenic
TGAGGGAGAGTGAAGGATTG+GGG 0.470927 1.1:-53063561 None:intergenic
GGCTGAGGAAGAGGATGAGG+AGG 0.474629 1.1:-53063656 None:intergenic
ACGGAGGGTGGTTTCGGAGA+GGG 0.477533 1.1:-53063586 None:intergenic
CGTGGGGAAGTTGAGTTTGA+AGG 0.477570 1.1:-53063483 None:intergenic
CGTGGGGTAGTTGGAAGGTG+GGG 0.481724 1.1:-53063511 None:intergenic
GTCCTCGTGTCGGTGCTCTT+CGG 0.484352 1.1:+53063861 MS.gene49344:CDS
GAGAGAGTTGTAAGTTGGAG+TGG 0.502950 1.1:-53063460 None:intergenic
AGTTGATGCGGAAGTGGTTG+AGG 0.503368 1.1:-53063620 None:intergenic
AGACGATGAGGGAGAGAGGG+TGG 0.503783 1.1:-53063686 None:intergenic
GTCGTCGCGCTCGTCTTCAC+CGG 0.504856 1.1:+53063825 MS.gene49344:CDS
CTTCTTCTTCCGTGACCACC+CGG 0.507928 1.1:+53063740 MS.gene49344:CDS
AGAGAGTTGTAAGTTGGAGT+GGG 0.514057 1.1:-53063459 None:intergenic
ACGTGGGGTAGTTGGAAGGT+GGG 0.516248 1.1:-53063512 None:intergenic
GAGGATGAGGAGGATGATGA+TGG 0.521356 1.1:-53063646 None:intergenic
AGAGTAGAATGAGGAGGAAG+CGG 0.522523 1.1:-53063791 None:intergenic
GAGGGAGTGAGGGAGAGTGA+AGG 0.523179 1.1:-53063568 None:intergenic
TCTAGTGTACCTCGTTCGCT+TGG 0.528961 1.1:-53063997 None:intergenic
AGCGGTCGTCGATGGTGAAA+CGG 0.536990 1.1:-53063773 None:intergenic
GTGAAACGGAAGAGGACGAC+CGG 0.538948 1.1:-53063759 None:intergenic
AGGCACGTGGGGTAGTTGGA+AGG 0.547236 1.1:-53063516 None:intergenic
AGAGGACGACCGGGTGGTCA+CGG 0.547677 1.1:-53063749 None:intergenic
CGTCGATGGTGAAACGGAAG+AGG 0.553573 1.1:-53063767 None:intergenic
GTGGGGAAGTTGAGTTTGAA+GGG 0.558559 1.1:-53063482 None:intergenic
GAGGAGGAAGCGGTCGTCGA+TGG 0.560409 1.1:-53063781 None:intergenic
GTCGGTGCTCTTCGGTGCTG+CGG 0.562357 1.1:+53063869 MS.gene49344:CDS
ACTACCCCACGTGCCTCCCA+TGG 0.562455 1.1:+53063523 MS.gene49344:CDS
CTGGCTTAACGTCCTCGTGT+CGG 0.579627 1.1:+53063851 MS.gene49344:CDS
GGTGCTCTTCGGTGCTGCGG+TGG 0.582059 1.1:+53063872 MS.gene49344:CDS
TGGCGTAGTTGATGCGGAAG+TGG 0.582115 1.1:-53063626 None:intergenic
GGAAGACGATGAGGGAGAGA+GGG 0.595788 1.1:-53063689 None:intergenic
TTTGCCATGGGAGGCACGTG+GGG 0.597252 1.1:-53063527 None:intergenic
GGGCAGAGAGTAGAATGAGG+AGG 0.599319 1.1:-53063797 None:intergenic
CACCGAAGAGCACCGACACG+AGG 0.603948 1.1:-53063863 None:intergenic
GGTGGTCACGGAAGAAGAAG+AGG 0.608401 1.1:-53063737 None:intergenic
GACGAGCGCGACGACTGTGA+GGG 0.612183 1.1:-53063817 None:intergenic
ACCAAGCGGCGAAGACGGCG+AGG 0.613183 1.1:-53063710 None:intergenic
TACGGAGGGTGGTTTCGGAG+AGG 0.616601 1.1:-53063587 None:intergenic
TGAGGGCAGAGAGTAGAATG+AGG 0.616996 1.1:-53063800 None:intergenic
GATTTACTTTCAGTTGTTGG+TGG 0.624407 1.1:+53063963 MS.gene49344:CDS
AGACGGCGAGGAAGACGATG+AGG 0.634290 1.1:-53063698 None:intergenic
GACGGCGAGGAAGACGATGA+GGG 0.639915 1.1:-53063697 None:intergenic
TGAAACGGAAGAGGACGACC+GGG 0.651587 1.1:-53063758 None:intergenic
AGACGAGCGCGACGACTGTG+AGG 0.675858 1.1:-53063818 None:intergenic
TGATGATGGCGTAGTTGATG+CGG 0.679858 1.1:-53063632 None:intergenic
GCTTCAATACCAAGCGAACG+AGG 0.681179 1.1:+53063988 MS.gene49344:CDS
GAAGAAGAGGAAGAACCAAG+CGG 0.686040 1.1:-53063724 None:intergenic
GAGGACGTTAAGCCAGACGC+CGG 0.719336 1.1:-53063844 None:intergenic
AACGGAAGAGGACGACCGGG+TGG 0.723292 1.1:-53063755 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GATGAAGAAGAGATCTTTGA+TGG + chr1.1:53063939-53063958 MS.gene49344:CDS 35.0%
GATTTACTTTCAGTTGTTGG+TGG + chr1.1:53063963-53063982 MS.gene49344:CDS 35.0%
GGTGATTTACTTTCAGTTGT+TGG + chr1.1:53063960-53063979 MS.gene49344:CDS 35.0%
! AGAGAGTTGTAAGTTGGAGT+GGG - chr1.1:53063462-53063481 None:intergenic 40.0%
! GAGTGAAGAAGTTTTGCCAT+GGG - chr1.1:53063542-53063561 None:intergenic 40.0%
! GGTTGAGGTTGCGTTTTATA+CGG - chr1.1:53063608-53063627 None:intergenic 40.0%
! TTTTATACGGAGGGTGGTTT+CGG - chr1.1:53063595-53063614 None:intergenic 40.0%
AGAGTAGAATGAGGAGGAAG+CGG - chr1.1:53063794-53063813 None:intergenic 45.0%
GAAGAAGAGGAAGAACCAAG+CGG - chr1.1:53063727-53063746 None:intergenic 45.0%
GAAGGGAGAGAGTTGTAAGT+TGG - chr1.1:53063468-53063487 None:intergenic 45.0%
GTGGGGAAGTTGAGTTTGAA+GGG - chr1.1:53063485-53063504 None:intergenic 45.0%
! GAGAGAGTTGTAAGTTGGAG+TGG - chr1.1:53063463-53063482 None:intergenic 45.0%
! GAGGTTGCGTTTTATACGGA+GGG - chr1.1:53063604-53063623 None:intergenic 45.0%
! GGAGTGAAGAAGTTTTGCCA+TGG - chr1.1:53063543-53063562 None:intergenic 45.0%
! GTAAGTTGGAGTGGGATAGA+TGG - chr1.1:53063454-53063473 None:intergenic 45.0%
! TGAAGAAGTTTTGCCATGGG+AGG - chr1.1:53063539-53063558 None:intergenic 45.0%
! TGAGGTTGCGTTTTATACGG+AGG - chr1.1:53063605-53063624 None:intergenic 45.0%
!! TGATGATGGCGTAGTTGATG+CGG - chr1.1:53063635-53063654 None:intergenic 45.0%
!! TTGTTTTGCATGCGGCGTTT+CGG + chr1.1:53063895-53063914 MS.gene49344:CDS 45.0%
AGTGAGGGAGAGTGAAGGAT+TGG - chr1.1:53063566-53063585 None:intergenic 50.0%
CGTGGGGAAGTTGAGTTTGA+AGG - chr1.1:53063486-53063505 None:intergenic 50.0%
GAGGATGAGGAGGATGATGA+TGG - chr1.1:53063649-53063668 None:intergenic 50.0%
GCTTCAATACCAAGCGAACG+AGG + chr1.1:53063988-53064007 MS.gene49344:CDS 50.0%
GTGAGGGAGAGTGAAGGATT+GGG - chr1.1:53063565-53063584 None:intergenic 50.0%
TCTAGTGTACCTCGTTCGCT+TGG - chr1.1:53064000-53064019 None:intergenic 50.0%
TGAGGGAGAGTGAAGGATTG+GGG - chr1.1:53063564-53063583 None:intergenic 50.0%
TGAGGGCAGAGAGTAGAATG+AGG - chr1.1:53063803-53063822 None:intergenic 50.0%
! AGTTGATGCGGAAGTGGTTG+AGG - chr1.1:53063623-53063642 None:intergenic 50.0%
! GTTGCGTTTTATACGGAGGG+TGG - chr1.1:53063601-53063620 None:intergenic 50.0%
!! TGCGGTGGTTGTTTTGCATG+CGG + chr1.1:53063887-53063906 MS.gene49344:CDS 50.0%
ACGTGGGGTAGTTGGAAGGT+GGG - chr1.1:53063515-53063534 None:intergenic 55.0%
AGCGGTCGTCGATGGTGAAA+CGG - chr1.1:53063776-53063795 None:intergenic 55.0%
AGGAAGACGATGAGGGAGAG+AGG - chr1.1:53063693-53063712 None:intergenic 55.0%
CGTCGATGGTGAAACGGAAG+AGG - chr1.1:53063770-53063789 None:intergenic 55.0%
CTGGCTTAACGTCCTCGTGT+CGG + chr1.1:53063851-53063870 MS.gene49344:CDS 55.0%
CTTCTTCTTCCGTGACCACC+CGG + chr1.1:53063740-53063759 MS.gene49344:CDS 55.0%
GAAGAACCAAGCGGCGAAGA+CGG - chr1.1:53063718-53063737 None:intergenic 55.0%
GGAAGACGATGAGGGAGAGA+GGG - chr1.1:53063692-53063711 None:intergenic 55.0%
GGGCAGAGAGTAGAATGAGG+AGG - chr1.1:53063800-53063819 None:intergenic 55.0%
GGTGGTCACGGAAGAAGAAG+AGG - chr1.1:53063740-53063759 None:intergenic 55.0%
GTGAAACGGAAGAGGACGAC+CGG - chr1.1:53063762-53063781 None:intergenic 55.0%
TGAAACGGAAGAGGACGACC+GGG - chr1.1:53063761-53063780 None:intergenic 55.0%
TGGTTTCGGAGAGGGAGTGA+GGG - chr1.1:53063581-53063600 None:intergenic 55.0%
! TGGCGTAGTTGATGCGGAAG+TGG - chr1.1:53063629-53063648 None:intergenic 55.0%
!! TTTTGCCATGGGAGGCACGT+GGG - chr1.1:53063531-53063550 None:intergenic 55.0%
ACGGAGGGTGGTTTCGGAGA+GGG - chr1.1:53063589-53063608 None:intergenic 60.0%
AGACGATGAGGGAGAGAGGG+TGG - chr1.1:53063689-53063708 None:intergenic 60.0%
AGACGGCGAGGAAGACGATG+AGG - chr1.1:53063701-53063720 None:intergenic 60.0%
AGGCACGTGGGGTAGTTGGA+AGG - chr1.1:53063519-53063538 None:intergenic 60.0%
CACGTGGGGTAGTTGGAAGG+TGG - chr1.1:53063516-53063535 None:intergenic 60.0%
CGTGGGGTAGTTGGAAGGTG+GGG - chr1.1:53063514-53063533 None:intergenic 60.0%
GACGGCGAGGAAGACGATGA+GGG - chr1.1:53063700-53063719 None:intergenic 60.0%
GAGGACGTTAAGCCAGACGC+CGG - chr1.1:53063847-53063866 None:intergenic 60.0%
GAGGGAGTGAGGGAGAGTGA+AGG - chr1.1:53063571-53063590 None:intergenic 60.0%
GGAGGCTGAGGAAGAGGATG+AGG - chr1.1:53063662-53063681 None:intergenic 60.0%
GGCTGAGGAAGAGGATGAGG+AGG - chr1.1:53063659-53063678 None:intergenic 60.0%
GGTAGAGGAGGCTGAGGAAG+AGG - chr1.1:53063668-53063687 None:intergenic 60.0%
GTGGTTTCGGAGAGGGAGTG+AGG - chr1.1:53063582-53063601 None:intergenic 60.0%
TACGGAGGGTGGTTTCGGAG+AGG - chr1.1:53063590-53063609 None:intergenic 60.0%
TGAGGGAGAGAGGGTGGTAG+AGG - chr1.1:53063683-53063702 None:intergenic 60.0%
! GTCCTCGTGTCGGTGCTCTT+CGG + chr1.1:53063861-53063880 MS.gene49344:CDS 60.0%
! TTTGCCATGGGAGGCACGTG+GGG - chr1.1:53063530-53063549 None:intergenic 60.0%
!! GTTTTGCCATGGGAGGCACG+TGG - chr1.1:53063532-53063551 None:intergenic 60.0%
AACGGAAGAGGACGACCGGG+TGG - chr1.1:53063758-53063777 None:intergenic 65.0%
ACTACCCCACGTGCCTCCCA+TGG + chr1.1:53063523-53063542 MS.gene49344:CDS 65.0%
AGACGAGCGCGACGACTGTG+AGG - chr1.1:53063821-53063840 None:intergenic 65.0%
AGAGGACGACCGGGTGGTCA+CGG - chr1.1:53063752-53063771 None:intergenic 65.0%
GACGAGCGCGACGACTGTGA+GGG - chr1.1:53063820-53063839 None:intergenic 65.0%
GAGGAGGAAGCGGTCGTCGA+TGG - chr1.1:53063784-53063803 None:intergenic 65.0%
GAGGGTGGTAGAGGAGGCTG+AGG - chr1.1:53063674-53063693 None:intergenic 65.0%
GGGAGAGAGGGTGGTAGAGG+AGG - chr1.1:53063680-53063699 None:intergenic 65.0%
GGGGTAGTTGGAAGGTGGGG+TGG - chr1.1:53063511-53063530 None:intergenic 65.0%
GTCGTCGCGCTCGTCTTCAC+CGG + chr1.1:53063825-53063844 MS.gene49344:CDS 65.0%
! TGGGAGGCACGTGGGGTAGT+TGG - chr1.1:53063523-53063542 None:intergenic 65.0%
!! CACCGAAGAGCACCGACACG+AGG - chr1.1:53063866-53063885 None:intergenic 65.0%
!! GTCGGTGCTCTTCGGTGCTG+CGG + chr1.1:53063869-53063888 MS.gene49344:CDS 65.0%
ACCAAGCGGCGAAGACGGCG+AGG - chr1.1:53063713-53063732 None:intergenic 70.0%
CGCTCGTCTTCACCGGCGTC+TGG + chr1.1:53063832-53063851 MS.gene49344:CDS 70.0%
TCCTCGCCGTCTTCGCCGCT+TGG + chr1.1:53063709-53063728 MS.gene49344:CDS 70.0%
TGGAAGGTGGGGTGGCGCGT+GGG - chr1.1:53063503-53063522 None:intergenic 70.0%
TTGGAAGGTGGGGTGGCGCG+TGG - chr1.1:53063504-53063523 None:intergenic 70.0%
!! GGTGCTCTTCGGTGCTGCGG+TGG + chr1.1:53063872-53063891 MS.gene49344:CDS 70.0%
GGAAGGTGGGGTGGCGCGTG+GGG - chr1.1:53063502-53063521 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 53063444 53064025 53063444 ID=MS.gene49344
chr1.1 mRNA 53063444 53064025 53063444 ID=MS.gene49344.t1;Parent=MS.gene49344
chr1.1 exon 53063444 53064025 53063444 ID=MS.gene49344.t1.exon1;Parent=MS.gene49344.t1
chr1.1 CDS 53063444 53064025 53063444 ID=cds.MS.gene49344.t1;Parent=MS.gene49344.t1
Gene Sequence

>MS.gene49344

ATGTCTTCCATCTATCCCACTCCAACTTACAACTCTCTCCCTTCAAACTCAACTTCCCCACGCGCCACCCCACCTTCCAACTACCCCACGTGCCTCCCATGGCAAAACTTCTTCACTCCCCAATCCTTCACTCTCCCTCACTCCCTCTCCGAAACCACCCTCCGTATAAAACGCAACCTCAACCACTTCCGCATCAACTACGCCATCATCATCCTCCTCATCCTCTTCCTCAGCCTCCTCTACCACCCTCTCTCCCTCATCGTCTTCCTCGCCGTCTTCGCCGCTTGGTTCTTCCTCTTCTTCTTCCGTGACCACCCGGTCGTCCTCTTCCGTTTCACCATCGACGACCGCTTCCTCCTCATTCTACTCTCTGCCCTCACAGTCGTCGCGCTCGTCTTCACCGGCGTCTGGCTTAACGTCCTCGTGTCGGTGCTCTTCGGTGCTGCGGTGGTTGTTTTGCATGCGGCGTTTCGGAGTATTGATGATTTGTATTTAGATGAAGAAGAGATCTTTGATGGTGATTTACTTTCAGTTGTTGGTGGTAGCTTCAATACCAAGCGAACGAGGTACACTAGAATGTAG

Protein sequence

>MS.gene49344.t1

MSSIYPTPTYNSLPSNSTSPRATPPSNYPTCLPWQNFFTPQSFTLPHSLSETTLRIKRNLNHFRINYAIIILLILFLSLLYHPLSLIVFLAVFAAWFFLFFFRDHPVVLFRFTIDDRFLLILLSALTVVALVFTGVWLNVLVSVLFGAAVVVLHAAFRSIDDLYLDEEEIFDGDLLSVVGGSFNTKRTRYTRM