AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062884

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062884.t1 MTR_4g071110 92.424 198 15 0 1 198 1 198 1.51e-119 339
MS.gene062884.t1 MTR_3g112510 51.034 145 51 4 14 138 83 227 3.37e-42 144
MS.gene062884.t1 MTR_8g076620 50.000 136 59 2 13 139 117 252 1.67e-41 143
MS.gene062884.t1 MTR_5g021130 44.654 159 57 4 15 142 98 256 4.15e-37 131
MS.gene062884.t1 MTR_5g089750 38.125 160 67 3 17 144 249 408 3.46e-29 112
MS.gene062884.t1 MTR_8g039110 36.571 175 73 3 6 142 113 287 3.90e-27 105
MS.gene062884.t1 MTR_3g014660 36.076 158 69 4 17 142 134 291 1.01e-23 96.3
MS.gene062884.t1 MTR_0363s0040 62.500 56 21 0 6 61 113 168 4.40e-20 85.1
MS.gene062884.t1 MTR_1g023230 68.085 47 15 0 15 61 120 166 2.74e-19 83.2
MS.gene062884.t1 MTR_0105s0070 81.818 33 6 0 19 51 44 76 1.30e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062884.t1 AT2G21400 50.758 132 49 2 11 137 4 124 3.43e-40 135
MS.gene062884.t1 AT2G21400 50.758 132 49 2 11 137 3 123 3.75e-40 135
MS.gene062884.t1 AT2G21400 49.265 136 60 2 11 137 3 138 6.90e-39 132
MS.gene062884.t1 AT2G21400 49.265 136 60 2 11 137 4 139 7.66e-39 132
MS.gene062884.t1 AT1G75520 37.327 217 87 6 14 193 122 326 2.24e-36 130
MS.gene062884.t1 AT5G66350 41.463 164 72 3 17 160 120 279 5.20e-36 128
MS.gene062884.t1 AT5G66350 41.463 164 72 3 17 160 120 279 7.10e-36 128
MS.gene062884.t1 AT5G66350 41.463 164 72 3 17 160 120 279 8.87e-36 128
MS.gene062884.t1 AT3G51060 46.809 141 55 3 15 135 142 282 2.67e-35 127
MS.gene062884.t1 AT2G18120 42.657 143 72 3 15 147 70 212 1.69e-34 122
MS.gene062884.t1 AT2G18120 42.069 145 72 3 15 147 70 214 7.90e-34 120
MS.gene062884.t1 AT4G36260 41.615 161 52 4 15 139 92 246 3.59e-32 118
MS.gene062884.t1 AT1G19790 39.444 180 75 4 15 160 117 296 4.76e-32 118
MS.gene062884.t1 AT1G19790 39.444 180 75 4 15 160 117 296 4.76e-32 118
MS.gene062884.t1 AT5G12330 34.518 197 84 4 17 176 112 300 2.90e-27 105
MS.gene062884.t1 AT5G12330 34.518 197 84 4 17 176 112 300 2.90e-27 105
MS.gene062884.t1 AT5G12330 34.518 197 84 4 17 176 199 387 4.11e-27 106
MS.gene062884.t1 AT3G54430 34.848 132 77 3 17 139 41 172 2.08e-20 84.3
MS.gene062884.t1 AT5G33210 65.957 47 16 0 15 61 15 61 4.72e-19 79.0
MS.gene062884.t1 AT5G12330 62.000 50 19 0 17 66 112 161 1.89e-18 80.5
MS.gene062884.t1 AT5G33210 65.957 47 16 0 15 61 50 96 3.06e-18 78.6

Find 47 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACATCCATTGCCATCTTTC+AGG 0.162920 4.1:-31845777 MS.gene062884:CDS
TTCTGATGAGTTCAAATTTC+CGG 0.205380 4.1:-31846091 MS.gene062884:CDS
AAGATGTATTCAACACAATT+AGG 0.212765 4.1:-31846660 MS.gene062884:CDS
AGGGAAAGAAGAAGTGTTAA+AGG 0.254491 4.1:-31846640 MS.gene062884:CDS
AATTTCTACACTTGTTTGAT+AGG 0.288184 4.1:+31845996 None:intergenic
TATCAAACAAGTGTAGAAAT+TGG 0.319031 4.1:-31845994 MS.gene062884:CDS
ACCACCTTCATGAACATAAA+AGG 0.327971 4.1:-31846452 MS.gene062884:CDS
GTATGGAAGCTTTGTTGATC+AGG 0.364960 4.1:+31845934 None:intergenic
ATGTGTTCAGGTGCGCTCTA+TGG 0.373967 4.1:-31846040 MS.gene062884:CDS
ATGCACAATCCTTCTTTGCT+TGG 0.390646 4.1:+31846592 None:intergenic
AGTGGTATTCTTTATGATCA+AGG 0.401384 4.1:-31845958 MS.gene062884:CDS
CTTGGATTCCTGCCGATAGA+AGG 0.408141 4.1:-31846506 MS.gene062884:CDS
AGATGTATTCAACACAATTA+GGG 0.426718 4.1:-31846659 MS.gene062884:CDS
GATCAAGGGAGTGTATAGTA+TGG 0.429220 4.1:+31845917 None:intergenic
GGCCACATTGACATGTGTTC+AGG 0.436853 4.1:-31846052 MS.gene062884:CDS
GGGAAAGAAGAAGTGTTAAA+GGG 0.452664 4.1:-31846639 MS.gene062884:CDS
ATTGGAGGACATGTATTTAG+TGG 0.464916 4.1:-31845976 MS.gene062884:CDS
CTGTGGGAACCAAGCAAAGA+AGG 0.482489 4.1:-31846601 MS.gene062884:CDS
GGCATACCGGGCCTGAAAGA+TGG 0.493287 4.1:+31845766 None:intergenic
CATTCTGTGACGCCTTCTAT+CGG 0.499159 4.1:+31846494 None:intergenic
CTGAAAGATGGCAATGGATG+TGG 0.502689 4.1:+31845778 None:intergenic
AAGTGCTTCTGATATGTGTT+TGG 0.503819 4.1:+31846526 None:intergenic
CTGTGACGCCTTCTATCGGC+AGG 0.519090 4.1:+31846498 None:intergenic
GATGGCAATGGATGTGGTGG+AGG 0.521208 4.1:+31845784 None:intergenic
GGACGGAACGGTTAATGAAA+CGG 0.532430 4.1:-31846019 MS.gene062884:CDS
CCATTGCCATCTTTCAGGCC+CGG 0.535194 4.1:-31845772 None:intergenic
GCAAGTGCAAGTGCAACTAT+AGG 0.535841 4.1:-31845838 MS.gene062884:CDS
TATGGAAGCTTTGTTGATCA+GGG 0.559692 4.1:+31845935 None:intergenic
GCCATGGAACTCGTAACAGC+CGG 0.560763 4.1:+31846072 None:intergenic
GTCTGAAATGTCAAGACTGT+GGG 0.561427 4.1:-31846617 MS.gene062884:CDS
TCCGGCTGTTACGAGTTCCA+TGG 0.567211 4.1:-31846073 MS.gene062884:CDS
CGATAGAAGGCGTCACAGAA+TGG 0.568956 4.1:-31846493 MS.gene062884:CDS
GCAATCCACACAGGTGATGA+TGG 0.569958 4.1:-31845862 MS.gene062884:CDS
CAAACAAGTGTAGAAATTGG+AGG 0.570503 4.1:-31845991 MS.gene062884:CDS
AACACATGTCAATGTGGCCA+TGG 0.579628 4.1:+31846056 None:intergenic
AGAAGGATTGTGCATACTCA+AGG 0.587247 4.1:-31846584 MS.gene062884:CDS
GTTCAGGTGCGCTCTATGGA+CGG 0.606942 4.1:-31846036 MS.gene062884:CDS
CCGGGCCTGAAAGATGGCAA+TGG 0.618050 4.1:+31845772 None:intergenic
AGTAGTAATGCAATCCACAC+AGG 0.618793 4.1:-31845871 MS.gene062884:CDS
TGAAGGTGGTGCTGATCAGA+AGG 0.627301 4.1:+31846465 None:intergenic
AAAGATGGCAATGGATGTGG+TGG 0.634340 4.1:+31845781 None:intergenic
AAACACATATCAGAAGCACT+TGG 0.635365 4.1:-31846524 MS.gene062884:CDS
GGTCTGAAATGTCAAGACTG+TGG 0.643818 4.1:-31846618 MS.gene062884:CDS
GGTGCGCTCTATGGACGGAA+CGG 0.668044 4.1:-31846031 MS.gene062884:CDS
CACCTGAACACATGTCAATG+TGG 0.680012 4.1:+31846050 None:intergenic
GGTGGTGCTGATCAGAAGGA+TGG 0.685704 4.1:+31846469 None:intergenic
TTGCACCATCATCACCTGTG+TGG 0.692440 4.1:+31845857 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAAAAAATGAACTATTTA+GGG + chr4.1:31846084-31846103 None:intergenic 15.0%
!! CTGAAATATTAGACATATTA+CGG + chr4.1:31846318-31846337 None:intergenic 20.0%
!! GGAAAAAAAATGAACTATTT+AGG + chr4.1:31846085-31846104 None:intergenic 20.0%
!! TTGAGTTAAAAGATCAAAAT+AGG + chr4.1:31846197-31846216 None:intergenic 20.0%
! AATTTCTACACTTGTTTGAT+AGG + chr4.1:31846437-31846456 None:intergenic 25.0%
! ATAACAGAAGAAACATATTG+AGG + chr4.1:31846106-31846125 None:intergenic 25.0%
! CGTAATATGTCTAATATTTC+AGG - chr4.1:31846316-31846335 MS.gene062884:intron 25.0%
! TATCAAACAAGTGTAGAAAT+TGG - chr4.1:31846436-31846455 MS.gene062884:CDS 25.0%
AGTGGTATTCTTTATGATCA+AGG - chr4.1:31846472-31846491 MS.gene062884:CDS 30.0%
CCTAATTGTGTTGAATACAT+CGG + chr4.1:31845773-31845792 None:intergenic 30.0%
TTCTGATGAGTTCAAATTTC+CGG - chr4.1:31846339-31846358 MS.gene062884:intron 30.0%
! AAGATTTTGTTGCTGATCAA+GGG + chr4.1:31846530-31846549 None:intergenic 30.0%
! TAAGATTTTGTTGCTGATCA+AGG + chr4.1:31846531-31846550 None:intergenic 30.0%
AAGTGCTTCTGATATGTGTT+TGG + chr4.1:31845907-31845926 None:intergenic 35.0%
ACCACCTTCATGAACATAAA+AGG - chr4.1:31845978-31845997 MS.gene062884:CDS 35.0%
AGAAGTTGCTGCAAAAACAA+AGG - chr4.1:31845872-31845891 MS.gene062884:CDS 35.0%
ATTGGAGGACATGTATTTAG+TGG - chr4.1:31846454-31846473 MS.gene062884:CDS 35.0%
CAAACAAGTGTAGAAATTGG+AGG - chr4.1:31846439-31846458 MS.gene062884:CDS 35.0%
GACATATTACGGTTGTGATT+AGG + chr4.1:31846307-31846326 None:intergenic 35.0%
GTATCCCTTGTACTTATCAT+TGG + chr4.1:31846277-31846296 None:intergenic 35.0%
TTACGGTTGTGATTAGGATA+TGG + chr4.1:31846301-31846320 None:intergenic 35.0%
! AATGAACTATTTAGGGCTCT+TGG + chr4.1:31846077-31846096 None:intergenic 35.0%
! TGTGCCTTTTATGTTCATGA+AGG + chr4.1:31845985-31846004 None:intergenic 35.0%
!! AAACACATATCAGAAGCACT+TGG - chr4.1:31845906-31845925 MS.gene062884:CDS 35.0%
!! AGGGAAAGAAGAAGTGTTAA+AGG - chr4.1:31845790-31845809 MS.gene062884:CDS 35.0%
!! GGGAAAGAAGAAGTGTTAAA+GGG - chr4.1:31845791-31845810 MS.gene062884:CDS 35.0%
!! TATGGAAGCTTTGTTGATCA+GGG + chr4.1:31846498-31846517 None:intergenic 35.0%
AGAAGGATTGTGCATACTCA+AGG - chr4.1:31845846-31845865 MS.gene062884:CDS 40.0%
AGTAGTAATGCAATCCACAC+AGG - chr4.1:31846559-31846578 MS.gene062884:CDS 40.0%
ATGCACAATCCTTCTTTGCT+TGG + chr4.1:31845841-31845860 None:intergenic 40.0%
! GATCAAGGGAGTGTATAGTA+TGG + chr4.1:31846516-31846535 None:intergenic 40.0%
! GCCTTTTATGTTCATGAAGG+TGG + chr4.1:31845982-31846001 None:intergenic 40.0%
! GTCTGAAATGTCAAGACTGT+GGG - chr4.1:31845813-31845832 MS.gene062884:CDS 40.0%
!! GTATGGAAGCTTTGTTGATC+AGG + chr4.1:31846499-31846518 None:intergenic 40.0%
AAAGATGGCAATGGATGTGG+TGG + chr4.1:31846652-31846671 None:intergenic 45.0%
AACACATGTCAATGTGGCCA+TGG + chr4.1:31846377-31846396 None:intergenic 45.0%
CACATCCATTGCCATCTTTC+AGG - chr4.1:31846653-31846672 MS.gene062884:CDS 45.0%
CACCTGAACACATGTCAATG+TGG + chr4.1:31846383-31846402 None:intergenic 45.0%
CATTCTGTGACGCCTTCTAT+CGG + chr4.1:31845939-31845958 None:intergenic 45.0%
CCCTTGTACTTATCATTGGC+CGG + chr4.1:31846273-31846292 None:intergenic 45.0%
CCGGCCAATGATAAGTACAA+GGG - chr4.1:31846270-31846289 MS.gene062884:intron 45.0%
CTGAAAGATGGCAATGGATG+TGG + chr4.1:31846655-31846674 None:intergenic 45.0%
GCAAGTGCAAGTGCAACTAT+AGG - chr4.1:31846592-31846611 MS.gene062884:CDS 45.0%
GGACGGAACGGTTAATGAAA+CGG - chr4.1:31846411-31846430 MS.gene062884:intron 45.0%
TCCGGCCAATGATAAGTACA+AGG - chr4.1:31846269-31846288 MS.gene062884:intron 45.0%
TGTACTTATCATTGGCCGGA+GGG + chr4.1:31846269-31846288 None:intergenic 45.0%
TTGTACTTATCATTGGCCGG+AGG + chr4.1:31846270-31846289 None:intergenic 45.0%
! GGTCTGAAATGTCAAGACTG+TGG - chr4.1:31845812-31845831 MS.gene062884:CDS 45.0%
ATGTGTTCAGGTGCGCTCTA+TGG - chr4.1:31846390-31846409 MS.gene062884:intron 50.0%
CTGTGGGAACCAAGCAAAGA+AGG - chr4.1:31845829-31845848 MS.gene062884:CDS 50.0%
CTTGGATTCCTGCCGATAGA+AGG - chr4.1:31845924-31845943 MS.gene062884:CDS 50.0%
GCAATCCACACAGGTGATGA+TGG - chr4.1:31846568-31846587 MS.gene062884:CDS 50.0%
GGCCACATTGACATGTGTTC+AGG - chr4.1:31846378-31846397 MS.gene062884:intron 50.0%
TTGCACCATCATCACCTGTG+TGG + chr4.1:31846576-31846595 None:intergenic 50.0%
!! CGATAGAAGGCGTCACAGAA+TGG - chr4.1:31845937-31845956 MS.gene062884:CDS 50.0%
!! TGAAGGTGGTGCTGATCAGA+AGG + chr4.1:31845968-31845987 None:intergenic 50.0%
ACTTATCATTGGCCGGAGGG+AGG + chr4.1:31846266-31846285 None:intergenic 55.0%
CTTATCATTGGCCGGAGGGA+GGG + chr4.1:31846265-31846284 None:intergenic 55.0%
GATGGCAATGGATGTGGTGG+AGG + chr4.1:31846649-31846668 None:intergenic 55.0%
GCCATGGAACTCGTAACAGC+CGG + chr4.1:31846361-31846380 None:intergenic 55.0%
GTTCAGGTGCGCTCTATGGA+CGG - chr4.1:31846394-31846413 MS.gene062884:intron 55.0%
TCCGGCTGTTACGAGTTCCA+TGG - chr4.1:31846357-31846376 MS.gene062884:intron 55.0%
TCTTCCTACTTCCCTCCCTC+CGG - chr4.1:31846251-31846270 MS.gene062884:intron 55.0%
!! GGTGGTGCTGATCAGAAGGA+TGG + chr4.1:31845964-31845983 None:intergenic 55.0%
CTGTGACGCCTTCTATCGGC+AGG + chr4.1:31845935-31845954 None:intergenic 60.0%
GGTGCGCTCTATGGACGGAA+CGG - chr4.1:31846399-31846418 MS.gene062884:intron 60.0%
TTGGCCGGAGGGAGGGAAGT+AGG + chr4.1:31846258-31846277 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 31845773 31846679 31845773 ID=MS.gene062884
chr4.1 mRNA 31845773 31846679 31845773 ID=MS.gene062884.t1;Parent=MS.gene062884
chr4.1 exon 31846427 31846679 31846427 ID=MS.gene062884.t1.exon1;Parent=MS.gene062884.t1
chr4.1 CDS 31846427 31846679 31846427 ID=cds.MS.gene062884.t1;Parent=MS.gene062884.t1
chr4.1 exon 31845773 31846114 31845773 ID=MS.gene062884.t1.exon2;Parent=MS.gene062884.t1
chr4.1 CDS 31845773 31846114 31845773 ID=cds.MS.gene062884.t1;Parent=MS.gene062884.t1
Gene Sequence

>MS.gene062884

ATGTATTCAACACAATTAGGGAAAGAAGAAGTGTTAAAGGGTCTGAAATGTCAAGACTGTGGGAACCAAGCAAAGAAGGATTGTGCATACTCAAGGTGCAGAAGTTGCTGCAAAAACAAAGGTTTTCACTGCCAAACACATATCAGAAGCACTTGGATTCCTGCCGATAGAAGGCGTCACAGAATGGACCATCCTTCTGATCAGCACCACCTTCATGAACATAAAAGGCACAAGCAGATCAACACTATTTCAAGTACTCTACATTTCTCAATTATGTATAAGTAATTATAACTCAAATTAGCCAAGAGCCCTAAATAGTTCATTTTTTTTCCTCAATATGTTTCTTCTGTTATTATTATATAATAATTTATGTCTTGAAAAATATCAACATATATCATAAAAAGTAGATATATTAATTAAGCCTATTTTGATCTTTTAACTCAAACATTCAATCTGATTTAAAAATTAGTCTTTTTTCTCTTCCTACTTCCCTCCCTCCGGCCAATGATAAGTACAAGGGATACTCCATATCCTAATCACAACCGTAATATGTCTAATATTTCAGGTTCTGATGAGTTCAAATTTCCGGCTGTTACGAGTTCCATGGCCACATTGACATGTGTTCAGGTGCGCTCTATGGACGGAACGGTTAATGAAACGGCCTATCAAACAAGTGTAGAAATTGGAGGACATGTATTTAGTGGTATTCTTTATGATCAAGGCCCTGATCAACAAAGCTTCCATACTATACACTCCCTTGATCAGCAACAAAATCTTAATCTTTTTAGTAGTAATGCAATCCACACAGGTGATGATGGTGCAAGTGCAAGTGCAACTATAGGTGCTACTGCTTCTCATCGTCGCTTTTTATTTCCTCCACCACATCCATTGCCATCTTTCAGGCCCG
Protein sequence

>MS.gene062884.t1

MYSTQLGKEEVLKGLKCQDCGNQAKKDCAYSRCRSCCKNKGFHCQTHIRSTWIPADRRRHRMDHPSDQHHLHEHKRHKQINTISSSDEFKFPAVTSSMATLTCVQVRSMDGTVNETAYQTSVEIGGHVFSGILYDQGPDQQSFHTIHSLDQQQNLNLFSSNAIHTGDDGASASATIGATASHRRFLFPPPHPLPSFRP