AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71773


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71773.t1 MTR_1g109510 95.062 162 3 1 1 162 22 178 1.55e-110 312
MS.gene71773.t1 MTR_1g069495 40.385 104 43 2 68 152 146 249 5.18e-17 76.3
MS.gene71773.t1 MTR_5g067350 32.653 147 77 4 23 152 187 328 3.51e-16 74.7
MS.gene71773.t1 MTR_1g085750 42.697 89 49 1 69 155 85 173 1.92e-15 70.1
MS.gene71773.t1 MTR_1g040675 36.879 141 65 5 18 152 53 175 5.04e-15 69.3
MS.gene71773.t1 MTR_4g124300 31.544 149 83 4 8 155 53 183 9.20e-15 68.6
MS.gene71773.t1 MTR_3g106850 28.358 134 90 2 21 152 77 206 9.97e-15 68.9
MS.gene71773.t1 MTR_7g110790 43.023 86 47 1 69 152 70 155 3.06e-14 66.6
MS.gene71773.t1 MTR_6g488150 35.811 148 69 6 25 152 94 235 3.15e-14 68.2
MS.gene71773.t1 MTR_5g030710 29.412 136 79 3 33 152 182 316 4.03e-14 68.9
MS.gene71773.t1 MTR_1g076270 36.290 124 59 4 33 152 64 171 4.17e-13 63.9
MS.gene71773.t1 MTR_1g093350 36.290 124 59 4 33 152 64 171 4.17e-13 63.9
MS.gene71773.t1 MTR_8g014520 37.624 101 46 2 69 152 157 257 6.94e-13 64.7
MS.gene71773.t1 MTR_8g014520 37.624 101 46 2 69 152 157 257 7.64e-13 64.7
MS.gene71773.t1 MTR_8g067530 31.081 148 76 5 25 152 196 337 8.05e-13 65.1
MS.gene71773.t1 MTR_2g101500 30.612 147 83 4 23 152 163 307 1.00e-12 64.7
MS.gene71773.t1 MTR_4g115075 34.524 84 48 1 69 152 129 205 4.09e-12 62.0
MS.gene71773.t1 MTR_8g103030 27.879 165 88 4 16 152 113 274 5.92e-12 62.4
MS.gene71773.t1 MTR_1g080860 32.374 139 73 4 33 152 98 234 6.79e-12 61.6
MS.gene71773.t1 MTR_1g080860 32.374 139 73 4 33 152 98 234 9.87e-12 61.6
MS.gene71773.t1 MTR_2g100780 34.951 103 48 2 69 152 149 251 3.25e-11 60.1
MS.gene71773.t1 MTR_2g100780 34.951 103 48 2 69 152 149 251 3.50e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71773.t1 AT2G01200 50.000 162 72 2 2 154 24 185 1.59e-51 163
MS.gene71773.t1 AT2G01200 50.000 162 72 2 2 154 24 185 1.59e-51 163
MS.gene71773.t1 AT1G15050 51.007 149 45 2 6 154 27 147 1.80e-46 149
MS.gene71773.t1 AT1G15050 51.007 149 45 2 6 154 59 179 2.43e-46 149
MS.gene71773.t1 AT2G33310 44.681 94 42 1 69 152 130 223 7.79e-21 85.9
MS.gene71773.t1 AT2G33310 44.681 94 42 1 69 152 130 223 7.79e-21 85.9
MS.gene71773.t1 AT2G33310 44.681 94 42 1 69 152 131 224 8.18e-21 85.9
MS.gene71773.t1 AT1G04550 45.556 90 42 1 68 150 125 214 2.25e-19 82.0
MS.gene71773.t1 AT4G28640 40.206 97 45 3 69 152 138 234 2.48e-14 68.6
MS.gene71773.t1 AT4G28640 40.206 97 45 3 69 152 138 234 2.65e-14 68.6
MS.gene71773.t1 AT4G28640 40.206 97 45 3 69 152 138 234 8.28e-14 67.8
MS.gene71773.t1 AT3G62100 43.529 85 47 1 69 152 84 168 8.79e-14 65.9
MS.gene71773.t1 AT1G52830 37.634 93 57 1 62 154 88 179 9.85e-14 65.9
MS.gene71773.t1 AT2G46990 41.111 90 52 1 69 157 86 175 1.34e-13 65.5
MS.gene71773.t1 AT3G17600 40.000 85 48 1 69 153 74 155 1.64e-13 64.7
MS.gene71773.t1 AT3G15540 39.773 88 51 2 68 154 97 183 1.04e-12 63.5
MS.gene71773.t1 AT3G16500 31.148 122 70 3 44 152 129 249 2.59e-12 63.2
MS.gene71773.t1 AT3G16500 31.148 122 70 3 44 152 129 249 2.78e-12 63.2
MS.gene71773.t1 AT1G51950 34.343 99 48 2 69 152 151 247 4.90e-12 62.4
MS.gene71773.t1 AT2G22670 28.302 159 90 6 16 152 144 300 5.13e-12 62.8
MS.gene71773.t1 AT2G22670 28.302 159 90 6 16 152 144 300 5.13e-12 62.8
MS.gene71773.t1 AT2G22670 28.302 159 90 6 16 152 144 300 5.40e-12 62.8
MS.gene71773.t1 AT2G22670 28.302 159 90 6 16 152 144 300 5.40e-12 62.8
MS.gene71773.t1 AT2G22670 28.302 159 90 6 16 152 161 317 5.45e-12 62.8
MS.gene71773.t1 AT5G25890 33.708 89 54 1 69 157 82 165 5.48e-12 61.2
MS.gene71773.t1 AT1G04240 32.258 124 70 3 33 152 65 178 1.58e-11 60.1
MS.gene71773.t1 AT4G29080 30.000 160 89 6 16 152 127 286 4.31e-11 60.1
MS.gene71773.t1 AT1G04240 32.258 124 70 3 33 152 165 278 4.33e-11 60.1
MS.gene71773.t1 AT5G65670 27.941 136 80 4 33 152 184 317 5.28e-11 60.1
MS.gene71773.t1 AT5G65670 27.941 136 80 4 33 152 184 317 5.85e-11 59.7
MS.gene71773.t1 AT1G04100 33.929 112 58 2 61 156 145 256 7.35e-11 59.3
MS.gene71773.t1 AT5G43700 30.714 140 81 5 17 152 47 174 7.38e-11 58.2
MS.gene71773.t1 AT3G04730 36.364 99 49 2 68 152 119 217 7.54e-11 58.9

Find 37 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGCTTGAATTCTTCATATT+AGG 0.248292 1.3:-74562453 None:intergenic
GGTATAAGATTATTTCAATC+TGG 0.393434 1.3:+74562923 MS.gene71773:CDS
AAAATTTGTATTCTTGATCA+TGG 0.399284 1.3:+74562588 MS.gene71773:CDS
ATTGATCTTGGTCTTAGTCT+TGG 0.403384 1.3:+74561945 MS.gene71773:CDS
TCAGGTAGCCAATCAGTATC+TGG 0.404191 1.3:+74562902 MS.gene71773:intron
AGTGTATGATGATGACCTTA+TGG 0.418403 1.3:+74562425 MS.gene71773:intron
ATTCAATTAGAAGACATGTT+TGG 0.424570 1.3:+74562630 MS.gene71773:CDS
AAACTTTGATGAAGAGATAG+AGG 0.443595 1.3:+74562500 MS.gene71773:CDS
ACAAGGATAGTGAAGACAAT+TGG 0.458182 1.3:+74562966 MS.gene71773:CDS
ATCTTATACCAGATACTGAT+TGG 0.459323 1.3:-74562910 None:intergenic
TCATATTAGGCCAATCCATA+AGG 0.461452 1.3:-74562440 None:intergenic
AAACATGTCTTCTAATTGAA+TGG 0.463927 1.3:-74562628 None:intergenic
GATGATGGCATAATTGATCT+TGG 0.492063 1.3:+74561933 MS.gene71773:CDS
AAGCCCATCTCTCATTGCTC+TGG 0.494319 1.3:-74562527 None:intergenic
ATGTGAAGGTTAACATGGAT+GGG 0.495408 1.3:+74562550 MS.gene71773:CDS
TATGTGAAGGTTAACATGGA+TGG 0.499449 1.3:+74562549 MS.gene71773:CDS
TAGAATGTGTGAAAAGGCTA+AGG 0.521536 1.3:+74563121 MS.gene71773:CDS
GGTCCAGAGCAATGAGAGAT+GGG 0.537453 1.3:+74562524 MS.gene71773:CDS
GGGTCCAGAGCAATGAGAGA+TGG 0.546013 1.3:+74562523 MS.gene71773:CDS
AACATGGATGGGGTCTCCAT+TGG 0.556874 1.3:+74562561 MS.gene71773:CDS
TATCAGGACAAACATGATGA+TGG 0.557533 1.3:+74561918 None:intergenic
AGTTTGTAGAATGTGTGAAA+AGG 0.572178 1.3:+74563115 MS.gene71773:CDS
AACTTTGATGAAGAGATAGA+GGG 0.577407 1.3:+74562501 MS.gene71773:CDS
GGATGAACACATACTTCCAC+AGG 0.585852 1.3:-74563006 None:intergenic
AGGATAGTGAAGACAATTGG+AGG 0.586064 1.3:+74562969 MS.gene71773:CDS
GGACTGTTGGTGATGTCCTG+TGG 0.599377 1.3:+74562990 MS.gene71773:CDS
TGGATGGGGTCTCCATTGGT+AGG 0.603415 1.3:+74562565 MS.gene71773:CDS
GGCTTATGTGAAGGTTAACA+TGG 0.603593 1.3:+74562545 MS.gene71773:CDS
AGGATTGCAAGAAAGAATGC+AGG 0.603908 1.3:+74563141 MS.gene71773:CDS
TGTGAAGGTTAACATGGATG+GGG 0.610516 1.3:+74562551 MS.gene71773:CDS
AGAGTACTCATTATTCTACA+AGG 0.631045 1.3:+74562949 MS.gene71773:CDS
ATGATGATGACCTTATGGAT+TGG 0.632385 1.3:+74562430 MS.gene71773:CDS
TGAGAGATGGGCTTATGTGA+AGG 0.637438 1.3:+74562536 MS.gene71773:CDS
GAAGACAATTGGAGGACTGT+TGG 0.640837 1.3:+74562977 MS.gene71773:CDS
ATTTGTATTCTTGATCATGG+AGG 0.642489 1.3:+74562591 MS.gene71773:CDS
ACTTTGATGAAGAGATAGAG+GGG 0.683990 1.3:+74562502 MS.gene71773:CDS
CTTTGATGAAGAGATAGAGG+GGG 0.700859 1.3:+74562503 MS.gene71773:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATTGAAACAATGAACA+AGG - chr1.3:74562023-74562042 None:intergenic 20.0%
!! AAAATTGAAACAATGAACAA+GGG - chr1.3:74562022-74562041 None:intergenic 20.0%
!! AAAATTTGTATTCTTGATCA+TGG + chr1.3:74562588-74562607 MS.gene71773:CDS 20.0%
!!! AAAACTTTTTAAAATGATGG+GGG - chr1.3:74562084-74562103 None:intergenic 20.0%
!!! AGAAAAGTGTTAAATGAAAA+GGG - chr1.3:74563030-74563049 None:intergenic 20.0%
!!! AGTTTGTATCAATCATTTTT+AGG - chr1.3:74562303-74562322 None:intergenic 20.0%
!!! CAAAACTTTTTAAAATGATG+GGG - chr1.3:74562085-74562104 None:intergenic 20.0%
!!! CTACATTTTATTATACTAGT+TGG + chr1.3:74563048-74563067 MS.gene71773:intron 20.0%
!!! GCAAAACTTTTTAAAATGAT+GGG - chr1.3:74562086-74562105 None:intergenic 20.0%
!!! TAGAAAAGTGTTAAATGAAA+AGG - chr1.3:74563031-74563050 None:intergenic 20.0%
!!! TGCAAAACTTTTTAAAATGA+TGG - chr1.3:74562087-74562106 None:intergenic 20.0%
!!! TTTGTAATGTTTTGTTAACA+GGG + chr1.3:74563092-74563111 MS.gene71773:intron 20.0%
! AAAACACTGTATGAAAAATG+AGG - chr1.3:74562234-74562253 None:intergenic 25.0%
! AAACATGTCTTCTAATTGAA+TGG - chr1.3:74562631-74562650 None:intergenic 25.0%
! AAATTGAAACAATGAACAAG+GGG - chr1.3:74562021-74562040 None:intergenic 25.0%
! ATTCAATTAGAAGACATGTT+TGG + chr1.3:74562630-74562649 MS.gene71773:CDS 25.0%
! GGTATAAGATTATTTCAATC+TGG + chr1.3:74562923-74562942 MS.gene71773:CDS 25.0%
! TAACTCACTCAAATAAGAAA+AGG - chr1.3:74562051-74562070 None:intergenic 25.0%
! TAGTGTAATGTAATGATGTT+TGG + chr1.3:74562398-74562417 MS.gene71773:intron 25.0%
!! AATACAAATTTTCCTACCAA+TGG - chr1.3:74562580-74562599 None:intergenic 25.0%
!! ATACAACTTATCAGTCATTT+TGG - chr1.3:74562871-74562890 None:intergenic 25.0%
!!! GTTTGTAATGTTTTGTTAAC+AGG + chr1.3:74563091-74563110 MS.gene71773:intron 25.0%
AAAATGAACCGATACATTCA+TGG + chr1.3:74562813-74562832 MS.gene71773:intron 30.0%
AAACTTTGATGAAGAGATAG+AGG + chr1.3:74562500-74562519 MS.gene71773:CDS 30.0%
AACTGTTCACTTTGATAAGA+TGG - chr1.3:74562706-74562725 None:intergenic 30.0%
AACTTTGATGAAGAGATAGA+GGG + chr1.3:74562501-74562520 MS.gene71773:CDS 30.0%
AGTTTGTAGAATGTGTGAAA+AGG + chr1.3:74563115-74563134 MS.gene71773:CDS 30.0%
ATCTTATACCAGATACTGAT+TGG - chr1.3:74562913-74562932 None:intergenic 30.0%
ATTTGTATTCTTGATCATGG+AGG + chr1.3:74562591-74562610 MS.gene71773:CDS 30.0%
CTAAACTAAATACAGCAGTA+AGG + chr1.3:74562324-74562343 MS.gene71773:intron 30.0%
CTATGTTAACACTTCATCTT+AGG + chr1.3:74563164-74563183 MS.gene71773:CDS 30.0%
GTGCTTGAATTCTTCATATT+AGG - chr1.3:74562456-74562475 None:intergenic 30.0%
GTTGTATAATTACCCTATTC+AGG + chr1.3:74562884-74562903 MS.gene71773:intron 30.0%
! AGAGTACTCATTATTCTACA+AGG + chr1.3:74562949-74562968 MS.gene71773:CDS 30.0%
! TCTCTTCATCAAAGTTTTCA+TGG - chr1.3:74562497-74562516 None:intergenic 30.0%
ACAAGGATAGTGAAGACAAT+TGG + chr1.3:74562966-74562985 MS.gene71773:CDS 35.0%
ACAAGTGCATTATTGACACA+AGG - chr1.3:74562666-74562685 None:intergenic 35.0%
ACTTTGATGAAGAGATAGAG+GGG + chr1.3:74562502-74562521 MS.gene71773:CDS 35.0%
ATGTGAAGGTTAACATGGAT+GGG + chr1.3:74562550-74562569 MS.gene71773:CDS 35.0%
TAGAATGTGTGAAAAGGCTA+AGG + chr1.3:74563121-74563140 MS.gene71773:CDS 35.0%
TATGTGAAGGTTAACATGGA+TGG + chr1.3:74562549-74562568 MS.gene71773:CDS 35.0%
TCATATTAGGCCAATCCATA+AGG - chr1.3:74562443-74562462 None:intergenic 35.0%
! AGTGTATGATGATGACCTTA+TGG + chr1.3:74562425-74562444 MS.gene71773:intron 35.0%
! ATGATGATGACCTTATGGAT+TGG + chr1.3:74562430-74562449 MS.gene71773:CDS 35.0%
! GATGATGGCATAATTGATCT+TGG + chr1.3:74561933-74561952 MS.gene71773:CDS 35.0%
!! ATTGATCTTGGTCTTAGTCT+TGG + chr1.3:74561945-74561964 MS.gene71773:CDS 35.0%
AGGATAGTGAAGACAATTGG+AGG + chr1.3:74562969-74562988 MS.gene71773:CDS 40.0%
AGGATTGCAAGAAAGAATGC+AGG + chr1.3:74563141-74563160 MS.gene71773:CDS 40.0%
CGAAGAGTCCATGAATGTAT+CGG - chr1.3:74562824-74562843 None:intergenic 40.0%
CTTTGATGAAGAGATAGAGG+GGG + chr1.3:74562503-74562522 MS.gene71773:CDS 40.0%
GGCTTATGTGAAGGTTAACA+TGG + chr1.3:74562545-74562564 MS.gene71773:CDS 40.0%
TGTGAAGGTTAACATGGATG+GGG + chr1.3:74562551-74562570 MS.gene71773:CDS 40.0%
! ACTGATTGGCTACCTGAATA+GGG - chr1.3:74562899-74562918 None:intergenic 40.0%
! TACTGATTGGCTACCTGAAT+AGG - chr1.3:74562900-74562919 None:intergenic 40.0%
GAAGACAATTGGAGGACTGT+TGG + chr1.3:74562977-74562996 MS.gene71773:CDS 45.0%
GGATGAACACATACTTCCAC+AGG - chr1.3:74563009-74563028 None:intergenic 45.0%
TCAGGTAGCCAATCAGTATC+TGG + chr1.3:74562902-74562921 MS.gene71773:intron 45.0%
! TGAGAGATGGGCTTATGTGA+AGG + chr1.3:74562536-74562555 MS.gene71773:CDS 45.0%
AACATGGATGGGGTCTCCAT+TGG + chr1.3:74562561-74562580 MS.gene71773:CDS 50.0%
AAGCCCATCTCTCATTGCTC+TGG - chr1.3:74562530-74562549 None:intergenic 50.0%
GGTCCAGAGCAATGAGAGAT+GGG + chr1.3:74562524-74562543 MS.gene71773:CDS 50.0%
GGGTCCAGAGCAATGAGAGA+TGG + chr1.3:74562523-74562542 MS.gene71773:CDS 55.0%
TGGATGGGGTCTCCATTGGT+AGG + chr1.3:74562565-74562584 MS.gene71773:CDS 55.0%
!! GGACTGTTGGTGATGTCCTG+TGG + chr1.3:74562990-74563009 MS.gene71773:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 74561924 74563185 74561924 ID=MS.gene71773
chr1.3 mRNA 74561924 74563185 74561924 ID=MS.gene71773.t1;Parent=MS.gene71773
chr1.3 exon 74561924 74562005 74561924 ID=MS.gene71773.t1.exon1;Parent=MS.gene71773.t1
chr1.3 CDS 74561924 74562005 74561924 ID=cds.MS.gene71773.t1;Parent=MS.gene71773.t1
chr1.3 exon 74562427 74562651 74562427 ID=MS.gene71773.t1.exon2;Parent=MS.gene71773.t1
chr1.3 CDS 74562427 74562651 74562427 ID=cds.MS.gene71773.t1;Parent=MS.gene71773.t1
chr1.3 exon 74562906 74563014 74562906 ID=MS.gene71773.t1.exon3;Parent=MS.gene71773.t1
chr1.3 CDS 74562906 74563014 74562906 ID=cds.MS.gene71773.t1;Parent=MS.gene71773.t1
chr1.3 exon 74563113 74563185 74563113 ID=MS.gene71773.t1.exon4;Parent=MS.gene71773.t1
chr1.3 CDS 74563113 74563185 74563113 ID=cds.MS.gene71773.t1;Parent=MS.gene71773.t1
Gene Sequence

>MS.gene71773

GACAAACATGATGATGGCATAATTGATCTTGGTCTTAGTCTTGGAACTGTTCAACATGATGCTTATCATTCTTCTGCTAACTGTATGAGTTCGTCCCCTTGTTCATTGTTTCAATTTTTCAATTCCTTTTCTTATTTGAGTGAGTTAAATTTTGATACCCCCATCATTTTAAAAAGTTTTGCATTGTTAACAAATTACAATCAATCATATATGACTTTAGAAGAAGTTATTATTATAGTGAACATTTTGACGATAATGATTAATTGACAGTGTAGAAAATCATTACACTAATGTATATAAATTAAATCCTCATTTTTCATACAGTGTTTTGTCAGATATTAAATGAATTTTGTATGTTGTCTTTAGCAAAAACAAACCTAAAAATGATTGATACAAACTACTAAACTAAATACAGCAGTAAGGTCTAAGTAGATAAATATTATAGATGAAAAGTAAACACTTATTTCAAATACATAGTGTAATGTAATGATGTTTGGATTCAGTGTATGATGATGACCTTATGGATTGGCCTAATATGAAGAATTCAAGCACAACACATTCTAGATCTGTCCATGAAAACTTTGATGAAGAGATAGAGGGGGTCCAGAGCAATGAGAGATGGGCTTATGTGAAGGTTAACATGGATGGGGTCTCCATTGGTAGGAAAATTTGTATTCTTGATCATGGAGGATACTCAAGTCTAGCCATTCAATTAGAAGACATGTTTGGTAAGTAGTGTCCTTGTGTCAATAATGCACTTGTCATATATTCACATTTCTCCATCTTATCAAAGTGAACAGTTTTAAAGAACTGATACTATAATATGATAAAATTAGTTGTACATCTATTTACATTTTAGTTTATAAATGTGTGATGCATTGTCACTGATAAAATGAACCGATACATTCATGGACTCTTCGAATAACATCTAACAAATTCAAAGACCAAAATGACTGATAAGTTGTATAATTACCCTATTCAGGTAGCCAATCAGTATCTGGTATAAGATTATTTCAATCTGGATCAGAGTACTCATTATTCTACAAGGATAGTGAAGACAATTGGAGGACTGTTGGTGATGTCCTGTGGAAGTATGTGTTCATCCCTTTTCATTTAACACTTTTCTACATTTTATTATACTAGTTGGACAATAATTATTTTTTGTTTGTTTGTAATGTTTTGTTAACAGGGAGTTTGTAGAATGTGTGAAAAGGCTAAGGATTGCAAGAAAGAATGCAGGCTATGTTAACACTTCATCTTAG

Protein sequence

>MS.gene71773.t1

DKHDDGIIDLGLSLGTVQHDAYHSSANLYDDDLMDWPNMKNSSTTHSRSVHENFDEEIEGVQSNERWAYVKVNMDGVSIGRKICILDHGGYSSLAIQLEDMFGSQSVSGIRLFQSGSEYSLFYKDSEDNWRTVGDVLWKEFVECVKRLRIARKNAGYVNTSS