AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0254550

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0254550 MtrunA17_Chr2g0315201 98.611 72 1 0 1 72 1 72 4.65e-48 155
Msa0254550 MtrunA17_Chr1g0154651 66.667 81 26 1 6 86 14 93 4.57e-30 107
Msa0254550 MtrunA17_Chr2g0315211 94.444 72 4 0 1 72 1 72 2.05e-28 104
Msa0254550 MtrunA17_Chr3g0141401 77.143 70 16 0 3 72 12 81 1.39e-23 91.7
Msa0254550 MtrunA17_Chr5g0403631 74.157 89 22 1 3 91 6 93 1.51e-22 89.0
Msa0254550 MtrunA17_Chr5g0408851 61.404 57 22 0 17 73 61 117 1.45e-18 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0254550 AT1G78700.1 91.667 72 6 0 1 72 1 72 4.68e-28 103
Msa0254550 AT4G18890.1 90.278 72 7 0 1 72 1 72 1.25e-26 99.4
Msa0254550 AT1G19350.5 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0254550 AT1G19350.1 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0254550 AT1G19350.6 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0254550 AT1G19350.4 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0254550 AT3G50750.1 83.582 67 11 0 6 72 14 80 1.44e-24 94.0
Msa0254550 AT1G19350.3 73.973 73 19 0 6 78 44 116 1.67e-24 94.7
Msa0254550 AT4G36780.1 81.159 69 13 0 6 74 16 84 1.86e-24 93.2
Msa0254550 AT1G75080.2 72.603 73 20 0 6 78 23 95 1.14e-22 89.7
Msa0254550 AT1G75080.1 72.603 73 20 0 6 78 23 95 1.14e-22 89.7
Msa0254550 AT5G45300.1 61.290 62 22 1 17 78 97 156 5.03e-19 80.5
Msa0254550 AT5G45300.2 61.290 62 22 1 17 78 97 156 5.55e-19 80.5
Msa0254550 AT5G45300.3 61.290 62 22 1 17 78 111 170 6.12e-19 80.5
Msa0254550 AT2G45880.1 55.000 60 27 0 11 70 74 133 1.31e-15 70.9

Find 41 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGGTGTAGTTAGTATATT+TGG 0.217831 2_2:+48088438 None:intergenic
GTTGATGTTAATGAGGATTA+TGG 0.283185 2_2:-48087640 Msa0254550:CDS
AGTATATTTGGAAATGGATT+TGG 0.293195 2_2:+48088450 None:intergenic
TCATTGTTATCACAATGTTT+AGG 0.355738 2_2:+48088199 None:intergenic
AATCCAAAGGTTGCATTTAG+TGG 0.362338 2_2:+48087670 None:intergenic
TTCTCTGGTTTGAGAATGTA+TGG 0.389954 2_2:-48088235 Msa0254550:CDS
GTAGTTAGTATATTTGGAAA+TGG 0.397691 2_2:+48088444 None:intergenic
ATGCCACTAAATGCAACCTT+TGG 0.398006 2_2:-48087673 Msa0254550:CDS
AGAAAAGAATTGAACTTTGA+AGG 0.412503 2_2:+48088383 None:intergenic
GAACTTTGAAGGAGAGAAAG+AGG 0.424311 2_2:+48088394 None:intergenic
TCAAAAGGGTGTTCACGAAA+TGG 0.427164 2_2:+48088360 None:intergenic
CATTGAGAGTAACTCTCAAA+AGG 0.443094 2_2:+48088345 None:intergenic
TTTGGAAATGGATTTGGAGG+TGG 0.455823 2_2:+48088456 None:intergenic
TTACGATAAGTTGTTCCATC+AGG 0.461183 2_2:+48088133 None:intergenic
AAATGCAACCTTTGGATTGA+CGG 0.466530 2_2:-48087665 Msa0254550:CDS
ATAGCTGCTAAGATCTTCTC+TGG 0.470421 2_2:-48088250 Msa0254550:CDS
AAAGCTCTTTGTAATGAAGC+TGG 0.472686 2_2:-48088169 Msa0254550:CDS
AGGTGGAGGGTGATCTTTGT+CGG 0.480030 2_2:+48088473 None:intergenic
GGAAATGGATTTGGAGGTGG+AGG 0.484848 2_2:+48088459 None:intergenic
GACGGTAGTTGATGTTAATG+AGG 0.487517 2_2:-48087647 Msa0254550:CDS
ATATTTGGAAATGGATTTGG+AGG 0.490012 2_2:+48088453 None:intergenic
TGTAATGAAAATAAAGGAAA+GGG 0.490496 2_2:+48088524 None:intergenic
AGGAGAGAAAGAGGGAGGTG+TGG 0.492949 2_2:+48088403 None:intergenic
TTCTCTCTCTCCTTCCATGT+TGG 0.499958 2_2:+48088304 None:intergenic
AGGTGTGGAAGTAGAAGAAG+TGG 0.501319 2_2:+48088418 None:intergenic
AAAGTGTGTAATGAAAATAA+AGG 0.508090 2_2:+48088518 None:intergenic
GAGTTACTCTCAATGACATC+TGG 0.509973 2_2:-48088337 Msa0254550:exon
AACTTTGAAGGAGAGAAAGA+GGG 0.529635 2_2:+48088395 None:intergenic
GGTTGGTCTGTTGAACCTGA+TGG 0.545542 2_2:-48088148 Msa0254550:CDS
ATTGAGAGTAACTCTCAAAA+GGG 0.547709 2_2:+48088346 None:intergenic
CTCTTTGTAATGAAGCTGGT+TGG 0.548313 2_2:-48088165 Msa0254550:CDS
GTGTAATGAAAATAAAGGAA+AGG 0.558624 2_2:+48088523 None:intergenic
GGTGTGGAAGTAGAAGAAGT+GGG 0.575717 2_2:+48088419 None:intergenic
TTTGAAGGAGAGAAAGAGGG+AGG 0.577067 2_2:+48088398 None:intergenic
GAAATGGATTTGGAGGTGGA+GGG 0.584278 2_2:+48088460 None:intergenic
TGATGGAACAACTTATCGTA+AGG 0.588204 2_2:-48088131 Msa0254550:intron
GTGTGGAAGTAGAAGAAGTG+GGG 0.600322 2_2:+48088420 None:intergenic
ATCAACTACCGTCAATCCAA+AGG 0.603498 2_2:+48087657 None:intergenic
CTGGTACAAGACTACCAACA+TGG 0.603713 2_2:-48088318 Msa0254550:CDS
AGGAGAGAGAGAACAACAAG+AGG 0.604704 2_2:-48088294 Msa0254550:CDS
TACAAGACTACCAACATGGA+AGG 0.634618 2_2:-48088314 Msa0254550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATTATAATATAATTTGA+TGG - chr2_2:48088193-48088212 Msa0254550:CDS 10.0%
!! GATATTATAATATAATTTGA+TGG - chr2_2:48088193-48088212 Msa0254550:CDS 10.0%
!! GATATTATAATATGATTTGA+CGG - chr2_2:48088274-48088293 Msa0254550:CDS 15.0%
!! GATATTATAATATGATTTGA+CGG - chr2_2:48088274-48088293 Msa0254550:CDS 15.0%
!! TGTAATGAAAATAAAGGAAA+GGG + chr2_2:48087645-48087664 None:intergenic 20.0%
!! AAAGTGTGTAATGAAAATAA+AGG + chr2_2:48087651-48087670 None:intergenic 20.0%
!! TTCTTTGCATTATTACATTA+TGG - chr2_2:48088064-48088083 Msa0254550:intron 20.0%
!! TGTAATGAAAATAAAGGAAA+GGG + chr2_2:48087645-48087664 None:intergenic 20.0%
!! AAAGTGTGTAATGAAAATAA+AGG + chr2_2:48087651-48087670 None:intergenic 20.0%
!! TTCTTTGCATTATTACATTA+TGG - chr2_2:48088064-48088083 Msa0254550:intron 20.0%
! GTGTAATGAAAATAAAGGAA+AGG + chr2_2:48087646-48087665 None:intergenic 25.0%
!! AGTATATTTGGAAATGGATT+TGG + chr2_2:48087719-48087738 None:intergenic 25.0%
! GTAGTTAGTATATTTGGAAA+TGG + chr2_2:48087725-48087744 None:intergenic 25.0%
! AGAAAAGAATTGAACTTTGA+AGG + chr2_2:48087786-48087805 None:intergenic 25.0%
! TCATTGTTATCACAATGTTT+AGG + chr2_2:48087970-48087989 None:intergenic 25.0%
! TAGTTTCAAAAATATCTAGG+TGG + chr2_2:48088243-48088262 None:intergenic 25.0%
!!! GGTTAGTTTCAAAAATATCT+AGG + chr2_2:48088246-48088265 None:intergenic 25.0%
!! TGTAAAAAGTTTTACACAGT+CGG - chr2_2:48088304-48088323 Msa0254550:CDS 25.0%
!!! GAAACCATCAATGTTTTAAA+AGG - chr2_2:48088418-48088437 Msa0254550:five_prime_UTR 25.0%
! GTGTAATGAAAATAAAGGAA+AGG + chr2_2:48087646-48087665 None:intergenic 25.0%
!! AGTATATTTGGAAATGGATT+TGG + chr2_2:48087719-48087738 None:intergenic 25.0%
! GTAGTTAGTATATTTGGAAA+TGG + chr2_2:48087725-48087744 None:intergenic 25.0%
! AGAAAAGAATTGAACTTTGA+AGG + chr2_2:48087786-48087805 None:intergenic 25.0%
! TCATTGTTATCACAATGTTT+AGG + chr2_2:48087970-48087989 None:intergenic 25.0%
! TAGTTTCAAAAATATCTAGG+TGG + chr2_2:48088243-48088262 None:intergenic 25.0%
!!! GGTTAGTTTCAAAAATATCT+AGG + chr2_2:48088246-48088265 None:intergenic 25.0%
!! TGTAAAAAGTTTTACACAGT+CGG - chr2_2:48088304-48088323 Msa0254550:CDS 25.0%
!!! GAAACCATCAATGTTTTAAA+AGG - chr2_2:48088418-48088437 Msa0254550:five_prime_UTR 25.0%
! ATATTTGGAAATGGATTTGG+AGG + chr2_2:48087716-48087735 None:intergenic 30.0%
ATTGAGAGTAACTCTCAAAA+GGG + chr2_2:48087823-48087842 None:intergenic 30.0%
!!! ACCATCAATGTTTTAAAAGG+TGG - chr2_2:48088421-48088440 Msa0254550:five_prime_UTR 30.0%
!!! ACCACCTTTTAAAACATTGA+TGG + chr2_2:48088425-48088444 None:intergenic 30.0%
!!! AATGTTTTAAAAGGTGGTTG+TGG - chr2_2:48088427-48088446 Msa0254550:five_prime_UTR 30.0%
GTTGATGTTAATGAGGATTA+TGG - chr2_2:48088526-48088545 Msa0254550:five_prime_UTR 30.0%
! ATATTTGGAAATGGATTTGG+AGG + chr2_2:48087716-48087735 None:intergenic 30.0%
ATTGAGAGTAACTCTCAAAA+GGG + chr2_2:48087823-48087842 None:intergenic 30.0%
!!! ACCATCAATGTTTTAAAAGG+TGG - chr2_2:48088421-48088440 Msa0254550:five_prime_UTR 30.0%
!!! ACCACCTTTTAAAACATTGA+TGG + chr2_2:48088425-48088444 None:intergenic 30.0%
!!! AATGTTTTAAAAGGTGGTTG+TGG - chr2_2:48088427-48088446 Msa0254550:five_prime_UTR 30.0%
GTTGATGTTAATGAGGATTA+TGG - chr2_2:48088526-48088545 Msa0254550:five_prime_UTR 30.0%
AAAGGAAAGGGAAAAAGTGA+AGG + chr2_2:48087633-48087652 None:intergenic 35.0%
TGGGGTGTAGTTAGTATATT+TGG + chr2_2:48087731-48087750 None:intergenic 35.0%
! AACTTTGAAGGAGAGAAAGA+GGG + chr2_2:48087774-48087793 None:intergenic 35.0%
CATTGAGAGTAACTCTCAAA+AGG + chr2_2:48087824-48087843 None:intergenic 35.0%
! TTCTCTGGTTTGAGAATGTA+TGG - chr2_2:48087931-48087950 Msa0254550:intron 35.0%
AAAGCTCTTTGTAATGAAGC+TGG - chr2_2:48087997-48088016 Msa0254550:intron 35.0%
TTACGATAAGTTGTTCCATC+AGG + chr2_2:48088036-48088055 None:intergenic 35.0%
TGATGGAACAACTTATCGTA+AGG - chr2_2:48088035-48088054 Msa0254550:intron 35.0%
TTAAAAGGTGGTTGTGGTAA+TGG - chr2_2:48088433-48088452 Msa0254550:five_prime_UTR 35.0%
AATCCAAAGGTTGCATTTAG+TGG + chr2_2:48088499-48088518 None:intergenic 35.0%
AAATGCAACCTTTGGATTGA+CGG - chr2_2:48088501-48088520 Msa0254550:five_prime_UTR 35.0%
AAAGGAAAGGGAAAAAGTGA+AGG + chr2_2:48087633-48087652 None:intergenic 35.0%
TGGGGTGTAGTTAGTATATT+TGG + chr2_2:48087731-48087750 None:intergenic 35.0%
! AACTTTGAAGGAGAGAAAGA+GGG + chr2_2:48087774-48087793 None:intergenic 35.0%
CATTGAGAGTAACTCTCAAA+AGG + chr2_2:48087824-48087843 None:intergenic 35.0%
! TTCTCTGGTTTGAGAATGTA+TGG - chr2_2:48087931-48087950 Msa0254550:intron 35.0%
AAAGCTCTTTGTAATGAAGC+TGG - chr2_2:48087997-48088016 Msa0254550:intron 35.0%
TTACGATAAGTTGTTCCATC+AGG + chr2_2:48088036-48088055 None:intergenic 35.0%
TGATGGAACAACTTATCGTA+AGG - chr2_2:48088035-48088054 Msa0254550:intron 35.0%
TTAAAAGGTGGTTGTGGTAA+TGG - chr2_2:48088433-48088452 Msa0254550:five_prime_UTR 35.0%
AATCCAAAGGTTGCATTTAG+TGG + chr2_2:48088499-48088518 None:intergenic 35.0%
AAATGCAACCTTTGGATTGA+CGG - chr2_2:48088501-48088520 Msa0254550:five_prime_UTR 35.0%
! TTTGGAAATGGATTTGGAGG+TGG + chr2_2:48087713-48087732 None:intergenic 40.0%
! GAACTTTGAAGGAGAGAAAG+AGG + chr2_2:48087775-48087794 None:intergenic 40.0%
!! TCAAAAGGGTGTTCACGAAA+TGG + chr2_2:48087809-48087828 None:intergenic 40.0%
GAGTTACTCTCAATGACATC+TGG - chr2_2:48087829-48087848 Msa0254550:intron 40.0%
TACAAGACTACCAACATGGA+AGG - chr2_2:48087852-48087871 Msa0254550:intron 40.0%
ATAGCTGCTAAGATCTTCTC+TGG - chr2_2:48087916-48087935 Msa0254550:intron 40.0%
CTCTTTGTAATGAAGCTGGT+TGG - chr2_2:48088001-48088020 Msa0254550:intron 40.0%
ATGCCACTAAATGCAACCTT+TGG - chr2_2:48088493-48088512 Msa0254550:five_prime_UTR 40.0%
ATCAACTACCGTCAATCCAA+AGG + chr2_2:48088512-48088531 None:intergenic 40.0%
! GACGGTAGTTGATGTTAATG+AGG - chr2_2:48088519-48088538 Msa0254550:five_prime_UTR 40.0%
! TTTGGAAATGGATTTGGAGG+TGG + chr2_2:48087713-48087732 None:intergenic 40.0%
! GAACTTTGAAGGAGAGAAAG+AGG + chr2_2:48087775-48087794 None:intergenic 40.0%
!! TCAAAAGGGTGTTCACGAAA+TGG + chr2_2:48087809-48087828 None:intergenic 40.0%
GAGTTACTCTCAATGACATC+TGG - chr2_2:48087829-48087848 Msa0254550:intron 40.0%
TACAAGACTACCAACATGGA+AGG - chr2_2:48087852-48087871 Msa0254550:intron 40.0%
ATAGCTGCTAAGATCTTCTC+TGG - chr2_2:48087916-48087935 Msa0254550:intron 40.0%
CTCTTTGTAATGAAGCTGGT+TGG - chr2_2:48088001-48088020 Msa0254550:intron 40.0%
ATGCCACTAAATGCAACCTT+TGG - chr2_2:48088493-48088512 Msa0254550:five_prime_UTR 40.0%
ATCAACTACCGTCAATCCAA+AGG + chr2_2:48088512-48088531 None:intergenic 40.0%
! GACGGTAGTTGATGTTAATG+AGG - chr2_2:48088519-48088538 Msa0254550:five_prime_UTR 40.0%
CGGAAAAATGAGAGAGTGAG+AGG + chr2_2:48087676-48087695 None:intergenic 45.0%
! GAAATGGATTTGGAGGTGGA+GGG + chr2_2:48087709-48087728 None:intergenic 45.0%
GTGTGGAAGTAGAAGAAGTG+GGG + chr2_2:48087749-48087768 None:intergenic 45.0%
GGTGTGGAAGTAGAAGAAGT+GGG + chr2_2:48087750-48087769 None:intergenic 45.0%
AGGTGTGGAAGTAGAAGAAG+TGG + chr2_2:48087751-48087770 None:intergenic 45.0%
TTTGAAGGAGAGAAAGAGGG+AGG + chr2_2:48087771-48087790 None:intergenic 45.0%
CTGGTACAAGACTACCAACA+TGG - chr2_2:48087848-48087867 Msa0254550:intron 45.0%
TTCTCTCTCTCCTTCCATGT+TGG + chr2_2:48087865-48087884 None:intergenic 45.0%
AGGAGAGAGAGAACAACAAG+AGG - chr2_2:48087872-48087891 Msa0254550:intron 45.0%
!! TTGTGGTAATGGTTGTGGCT+CGG - chr2_2:48088444-48088463 Msa0254550:five_prime_UTR 45.0%
CGGAAAAATGAGAGAGTGAG+AGG + chr2_2:48087676-48087695 None:intergenic 45.0%
! GAAATGGATTTGGAGGTGGA+GGG + chr2_2:48087709-48087728 None:intergenic 45.0%
GTGTGGAAGTAGAAGAAGTG+GGG + chr2_2:48087749-48087768 None:intergenic 45.0%
GGTGTGGAAGTAGAAGAAGT+GGG + chr2_2:48087750-48087769 None:intergenic 45.0%
AGGTGTGGAAGTAGAAGAAG+TGG + chr2_2:48087751-48087770 None:intergenic 45.0%
TTTGAAGGAGAGAAAGAGGG+AGG + chr2_2:48087771-48087790 None:intergenic 45.0%
CTGGTACAAGACTACCAACA+TGG - chr2_2:48087848-48087867 Msa0254550:intron 45.0%
TTCTCTCTCTCCTTCCATGT+TGG + chr2_2:48087865-48087884 None:intergenic 45.0%
AGGAGAGAGAGAACAACAAG+AGG - chr2_2:48087872-48087891 Msa0254550:intron 45.0%
!! TTGTGGTAATGGTTGTGGCT+CGG - chr2_2:48088444-48088463 Msa0254550:five_prime_UTR 45.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_2:48088186-48088205 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_2:48088186-48088205 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_2:48088186-48088205 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_2:48088186-48088205 None:intergenic 5.0%
AGGTGGAGGGTGATCTTTGT+CGG + chr2_2:48087696-48087715 None:intergenic 50.0%
! GGAAATGGATTTGGAGGTGG+AGG + chr2_2:48087710-48087729 None:intergenic 50.0%
!! GGTTGGTCTGTTGAACCTGA+TGG - chr2_2:48088018-48088037 Msa0254550:intron 50.0%
!! GGTGGTTGTGGTAATGGTTG+TGG - chr2_2:48088439-48088458 Msa0254550:five_prime_UTR 50.0%
AGGTGGAGGGTGATCTTTGT+CGG + chr2_2:48087696-48087715 None:intergenic 50.0%
! GGAAATGGATTTGGAGGTGG+AGG + chr2_2:48087710-48087729 None:intergenic 50.0%
!! GGTTGGTCTGTTGAACCTGA+TGG - chr2_2:48088018-48088037 Msa0254550:intron 50.0%
!! GGTGGTTGTGGTAATGGTTG+TGG - chr2_2:48088439-48088458 Msa0254550:five_prime_UTR 50.0%
AGGAGAGAAAGAGGGAGGTG+TGG + chr2_2:48087766-48087785 None:intergenic 55.0%
AGGAGAGAAAGAGGGAGGTG+TGG + chr2_2:48087766-48087785 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 48087630 48088558 48087630 ID=Msa0254550;Name=Msa0254550
chr2_2 mRNA 48087630 48088558 48087630 ID=Msa0254550-mRNA-1;Parent=Msa0254550;Name=Msa0254550-mRNA-1;_AED=0.53;_eAED=0.53;_QI=211|0|0.5|0.5|1|1|2|0|97
chr2_2 exon 48087630 48087707 48087630 ID=Msa0254550-mRNA-1:exon:14546;Parent=Msa0254550-mRNA-1
chr2_2 exon 48088132 48088558 48088132 ID=Msa0254550-mRNA-1:exon:14545;Parent=Msa0254550-mRNA-1
chr2_2 five_prime_UTR 48088348 48088558 48088348 ID=Msa0254550-mRNA-1:five_prime_utr;Parent=Msa0254550-mRNA-1
chr2_2 CDS 48088132 48088347 48088132 ID=Msa0254550-mRNA-1:cds;Parent=Msa0254550-mRNA-1
chr2_2 CDS 48087630 48087707 48087630 ID=Msa0254550-mRNA-1:cds;Parent=Msa0254550-mRNA-1
Gene Sequence

>Msa0254550

ATGACATCTGGTACAAGACTACCAACATGGAAGGAGAGAGAGAACAACAAGAGGAGAGAGAGAAGAAGAAGAGCTATAGCTGCTAAGATCTTCTCTGGTTTGAGAATGTATGGTAACTTTAGATTACCTAAACATTGTGATAACAATGAAGTTCTTAAAGCTCTTTGTAATGAAGCTGGTTGGTCTGTTGAACCTGATGGAACAACTTATCGTAAGTGTTACAGTCAAATGCCACTAAATGCAACCTTTGGATTGACGGTAGTTGATGTTAATGAGGATTATGGTCGAATGTGA
Protein sequence

>Msa0254550

MTSGTRLPTWKERENNKRRERRRRAIAAKIFSGLRMYGNFRLPKHCDNNEVLKALCNEAGWSVEPDGTTYRKCYSQMPLNATFGLTVVDVNEDYGRM*