AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180004929.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180004929.01.T01 MTR_1g089750 74.545 165 16 3 12 150 12 176 3.21e-80 234
MsG0180004929.01.T01 MTR_1g089750 73.913 161 16 3 16 150 1 161 3.18e-77 226
MsG0180004929.01.T01 MTR_0019s0310 59.091 176 44 2 1 150 1 174 3.28e-65 196
MsG0180004929.01.T01 MTR_6g055750 59.091 176 44 2 1 150 1 174 3.66e-65 196
MsG0180004929.01.T01 MTR_6g027250 55.901 161 43 2 1 135 1 159 1.76e-55 171
MsG0180004929.01.T01 MTR_0019s0330 83.951 81 13 0 63 143 26 106 7.73e-46 145
MsG0180004929.01.T01 MTR_0019s0270 84.416 77 12 0 63 139 46 122 4.77e-44 142
MsG0180004929.01.T01 MTR_6g027240 79.452 73 15 0 63 135 24 96 6.85e-40 130
MsG0180004929.01.T01 MTR_7g013320 76.119 67 6 1 63 129 57 113 8.67e-29 102
MsG0180004929.01.T01 MTR_6g055760 84.375 32 5 0 72 103 40 71 4.24e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180004929.01.T01 AT3G63030 46.667 135 46 3 21 129 25 159 4.66e-35 120
MsG0180004929.01.T01 AT4G22745 44.138 145 54 4 15 132 45 189 4.30e-32 113

Find 44 sgRNAs with CRISPR-Local

Find 111 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGTTGCTCAATAAATTC+TGG 0.227479 1:-84521086 None:intergenic
TGGTGTCTTGCATAATCTTT+GGG 0.244821 1:-84521061 None:intergenic
ATGGTGTCTTGCATAATCTT+TGG 0.279956 1:-84521062 None:intergenic
GTTTATTTCTTTCTCTCTCT+TGG 0.362956 1:-84519671 None:intergenic
AATGCAAACTTTGCATGAAA+TGG 0.372986 1:+84520705 MsG0180004929.01.T01:CDS
GCTAGAAGAAGATGGAGTTT+TGG 0.380480 1:-84519786 None:intergenic
TAGAAAGGATTACTCTAAGT+TGG 0.402694 1:+84520920 MsG0180004929.01.T01:CDS
ATATGCTGCTATCTCATTGC+GGG 0.412618 1:-84520982 None:intergenic
TCTGTTGCTCAATAAATTCT+GGG 0.422405 1:-84521085 None:intergenic
ACAAGGTTTCAAGAGAATCT+TGG 0.424100 1:+84520893 MsG0180004929.01.T01:CDS
ATTTCTTTCTCTCTCTTGGT+AGG 0.428735 1:-84519667 None:intergenic
TGCTACAATCAAAAGGCTCT+CGG 0.434619 1:-84520777 None:intergenic
CTGAGACAGTGTTTAGAGTT+CGG 0.434849 1:-84519720 None:intergenic
TTCTCTCTCTTGGTAGGTGG+TGG 0.441356 1:-84519661 None:intergenic
GAGAATCTTGGTGCTTAGAA+AGG 0.448776 1:+84520905 MsG0180004929.01.T01:CDS
TTGTTTGCTGAATCAATGTC+GGG 0.454590 1:+84519761 MsG0180004929.01.T01:exon
TCTTACTACATCACACCTAC+AGG 0.516283 1:+84520945 MsG0180004929.01.T01:CDS
CATATATATCAACTGAGCCC+TGG 0.521418 1:-84520676 None:intergenic
TCTTTCTCTCTCTTGGTAGG+TGG 0.531104 1:-84519664 None:intergenic
ACTGAGCCCTGGGTCATCGC+CGG 0.538613 1:-84520665 None:intergenic
AAATAAACAACTGTTCCGTT+CGG 0.538892 1:+84519686 MsG0180004929.01.T01:five_prime_UTR
TTTGTTTGCTGAATCAATGT+CGG 0.540179 1:+84519760 MsG0180004929.01.T01:exon
AGAATTTATTGAGCAACAGA+AGG 0.543104 1:+84521088 MsG0180004929.01.T01:CDS
ATATATATCAACTGAGCCCT+GGG 0.551958 1:-84520675 None:intergenic
GCAGATACACCACTGGGTTG+AGG 0.552234 1:-84521017 None:intergenic
AACTCCATCTTCTTCTAGCA+AGG 0.558032 1:+84519790 MsG0180004929.01.T01:CDS
AAGATTCTCTTGAAACCTTG+TGG 0.558153 1:-84520891 None:intergenic
AGTACCTTGCTAGAAGAAGA+TGG 0.558912 1:-84519794 None:intergenic
ACAGAGACCGGCGATGACCC+AGG 0.559040 1:+84520658 MsG0180004929.01.T01:intron
GGTGGTGGCGTTTATAAGAG+AGG 0.577882 1:-84519646 None:intergenic
CAGAGACCGGCGATGACCCA+GGG 0.581876 1:+84520659 MsG0180004929.01.T01:intron
ATCCGCAGCAGATACACCAC+TGG 0.582537 1:-84521024 None:intergenic
TTGATACACAAGAGGAGTTG+AGG 0.595636 1:+84520735 MsG0180004929.01.T01:CDS
TAAACAACTGTTCCGTTCGG+TGG 0.609115 1:+84519689 MsG0180004929.01.T01:five_prime_UTR
ACCCAGTGGTGTATCTGCTG+CGG 0.611469 1:+84521022 MsG0180004929.01.T01:CDS
GATATGCTGCTATCTCATTG+CGG 0.625471 1:-84520983 None:intergenic
TTGCTCAATAAATTCTGGGA+TGG 0.634957 1:-84521081 None:intergenic
GAGAGTGATTGATACACAAG+AGG 0.640381 1:+84520727 MsG0180004929.01.T01:CDS
GGTGTCTTGCATAATCTTTG+GGG 0.668330 1:-84521060 None:intergenic
GCTCTCGGATGATCTTATGA+CGG 0.668353 1:-84520762 None:intergenic
TAACATCCAAAGACTCCACA+AGG 0.677602 1:+84520876 MsG0180004929.01.T01:intron
TCCGCAGCAGATACACCACT+GGG 0.695152 1:-84521023 None:intergenic
TCGGAGAAGATACCACCGAA+CGG 0.717114 1:-84519701 None:intergenic
AAAGATCATCCTCAACCCAG+TGG 0.719856 1:+84521008 MsG0180004929.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAACCCTAAAAAAAAAT+AGG - Chr1:84519850-84519869 None:intergenic 20.0%
!! AGAAAAATAGTTGAAAACTA+AGG - Chr1:84519877-84519896 None:intergenic 20.0%
!! ATATTGAATATGATTCTTCT+CGG + Chr1:84520833-84520852 MsG0180004929.01.T01:intron 20.0%
!! CTCAATATAAAAACCTAATA+TGG - Chr1:84520496-84520515 None:intergenic 20.0%
!! GAAAAATAGTTGAAAACTAA+GGG - Chr1:84519876-84519895 None:intergenic 20.0%
!! TGGATTATTAAGTCTTTATT+GGG + Chr1:84520626-84520645 MsG0180004929.01.T01:intron 20.0%
!!! ATGGATTATTAAGTCTTTAT+TGG + Chr1:84520625-84520644 MsG0180004929.01.T01:intron 20.0%
!!! TACTTGTTAATTGAATTGAA+GGG + Chr1:84519957-84519976 MsG0180004929.01.T01:intron 20.0%
!!! TCGATTCCTATTTTTTTTTA+GGG + Chr1:84519841-84519860 MsG0180004929.01.T01:intron 20.0%
!!! TGTTAATTTCTGTTTTGAAT+GGG + Chr1:84520097-84520116 MsG0180004929.01.T01:intron 20.0%
!!! TTACTTGTTAATTGAATTGA+AGG + Chr1:84519956-84519975 MsG0180004929.01.T01:intron 20.0%
!! CTATTCTTGTTAACTCTTTT+GGG + Chr1:84519901-84519920 MsG0180004929.01.T01:intron 25.0%
!! TCTATTCTTGTTAACTCTTT+TGG + Chr1:84519900-84519919 MsG0180004929.01.T01:intron 25.0%
!!! CTCGATTCCTATTTTTTTTT+AGG + Chr1:84519840-84519859 MsG0180004929.01.T01:intron 25.0%
!!! GATGTTCTTTTTTCGTTTTA+GGG + Chr1:84519926-84519945 MsG0180004929.01.T01:intron 25.0%
!!! GTGTTAATTTCTGTTTTGAA+TGG + Chr1:84520096-84520115 MsG0180004929.01.T01:intron 25.0%
!!! GTTAATTTCTGTTTTGAATG+GGG + Chr1:84520098-84520117 MsG0180004929.01.T01:intron 25.0%
!!! TGATGTTCTTTTTTCGTTTT+AGG + Chr1:84519925-84519944 MsG0180004929.01.T01:intron 25.0%
!!! TTGGTTTTTTGTCAATAGTA+TGG + Chr1:84520606-84520625 MsG0180004929.01.T01:intron 25.0%
AAAAATAATCTTACGCACCT+AGG - Chr1:84520026-84520045 None:intergenic 30.0%
AAATAAACAACTGTTCCGTT+CGG + Chr1:84519686-84519705 MsG0180004929.01.T01:five_prime_UTR 30.0%
AATATCAGATCTGCAACAAA+AGG + Chr1:84520219-84520238 MsG0180004929.01.T01:intron 30.0%
AATGCAAACTTTGCATGAAA+TGG + Chr1:84520705-84520724 MsG0180004929.01.T01:CDS 30.0%
AGAATTTATTGAGCAACAGA+AGG + Chr1:84521088-84521107 MsG0180004929.01.T01:CDS 30.0%
ATTGTTAAACCAAGATAGAG+TGG + Chr1:84520129-84520148 MsG0180004929.01.T01:intron 30.0%
GAATCATATTCAATATCAGC+AGG - Chr1:84520829-84520848 None:intergenic 30.0%
GTAGGAGTAAAAAGGTTTAA+GGG + Chr1:84520394-84520413 MsG0180004929.01.T01:intron 30.0%
TAGAAAGGATTACTCTAAGT+TGG + Chr1:84520920-84520939 MsG0180004929.01.T01:CDS 30.0%
TCAAAATCGTAGGAGTAAAA+AGG + Chr1:84520386-84520405 MsG0180004929.01.T01:intron 30.0%
TCTGTTGCTCAATAAATTCT+GGG - Chr1:84521088-84521107 None:intergenic 30.0%
TGAAATCCAGACAAATCAAA+GGG - Chr1:84520369-84520388 None:intergenic 30.0%
TTCTGTTGCTCAATAAATTC+TGG - Chr1:84521089-84521108 None:intergenic 30.0%
TTGAAATCCAGACAAATCAA+AGG - Chr1:84520370-84520389 None:intergenic 30.0%
! GTTTATTTCTTTCTCTCTCT+TGG - Chr1:84519674-84519693 None:intergenic 30.0%
! TTGCTAAATTGTTTCTCTTC+CGG + Chr1:84520325-84520344 MsG0180004929.01.T01:intron 30.0%
! TTTGTTTGCTGAATCAATGT+CGG + Chr1:84519760-84519779 MsG0180004929.01.T01:exon 30.0%
!!! GCTTATCACTTTTTTAACAC+AGG + Chr1:84520581-84520600 MsG0180004929.01.T01:intron 30.0%
!!! TGTGCAGATTTTTTTTATCC+TGG + Chr1:84520050-84520069 MsG0180004929.01.T01:intron 30.0%
AAGATTCTCTTGAAACCTTG+TGG - Chr1:84520894-84520913 None:intergenic 35.0%
AATATGATTCTTCTCGGACA+TGG + Chr1:84520839-84520858 MsG0180004929.01.T01:intron 35.0%
ACAAGGTTTCAAGAGAATCT+TGG + Chr1:84520893-84520912 MsG0180004929.01.T01:CDS 35.0%
AGGAACTGTGATACCATATT+AGG + Chr1:84520480-84520499 MsG0180004929.01.T01:intron 35.0%
ATATATATCAACTGAGCCCT+GGG - Chr1:84520678-84520697 None:intergenic 35.0%
ATATGATTCTTCTCGGACAT+GGG + Chr1:84520840-84520859 MsG0180004929.01.T01:intron 35.0%
ATGGTGTCTTGCATAATCTT+TGG - Chr1:84521065-84521084 None:intergenic 35.0%
ATTTCTTTCTCTCTCTTGGT+AGG - Chr1:84519670-84519689 None:intergenic 35.0%
CAGAAAATTCCACTCTATCT+TGG - Chr1:84520141-84520160 None:intergenic 35.0%
CGTAGGAGTAAAAAGGTTTA+AGG + Chr1:84520393-84520412 MsG0180004929.01.T01:intron 35.0%
GTTATGCTGCTGTTAAGTAT+GGG + Chr1:84520191-84520210 MsG0180004929.01.T01:intron 35.0%
TGGTGTCTTGCATAATCTTT+GGG - Chr1:84521064-84521083 None:intergenic 35.0%
TGTCTGGATTTCAAAATCGT+AGG + Chr1:84520376-84520395 MsG0180004929.01.T01:intron 35.0%
TGTTATGCTGCTGTTAAGTA+TGG + Chr1:84520190-84520209 MsG0180004929.01.T01:intron 35.0%
TTCAATTTGATTCCGTACCT+AGG + Chr1:84520006-84520025 MsG0180004929.01.T01:intron 35.0%
! GCCTTTTTGCTACAATCAAA+AGG - Chr1:84520787-84520806 None:intergenic 35.0%
! TCTAGTTTCTCATAAGATCC+AGG - Chr1:84520071-84520090 None:intergenic 35.0%
! TTGCTCAATAAATTCTGGGA+TGG - Chr1:84521084-84521103 None:intergenic 35.0%
! TTGTTTGCTGAATCAATGTC+GGG + Chr1:84519761-84519780 MsG0180004929.01.T01:exon 35.0%
! TTTTGCATGTCTGGATTATC+CGG + Chr1:84520419-84520438 MsG0180004929.01.T01:intron 35.0%
!! GCCTTTTGATTGTAGCAAAA+AGG + Chr1:84520783-84520802 MsG0180004929.01.T01:CDS 35.0%
!!! CACTTTTTTAACACAGGACT+TGG + Chr1:84520587-84520606 MsG0180004929.01.T01:intron 35.0%
!!! GTTCTCAGTTTTTTACCTGT+AGG - Chr1:84520963-84520982 None:intergenic 35.0%
!!! TTAAGGGTTTTTTGCATGTC+TGG + Chr1:84520410-84520429 MsG0180004929.01.T01:intron 35.0%
AACTCCATCTTCTTCTAGCA+AGG + Chr1:84519790-84519809 MsG0180004929.01.T01:CDS 40.0%
ACACTCTACACCATATAAGC+CGG - Chr1:84520536-84520555 None:intergenic 40.0%
AGACAAATCAAAGGGCTTTG+CGG - Chr1:84520361-84520380 None:intergenic 40.0%
AGTACCTTGCTAGAAGAAGA+TGG - Chr1:84519797-84519816 None:intergenic 40.0%
AGTCTAACTCATCCCAAAAC+CGG + Chr1:84520514-84520533 MsG0180004929.01.T01:intron 40.0%
ATATGCTGCTATCTCATTGC+GGG - Chr1:84520985-84521004 None:intergenic 40.0%
CATATATATCAACTGAGCCC+TGG - Chr1:84520679-84520698 None:intergenic 40.0%
GAGAGTGATTGATACACAAG+AGG + Chr1:84520727-84520746 MsG0180004929.01.T01:CDS 40.0%
GATATGCTGCTATCTCATTG+CGG - Chr1:84520986-84521005 None:intergenic 40.0%
GATTATCCGGACAAATCAGA+GGG + Chr1:84520432-84520451 MsG0180004929.01.T01:intron 40.0%
GGTGTCTTGCATAATCTTTG+GGG - Chr1:84521063-84521082 None:intergenic 40.0%
TAACATCCAAAGACTCCACA+AGG + Chr1:84520876-84520895 MsG0180004929.01.T01:intron 40.0%
TAATCTTACGCACCTAGGTA+CGG - Chr1:84520021-84520040 None:intergenic 40.0%
TCTTACTACATCACACCTAC+AGG + Chr1:84520945-84520964 MsG0180004929.01.T01:CDS 40.0%
TGCTACAATCAAAAGGCTCT+CGG - Chr1:84520780-84520799 None:intergenic 40.0%
TTGAAACCTTGTGGAGTCTT+TGG - Chr1:84520885-84520904 None:intergenic 40.0%
TTGATACACAAGAGGAGTTG+AGG + Chr1:84520735-84520754 MsG0180004929.01.T01:CDS 40.0%
TTGTGGAGTCTTTGGATGTT+AGG - Chr1:84520877-84520896 None:intergenic 40.0%
! CTGAGACAGTGTTTAGAGTT+CGG - Chr1:84519723-84519742 None:intergenic 40.0%
! GCTAGAAGAAGATGGAGTTT+TGG - Chr1:84519789-84519808 None:intergenic 40.0%
!! ACACCATATAAGCCGGTTTT+GGG - Chr1:84520529-84520548 None:intergenic 40.0%
!! GAGAATCTTGGTGCTTAGAA+AGG + Chr1:84520905-84520924 MsG0180004929.01.T01:CDS 40.0%
!! TACACCATATAAGCCGGTTT+TGG - Chr1:84520530-84520549 None:intergenic 40.0%
AAAGATCATCCTCAACCCAG+TGG + Chr1:84521008-84521027 MsG0180004929.01.T01:CDS 45.0%
ATGCTGCTGTTAAGTATGGG+TGG + Chr1:84520194-84520213 MsG0180004929.01.T01:intron 45.0%
GCTCTCGGATGATCTTATGA+CGG - Chr1:84520765-84520784 None:intergenic 45.0%
GGATTATCCGGACAAATCAG+AGG + Chr1:84520431-84520450 MsG0180004929.01.T01:intron 45.0%
GGGTTTATTGTGACAGAGAC+CGG + Chr1:84520646-84520665 MsG0180004929.01.T01:intron 45.0%
TAAACAACTGTTCCGTTCGG+TGG + Chr1:84519689-84519708 MsG0180004929.01.T01:five_prime_UTR 45.0%
TCTTTCTCTCTCTTGGTAGG+TGG - Chr1:84519667-84519686 None:intergenic 45.0%
! CATCCCAAAACCGGCTTATA+TGG + Chr1:84520523-84520542 MsG0180004929.01.T01:intron 45.0%
! TCAAAGCCCTCTGATTTGTC+CGG - Chr1:84520441-84520460 None:intergenic 45.0%
!! GCAAAGCCCTTTGATTTGTC+TGG + Chr1:84520360-84520379 MsG0180004929.01.T01:intron 45.0%
TCGGAGAAGATACCACCGAA+CGG - Chr1:84519704-84519723 None:intergenic 50.0%
TTCTCTCTCTTGGTAGGTGG+TGG - Chr1:84519664-84519683 None:intergenic 50.0%
! GGTGGTGGCGTTTATAAGAG+AGG - Chr1:84519649-84519668 None:intergenic 50.0%
!! TCAGAGGGCTTTGAAAAGCG+CGG + Chr1:84520447-84520466 MsG0180004929.01.T01:intron 50.0%
ACCCAGTGGTGTATCTGCTG+CGG + Chr1:84521022-84521041 MsG0180004929.01.T01:CDS 55.0%
ATCCGCAGCAGATACACCAC+TGG - Chr1:84521027-84521046 None:intergenic 55.0%
GCAGATACACCACTGGGTTG+AGG - Chr1:84521020-84521039 None:intergenic 55.0%
TCAAAGGGCTTTGCGGAGCA+CGG - Chr1:84520354-84520373 None:intergenic 55.0%
TCCGCAGCAGATACACCACT+GGG - Chr1:84521026-84521045 None:intergenic 55.0%
! AAAAGCGCGGGAGTTGGAAG+AGG + Chr1:84520460-84520479 MsG0180004929.01.T01:intron 55.0%
!! CAGAGGGCTTTGAAAAGCGC+GGG + Chr1:84520448-84520467 MsG0180004929.01.T01:intron 55.0%
!! GCTTTGAAAAGCGCGGGAGT+TGG + Chr1:84520454-84520473 MsG0180004929.01.T01:intron 55.0%
ACAGAGACCGGCGATGACCC+AGG + Chr1:84520658-84520677 MsG0180004929.01.T01:intron 65.0%
ACTGAGCCCTGGGTCATCGC+CGG - Chr1:84520668-84520687 None:intergenic 65.0%
CAGAGACCGGCGATGACCCA+GGG + Chr1:84520659-84520678 MsG0180004929.01.T01:intron 65.0%
GCTTTGCGGAGCACGGAGAC+CGG - Chr1:84520347-84520366 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 84519603 84521154 84519603 ID=MsG0180004929.01;Name=MsG0180004929.01
Chr1 mRNA 84519603 84521154 84519603 ID=MsG0180004929.01.T01;Parent=MsG0180004929.01;Name=MsG0180004929.01.T01;_AED=0.49;_eAED=0.49;_QI=173|0.5|0.33|1|0.5|0.33|3|0|150
Chr1 exon 84519603 84519811 84519603 ID=MsG0180004929.01.T01:exon:9292;Parent=MsG0180004929.01.T01
Chr1 exon 84520662 84520811 84520662 ID=MsG0180004929.01.T01:exon:9293;Parent=MsG0180004929.01.T01
Chr1 exon 84520888 84521154 84520888 ID=MsG0180004929.01.T01:exon:9294;Parent=MsG0180004929.01.T01
Chr1 five_prime_UTR 84519603 84519775 84519603 ID=MsG0180004929.01.T01:five_prime_utr;Parent=MsG0180004929.01.T01
Chr1 CDS 84519776 84519811 84519776 ID=MsG0180004929.01.T01:cds;Parent=MsG0180004929.01.T01
Chr1 CDS 84520662 84520811 84520662 ID=MsG0180004929.01.T01:cds;Parent=MsG0180004929.01.T01
Chr1 CDS 84520888 84521154 84520888 ID=MsG0180004929.01.T01:cds;Parent=MsG0180004929.01.T01
Gene Sequence

>MsG0180004929.01.T01

ATGTCGGGCTCCAAAACTCCATCTTCTTCTAGCAAGAGACCGGCGATGACCCAGGGCTCAGTTGATATATATGCTGCACAATGCAAACTTTGCATGAAATGGAGAGTGATTGATACACAAGAGGAGTTGAGGAGATCCGTCATAAGATCATCCGAGAGCCTTTTGATTGTAGCAAAAAGGCTAATCACTCCACAAGGTTTCAAGAGAATCTTGGTGCTTAGAAAGGATTACTCTAAGTTGGACTCTTACTACATCACACCTACAGGTAAAAAACTGAGAACCCGCAATGAGATAGCAGCATATCTTAAAGATCATCCTCAACCCAGTGGTGTATCTGCTGCGGATTTTGATTTTTCATCCCCAAAGATTATGCAAGACACCATCCCAGAATTTATTGAGCAACAGAAGGATTCTGCAAACAAAAAAGCTAAGATATCTAAAGATGAAGTTTGA
Protein sequence

>MsG0180004929.01.T01

MSGSKTPSSSSKRPAMTQGSVDIYAAQCKLCMKWRVIDTQEELRRSVIRSSESLLIVAKRLITPQGFKRILVLRKDYSKLDSYYITPTGKKLRTRNEIAAYLKDHPQPSGVSAADFDFSSPKIMQDTIPEFIEQQKDSANKKAKISKDEV*