AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180005656.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005656.01.T01 MTR_1g105305 95.858 169 7 0 39 207 31 199 1.18e-116 330
MsG0180005656.01.T01 MTR_5g005710 67.429 175 51 1 39 207 27 201 1.12e-86 254
MsG0180005656.01.T01 MTR_7g113640 40.972 144 82 2 37 177 26 169 2.47e-30 110
MsG0180005656.01.T01 MTR_1g082770 38.194 144 86 3 40 181 34 176 1.05e-29 109
MsG0180005656.01.T01 MTR_1g082830 34.211 152 92 3 34 177 36 187 2.61e-26 101
MsG0180005656.01.T01 MTR_1g082790 33.913 115 75 1 39 152 46 160 7.33e-18 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005656.01.T01 AT3G06035 58.382 173 68 2 39 207 27 199 8.19e-70 211
MsG0180005656.01.T01 AT5G19250 65.541 148 51 0 37 184 26 173 2.79e-67 205
MsG0180005656.01.T01 AT1G54860 46.853 143 74 2 36 176 27 169 9.72e-45 148
MsG0180005656.01.T01 AT5G19240 46.541 159 79 3 44 200 33 187 1.04e-44 147
MsG0180005656.01.T01 AT5G19230 51.449 138 58 2 40 177 29 157 1.24e-39 134
MsG0180005656.01.T01 AT5G19230 51.449 138 58 2 40 177 29 157 1.24e-39 134

Find 58 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATTGACATTTAGCTAAA+AGG 0.190847 1:+94565509 None:intergenic
GTTATGCCTGCCTGTGTTCC+TGG 0.264326 1:-94565460 MsG0180005656.01.T01:CDS
TCCAACTTTGGAATTCAAAT+TGG 0.272104 1:+94565267 None:intergenic
TGAGAGAGATAATCTTTATC+AGG 0.299934 1:-94565701 MsG0180005656.01.T01:CDS
TGACATTTAGCTAAAAGGTT+TGG 0.301742 1:+94565514 None:intergenic
AGCTAAAAGGTTTGGGTAGT+TGG 0.318984 1:+94565522 None:intergenic
GTATTGGCTCAGAAGATAAC+TGG 0.333128 1:-94565354 MsG0180005656.01.T01:CDS
GACATTTAGCTAAAAGGTTT+GGG 0.340607 1:+94565515 None:intergenic
TTAGGCCATGTTTCAGTGTC+AGG 0.357277 1:+94566592 None:intergenic
GCAATAAATCATTCCAACTT+TGG 0.358521 1:+94565255 None:intergenic
TACATGGTTGATTCTTGAAT+TGG 0.360348 1:+94565593 None:intergenic
ATTGGCAGCATTAGAACTAT+AGG 0.374058 1:+94565285 None:intergenic
TTGGCAGCATTAGAACTATA+GGG 0.380106 1:+94565286 None:intergenic
TGACAACAATAACAACCCTT+TGG 0.384688 1:+94564969 None:intergenic
CATCCTCTAGGTATCATAAC+AGG 0.398840 1:+94565203 None:intergenic
GCCAATTTGAATTCCAAAGT+TGG 0.400976 1:-94565268 MsG0180005656.01.T01:CDS
TTCAGTGTCAGGTATAAGTT+TGG 0.401126 1:+94566603 None:intergenic
GACAACAATAACAACCCTTT+GGG 0.402331 1:+94564970 None:intergenic
GACACACAGTATACAGGAAT+TGG 0.421140 1:-94565376 MsG0180005656.01.T01:CDS
TGCTCAATTCTCTTGTTAGC+TGG 0.427277 1:-94565235 MsG0180005656.01.T01:CDS
AACCTTTGTATGGTAGCATT+CGG 0.428535 1:+94565134 None:intergenic
ATTCAAGTAAAACCTTTGTA+TGG 0.450341 1:+94565124 None:intergenic
CTCAACGACACACAGTATAC+AGG 0.481619 1:-94565382 MsG0180005656.01.T01:CDS
TTGACCACTGACACTCCAAC+AGG 0.483770 1:-94565319 MsG0180005656.01.T01:CDS
TTTGGGTAGTTGGAGAATTG+AGG 0.485525 1:+94565532 None:intergenic
GGCATGCAAGAAAGAGACTT+TGG 0.492091 1:-94566643 MsG0180005656.01.T01:CDS
ATTGGCTATTTCTGATACAA+AGG 0.497292 1:-94565491 MsG0180005656.01.T01:CDS
ACGAGGCTTGAAGCTAGGCC+AGG 0.504069 1:+94565442 None:intergenic
TGAAGCTAGGCCAGGAACAC+AGG 0.509872 1:+94565450 None:intergenic
GCTAGGCCAGGAACACAGGC+AGG 0.513127 1:+94565454 None:intergenic
GGTAGCATTCGGTTTCTGAC+TGG 0.515517 1:+94565145 None:intergenic
GAGAATTGAGGTTCAGTACC+TGG 0.522201 1:+94565544 None:intergenic
AGGAGAGTCTTGTTCCCAAA+GGG 0.529687 1:-94564984 MsG0180005656.01.T01:three_prime_UTR
CAGGTATAAGTTTGGTTCTG+AGG 0.530035 1:+94566611 None:intergenic
GCTATTTCTGATACAAAGGA+TGG 0.531181 1:-94565487 MsG0180005656.01.T01:CDS
CAGTATACAGGAATTGGTAT+TGG 0.536270 1:-94565370 MsG0180005656.01.T01:CDS
GCACCTGTGGTATTTGTACA+TGG 0.542966 1:+94565577 None:intergenic
GACATCATACTGACACTGAT+GGG 0.545161 1:+94566538 None:intergenic
CTGTTATGATACCTAGAGGA+TGG 0.559307 1:-94565202 MsG0180005656.01.T01:exon
AGACATCATACTGACACTGA+TGG 0.562240 1:+94566537 None:intergenic
TCGTGAAGTTAGTGAGGACG+AGG 0.562843 1:+94565425 None:intergenic
TGAGGACGAGGCTTGAAGCT+AGG 0.566605 1:+94565437 None:intergenic
GTTTCCTGTTGGAGTGTCAG+TGG 0.576612 1:+94565315 None:intergenic
GAGATTTCGTGAAGTTAGTG+AGG 0.582648 1:+94565419 None:intergenic
TAGGAGAGTCTTGTTCCCAA+AGG 0.591193 1:-94564985 MsG0180005656.01.T01:three_prime_UTR
GAGAGAGATAATCTTTATCA+GGG 0.592178 1:-94565700 MsG0180005656.01.T01:CDS
ACTGTCAATAGCCATCCTCT+AGG 0.605574 1:+94565191 None:intergenic
TTATACCTGACACTGAAACA+TGG 0.607114 1:-94566597 MsG0180005656.01.T01:CDS
TGGTACTGTATTAGCACCTG+TGG 0.607702 1:+94565564 None:intergenic
TGGCAGCATTAGAACTATAG+GGG 0.612217 1:+94565287 None:intergenic
CACTGATGGGGACATTGCAA+CGG 0.615123 1:+94566551 None:intergenic
ACAGGTGCTAATACAGTACC+AGG 0.621692 1:-94565562 MsG0180005656.01.T01:CDS
TTTCCTGTTATGATACCTAG+AGG 0.629858 1:-94565206 MsG0180005656.01.T01:exon
CAACCATGTACAAATACCAC+AGG 0.631778 1:-94565580 MsG0180005656.01.T01:CDS
AACCGAATGCTACCATACAA+AGG 0.658980 1:-94565136 MsG0180005656.01.T01:three_prime_UTR
ACATCATACTGACACTGATG+GGG 0.659818 1:+94566539 None:intergenic
GGCAGCATTAGAACTATAGG+GGG 0.666389 1:+94565288 None:intergenic
TATGAAACAATAGTAACACG+AGG 0.774462 1:+94565042 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATAATATCATTTTTTAACT+TGG - Chr1:94566627-94566646 MsG0180005656.01.T01:CDS 10.0%
!! CAGCTTCAAAAAAAAAAAAA+TGG - Chr1:94565214-94565233 MsG0180005656.01.T01:exon 20.0%
!! GAATGTAAAGTAAGAAAAAT+AGG - Chr1:94566570-94566589 MsG0180005656.01.T01:CDS 20.0%
!!! ATAAAAACATTTACCACTTT+TGG + Chr1:94565131-94565150 None:intergenic 20.0%
!!! ATTTTGACCAATTCAAAATA+TGG + Chr1:94565386-94565405 None:intergenic 20.0%
!!! GTTTTACTTGAATGTTAAAA+TGG - Chr1:94566460-94566479 MsG0180005656.01.T01:intron 20.0%
! ATTCAAGTAAAACCTTTGTA+TGG + Chr1:94566453-94566472 None:intergenic 25.0%
! ATTCATGAGATTAATGTCAT+AGG - Chr1:94565451-94565470 MsG0180005656.01.T01:CDS 25.0%
! ATTCATGAGATTAATGTCAT+TGG - Chr1:94565451-94565470 MsG0180005656.01.T01:CDS 25.0%
! TATCCAGTTAAATGTGATAA+CGG - Chr1:94565302-94565321 MsG0180005656.01.T01:CDS 25.0%
!! TTAGAAATGACAACGTTTTT+AGG + Chr1:94565003-94565022 None:intergenic 25.0%
!!! TCTTAGACCATATTTTGAAT+TGG - Chr1:94565376-94565395 MsG0180005656.01.T01:CDS 25.0%
CCAATTGACATTTAGCTAAA+AGG + Chr1:94566068-94566087 None:intergenic 30.0%
GACATTTAGCTAAAAGGTTT+GGG + Chr1:94566062-94566081 None:intergenic 30.0%
GAGAGAGATAATCTTTATCA+GGG - Chr1:94565874-94565893 MsG0180005656.01.T01:intron 30.0%
GCAATAAATCATTCCAACTT+TGG + Chr1:94566322-94566341 None:intergenic 30.0%
TATGAAACAATAGTAACACG+AGG + Chr1:94566535-94566554 None:intergenic 30.0%
TGACATTTAGCTAAAAGGTT+TGG + Chr1:94566063-94566082 None:intergenic 30.0%
TGAGAGAGATAATCTTTATC+AGG - Chr1:94565873-94565892 MsG0180005656.01.T01:intron 30.0%
TGCAGAAAAAACATTGAACA+GGG + Chr1:94565851-94565870 None:intergenic 30.0%
TGTCAGTGAACAAAATGATT+TGG + Chr1:94565745-94565764 None:intergenic 30.0%
TTTCAGCTTCATTGTGTATA+TGG + Chr1:94565811-94565830 None:intergenic 30.0%
! CACTTTTGGATTCTATATGT+GGG + Chr1:94565117-94565136 None:intergenic 30.0%
! TACATGGTTGATTCTTGAAT+TGG + Chr1:94565984-94566003 None:intergenic 30.0%
!! ATTGGCTATTTCTGATACAA+AGG - Chr1:94566083-94566102 MsG0180005656.01.T01:intron 30.0%
!! CCTTTTAGCTAAATGTCAAT+TGG - Chr1:94566065-94566084 MsG0180005656.01.T01:intron 30.0%
!! TCCAACTTTGGAATTCAAAT+TGG + Chr1:94566310-94566329 None:intergenic 30.0%
!! TGGTAAATGTTTTTATGCTG+TGG - Chr1:94565135-94565154 MsG0180005656.01.T01:three_prime_UTR 30.0%
AACCTTTGTATGGTAGCATT+CGG + Chr1:94566443-94566462 None:intergenic 35.0%
ATGCCTCTTAAAACATTCAC+TGG - Chr1:94565644-94565663 MsG0180005656.01.T01:CDS 35.0%
ATTGGCAGCATTAGAACTAT+AGG + Chr1:94566292-94566311 None:intergenic 35.0%
CAGAAGAATAGAGAGAACTT+GGG + Chr1:94565245-94565264 None:intergenic 35.0%
CAGTATACAGGAATTGGTAT+TGG - Chr1:94566204-94566223 MsG0180005656.01.T01:intron 35.0%
CCACATATAGAATCCAAAAG+TGG - Chr1:94565115-94565134 MsG0180005656.01.T01:three_prime_UTR 35.0%
CTAAGCTTGAAATGAGTCAT+GGG + Chr1:94565524-94565543 None:intergenic 35.0%
CTAGCTTATGCTTCAAGAAA+TGG - Chr1:94565058-94565077 MsG0180005656.01.T01:three_prime_UTR 35.0%
CTGCAGAAAAAACATTGAAC+AGG + Chr1:94565852-94565871 None:intergenic 35.0%
GACAACAATAACAACCCTTT+GGG + Chr1:94566607-94566626 None:intergenic 35.0%
GCCAATTTGAATTCCAAAGT+TGG - Chr1:94566306-94566325 MsG0180005656.01.T01:intron 35.0%
TCACCGTTATCACATTTAAC+TGG + Chr1:94565308-94565327 None:intergenic 35.0%
TGACAACAATAACAACCCTT+TGG + Chr1:94566608-94566627 None:intergenic 35.0%
TTATACCTGACACTGAAACA+TGG - Chr1:94564977-94564996 MsG0180005656.01.T01:three_prime_UTR 35.0%
TTCAGTGTCAGGTATAAGTT+TGG + Chr1:94564974-94564993 None:intergenic 35.0%
TTGGCAGCATTAGAACTATA+GGG + Chr1:94566291-94566310 None:intergenic 35.0%
TTTCCTGTTATGATACCTAG+AGG - Chr1:94566368-94566387 MsG0180005656.01.T01:intron 35.0%
! TACCTAAGTTTGCTTGAACT+GGG + Chr1:94565091-94565110 None:intergenic 35.0%
! TTACCTAAGTTTGCTTGAAC+TGG + Chr1:94565092-94565111 None:intergenic 35.0%
!! CCACTTTTGGATTCTATATG+TGG + Chr1:94565118-94565137 None:intergenic 35.0%
!! GCTATTTCTGATACAAAGGA+TGG - Chr1:94566087-94566106 MsG0180005656.01.T01:intron 35.0%
!! TGTCCAGTGAATGTTTTAAG+AGG + Chr1:94565650-94565669 None:intergenic 35.0%
AACCGAATGCTACCATACAA+AGG - Chr1:94566438-94566457 MsG0180005656.01.T01:intron 40.0%
ACAGGGTAAGTGTAGTGTAA+TGG + Chr1:94565834-94565853 None:intergenic 40.0%
ACATCATACTGACACTGATG+GGG + Chr1:94565038-94565057 None:intergenic 40.0%
AGACATCATACTGACACTGA+TGG + Chr1:94565040-94565059 None:intergenic 40.0%
AGCTAAAAGGTTTGGGTAGT+TGG + Chr1:94566055-94566074 None:intergenic 40.0%
CAACCATGTACAAATACCAC+AGG - Chr1:94565994-94566013 MsG0180005656.01.T01:intron 40.0%
CATCCTCTAGGTATCATAAC+AGG + Chr1:94566374-94566393 None:intergenic 40.0%
CCAAGTTCTCTCTATTCTTC+TGG - Chr1:94565243-94565262 MsG0180005656.01.T01:CDS 40.0%
CCAGAAGAATAGAGAGAACT+TGG + Chr1:94565246-94565265 None:intergenic 40.0%
CTGTTATGATACCTAGAGGA+TGG - Chr1:94566372-94566391 MsG0180005656.01.T01:intron 40.0%
GACACACAGTATACAGGAAT+TGG - Chr1:94566198-94566217 MsG0180005656.01.T01:intron 40.0%
GACATCATACTGACACTGAT+GGG + Chr1:94565039-94565058 None:intergenic 40.0%
GAGATTTCGTGAAGTTAGTG+AGG + Chr1:94566158-94566177 None:intergenic 40.0%
GCTAAGCTTGAAATGAGTCA+TGG + Chr1:94565525-94565544 None:intergenic 40.0%
TGCTCAATTCTCTTGTTAGC+TGG - Chr1:94566339-94566358 MsG0180005656.01.T01:intron 40.0%
TGGCAGCATTAGAACTATAG+GGG + Chr1:94566290-94566309 None:intergenic 40.0%
TTGAAGCTGAGTTATACCAG+AGG + Chr1:94565203-94565222 None:intergenic 40.0%
TTGAGTAATGCACAGATGAC+AGG + Chr1:94565675-94565694 None:intergenic 40.0%
TTTGGGTAGTTGGAGAATTG+AGG + Chr1:94566045-94566064 None:intergenic 40.0%
! ACCTAAGTTTGCTTGAACTG+GGG + Chr1:94565090-94565109 None:intergenic 40.0%
! TAGCACAATTCAAGTTCCTC+TGG - Chr1:94565184-94565203 MsG0180005656.01.T01:three_prime_UTR 40.0%
! TCTCAGTTGTGACCTTTTTC+TGG - Chr1:94565766-94565785 MsG0180005656.01.T01:intron 40.0%
!! CAGGTATAAGTTTGGTTCTG+AGG + Chr1:94564966-94564985 None:intergenic 40.0%
!! GGTCAGCTATTTTATCAGCA+AGG + Chr1:94565963-94565982 None:intergenic 40.0%
!! GTATTGGCTCAGAAGATAAC+TGG - Chr1:94566220-94566239 MsG0180005656.01.T01:intron 40.0%
ACAGGTGCTAATACAGTACC+AGG - Chr1:94566012-94566031 MsG0180005656.01.T01:intron 45.0%
ACTGTCAATAGCCATCCTCT+AGG + Chr1:94566386-94566405 None:intergenic 45.0%
CTCAACGACACACAGTATAC+AGG - Chr1:94566192-94566211 MsG0180005656.01.T01:intron 45.0%
GAGAATTGAGGTTCAGTACC+TGG + Chr1:94566033-94566052 None:intergenic 45.0%
GCACCTGTGGTATTTGTACA+TGG + Chr1:94566000-94566019 None:intergenic 45.0%
GGAACTTGAATTGTGCTAGC+TGG + Chr1:94565182-94565201 None:intergenic 45.0%
GGCAGCATTAGAACTATAGG+GGG + Chr1:94566289-94566308 None:intergenic 45.0%
TGGTACTGTATTAGCACCTG+TGG + Chr1:94566013-94566032 None:intergenic 45.0%
TGTGCATGTGTGCCAGAAAA+AGG + Chr1:94565781-94565800 None:intergenic 45.0%
TTAGGCCATGTTTCAGTGTC+AGG + Chr1:94564985-94565004 None:intergenic 45.0%
! CCTAAGTTTGCTTGAACTGG+GGG + Chr1:94565089-94565108 None:intergenic 45.0%
!! AGGAGAGTCTTGTTCCCAAA+GGG - Chr1:94566590-94566609 MsG0180005656.01.T01:CDS 45.0%
!! TAGGAGAGTCTTGTTCCCAA+AGG - Chr1:94566589-94566608 MsG0180005656.01.T01:CDS 45.0%
CACTGATGGGGACATTGCAA+CGG + Chr1:94565026-94565045 None:intergenic 50.0%
CCCCCAGTTCAAGCAAACTT+AGG - Chr1:94565086-94565105 MsG0180005656.01.T01:three_prime_UTR 50.0%
GGTAGCATTCGGTTTCTGAC+TGG + Chr1:94566432-94566451 None:intergenic 50.0%
TAGGGGGCAAAGTTTCCTGT+TGG + Chr1:94566273-94566292 None:intergenic 50.0%
TCATCGCAGTCGCGAGATTA+GGG + Chr1:94565598-94565617 None:intergenic 50.0%
TCGTGAAGTTAGTGAGGACG+AGG + Chr1:94566152-94566171 None:intergenic 50.0%
TTCATCGCAGTCGCGAGATT+AGG + Chr1:94565599-94565618 None:intergenic 50.0%
TTGACCACTGACACTCCAAC+AGG - Chr1:94566255-94566274 MsG0180005656.01.T01:intron 50.0%
! GTGCTAGCTGGTGCTTTTAG+AGG + Chr1:94565170-94565189 None:intergenic 50.0%
! GTTTCCTGTTGGAGTGTCAG+TGG + Chr1:94566262-94566281 None:intergenic 50.0%
GTTATGCCTGCCTGTGTTCC+TGG - Chr1:94566114-94566133 MsG0180005656.01.T01:intron 55.0%
TGAAGCTAGGCCAGGAACAC+AGG + Chr1:94566127-94566146 None:intergenic 55.0%
TGAGGACGAGGCTTGAAGCT+AGG + Chr1:94566140-94566159 None:intergenic 55.0%
ACGAGGCTTGAAGCTAGGCC+AGG + Chr1:94566135-94566154 None:intergenic 60.0%
GCTAGGCCAGGAACACAGGC+AGG + Chr1:94566123-94566142 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 94564934 94566662 94564934 ID=MsG0180005656.01;Name=MsG0180005656.01
Chr1 mRNA 94564934 94566662 94564934 ID=MsG0180005656.01.T01;Parent=MsG0180005656.01;Name=MsG0180005656.01.T01;_AED=0.32;_eAED=0.41;_QI=0|0|0.5|1|1|1|2|282|207
Chr1 exon 94564934 94565724 94564934 ID=MsG0180005656.01.T01:exon:50136;Parent=MsG0180005656.01.T01
Chr1 exon 94566548 94566662 94566548 ID=MsG0180005656.01.T01:exon:50135;Parent=MsG0180005656.01.T01
Chr1 CDS 94566548 94566662 94566548 ID=MsG0180005656.01.T01:cds;Parent=MsG0180005656.01.T01
Chr1 CDS 94565216 94565724 94565216 ID=MsG0180005656.01.T01:cds;Parent=MsG0180005656.01.T01
Chr1 three_prime_UTR 94564934 94565215 94564934 ID=MsG0180005656.01.T01:three_prime_utr;Parent=MsG0180005656.01.T01
Gene Sequence

>MsG0180005656.01.T01

ATGCAAGAAAGAGACTTTGGAACAGCTATCCTCAGAACCAAACTTATACCTGACACTGAAACATGGCCTAAAAACGTTGTCATTTCTAACCGTTGCAATGTCCCCATCAGTGTCAATGAGAGAGATAATCTTTATCAGGGTATCAACAAGTATCGAGCATCATTAAACTTGAAATCTCTCACAAAAAATAAAAATGCAGATTGCCTTGCTGATAAAATAGCTGACCAATTCAAGAATCAACCATGTACAAATACCACAGGTGCTAATACAGTACCAGGTACTGAACCTCAATTCTCCAACTACCCAAACCTTTTAGCTAAATGTCAATTGGCTATTTCTGATACAAAGGATGGAGCTGTTATGCCTGCCTGTGTTCCTGGCCTAGCTTCAAGCCTCGTCCTCACTAACTTCACGAAATCTCTCTACTCACAGAATCTCAACGACACACAGTATACAGGAATTGGTATTGGCTCAGAAGATAACTGGATTGTCGTTGTCTTGACCACTGACACTCCAACAGGAAACTTTGCCCCCTATAGTTCTAATGCTGCCAATTTGAATTCCAAAGTTGGAATGATTTATTGCTCAATTCTCTTGTTAGCTGGCAAAATTTTCCTGTTATGA
Protein sequence

>MsG0180005656.01.T01

MQERDFGTAILRTKLIPDTETWPKNVVISNRCNVPISVNERDNLYQGINKYRASLNLKSLTKNKNADCLADKIADQFKNQPCTNTTGANTVPGTEPQFSNYPNLLAKCQLAISDTKDGAVMPACVPGLASSLVLTNFTKSLYSQNLNDTQYTGIGIGSEDNWIVVVLTTDTPTGNFAPYSSNAANLNSKVGMIYCSILLLAGKIFLL*