AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071846

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071846.t1 MTR_2g035220 81.529 157 4 1 1 132 1 157 2.14e-82 238
MS.gene071846.t1 MTR_2g035210 78.981 157 8 1 1 132 1 157 4.52e-80 233
MS.gene071846.t1 MTR_2g035190 77.707 157 10 1 1 132 1 157 4.19e-78 228
MS.gene071846.t1 MTR_2g035320 75.159 157 14 1 1 132 1 157 4.77e-76 223
MS.gene071846.t1 MTR_6g033450 55.414 157 45 1 1 132 1 157 5.04e-48 152
MS.gene071846.t1 MTR_4g120970 55.414 157 45 1 1 132 1 157 5.04e-48 152
MS.gene071846.t1 MTR_2g035100 54.140 157 47 1 1 132 1 157 5.33e-48 151
MS.gene071846.t1 MTR_2g035105 53.503 157 48 1 1 132 1 157 3.94e-47 149
MS.gene071846.t1 MTR_2g035150 53.503 157 48 1 1 132 1 157 1.21e-46 148
MS.gene071846.t1 MTR_2g035130 51.592 157 51 1 1 132 1 157 6.33e-45 144
MS.gene071846.t1 MTR_2g035120 49.682 157 54 1 1 132 1 157 4.57e-42 136
MS.gene071846.t1 MTR_2g035320 85.526 76 11 0 57 132 47 122 4.43e-41 133
MS.gene071846.t1 MTR_2g035170 41.096 146 61 1 12 132 12 157 2.51e-31 109
MS.gene071846.t1 MTR_4g120940 65.278 72 25 0 61 132 48 119 7.90e-24 89.4
MS.gene071846.t1 MTR_4g120950 36.076 158 75 4 1 132 1 158 3.45e-22 86.3
MS.gene071846.t1 MTR_4g120760 30.573 157 83 2 1 131 1 157 2.83e-21 84.0
MS.gene071846.t1 MTR_4g120760 30.573 157 83 2 1 131 1 157 2.89e-21 84.0
MS.gene071846.t1 MTR_2g435310 28.205 156 86 2 1 130 1 156 5.69e-20 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATACATTTACTTAATAATT+AGG 0.132764 2.2:+53677904 None:intergenic
GATAATTTCTTGATGGTTCC+TGG 0.258662 2.2:+53679316 None:intergenic
CTTGATAAGTCCAGTTCCTT+TGG 0.324632 2.2:+53677954 None:intergenic
GGCCATTGAGGGCTACGTTT+TGG 0.338863 2.2:-53677932 MS.gene071846:CDS
ATACATTTACTTAATAATTA+GGG 0.345110 2.2:+53677905 None:intergenic
TGGGCAGCTGGAATCACCTT+TGG 0.352078 2.2:+53679370 None:intergenic
TACAGCATAGTGGGAGGAAC+AGG 0.371602 2.2:-53678120 MS.gene071846:intron
GGGCAGCTGGAATCACCTTT+GGG 0.381427 2.2:+53679371 None:intergenic
AAGTCCAGTTCCTTTGGCTT+TGG 0.382566 2.2:+53677960 None:intergenic
AGATAGAGTTGCATCACCTT+TGG 0.394288 2.2:+53678002 None:intergenic
AGAGCTTTGTAGAGTTTAGC+TGG 0.394931 2.2:+53679418 None:intergenic
CTTCAACAATTTCAACACTC+TGG 0.405408 2.2:+53679350 None:intergenic
AGACATGGATAATTTCTTGA+TGG 0.415791 2.2:+53679309 None:intergenic
GAGACCAAAGCCAAAGGAAC+TGG 0.425614 2.2:-53677964 MS.gene071846:CDS
AGTGTTGTGGCTGGCTCTGA+TGG 0.429803 2.2:-53678060 MS.gene071846:CDS
ATTTCAACACTCTGGGCAGC+TGG 0.438114 2.2:+53679358 None:intergenic
GTTGAAATTGTTGAAGGAAA+TGG 0.443294 2.2:-53679343 MS.gene071846:CDS
TTCAACAATTTCAACACTCT+GGG 0.491385 2.2:+53679351 None:intergenic
CAAAGGAACTGGACTTATCA+AGG 0.497615 2.2:-53677953 MS.gene071846:CDS
CAGAGTGTTGAAATTGTTGA+AGG 0.502542 2.2:-53679349 MS.gene071846:CDS
GGACTTATCAAGGCCATTGA+GGG 0.514208 2.2:-53677943 MS.gene071846:CDS
TGCCAAAACGTAGCCCTCAA+TGG 0.516239 2.2:+53677930 None:intergenic
GAGTTGCATCACCTTTGGTA+TGG 0.537356 2.2:+53678007 None:intergenic
GTTGTGGCTGGCTCTGATGG+TGG 0.558406 2.2:-53678057 MS.gene071846:CDS
TTTCACTGAAATCTTAACAA+TGG 0.567421 2.2:+53678032 None:intergenic
TTATCAATTACCTTCAGACA+TGG 0.569245 2.2:+53679294 None:intergenic
TGGACTTATCAAGGCCATTG+AGG 0.572485 2.2:-53677944 MS.gene071846:CDS
GAAATTGTTGAAGGAAATGG+TGG 0.582127 2.2:-53679340 MS.gene071846:CDS
GTTGAAGGAAATGGTGGACC+AGG 0.585895 2.2:-53679334 MS.gene071846:CDS
TTCGAGACAAGTGTTGTGGC+TGG 0.589865 2.2:-53678069 MS.gene071846:CDS
AAGAAATTATCCATGTCTGA+AGG 0.597444 2.2:-53679304 MS.gene071846:intron
CATAGTGGGAGGAACAGGGT+TGG 0.609437 2.2:-53678115 MS.gene071846:intron
TGCTGATGAAATCATCCCAA+AGG 0.616025 2.2:-53679386 MS.gene071846:CDS
TCAGTGAAATACCATACCAA+AGG 0.652605 2.2:-53678018 MS.gene071846:CDS
TGAATTCGAGACAAGTGTTG+TGG 0.660471 2.2:-53678073 MS.gene071846:CDS
CGTGAGGAGACCAAAGCCAA+AGG 0.666854 2.2:-53677970 MS.gene071846:CDS
TCTATCTGAAGCAGTACGTG+AGG 0.676642 2.2:-53677986 MS.gene071846:CDS
ACAGCATAGTGGGAGGAACA+GGG 0.682935 2.2:-53678119 MS.gene071846:intron
TGATGAACATGTCTCAACTG+TGG 0.723859 2.2:-53679443 MS.gene071846:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAATAAATAATAAATAA+CGG - chr2.2:53678331-53678350 MS.gene071846:intron 0.0%
!! AATTTGTATATAAATTATGA+TGG - chr2.2:53679158-53679177 MS.gene071846:intron 10.0%
!! ATTTGTATATAAATTATGAT+GGG - chr2.2:53679159-53679178 MS.gene071846:intron 10.0%
!! TTAATAACTTAATTGTAAAT+AGG - chr2.2:53678677-53678696 MS.gene071846:intron 10.0%
!! AAGAAACTATAACATTTAAA+CGG - chr2.2:53678989-53679008 MS.gene071846:intron 15.0%
!! AATTTAACTAAAGATTGTTT+CGG + chr2.2:53679117-53679136 None:intergenic 15.0%
!! ACATAAATTCTCAATAAATT+TGG + chr2.2:53678391-53678410 None:intergenic 15.0%
!! ATAATTTCAACTATCAATTA+TGG - chr2.2:53678604-53678623 MS.gene071846:intron 15.0%
!! TAATTTCAACTATCAATTAT+GGG - chr2.2:53678605-53678624 MS.gene071846:intron 15.0%
!!! TTTATTTTTTCCATGAAAAA+TGG + chr2.2:53678309-53678328 None:intergenic 15.0%
!! CTTATTATCATTTACGAATA+TGG + chr2.2:53678704-53678723 None:intergenic 20.0%
!! TTCAATTCAAGTATTTGAAT+AGG - chr2.2:53678187-53678206 MS.gene071846:intron 20.0%
!!! AACGGTTTATTTTTTTTTTC+CGG - chr2.2:53679007-53679026 MS.gene071846:intron 20.0%
!!! AGTTCAAGTTTAGAATTTTA+CGG + chr2.2:53678426-53678445 None:intergenic 20.0%
!!! TGAAGCTTTAAATTTATTGA+TGG + chr2.2:53678278-53678297 None:intergenic 20.0%
! AAAATACCAAAATACCTTCA+CGG - chr2.2:53678818-53678837 MS.gene071846:intron 25.0%
! TTTCACTGAAATCTTAACAA+TGG + chr2.2:53679349-53679368 None:intergenic 25.0%
!! TTGAATTCAACAACTCTTTT+TGG + chr2.2:53678172-53678191 None:intergenic 25.0%
!! TTTCAATGTTTTCAACTTCA+TGG - chr2.2:53678632-53678651 MS.gene071846:intron 25.0%
!! TTTTCAACTTCATGGTAAAT+AGG - chr2.2:53678640-53678659 MS.gene071846:intron 25.0%
!!! AAGGTATTTTGGTATTTTCA+CGG + chr2.2:53678816-53678835 None:intergenic 25.0%
AAGAAATTATCCATGTCTGA+AGG - chr2.2:53678074-53678093 MS.gene071846:CDS 30.0%
AATCAGCCTAACATAATATG+TGG - chr2.2:53678735-53678754 MS.gene071846:intron 30.0%
AGACATGGATAATTTCTTGA+TGG + chr2.2:53678072-53678091 None:intergenic 30.0%
ATCGGAGATTTGAAAGTAAT+TGG + chr2.2:53679092-53679111 None:intergenic 30.0%
CTCTCAAATTTGAGAATTGA+AGG - chr2.2:53678227-53678246 MS.gene071846:intron 30.0%
CTTCAATTCTCAAATTTGAG+AGG + chr2.2:53678229-53678248 None:intergenic 30.0%
GTTGAAATTGTTGAAGGAAA+TGG - chr2.2:53678035-53678054 MS.gene071846:CDS 30.0%
TACAATTCATGCAAAGGTTA+TGG - chr2.2:53678358-53678377 MS.gene071846:intron 30.0%
TAGAGACGTGTAAATGTTAT+AGG + chr2.2:53678966-53678985 None:intergenic 30.0%
TGTAGACCACATATTATGTT+AGG + chr2.2:53678744-53678763 None:intergenic 30.0%
TTATCAATTACCTTCAGACA+TGG + chr2.2:53678087-53678106 None:intergenic 30.0%
TTCAACAATTTCAACACTCT+GGG + chr2.2:53678030-53678049 None:intergenic 30.0%
! TAATTTGTGTAGCACAAAGT+CGG + chr2.2:53679204-53679223 None:intergenic 30.0%
!! AATTATGATGGGTGTATTGT+AGG - chr2.2:53679170-53679189 MS.gene071846:intron 30.0%
!! CAAAGAACAACCATTTTTCA+TGG - chr2.2:53678296-53678315 MS.gene071846:intron 30.0%
AAATTAGAAGCAGTGGAATG+AGG - chr2.2:53679218-53679237 MS.gene071846:intron 35.0%
CCAGTGAATCACTATTACAA+TGG + chr2.2:53678508-53678527 None:intergenic 35.0%
CCATTGTAATAGTGATTCAC+TGG - chr2.2:53678505-53678524 MS.gene071846:intron 35.0%
CTAAAGATTGTTTCGGTCAT+CGG + chr2.2:53679110-53679129 None:intergenic 35.0%
CTTCAACAATTTCAACACTC+TGG + chr2.2:53678031-53678050 None:intergenic 35.0%
GAAATTGTTGAAGGAAATGG+TGG - chr2.2:53678038-53678057 MS.gene071846:CDS 35.0%
GGGATATACAATTCATGCAA+AGG - chr2.2:53678352-53678371 MS.gene071846:intron 35.0%
TCAGTGAAATACCATACCAA+AGG - chr2.2:53679360-53679379 MS.gene071846:CDS 35.0%
TGTGGTCTACAACTATAACA+TGG - chr2.2:53678753-53678772 MS.gene071846:intron 35.0%
TTTGAGAATTGAAGGAGACA+TGG - chr2.2:53678235-53678254 MS.gene071846:intron 35.0%
! GATAATTTCTTGATGGTTCC+TGG + chr2.2:53678065-53678084 None:intergenic 35.0%
! TTGGTATTTTCACGGTACAT+TGG + chr2.2:53678808-53678827 None:intergenic 35.0%
!! CAGAGTGTTGAAATTGTTGA+AGG - chr2.2:53678029-53678048 MS.gene071846:CDS 35.0%
!!! TAACTACCGTGAAGGTATTT+TGG + chr2.2:53678827-53678846 None:intergenic 35.0%
ACCAACAATCAACTCTAGTC+CGG + chr2.2:53679029-53679048 None:intergenic 40.0%
ACTTGAACTCAAATCACACC+AGG - chr2.2:53678437-53678456 MS.gene071846:intron 40.0%
AGATAGAGTTGCATCACCTT+TGG + chr2.2:53679379-53679398 None:intergenic 40.0%
AGTGATGGTTAAATGTCGCT+TGG - chr2.2:53678880-53678899 MS.gene071846:intron 40.0%
CAAAGGAACTGGACTTATCA+AGG - chr2.2:53679425-53679444 MS.gene071846:CDS 40.0%
CACGGTACATTGGAGTAAAA+AGG + chr2.2:53678798-53678817 None:intergenic 40.0%
CTTGAACTCAAATCACACCA+GGG - chr2.2:53678438-53678457 MS.gene071846:intron 40.0%
CTTGATAAGTCCAGTTCCTT+TGG + chr2.2:53679427-53679446 None:intergenic 40.0%
GCTACACAAATTAGAAGCAG+TGG - chr2.2:53679211-53679230 MS.gene071846:intron 40.0%
GGATACAACTACAGCATAGT+GGG - chr2.2:53679249-53679268 MS.gene071846:intron 40.0%
TCACTCAGCAAATGTTGTTG+TGG - chr2.2:53678853-53678872 MS.gene071846:intron 40.0%
TGATGAACATGTCTCAACTG+TGG - chr2.2:53677935-53677954 MS.gene071846:CDS 40.0%
TGCTGATGAAATCATCCCAA+AGG - chr2.2:53677992-53678011 MS.gene071846:CDS 40.0%
! AGAGCTTTGTAGAGTTTAGC+TGG + chr2.2:53677963-53677982 None:intergenic 40.0%
! GTGATGGTTAAATGTCGCTT+GGG - chr2.2:53678881-53678900 MS.gene071846:intron 40.0%
! TGAATTCGAGACAAGTGTTG+TGG - chr2.2:53679305-53679324 MS.gene071846:CDS 40.0%
! TGATGGTTAAATGTCGCTTG+GGG - chr2.2:53678882-53678901 MS.gene071846:intron 40.0%
!! AAATGTCGCTTGGGGTATTT+TGG - chr2.2:53678890-53678909 MS.gene071846:intron 40.0%
!! TATGATGGGTGTATTGTAGG+TGG - chr2.2:53679173-53679192 MS.gene071846:intron 40.0%
AGTTAACCGCCACAAGTAGT+TGG + chr2.2:53678476-53678495 None:intergenic 45.0%
CAGTGGAATGAGGCAAACTT+GGG - chr2.2:53679228-53679247 MS.gene071846:intron 45.0%
CTTGTGGCGGTTAACTAGAA+AGG - chr2.2:53678480-53678499 MS.gene071846:intron 45.0%
GAAGATCCAACTACTTGTGG+CGG - chr2.2:53678467-53678486 MS.gene071846:intron 45.0%
GAGTTGCATCACCTTTGGTA+TGG + chr2.2:53679374-53679393 None:intergenic 45.0%
GGACTTATCAAGGCCATTGA+GGG - chr2.2:53679435-53679454 MS.gene071846:CDS 45.0%
GGGATACAACTACAGCATAG+TGG - chr2.2:53679248-53679267 MS.gene071846:intron 45.0%
TCAAATCACACCAGGGTAAG+CGG - chr2.2:53678445-53678464 MS.gene071846:intron 45.0%
TGGACTTATCAAGGCCATTG+AGG - chr2.2:53679434-53679453 MS.gene071846:CDS 45.0%
TGTTGTTGTGGAGTGAGTGA+TGG - chr2.2:53678865-53678884 MS.gene071846:intron 45.0%
! AAGTCCAGTTCCTTTGGCTT+TGG + chr2.2:53679421-53679440 None:intergenic 45.0%
! TACAACTACAGCATAGTGGG+AGG - chr2.2:53679252-53679271 MS.gene071846:intron 45.0%
! TCCGGACTAGAGTTGATTGT+TGG - chr2.2:53679025-53679044 MS.gene071846:intron 45.0%
! TCTATCTGAAGCAGTACGTG+AGG - chr2.2:53679392-53679411 MS.gene071846:CDS 45.0%
!! ATAAATAAATAATAAATAAC+GGG - chr2.2:53678332-53678351 MS.gene071846:intron 5.0%
!!! TTAAATTTTATTTACATTTA+AGG - chr2.2:53679130-53679149 MS.gene071846:intron 5.0%
ATTTCAACACTCTGGGCAGC+TGG + chr2.2:53678023-53678042 None:intergenic 50.0%
GAGACCAAAGCCAAAGGAAC+TGG - chr2.2:53679414-53679433 MS.gene071846:CDS 50.0%
GCAGTGGAATGAGGCAAACT+TGG - chr2.2:53679227-53679246 MS.gene071846:intron 50.0%
GCGGAAGATCCAACTACTTG+TGG - chr2.2:53678464-53678483 MS.gene071846:intron 50.0%
TGCCAAAACGTAGCCCTCAA+TGG + chr2.2:53679451-53679470 None:intergenic 50.0%
TTCACTGGTGCTTGCTCTTG+TGG - chr2.2:53678520-53678539 MS.gene071846:intron 50.0%
! ACAGCATAGTGGGAGGAACA+GGG - chr2.2:53679259-53679278 MS.gene071846:intron 50.0%
! TACAGCATAGTGGGAGGAAC+AGG - chr2.2:53679258-53679277 MS.gene071846:intron 50.0%
! TTCGAGACAAGTGTTGTGGC+TGG - chr2.2:53679309-53679328 MS.gene071846:CDS 50.0%
!! GTTGAAGGAAATGGTGGACC+AGG - chr2.2:53678044-53678063 MS.gene071846:CDS 50.0%
CGTGAGGAGACCAAAGCCAA+AGG - chr2.2:53679408-53679427 MS.gene071846:CDS 55.0%
GACAGCGCTAACTACCGTGA+AGG + chr2.2:53678835-53678854 None:intergenic 55.0%
GGGCAGCTGGAATCACCTTT+GGG + chr2.2:53678010-53678029 None:intergenic 55.0%
GTTGGATCTTCCGCTTACCC+TGG + chr2.2:53678458-53678477 None:intergenic 55.0%
TGGGCAGCTGGAATCACCTT+TGG + chr2.2:53678011-53678030 None:intergenic 55.0%
! CATAGTGGGAGGAACAGGGT+TGG - chr2.2:53679263-53679282 MS.gene071846:intron 55.0%
! GGCCATTGAGGGCTACGTTT+TGG - chr2.2:53679446-53679465 MS.gene071846:CDS 55.0%
!! AGTGTTGTGGCTGGCTCTGA+TGG - chr2.2:53679318-53679337 MS.gene071846:CDS 55.0%
!! GTTGTGGCTGGCTCTGATGG+TGG - chr2.2:53679321-53679340 MS.gene071846:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53677915 53679485 53677915 ID=MS.gene071846
chr2.2 mRNA 53677915 53679485 53677915 ID=MS.gene071846.t1;Parent=MS.gene071846
chr2.2 exon 53679305 53679485 53679305 ID=MS.gene071846.t1.exon1;Parent=MS.gene071846.t1
chr2.2 CDS 53679305 53679485 53679305 ID=cds.MS.gene071846.t1;Parent=MS.gene071846.t1
chr2.2 exon 53677915 53678132 53677915 ID=MS.gene071846.t1.exon2;Parent=MS.gene071846.t1
chr2.2 CDS 53677915 53678132 53677915 ID=cds.MS.gene071846.t1;Parent=MS.gene071846.t1
Gene Sequence

>MS.gene071846

ATGGGTGTTTTTGTTTTCATTGATGAACATGTCTCAACTGTGGCTCCAGCTAAACTCTACAAAGCTCTTGCAAAAGATGCTGATGAAATCATCCCAAAGGTGATTCCAGCTGCCCAGAGTGTTGAAATTGTTGAAGGAAATGGTGGACCAGGAACCATCAAGAAATTATCCATGTCTGAAGGTAATTGATAAAGAGCATATACTATATTCTGCAAAAAAAAATAAACTTTATTAATTAGTAATTCAATTGTGTACCAAAAAGAGTTGTTGAATTCAATTCAAGTATTTGAATAGGCATATACGATGTGAAACCTCTCAAATTTGAGAATTGAAGGAGACATGGTGATAAATAAGCTTAGTCCATCAATAAATTTAAAGCTTCAAAGAACAACCATTTTTCATGGAAAAAATAAATAAATAAATAAATAATAAATAACGGGATATACAATTCATGCAAAGGTTATGGAGAATCACCAAATTTATTGAGAATTTATGTATAACTTGTAAACCGTAAAATTCTAAACTTGAACTCAAATCACACCAGGGTAAGCGGAAGATCCAACTACTTGTGGCGGTTAACTAGAAAGGAACCATTGTAATAGTGATTCACTGGTGCTTGCTCTTGTGGTATATATTAGTCAAATATTCAAATGAAATGAATGATCAAATTAAAACTAAATTTAGTTAAAATAATTTCAACTATCAATTATGGGTCATTTTCAATGTTTTCAACTTCATGGTAAATAGGTCATTTTCAAAAAATTAATAACTTAATTGTAAATAGGTCCATATTCGTAAATGATAATAAGATCAACTTTATAATCAGCCTAACATAATATGTGGTCTACAACTATAACATGGAAATTGCTCTTCTCGCTTTCCTTTTTACTCCAATGTACCGTGAAAATACCAAAATACCTTCACGGTAGTTAGCGCTGTCACTCAGCAAATGTTGTTGTGGAGTGAGTGATGGTTAAATGTCGCTTGGGGTATTTTGGTATTTTTGCAGTGTTTGAAAAGAAAAAATGAAAGTGAGAAAAATTGCTTTCCTATAACATTTACACGTCTCTAAAAAAGAAACTATAACATTTAAACGGTTTATTTTTTTTTTCCGGACTAGAGTTGATTGTTGGTATAGTTAAATCAGATTCAGCAATCAAGTGATTAATGATATCCAATTACTTTCAAATCTCCGATGACCGAAACAATCTTTAGTTAAATTTTATTTACATTTAAGGAACAAAATTTGTATATAAATTATGATGGGTGTATTGTAGGTGGCAAAACCGACTTTGTGCTACACAAATTAGAAGCAGTGGAATGAGGCAAACTTGGGATACAACTACAGCATAGTGGGAGGAACAGGGTTGGATGAAAGTTTAGAGAAAGTTGAATTCGAGACAAGTGTTGTGGCTGGCTCTGATGGTGGATCCATTGTTAAGATTTCAGTGAAATACCATACCAAAGGTGATGCAACTCTATCTGAAGCAGTACGTGAGGAGACCAAAGCCAAAGGAACTGGACTTATCAAGGCCATTGAGGGCTACGTTTTGGCAAACCCTAATTATTAA
Protein sequence

>MS.gene071846.t1

MGVFVFIDEHVSTVAPAKLYKALAKDADEIIPKVIPAAQSVEIVEGNGGPGTIKKLSMSEVGGTGLDESLEKVEFETSVVAGSDGGSIVKISVKYHTKGDATLSEAVREETKAKGTGLIKAIEGYVLANPNY