AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene72849

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72849.t1 MTR_5g027020 94.958 357 18 0 1 357 1 357 0.0 709
MS.gene72849.t1 MTR_1g038390 54.545 77 30 2 220 291 4 80 3.84e-20 85.5
MS.gene72849.t1 MTR_3g073000 23.306 369 193 15 10 352 13 317 4.45e-13 70.1
MS.gene72849.t1 MTR_3g073000 23.306 369 193 15 10 352 13 317 4.77e-13 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene72849.t1 AT2G19640 45.128 390 163 8 8 354 11 392 2.00e-113 335
MS.gene72849.t1 AT2G19640 48.515 303 140 6 8 302 11 305 1.38e-97 293
MS.gene72849.t1 AT2G17900 24.332 337 208 14 10 337 18 316 1.16e-13 72.4

Find 62 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAACCTCTCTCTTGAAAT+TGG 0.182162 5.1:+17665663 MS.gene72849:CDS
GTAAATTCCATAAGCCTTAA+TGG 0.186663 5.1:-17666271 None:intergenic
GGGATTCAGTGAGGATTATT+TGG 0.209184 5.1:-17665741 None:intergenic
GAAAGTAAAGTTTGAAGTTT+TGG 0.250619 5.1:-17666060 None:intergenic
CTGAAGCAGTTGTGACAATA+AGG 0.255076 5.1:-17665811 None:intergenic
CAAAGATCCATTAAGGCTTA+TGG 0.268080 5.1:+17666264 MS.gene72849:CDS
TGGATCTTTGAGGACCCTTT+TGG 0.292191 5.1:-17666251 None:intergenic
CAAACTTTACTTTCACTTCA+TGG 0.305377 5.1:+17666069 MS.gene72849:CDS
TAATCAAATCTGCATGCATT+AGG 0.315519 5.1:-17666327 None:intergenic
TGAGATCTTGTGTTGCAATA+AGG 0.317003 5.1:-17665711 None:intergenic
TTCATGTGGGGTGGACAAAA+AGG 0.320238 5.1:-17666153 None:intergenic
GAAAGTTGACCCTGCTACTT+AGG 0.333316 5.1:+17666701 MS.gene72849:CDS
AAACTTAGCATTATCAACTA+TGG 0.347178 5.1:-17666112 None:intergenic
GGTGCAAGATTGAAGCAAAT+TGG 0.355945 5.1:+17666523 MS.gene72849:CDS
ATAAGGCCTCTACCTTTGTT+AGG 0.358422 5.1:-17665694 None:intergenic
GGGTCCTCAAAGATCCATTA+AGG 0.360632 5.1:+17666257 MS.gene72849:CDS
GGAGAATTGTGCAGGTACTA+TGG 0.393903 5.1:+17666614 MS.gene72849:CDS
ACTATGGAATCATGATCATT+AGG 0.397254 5.1:-17666096 None:intergenic
AATCAAATCTGCATGCATTA+GGG 0.408868 5.1:-17666326 None:intergenic
CCAAATAAGACCTAAGTAGC+AGG 0.442970 5.1:-17666711 None:intergenic
ATTGAAGCAAATTGGAATGA+TGG 0.446384 5.1:+17666531 MS.gene72849:CDS
AATGGAACCTTATACCCAAA+AGG 0.447342 5.1:+17666236 MS.gene72849:CDS
GTGAGAGGAATTGAGGGCAT+TGG 0.448917 5.1:-17665908 None:intergenic
TCAATTCCTCTCACTCATCT+TGG 0.489766 5.1:+17665917 MS.gene72849:CDS
TAGCAGAATAGAGAAGAAGA+GGG 0.491920 5.1:-17665762 None:intergenic
AAGATGAGTGAGAGGAATTG+AGG 0.492387 5.1:-17665915 None:intergenic
AGATGAGTGAGAGGAATTGA+GGG 0.494037 5.1:-17665914 None:intergenic
TGCATGCAGATTTGATTATG+TGG 0.500019 5.1:+17666332 MS.gene72849:CDS
ATGGAACCTTATACCCAAAA+GGG 0.516328 5.1:+17666237 MS.gene72849:CDS
TGAAGCAGTTGTGACAATAA+GGG 0.517249 5.1:-17665810 None:intergenic
GTAGCAGAATAGAGAAGAAG+AGG 0.521798 5.1:-17665763 None:intergenic
GCTCCTCTGCCTCCAAAAGA+TGG 0.525196 5.1:+17666636 MS.gene72849:CDS
TAAGCCTTAATGGATCTTTG+AGG 0.528933 5.1:-17666261 None:intergenic
CATGGAAATGTTTGTGAAGG+TGG 0.530274 5.1:-17665841 None:intergenic
GAAGAAGAGGGGATTCAGTG+AGG 0.537045 5.1:-17665750 None:intergenic
AGCAGAATAGAGAAGAAGAG+GGG 0.546586 5.1:-17665761 None:intergenic
AAAAGGTAGTTTGAGCAAGA+AGG 0.551661 5.1:-17665865 None:intergenic
AAATGTTTGTGAAGGTGGTA+AGG 0.557933 5.1:-17665836 None:intergenic
TTGATTGAGGATGTTGCTGT+TGG 0.558045 5.1:+17666402 MS.gene72849:CDS
ATCTAAGTTTGTTTGTGACA+AGG 0.563087 5.1:+17666593 MS.gene72849:CDS
TTTCTGATAATGGTGAAGTG+GGG 0.567781 5.1:-17665969 None:intergenic
GCAACACAAGATCTCAAAGC+TGG 0.580231 5.1:+17665718 MS.gene72849:CDS
CACATACCTAACAAAGGTAG+AGG 0.580606 5.1:+17665688 MS.gene72849:CDS
GAGGGTGTATGAGAGAAAAG+AGG 0.582689 5.1:-17665787 None:intergenic
GAAGCAGTTGTGACAATAAG+GGG 0.584478 5.1:-17665809 None:intergenic
GTGCTCCAATTTCAAGAGAG+AGG 0.586066 5.1:-17665668 None:intergenic
TAGTTTGAGCAAGAAGGACA+TGG 0.592796 5.1:-17665859 None:intergenic
TCAGTATTATGTTCATCACC+AGG 0.593180 5.1:-17666366 None:intergenic
AGATTTGATTATGTGGAAAG+TGG 0.595188 5.1:+17666339 MS.gene72849:CDS
TATGTGGAAAGTGGTGAACC+TGG 0.596809 5.1:+17666348 MS.gene72849:CDS
CAAATAAGACCTAAGTAGCA+GGG 0.606280 5.1:-17666710 None:intergenic
ACATGACCAAGATGAGTGAG+AGG 0.606296 5.1:-17665923 None:intergenic
TGTGACAAGGAGAATTGTGC+AGG 0.619538 5.1:+17666606 MS.gene72849:CDS
AGGAATTGAGGGCATTGGAG+AGG 0.625591 5.1:-17665903 None:intergenic
GCTTGAACTTGAAGTTCACA+AGG 0.648973 5.1:-17665994 None:intergenic
CAGTTGTGACAATAAGGGGA+GGG 0.650828 5.1:-17665805 None:intergenic
GCAGTTGTGACAATAAGGGG+AGG 0.655954 5.1:-17665806 None:intergenic
GGACATGGAAATGTTTGTGA+AGG 0.669839 5.1:-17665844 None:intergenic
TTGGAGCACATACCTAACAA+AGG 0.675712 5.1:+17665682 MS.gene72849:CDS
TTAGATAAGAAAATCACATG+TGG 0.682821 5.1:-17666576 None:intergenic
ATGCATTAGGGATACAACCA+TGG 0.710306 5.1:-17666314 None:intergenic
TTAATAAGGATTACTCAACA+AGG 0.716109 5.1:+17666454 MS.gene72849:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATACTGATATTGTTTTT+AGG + chr5.1:17666379-17666398 MS.gene72849:CDS 15.0%
!!! AAGCTATTTTAGGATTAATA+AGG + chr5.1:17666440-17666459 MS.gene72849:CDS 20.0%
!!! ATTAAACTCTTTTTGCTTAA+TGG + chr5.1:17666218-17666237 MS.gene72849:CDS 20.0%
! AAACTTAGCATTATCAACTA+TGG - chr5.1:17666115-17666134 None:intergenic 25.0%
! TTAATAAGGATTACTCAACA+AGG + chr5.1:17666454-17666473 MS.gene72849:CDS 25.0%
! TTAGATAAGAAAATCACATG+TGG - chr5.1:17666579-17666598 None:intergenic 25.0%
!! AACAAGGAAAAAGATTTTGA+TGG + chr5.1:17666470-17666489 MS.gene72849:CDS 25.0%
!! GGTTAAAAAAAGTAGCTTTT+TGG - chr5.1:17666296-17666315 None:intergenic 25.0%
!! TTAGATTTTTCACCATCTTT+TGG - chr5.1:17666651-17666670 None:intergenic 25.0%
!!! AAAGCTACTTTTTTTAACCA+TGG + chr5.1:17666297-17666316 MS.gene72849:CDS 25.0%
!!! AGATTTGCATAAGCTATTTT+AGG + chr5.1:17666430-17666449 MS.gene72849:CDS 25.0%
!!! GAAAGTAAAGTTTGAAGTTT+TGG - chr5.1:17666063-17666082 None:intergenic 25.0%
!!! TATTGTTTTTAGGTTGATTG+AGG + chr5.1:17666389-17666408 MS.gene72849:CDS 25.0%
AATCAAATCTGCATGCATTA+GGG - chr5.1:17666329-17666348 None:intergenic 30.0%
ACTATGGAATCATGATCATT+AGG - chr5.1:17666099-17666118 None:intergenic 30.0%
AGATTTGATTATGTGGAAAG+TGG + chr5.1:17666339-17666358 MS.gene72849:CDS 30.0%
ATTGAAGCAAATTGGAATGA+TGG + chr5.1:17666531-17666550 MS.gene72849:CDS 30.0%
CAAACTTTACTTTCACTTCA+TGG + chr5.1:17666069-17666088 MS.gene72849:CDS 30.0%
GTAAATTCCATAAGCCTTAA+TGG - chr5.1:17666274-17666293 None:intergenic 30.0%
TAATCAAATCTGCATGCATT+AGG - chr5.1:17666330-17666349 None:intergenic 30.0%
TTCAGCTGAAAAATTCATGT+GGG - chr5.1:17666169-17666188 None:intergenic 30.0%
! ATCTAAGTTTGTTTGTGACA+AGG + chr5.1:17666593-17666612 MS.gene72849:CDS 30.0%
! TCACAAGGTTTTTCTGATAA+TGG - chr5.1:17665982-17666001 None:intergenic 30.0%
!! AAGATTTTGATGGAGGATTA+TGG + chr5.1:17666480-17666499 MS.gene72849:CDS 30.0%
!! AAGGAAAAAGATTTTGATGG+AGG + chr5.1:17666473-17666492 MS.gene72849:CDS 30.0%
!! AGTAAAGTTTGAAGTTTTGG+AGG - chr5.1:17666060-17666079 None:intergenic 30.0%
!!! GTAAAGTTTGAAGTTTTGGA+GGG - chr5.1:17666059-17666078 None:intergenic 30.0%
!!! TAAAGTTTGAAGTTTTGGAG+GGG - chr5.1:17666058-17666077 None:intergenic 30.0%
!!! TTTTCTGATAATGGTGAAGT+GGG - chr5.1:17665973-17665992 None:intergenic 30.0%
!!! TTTTTCTGATAATGGTGAAG+TGG - chr5.1:17665974-17665993 None:intergenic 30.0%
AAAAGGTAGTTTGAGCAAGA+AGG - chr5.1:17665868-17665887 None:intergenic 35.0%
AAATGTTTGTGAAGGTGGTA+AGG - chr5.1:17665839-17665858 None:intergenic 35.0%
AATGGAACCTTATACCCAAA+AGG + chr5.1:17666236-17666255 MS.gene72849:CDS 35.0%
ATGGAACCTTATACCCAAAA+GGG + chr5.1:17666237-17666256 MS.gene72849:CDS 35.0%
CAAAGATCCATTAAGGCTTA+TGG + chr5.1:17666264-17666283 MS.gene72849:CDS 35.0%
GTTCAGCTGAAAAATTCATG+TGG - chr5.1:17666170-17666189 None:intergenic 35.0%
TAGCAGAATAGAGAAGAAGA+GGG - chr5.1:17665765-17665784 None:intergenic 35.0%
TCAGCTGAAAAATTCATGTG+GGG - chr5.1:17666168-17666187 None:intergenic 35.0%
TCAGTATTATGTTCATCACC+AGG - chr5.1:17666369-17666388 None:intergenic 35.0%
TGAAGCAGTTGTGACAATAA+GGG - chr5.1:17665813-17665832 None:intergenic 35.0%
TGAGATCTTGTGTTGCAATA+AGG - chr5.1:17665714-17665733 None:intergenic 35.0%
TGCATGCAGATTTGATTATG+TGG + chr5.1:17666332-17666351 MS.gene72849:CDS 35.0%
TTCAACCTCTCTCTTGAAAT+TGG + chr5.1:17665663-17665682 MS.gene72849:CDS 35.0%
! GATTTTTCACCATCTTTTGG+AGG - chr5.1:17666648-17666667 None:intergenic 35.0%
! GTTTTGCTTGTGAATGTGAT+AGG + chr5.1:17666502-17666521 MS.gene72849:CDS 35.0%
! TAAGCCTTAATGGATCTTTG+AGG - chr5.1:17666264-17666283 None:intergenic 35.0%
!! TTTCTGATAATGGTGAAGTG+GGG - chr5.1:17665972-17665991 None:intergenic 35.0%
AAGATGAGTGAGAGGAATTG+AGG - chr5.1:17665918-17665937 None:intergenic 40.0%
AGATGAGTGAGAGGAATTGA+GGG - chr5.1:17665917-17665936 None:intergenic 40.0%
AGCAGAATAGAGAAGAAGAG+GGG - chr5.1:17665764-17665783 None:intergenic 40.0%
ATAAGGCCTCTACCTTTGTT+AGG - chr5.1:17665697-17665716 None:intergenic 40.0%
ATGCATTAGGGATACAACCA+TGG - chr5.1:17666317-17666336 None:intergenic 40.0%
CACATACCTAACAAAGGTAG+AGG + chr5.1:17665688-17665707 MS.gene72849:CDS 40.0%
CATGGAAATGTTTGTGAAGG+TGG - chr5.1:17665844-17665863 None:intergenic 40.0%
CTGAAGCAGTTGTGACAATA+AGG - chr5.1:17665814-17665833 None:intergenic 40.0%
GAAGCAGTTGTGACAATAAG+GGG - chr5.1:17665812-17665831 None:intergenic 40.0%
GCTTGAACTTGAAGTTCACA+AGG - chr5.1:17665997-17666016 None:intergenic 40.0%
GGACATGGAAATGTTTGTGA+AGG - chr5.1:17665847-17665866 None:intergenic 40.0%
GGGATTCAGTGAGGATTATT+TGG - chr5.1:17665744-17665763 None:intergenic 40.0%
GGTGCAAGATTGAAGCAAAT+TGG + chr5.1:17666523-17666542 MS.gene72849:CDS 40.0%
GTAGCAGAATAGAGAAGAAG+AGG - chr5.1:17665766-17665785 None:intergenic 40.0%
TAGTTTGAGCAAGAAGGACA+TGG - chr5.1:17665862-17665881 None:intergenic 40.0%
TCAATTCCTCTCACTCATCT+TGG + chr5.1:17665917-17665936 MS.gene72849:CDS 40.0%
TTGATTGAGGATGTTGCTGT+TGG + chr5.1:17666402-17666421 MS.gene72849:CDS 40.0%
TTGGAGCACATACCTAACAA+AGG + chr5.1:17665682-17665701 MS.gene72849:CDS 40.0%
! GTTCTTGAGTGCAACTTTTG+TGG + chr5.1:17666672-17666691 MS.gene72849:CDS 40.0%
ACATGACCAAGATGAGTGAG+AGG - chr5.1:17665926-17665945 None:intergenic 45.0%
CAGTTGTGACAATAAGGGGA+GGG - chr5.1:17665808-17665827 None:intergenic 45.0%
GCAACACAAGATCTCAAAGC+TGG + chr5.1:17665718-17665737 MS.gene72849:CDS 45.0%
GCTGAAAAATTCATGTGGGG+TGG - chr5.1:17666165-17666184 None:intergenic 45.0%
GGAGAATTGTGCAGGTACTA+TGG + chr5.1:17666614-17666633 MS.gene72849:CDS 45.0%
GGGTCCTCAAAGATCCATTA+AGG + chr5.1:17666257-17666276 MS.gene72849:CDS 45.0%
GTGCTCCAATTTCAAGAGAG+AGG - chr5.1:17665671-17665690 None:intergenic 45.0%
TATGTGGAAAGTGGTGAACC+TGG + chr5.1:17666348-17666367 MS.gene72849:CDS 45.0%
TGTGACAAGGAGAATTGTGC+AGG + chr5.1:17666606-17666625 MS.gene72849:CDS 45.0%
TTCATGTGGGGTGGACAAAA+AGG - chr5.1:17666156-17666175 None:intergenic 45.0%
! GAGGGTGTATGAGAGAAAAG+AGG - chr5.1:17665790-17665809 None:intergenic 45.0%
!! GGATCTTTGAGGACCCTTTT+GGG - chr5.1:17666253-17666272 None:intergenic 45.0%
!! TGAGGACCCTTTTGGGTATA+AGG - chr5.1:17666246-17666265 None:intergenic 45.0%
!! TGGATCTTTGAGGACCCTTT+TGG - chr5.1:17666254-17666273 None:intergenic 45.0%
!!! GGCATTTTTGGCTGCAGAAA+AGG - chr5.1:17665885-17665904 None:intergenic 45.0%
GAAGAAGAGGGGATTCAGTG+AGG - chr5.1:17665753-17665772 None:intergenic 50.0%
GCAGTTGTGACAATAAGGGG+AGG - chr5.1:17665809-17665828 None:intergenic 50.0%
! GTGAGAGGAATTGAGGGCAT+TGG - chr5.1:17665911-17665930 None:intergenic 50.0%
!! AGGAATTGAGGGCATTGGAG+AGG - chr5.1:17665906-17665925 None:intergenic 50.0%
!! TCACCATCTTTTGGAGGCAG+AGG - chr5.1:17666642-17666661 None:intergenic 50.0%
!!! GGGCATTGGAGAGGCATTTT+TGG - chr5.1:17665897-17665916 None:intergenic 50.0%
GCTCCTCTGCCTCCAAAAGA+TGG + chr5.1:17666636-17666655 MS.gene72849:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 17665649 17666722 17665649 ID=MS.gene72849
chr5.1 mRNA 17665649 17666722 17665649 ID=MS.gene72849.t1;Parent=MS.gene72849
chr5.1 exon 17665649 17666722 17665649 ID=MS.gene72849.t1.exon1;Parent=MS.gene72849.t1
chr5.1 CDS 17665649 17666722 17665649 ID=cds.MS.gene72849.t1;Parent=MS.gene72849.t1
Gene Sequence

>MS.gene72849

ATGGCTGCTCAAACTTCAACCTCTCTCTTGAAATTGGAGCACATACCTAACAAAGGTAGAGGCCTTATTGCAACACAAGATCTCAAAGCTGGCCAAATAATCCTCACTGAATCCCCTCTTCTTCTCTATTCTGCTACACCTCTTTTCTCTCATACACCCTCCCCTTATTGTCACAACTGCTTCAGAACCTTACCACCTTCACAAACATTTCCATGTCCTTCTTGCTCAAACTACCTTTTCTGCAGCCAAAAATGCCTCTCCAATGCCCTCAATTCCTCTCACTCATCTTGGTCATGTCAAACACTCTCTCATCTTCAAAACCCCACTTCACCATTATCAGAAAAACCTTGTGAACTTCAAGTTCAAGCTCGTTTGATTGTTGCTGCTTACAATCTTGCTATTCACACCCCTCCAAAACTTCAAACTTTACTTTCACTTCATGGTAGTCCTAATGATCATGATTCCATAGTTGATAATGCTAAGTTTATTCATGCTCTTATCTCACCTTTTTGTCCACCCCACATGAATTTTTCAGCTGAACTAGCTGCTAAAGTCATTGCTAAAGAAAGATTAAACTCTTTTTGCTTAATGGAACCTTATACCCAAAAGGGTCCTCAAAGATCCATTAAGGCTTATGGAATTTACCAAAAAGCTACTTTTTTTAACCATGGTTGTATCCCTAATGCATGCAGATTTGATTATGTGGAAAGTGGTGAACCTGGTGATGAACATAATACTGATATTGTTTTTAGGTTGATTGAGGATGTTGCTGTTGGAAGTGAGATTTGCATAAGCTATTTTAGGATTAATAAGGATTACTCAACAAGGAAAAAGATTTTGATGGAGGATTATGGTTTTGCTTGTGAATGTGATAGGTGCAAGATTGAAGCAAATTGGAATGATGGAGAGAACAAGTACAGTGATCTGCCACATGTGATTTTCTTATCTAAGTTTGTTTGTGACAAGGAGAATTGTGCAGGTACTATGGCTCCTCTGCCTCCAAAAGATGGTGAAAAATCTAATGTTCTTGAGTGCAACTTTTGTGGTAATTTGAAAGTTGACCCTGCTACTTAG
Protein sequence

>MS.gene72849.t1

MAAQTSTSLLKLEHIPNKGRGLIATQDLKAGQIILTESPLLLYSATPLFSHTPSPYCHNCFRTLPPSQTFPCPSCSNYLFCSQKCLSNALNSSHSSWSCQTLSHLQNPTSPLSEKPCELQVQARLIVAAYNLAIHTPPKLQTLLSLHGSPNDHDSIVDNAKFIHALISPFCPPHMNFSAELAAKVIAKERLNSFCLMEPYTQKGPQRSIKAYGIYQKATFFNHGCIPNACRFDYVESGEPGDEHNTDIVFRLIEDVAVGSEICISYFRINKDYSTRKKILMEDYGFACECDRCKIEANWNDGENKYSDLPHVIFLSKFVCDKENCAGTMAPLPPKDGEKSNVLECNFCGNLKVDPAT