AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64657

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64657.t1 MTR_5g079710 92.982 171 6 2 1 171 1 165 4.93e-111 317
MS.gene64657.t1 MTR_4g052040 47.619 168 78 4 6 166 4 168 9.23e-39 130
MS.gene64657.t1 MTR_4g052060 41.071 168 92 4 3 167 1 164 5.26e-32 113
MS.gene64657.t1 MTR_0907s0020 59.420 69 28 0 97 165 102 170 1.14e-23 92.0
MS.gene64657.t1 MTR_7g105790 36.932 176 86 5 6 161 4 174 3.12e-23 91.7
MS.gene64657.t1 MTR_8g103520 44.304 79 44 0 88 166 215 293 2.35e-18 80.5
MS.gene64657.t1 MTR_3g111780 50.725 69 34 0 94 162 195 263 1.10e-12 64.7
MS.gene64657.t1 MTR_5g075210 39.189 74 45 0 88 161 271 344 1.82e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64657.t1 AT3G52525 60.317 63 25 0 98 160 67 129 3.55e-21 85.1
MS.gene64657.t1 AT5G19650 53.030 66 31 0 97 162 154 219 5.67e-21 86.3
MS.gene64657.t1 AT2G36026 60.656 61 24 0 102 162 91 151 7.00e-20 82.4
MS.gene64657.t1 AT2G18500 48.387 62 32 0 95 156 224 285 1.00e-16 76.3
MS.gene64657.t1 AT5G22240 45.205 73 40 0 91 163 90 162 1.67e-15 71.2
MS.gene64657.t1 AT1G06920 40.580 69 41 0 94 162 240 308 6.71e-13 65.9

Find 31 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGAAGAATTGAGGCTATT+AGG 0.197369 5.2:+67776104 None:intergenic
CCATCACCACAAAGCTTCTT+AGG 0.222603 5.2:+67775759 None:intergenic
CTCTATACTTCAAATGATAT+TGG 0.278958 5.2:-67775904 MS.gene64657:CDS
TGGAAGAATTGAGGCTATTA+GGG 0.332981 5.2:+67776105 None:intergenic
TGTCATTGTTGAAGCGTTCA+TGG 0.333768 5.2:-67775802 MS.gene64657:CDS
GCAACAATAATAATAATTAT+AGG 0.367952 5.2:-67776007 MS.gene64657:CDS
AGAGGGTTCAAGTACGTTAG+AGG 0.399454 5.2:+67776163 None:intergenic
ATTGGAGAGAGAGATTTATT+CGG 0.406374 5.2:-67775886 MS.gene64657:CDS
CCTAAGAAGCTTTGTGGTGA+TGG 0.449802 5.2:-67775759 MS.gene64657:CDS
ATATTTCCTAAGAAGCTTTG+TGG 0.453226 5.2:-67775765 MS.gene64657:CDS
GGCATCGGCGTCGTGGGAAG+TGG 0.454480 5.2:+67776082 None:intergenic
TTTGTCCTCGGTGTTGGCAT+CGG 0.463745 5.2:+67776067 None:intergenic
GAAATCTTTGTCCTCGGTGT+TGG 0.500764 5.2:+67776061 None:intergenic
GGTGTTGGCATCGGCGTCGT+GGG 0.511237 5.2:+67776076 None:intergenic
CGGTGTTGGCATCGGCGTCG+TGG 0.524524 5.2:+67776075 None:intergenic
TTCTCATCTAACAAAAGTTG+TGG 0.528866 5.2:-67776203 MS.gene64657:CDS
ATCGGCGTCGTGGGAAGTGG+TGG 0.551552 5.2:+67776085 None:intergenic
GAGTTTCGAAAATCTTCATA+CGG 0.557400 5.2:+67775924 None:intergenic
TGCTGTTGAGAAGGAATCGA+AGG 0.559087 5.2:-67775949 MS.gene64657:CDS
GAGGGTTCAAGTACGTTAGA+GGG 0.563551 5.2:+67776164 None:intergenic
AGATAGCATTGCTGTTGAGA+AGG 0.569048 5.2:-67775958 MS.gene64657:CDS
GCCGTTGTCGTTCGAGATGG+TGG 0.578742 5.2:+67776031 None:intergenic
GGGAAGTGGTGGAAGAATTG+AGG 0.591377 5.2:+67776096 None:intergenic
GTTGTCGTTCGAGATGGTGG+TGG 0.591904 5.2:+67776034 None:intergenic
GCTGCCGTTGTCGTTCGAGA+TGG 0.601950 5.2:+67776028 None:intergenic
GACGTGTGAAGGACATGTGA+AGG 0.602789 5.2:-67775734 None:intergenic
GGAAGTGAAATCTTTGTCCT+CGG 0.630018 5.2:+67776055 None:intergenic
ACCACCATCTCGAACGACAA+CGG 0.631485 5.2:-67776032 MS.gene64657:CDS
ACGCTTCAACAATGACATGA+TGG 0.645246 5.2:+67775808 None:intergenic
TGGTGATGGTAGACGTGTGA+AGG 0.668871 5.2:-67775745 MS.gene64657:CDS
CGACGCCGATGCCAACACCG+AGG 0.730176 5.2:-67776072 MS.gene64657:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GCAACAATAATAATAATTAT+AGG - chr5.2:67775975-67775994 MS.gene64657:CDS 15.0%
!!! TAATTATAGGATTTTAAAGC+CGG - chr5.2:67775988-67776007 MS.gene64657:CDS 20.0%
! CTCTATACTTCAAATGATAT+TGG - chr5.2:67776078-67776097 MS.gene64657:CDS 25.0%
!! AACTTTTGTTAGATGAGAAA+AGG + chr5.2:67775778-67775797 None:intergenic 25.0%
!! ACTTTTGTTAGATGAGAAAA+GGG + chr5.2:67775777-67775796 None:intergenic 25.0%
!! TTTTGACAAAAGGAGATTTT+AGG + chr5.2:67775851-67775870 None:intergenic 25.0%
!!! AATTATAGGATTTTAAAGCC+GGG - chr5.2:67775989-67776008 MS.gene64657:CDS 25.0%
ATATTTCCTAAGAAGCTTTG+TGG - chr5.2:67776217-67776236 MS.gene64657:CDS 30.0%
ATTGGAGAGAGAGATTTATT+CGG - chr5.2:67776096-67776115 MS.gene64657:CDS 30.0%
GAGTTTCGAAAATCTTCATA+CGG + chr5.2:67776061-67776080 None:intergenic 30.0%
TTCTCATCTAACAAAAGTTG+TGG - chr5.2:67775779-67775798 MS.gene64657:CDS 30.0%
!!! GAGATTTTAGGTTTTTGAGA+GGG + chr5.2:67775839-67775858 None:intergenic 30.0%
TGGAAGAATTGAGGCTATTA+GGG + chr5.2:67775880-67775899 None:intergenic 35.0%
!! CTATCTATGAGTTTTGTACC+CGG + chr5.2:67776010-67776029 None:intergenic 35.0%
!!! AGGGTTTGTGTTTTGACAAA+AGG + chr5.2:67775861-67775880 None:intergenic 35.0%
!!! GGAGATTTTAGGTTTTTGAG+AGG + chr5.2:67775840-67775859 None:intergenic 35.0%
ACGCTTCAACAATGACATGA+TGG + chr5.2:67776177-67776196 None:intergenic 40.0%
GGAAGTGAAATCTTTGTCCT+CGG + chr5.2:67775930-67775949 None:intergenic 40.0%
GTGGAAGAATTGAGGCTATT+AGG + chr5.2:67775881-67775900 None:intergenic 40.0%
! AGATAGCATTGCTGTTGAGA+AGG - chr5.2:67776024-67776043 MS.gene64657:CDS 40.0%
! TGTCATTGTTGAAGCGTTCA+TGG - chr5.2:67776180-67776199 MS.gene64657:CDS 40.0%
!! ATGAGAAAAGGGTTTTGACG+AGG + chr5.2:67775766-67775785 None:intergenic 40.0%
AGAGGGTTCAAGTACGTTAG+AGG + chr5.2:67775822-67775841 None:intergenic 45.0%
CCATCACCACAAAGCTTCTT+AGG + chr5.2:67776226-67776245 None:intergenic 45.0%
GAGGGTTCAAGTACGTTAGA+GGG + chr5.2:67775821-67775840 None:intergenic 45.0%
TGCTGTTGAGAAGGAATCGA+AGG - chr5.2:67776033-67776052 MS.gene64657:CDS 45.0%
! CCTAAGAAGCTTTGTGGTGA+TGG - chr5.2:67776223-67776242 MS.gene64657:CDS 45.0%
! GAAATCTTTGTCCTCGGTGT+TGG + chr5.2:67775924-67775943 None:intergenic 45.0%
ACCACCATCTCGAACGACAA+CGG - chr5.2:67775950-67775969 MS.gene64657:CDS 50.0%
! GGGAAGTGGTGGAAGAATTG+AGG + chr5.2:67775889-67775908 None:intergenic 50.0%
!! TGGTGATGGTAGACGTGTGA+AGG - chr5.2:67776237-67776256 MS.gene64657:CDS 50.0%
!! TTTGTCCTCGGTGTTGGCAT+CGG + chr5.2:67775918-67775937 None:intergenic 50.0%
! GTTGTCGTTCGAGATGGTGG+TGG + chr5.2:67775951-67775970 None:intergenic 55.0%
GCCGTTGTCGTTCGAGATGG+TGG + chr5.2:67775954-67775973 None:intergenic 60.0%
GCTGCCGTTGTCGTTCGAGA+TGG + chr5.2:67775957-67775976 None:intergenic 60.0%
ATCGGCGTCGTGGGAAGTGG+TGG + chr5.2:67775900-67775919 None:intergenic 65.0%
!! GGTGTTGGCATCGGCGTCGT+GGG + chr5.2:67775909-67775928 None:intergenic 65.0%
CGACGCCGATGCCAACACCG+AGG - chr5.2:67775910-67775929 MS.gene64657:CDS 70.0%
!! CGGTGTTGGCATCGGCGTCG+TGG + chr5.2:67775910-67775929 None:intergenic 70.0%
!! GGCATCGGCGTCGTGGGAAG+TGG + chr5.2:67775903-67775922 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 67775737 67776267 67775737 ID=MS.gene64657
chr5.2 mRNA 67775737 67776267 67775737 ID=MS.gene64657.t1;Parent=MS.gene64657
chr5.2 exon 67775737 67776267 67775737 ID=MS.gene64657.t1.exon1;Parent=MS.gene64657.t1
chr5.2 CDS 67775737 67776267 67775737 ID=cds.MS.gene64657.t1;Parent=MS.gene64657.t1
Gene Sequence

>MS.gene64657

ATGTCTTTCAATTTCAACAAGAGAAGCCTCGTCAAAACCCTTTTCTCATCTAACAAAAGTTGTGGTTGCATCAAAATAAAACCCTCTAACGTACTTGAACCCTCTCAAAAACCTAAAATCTCCTTTTGTCAAAACACAAACCCTAATAGCCTCAATTCTTCCACCACTTCCCACGACGCCGATGCCAACACCGAGGACAAAGATTTCACTTCCACCACCATCTCGAACGACAACGGCAGCAACAATAATAATAATTATAGGATTTTAAAGCCGGGTACAAAACTCATAGATAGCATTGCTGTTGAGAAGGAATCGAAGGAGCCGTATGAAGATTTTCGAAACTCTATACTTCAAATGATATTGGAGAGAGAGATTTATTCGGAAAATGATCTTCAAGAATTACTTGAGTGTTTTCTTCAGCTTAATGCAAAGTGTCACCATCATGTCATTGTTGAAGCGTTCATGGAGACATGTGAAGAAATATTTCCTAAGAAGCTTTGTGGTGATGGTAGACGTGTGAAGGACATGTGA
Protein sequence

>MS.gene64657.t1

MSFNFNKRSLVKTLFSSNKSCGCIKIKPSNVLEPSQKPKISFCQNTNPNSLNSSTTSHDADANTEDKDFTSTTISNDNGSNNNNNYRILKPGTKLIDSIAVEKESKEPYEDFRNSILQMILEREIYSENDLQELLECFLQLNAKCHHHVIVEAFMETCEEIFPKKLCGDGRRVKDM