AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027432

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027432.t1 MTR_4g046737 86.486 74 10 0 1 74 1 74 9.28e-43 133
MS.gene027432.t1 MTR_2g088730 70.000 50 15 0 24 73 30 79 5.32e-20 76.3
MS.gene027432.t1 MTR_5g009460 65.217 46 16 0 26 71 37 82 6.62e-18 71.2
MS.gene027432.t1 MTR_2g023100 49.333 75 35 2 1 73 1 74 6.99e-18 70.5
MS.gene027432.t1 MTR_0247s0040 58.537 41 17 0 28 68 65 105 5.92e-13 60.5
MS.gene027432.t1 MTR_4g485530 58.537 41 17 0 28 68 70 110 1.43e-12 59.7
MS.gene027432.t1 MTR_4g100720 63.415 41 15 0 28 68 71 111 2.49e-12 58.9
MS.gene027432.t1 MTR_8g060940 58.537 41 17 0 28 68 65 105 3.45e-12 59.3
MS.gene027432.t1 MTR_4g073420 58.537 41 17 0 28 68 70 110 3.56e-12 59.7
MS.gene027432.t1 MTR_5g079670 56.098 41 18 0 28 68 69 109 4.65e-12 58.5
MS.gene027432.t1 MTR_0197s0010 54.545 44 20 0 28 71 59 102 5.71e-12 58.5
MS.gene027432.t1 MTR_3g083540 57.143 42 18 0 27 68 98 139 7.72e-12 58.9
MS.gene027432.t1 MTR_4g125520 57.500 40 16 1 29 68 72 110 1.47e-11 58.2
MS.gene027432.t1 MTR_8g027345 56.098 41 18 0 28 68 70 110 2.80e-11 57.4
MS.gene027432.t1 MTR_7g117730 57.143 42 17 1 30 71 73 113 2.81e-11 57.0
MS.gene027432.t1 MTR_7g017260 56.098 41 18 0 28 68 85 125 2.84e-11 57.0
MS.gene027432.t1 MTR_3g103570 50.000 42 21 0 28 69 71 112 8.14e-11 55.8
MS.gene027432.t1 MTR_1g017140 52.381 42 20 0 28 69 71 112 8.17e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027432.t1 AT2G46410 65.957 47 16 0 26 72 36 82 9.44e-17 68.2
MS.gene027432.t1 AT1G01380 68.293 41 13 0 26 66 32 72 1.35e-15 65.1
MS.gene027432.t1 AT5G53200 58.696 46 19 0 26 71 31 76 3.95e-14 62.0
MS.gene027432.t1 AT4G01060 63.415 41 15 0 26 66 31 71 8.86e-14 60.1
MS.gene027432.t1 AT4G01060 63.415 41 15 0 26 66 33 73 9.51e-14 60.1
MS.gene027432.t1 AT4G01060 63.415 41 15 0 26 66 30 70 9.54e-14 60.1
MS.gene027432.t1 AT2G30420 56.522 46 20 0 26 71 38 83 1.61e-12 58.2
MS.gene027432.t1 AT1G22640 58.537 41 17 0 28 68 13 53 2.95e-12 58.9
MS.gene027432.t1 AT4G38620 58.537 41 17 0 28 68 70 110 4.63e-12 59.3
MS.gene027432.t1 AT1G22640 58.537 41 17 0 28 68 70 110 6.37e-12 58.9
MS.gene027432.t1 AT5G14750 52.273 44 21 0 28 71 13 56 1.07e-11 56.6
MS.gene027432.t1 AT5G14750 52.273 44 21 0 28 71 13 56 1.07e-11 56.6
MS.gene027432.t1 AT5G35550 62.500 40 14 1 29 68 77 115 1.77e-11 57.8
MS.gene027432.t1 AT3G49690 54.762 42 19 0 28 69 71 112 1.82e-11 57.8
MS.gene027432.t1 AT4G09460 51.220 41 20 0 28 68 70 110 2.14e-11 57.0
MS.gene027432.t1 AT5G14750 52.273 44 21 0 28 71 40 83 2.15e-11 56.2
MS.gene027432.t1 AT3G27920 50.000 48 24 0 24 71 68 115 2.72e-11 57.0
MS.gene027432.t1 AT2G30424 48.077 52 24 1 26 74 34 85 2.90e-11 54.3
MS.gene027432.t1 AT3G13540 58.537 41 17 0 28 68 81 121 3.05e-11 57.0
MS.gene027432.t1 AT2G30432 52.174 46 22 0 26 71 33 78 3.54e-11 53.9
MS.gene027432.t1 AT5G14750 52.273 44 21 0 28 71 74 117 4.12e-11 56.2
MS.gene027432.t1 AT5G65790 52.381 42 20 0 28 69 71 112 6.23e-11 56.6

Find 13 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGGAAATGCTTATTAAAA+TGG 0.190572 4.2:-53727027 MS.gene027432:CDS
ATCTCTTCTGCTGTTCTTCC+AGG 0.213845 4.2:+53726671 None:intergenic
AAATGGTTTATAATCTTGTT+GGG 0.339232 4.2:-53727010 MS.gene027432:CDS
TTGATTGCTGGAAGAATTCC+TGG 0.342209 4.2:-53726689 MS.gene027432:CDS
AAAATGGTTTATAATCTTGT+TGG 0.380870 4.2:-53727011 MS.gene027432:CDS
CATAGGTGGTCATTGATTGC+TGG 0.399125 4.2:-53726701 MS.gene027432:intron
TCAACCTTTGAACCTTGGTC+TGG 0.418134 4.2:+53727062 None:intergenic
AAAATTCAACCTTTGAACCT+TGG 0.444402 4.2:+53727057 None:intergenic
TTTATAATCTTGTTGGGGAG+AGG 0.507013 4.2:-53727004 MS.gene027432:intron
AATGGTTTATAATCTTGTTG+GGG 0.563787 4.2:-53727009 MS.gene027432:CDS
GCAACCAGACCAAGGTTCAA+AGG 0.564494 4.2:-53727066 MS.gene027432:CDS
AATGTTTCAACAGATTCCAA+AGG 0.613753 4.2:-53727213 MS.gene027432:intron
ACAGATCAGCAACCAGACCA+AGG 0.650716 4.2:-53727074 MS.gene027432:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAAAGTTACAATTTA+AGG + chr4.2:53726901-53726920 None:intergenic 10.0%
!! AAAATGGTTTATAATCTTGT+TGG - chr4.2:53726860-53726879 MS.gene027432:intron 20.0%
!! AAATGGTTTATAATCTTGTT+GGG - chr4.2:53726861-53726880 MS.gene027432:intron 20.0%
!! ATAACATCAATAACAAAGTT+TGG + chr4.2:53726942-53726961 None:intergenic 20.0%
!! ATTTCTCTTAGTCAATAAAA+TGG + chr4.2:53726765-53726784 None:intergenic 20.0%
!!! ATTTTATTGACTAAGAGAAA+TGG - chr4.2:53726764-53726783 MS.gene027432:intron 20.0%
!!! TGTCTTTTATAGCTAATTAA+TGG - chr4.2:53726698-53726717 MS.gene027432:CDS 20.0%
! AATGGTTTATAATCTTGTTG+GGG - chr4.2:53726862-53726881 MS.gene027432:intron 25.0%
! AGAGGAAATGCTTATTAAAA+TGG - chr4.2:53726844-53726863 MS.gene027432:intron 25.0%
! CAGAAGAGATAGAAAAATAT+TGG - chr4.2:53727213-53727232 MS.gene027432:intron 25.0%
! TAAAAGACATGCATTCTAAA+AGG + chr4.2:53726687-53726706 None:intergenic 25.0%
!! AAAAGACATGCATTCTAAAA+GGG + chr4.2:53726686-53726705 None:intergenic 25.0%
!! ATGAATGTGTATTTTCTCAT+AGG - chr4.2:53727153-53727172 MS.gene027432:intron 25.0%
!!! ATCTGTTGAAACATTTTTAG+AGG + chr4.2:53726653-53726672 None:intergenic 25.0%
AAAATTCAACCTTTGAACCT+TGG + chr4.2:53726817-53726836 None:intergenic 30.0%
AATGTTTCAACAGATTCCAA+AGG - chr4.2:53726658-53726677 MS.gene027432:CDS 30.0%
GTCTAGTGTTTGTGTTTATT+TGG + chr4.2:53726978-53726997 None:intergenic 30.0%
! AATGTGTATTTTCTCATAGG+TGG - chr4.2:53727156-53727175 MS.gene027432:intron 30.0%
! TTTGGAATGAAAGTGAAAAG+AGG + chr4.2:53726924-53726943 None:intergenic 30.0%
TTTATAATCTTGTTGGGGAG+AGG - chr4.2:53726867-53726886 MS.gene027432:intron 35.0%
!! GGTTGAATTTTCTGAAGAAG+AGG - chr4.2:53726826-53726845 MS.gene027432:intron 35.0%
AACACTGCATGTATTCCTGT+TGG - chr4.2:53727033-53727052 MS.gene027432:CDS 40.0%
TACACATGTGAATGTCCAAC+AGG + chr4.2:53727051-53727070 None:intergenic 40.0%
TTGATTGCTGGAAGAATTCC+TGG - chr4.2:53727182-53727201 MS.gene027432:intron 40.0%
! AAACCTTCGATCTAGAGTGT+CGG - chr4.2:53727082-53727101 MS.gene027432:intron 40.0%
!! GCATTCTAAAAGGGTACCTT+TGG + chr4.2:53726677-53726696 None:intergenic 40.0%
ATCTCTTCTGCTGTTCTTCC+AGG + chr4.2:53727203-53727222 None:intergenic 45.0%
CTCTAGATCGAAGGTTTGTC+TGG + chr4.2:53727079-53727098 None:intergenic 45.0%
TCAACCTTTGAACCTTGGTC+TGG + chr4.2:53726812-53726831 None:intergenic 45.0%
! CATAGGTGGTCATTGATTGC+TGG - chr4.2:53727170-53727189 MS.gene027432:intron 45.0%
ACACCGACACTCTAGATCGA+AGG + chr4.2:53727088-53727107 None:intergenic 50.0%
ACAGATCAGCAACCAGACCA+AGG - chr4.2:53726797-53726816 MS.gene027432:intron 50.0%
GCAACCAGACCAAGGTTCAA+AGG - chr4.2:53726805-53726824 MS.gene027432:intron 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 53726631 53727262 53726631 ID=MS.gene027432
chr4.2 mRNA 53726631 53727262 53726631 ID=MS.gene027432.t1;Parent=MS.gene027432
chr4.2 exon 53727214 53727262 53727214 ID=MS.gene027432.t1.exon1;Parent=MS.gene027432.t1
chr4.2 CDS 53727214 53727262 53727214 ID=cds.MS.gene027432.t1;Parent=MS.gene027432.t1
chr4.2 exon 53727005 53727092 53727005 ID=MS.gene027432.t1.exon2;Parent=MS.gene027432.t1
chr4.2 CDS 53727005 53727092 53727005 ID=cds.MS.gene027432.t1;Parent=MS.gene027432.t1
chr4.2 exon 53726631 53726718 53726631 ID=MS.gene027432.t1.exon3;Parent=MS.gene027432.t1
chr4.2 CDS 53726631 53726718 53726631 ID=cds.MS.gene027432.t1;Parent=MS.gene027432.t1
Gene Sequence

>MS.gene027432

ATGGCTGACTCAGAACACTCCTCTAAAAATGTTTCAACAGATTCCAAAGGTACCCTTTTAGAATGCATGTCTTTTATAGCTAATTAATGGATTTATCATGATTATTGATTTCAAATACTTTTTTTTATACACCATTTTATTGACTAAGAGAAATGGCATGTATTTTACAGATCAGCAACCAGACCAAGGTTCAAAGGTTGAATTTTCTGAAGAAGAGGAAATGCTTATTAAAATGGTTTATAATCTTGTTGGGGAGAGGTTAGTAGACCTTAAATTGTAACTTTTTTTTACCTCTTTTCACTTTCATTCCAAACTTTGTTATTGATGTTATAATCTACGAAGTACCAAATAAACACAAACACTAGACACGAAAGTAGCACTCACGTTAACACTTACGAAAGTAACACTGCATGTATTCCTGTTGGACATTCACATGTGTACGACACCAGACAAACCTTCGATCTAGAGTGTCGGTGTTATGACTATGCATATTTCTTTTATTTCAACTATTACTATTTGATGATGAATGTGTATTTTCTCATAGGTGGTCATTGATTGCTGGAAGAATTCCTGGAAGAACAGCAGAAGAGATAGAAAAATATTGGAATTCAAGACACTCGACTAGCAAATGA
Protein sequence

>MS.gene027432.t1

MADSEHSSKNVSTDSKDQQPDQGSKVEFSEEEEMLIKMVYNLVGERWSLIAGRIPGRTAEEIEKYWNSRHSTSK