AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27207

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27207.t1 MTR_2g023890 90.654 107 10 0 1 107 1 107 5.51e-68 207
MS.gene27207.t1 MTR_2g088020 51.818 110 49 3 1 107 1 109 2.53e-25 98.6
MS.gene27207.t1 MTR_4g049730 47.664 107 48 3 3 107 1 101 9.49e-24 94.4
MS.gene27207.t1 MTR_0154s0040 44.444 108 57 3 3 107 1 108 1.83e-19 82.0
MS.gene27207.t1 MTR_0189s0010 44.954 109 57 3 2 107 20 128 4.97e-19 80.9
MS.gene27207.t1 MTR_0154s0020 43.519 108 58 3 3 107 1 108 1.96e-18 79.0
MS.gene27207.t1 MTR_5g017110 41.414 99 54 2 4 98 3 101 6.23e-18 77.8
MS.gene27207.t1 MTR_5g017140 40.000 100 56 2 3 98 1 100 6.98e-16 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27207.t1 AT1G05100 55.660 106 40 4 3 102 1 105 5.81e-31 112
MS.gene27207.t1 AT2G32510 53.271 107 47 3 3 107 1 106 1.87e-30 112
MS.gene27207.t1 AT5G55090 51.579 95 44 1 4 98 5 97 3.04e-23 93.2
MS.gene27207.t1 AT5G55090 51.579 95 44 1 4 98 67 159 3.75e-23 93.2
MS.gene27207.t1 AT4G26890 50.000 98 47 1 1 98 1 96 2.23e-21 88.2
MS.gene27207.t1 AT3G50310 36.111 108 63 3 3 104 1 108 4.19e-15 70.1
MS.gene27207.t1 AT5G67080 37.273 110 61 4 3 104 1 110 6.70e-13 63.9
MS.gene27207.t1 AT4G36950 39.796 98 54 2 3 95 1 98 2.14e-12 62.4

Find 31 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAGCTGATCGTTGCCATTC+TGG 0.305456 2.1:+65099795 MS.gene27207:CDS
TAATTTGTTCAACTTGTTCA+TGG 0.313762 2.1:+65099956 MS.gene27207:CDS
TGTGAAGTCACCTTTGAAAA+TGG 0.369780 2.1:+65099930 MS.gene27207:CDS
CCTTGGTAGCTCACAATTTG+TGG 0.394674 2.1:-65099906 None:intergenic
GATGCAGTACGCAATGGAAA+TGG 0.442392 2.1:+65100005 MS.gene27207:CDS
CATACTTTCTAATATGTCAA+TGG 0.451822 2.1:+65099722 None:intergenic
TTCACCGCTCGGAGTTATTG+AGG 0.475715 2.1:+65099850 MS.gene27207:CDS
TTTCTAATATGTCAATGGAT+TGG 0.476690 2.1:+65099727 None:intergenic
TTCTGGTGGTGAAGTGTTTG+CGG 0.478886 2.1:+65099812 MS.gene27207:CDS
GTTCATGGAGTATGCACCTA+AGG 0.485777 2.1:+65099971 MS.gene27207:CDS
AATTTGTGGACACTTTAACT+TGG 0.509208 2.1:-65099892 None:intergenic
GTCTACAGAGTTTCACCGCT+CGG 0.535285 2.1:+65099839 MS.gene27207:CDS
GCATCTGAAAGAGTTCCCTT+AGG 0.541096 2.1:-65099987 None:intergenic
TGTCTTCTGCAACAGCTCGC+AGG 0.543521 2.1:+65100655 MS.gene27207:CDS
AGACGGTGGCGGTCGAGCCA+CGG 0.554526 2.1:-65099770 None:intergenic
ATGTCAATGGATTGGACTAG+AGG 0.558116 2.1:+65099735 MS.gene27207:CDS
CAAACACTTCACCACCAGAA+TGG 0.558159 2.1:-65099809 None:intergenic
CAAAGGTGACTTCACAACCT+TGG 0.558218 2.1:-65099923 None:intergenic
TGGACTAGAGGCAGAATCAT+CGG 0.559418 2.1:+65099747 MS.gene27207:CDS
GCTGTTGCAGAAGACAGCAC+TGG 0.560735 2.1:-65100648 None:intergenic
CTTTCAGATGCAGTACGCAA+TGG 0.568154 2.1:+65099999 MS.gene27207:CDS
CCACAAATTGTGAGCTACCA+AGG 0.578561 2.1:+65099906 MS.gene27207:CDS
AGAGGCAGAATCATCGGCCG+TGG 0.582406 2.1:+65099753 MS.gene27207:CDS
TTCATGGAGTATGCACCTAA+GGG 0.599689 2.1:+65099972 MS.gene27207:CDS
GCAACGATCAGCTACGTAGA+CGG 0.609565 2.1:-65099787 None:intergenic
ATCAGCTACGTAGACGGTGG+CGG 0.615601 2.1:-65099781 None:intergenic
CTGTTGCAGAAGACAGCACT+GGG 0.621221 2.1:-65100647 None:intergenic
AAATGGAATTGAAGAAGCTA+CGG 0.622381 2.1:+65100022 MS.gene27207:CDS
GCTGATCGTTGCCATTCTGG+TGG 0.700015 2.1:+65099798 MS.gene27207:CDS
CTTTCCTCAATAACTCCGAG+CGG 0.710893 2.1:-65099854 None:intergenic
ACGATCAGCTACGTAGACGG+TGG 0.714769 2.1:-65099784 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTGTTTATAATTGCTTTT+TGG + chr2.1:65100464-65100483 MS.gene27207:intron 15.0%
!! TTAACTATCTTCATTTGAAT+GGG + chr2.1:65100078-65100097 MS.gene27207:intron 20.0%
!!! ATTATATTTTGAAGCTCAAT+TGG + chr2.1:65100622-65100641 MS.gene27207:intron 20.0%
! AAAGAAGGAGAATTGATAAA+GGG + chr2.1:65100343-65100362 MS.gene27207:intron 25.0%
! ACTAAAATAGACATAGCTAA+AGG + chr2.1:65100311-65100330 MS.gene27207:intron 25.0%
! CATATAAAATACATCCTGTT+TGG - chr2.1:65100600-65100619 None:intergenic 25.0%
! CTTAACTATCTTCATTTGAA+TGG + chr2.1:65100077-65100096 MS.gene27207:intron 25.0%
! TAAACAAACTGAATGTTGTT+TGG + chr2.1:65100252-65100271 MS.gene27207:intron 25.0%
! TAAAGAAGGAGAATTGATAA+AGG + chr2.1:65100342-65100361 MS.gene27207:intron 25.0%
! TAAAGGAGAATTGATAAAGA+AGG + chr2.1:65100328-65100347 MS.gene27207:intron 25.0%
!! CAAATTAACACCATTTTCAA+AGG - chr2.1:65099943-65099962 None:intergenic 25.0%
!! TGAGAGAATTGATTTATGTT+TGG + chr2.1:65100208-65100227 MS.gene27207:intron 25.0%
!!! AAACCAAACATGTTGTTTTT+TGG + chr2.1:65100522-65100541 MS.gene27207:intron 25.0%
!!! AACTGCTTATAATTGCTTTT+TGG + chr2.1:65100549-65100568 MS.gene27207:intron 25.0%
!!! TAATTTGTTCAACTTGTTCA+TGG + chr2.1:65099956-65099975 MS.gene27207:CDS 25.0%
AAAATACATCCTGTTTGGTT+TGG - chr2.1:65100595-65100614 None:intergenic 30.0%
AAATGGAATTGAAGAAGCTA+CGG + chr2.1:65100022-65100041 MS.gene27207:CDS 30.0%
AATTTGTGGACACTTTAACT+TGG - chr2.1:65099895-65099914 None:intergenic 30.0%
ATAGTGCATTGTGATTTGAA+GGG + chr2.1:65100101-65100120 MS.gene27207:intron 30.0%
GAATTGATAAAGGGCAATAA+AGG + chr2.1:65100352-65100371 MS.gene27207:intron 30.0%
GGGCAATAAAGGAAAATAAT+AGG + chr2.1:65100363-65100382 MS.gene27207:intron 30.0%
TAGCCAAAAAACAACATGTT+TGG - chr2.1:65100528-65100547 None:intergenic 30.0%
! AGTTATGATTTGTAGCTTCA+TGG + chr2.1:65100439-65100458 MS.gene27207:intron 30.0%
GATAGTGCATTGTGATTTGA+AGG + chr2.1:65100100-65100119 MS.gene27207:intron 35.0%
! TGTGAAGTCACCTTTGAAAA+TGG + chr2.1:65099930-65099949 MS.gene27207:CDS 35.0%
ATGCACGTCAAATTCTGCTA+GGG + chr2.1:65100054-65100073 MS.gene27207:intron 40.0%
TATGCACGTCAAATTCTGCT+AGG + chr2.1:65100053-65100072 MS.gene27207:intron 40.0%
TCTGAAAAGCCAAACCAAAC+AGG + chr2.1:65100583-65100602 MS.gene27207:intron 40.0%
TTCATGGAGTATGCACCTAA+GGG + chr2.1:65099972-65099991 MS.gene27207:CDS 40.0%
!! ATGTCAATGGATTGGACTAG+AGG + chr2.1:65099735-65099754 MS.gene27207:CDS 40.0%
CAAACACTTCACCACCAGAA+TGG - chr2.1:65099812-65099831 None:intergenic 45.0%
CAAAGGTGACTTCACAACCT+TGG - chr2.1:65099926-65099945 None:intergenic 45.0%
CCACAAATTGTGAGCTACCA+AGG + chr2.1:65099906-65099925 MS.gene27207:CDS 45.0%
CTTTCAGATGCAGTACGCAA+TGG + chr2.1:65099999-65100018 MS.gene27207:CDS 45.0%
CTTTCCTCAATAACTCCGAG+CGG - chr2.1:65099857-65099876 None:intergenic 45.0%
GATGCAGTACGCAATGGAAA+TGG + chr2.1:65100005-65100024 MS.gene27207:CDS 45.0%
GCATCTGAAAGAGTTCCCTT+AGG - chr2.1:65099990-65100009 None:intergenic 45.0%
GGAATTGAAGAAGCTACGGT+GGG + chr2.1:65100026-65100045 MS.gene27207:intron 45.0%
GTTCATGGAGTATGCACCTA+AGG + chr2.1:65099971-65099990 MS.gene27207:CDS 45.0%
TGGAATTGAAGAAGCTACGG+TGG + chr2.1:65100025-65100044 MS.gene27207:intron 45.0%
TTGAAGGGACAGAACGTGTT+TGG + chr2.1:65100116-65100135 MS.gene27207:intron 45.0%
! CCTTGGTAGCTCACAATTTG+TGG - chr2.1:65099909-65099928 None:intergenic 45.0%
! TGGACTAGAGGCAGAATCAT+CGG + chr2.1:65099747-65099766 MS.gene27207:CDS 45.0%
! TTCTGGTGGTGAAGTGTTTG+CGG + chr2.1:65099812-65099831 MS.gene27207:CDS 45.0%
CTGTTGCAGAAGACAGCACT+GGG - chr2.1:65100650-65100669 None:intergenic 50.0%
GCAACGATCAGCTACGTAGA+CGG - chr2.1:65099790-65099809 None:intergenic 50.0%
GTAGCTGATCGTTGCCATTC+TGG + chr2.1:65099795-65099814 MS.gene27207:CDS 50.0%
GTCTACAGAGTTTCACCGCT+CGG + chr2.1:65099839-65099858 MS.gene27207:CDS 50.0%
TTCACCGCTCGGAGTTATTG+AGG + chr2.1:65099850-65099869 MS.gene27207:CDS 50.0%
ACGATCAGCTACGTAGACGG+TGG - chr2.1:65099787-65099806 None:intergenic 55.0%
ATCAGCTACGTAGACGGTGG+CGG - chr2.1:65099784-65099803 None:intergenic 55.0%
GCTGATCGTTGCCATTCTGG+TGG + chr2.1:65099798-65099817 MS.gene27207:CDS 55.0%
GCTGTTGCAGAAGACAGCAC+TGG - chr2.1:65100651-65100670 None:intergenic 55.0%
TGTCTTCTGCAACAGCTCGC+AGG + chr2.1:65100655-65100674 MS.gene27207:CDS 55.0%
AGAGGCAGAATCATCGGCCG+TGG + chr2.1:65099753-65099772 MS.gene27207:CDS 60.0%
! AGACGGTGGCGGTCGAGCCA+CGG - chr2.1:65099773-65099792 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 65099735 65100686 65099735 ID=MS.gene27207
chr2.1 mRNA 65099735 65100686 65099735 ID=MS.gene27207.t1;Parent=MS.gene27207
chr2.1 exon 65099735 65100043 65099735 ID=MS.gene27207.t1.exon1;Parent=MS.gene27207.t1
chr2.1 CDS 65099735 65100043 65099735 ID=cds.MS.gene27207.t1;Parent=MS.gene27207.t1
chr2.1 exon 65100636 65100686 65100636 ID=MS.gene27207.t1.exon2;Parent=MS.gene27207.t1
chr2.1 CDS 65100636 65100686 65100636 ID=cds.MS.gene27207.t1;Parent=MS.gene27207.t1
Gene Sequence

>MS.gene27207

ATGTCAATGGATTGGACTAGAGGCAGAATCATCGGCCGTGGCTCGACCGCCACCGTCTACGTAGCTGATCGTTGCCATTCTGGTGGTGAAGTGTTTGCGGTGAAGTCTACAGAGTTTCACCGCTCGGAGTTATTGAGGAAAGAGCAACAAATTCTCTCCAAGTTAAAGTGTCCACAAATTGTGAGCTACCAAGGTTGTGAAGTCACCTTTGAAAATGGTGTTAATTTGTTCAACTTGTTCATGGAGTATGCACCTAAGGGAACTCTTTCAGATGCAGTACGCAATGGAAATGGAATTGAAGAAGCTACGGTGGGATTCTATGCACGTCAAATTCTGCTAGGGCTTAACTATCTTCATTTGAATGGGATAGTGCATTGTGATTTGAAGGGACAGAACGTGTTTGGTTCAGCTTTGAATATAATTGATTCTGAGAGAATTGATTCTGATAGAATTGATTCTGACAGAATTGATTCTGAGAGAATTGATTTATGTTTGGATACAATTATGTAGAATTGATTAAACAAACTGAATGTTGTTTGGATGATTTTGATCAAAATTGCTTTTGAATGTATAATTACTAAAATAGACATAGCTAAAGGAGAATTGATAAAGAAGGAGAATTGATAAAGGGCAATAAAGGAAAATAATAGGTTGTAATAATAAAATATACAATTTACTGTATAATTGATTCTAGAAAAGCTAGAAGTTATGATTTGTAGCTTCATGGAGAATTGTTTATAATTGCTTTTTGGCTAGAATTGCTTCTGAAAAGCAATTCTGAAAAGTCAAACCAAACATGTTGTTTTTTGGCTAGAACTGCTTATAATTGCTTTTTGGCTAGAATTGCTTCTGAAAAGCCAAACCAAACAGGATGTATTTTATATGACATTATATTTTGAAGCTCAATTGGTACCCAGTGCTGTCTTCTGCAACAGCTCGCAGGATGTGCTGA
Protein sequence

>MS.gene27207.t1

MSMDWTRGRIIGRGSTATVYVADRCHSGGEVFAVKSTEFHRSELLRKEQQILSKLKCPQIVSYQGCEVTFENGVNLFNLFMEYAPKGTLSDAVRNGNGIEEATLNWYPVLSSATARRMC