AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64299

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64299.t1 MTR_1g046810 87.382 317 39 1 1 317 1 316 0.0 539
MS.gene64299.t1 MTR_1g052185 37.202 336 119 14 5 317 12 278 1.87e-39 140
MS.gene64299.t1 MTR_1g085590 37.324 284 109 12 72 316 17 270 1.20e-28 112
MS.gene64299.t1 MTR_1g053530 37.004 227 95 7 63 282 39 224 1.46e-27 108
MS.gene64299.t1 MTR_1g063150 36.697 218 55 8 94 311 36 170 3.29e-25 100
MS.gene64299.t1 MTR_1g063140 40.606 165 43 8 148 311 2 112 8.34e-16 74.7
MS.gene64299.t1 MTR_5g098470 30.000 210 84 9 14 211 46 204 4.11e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 60 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGAAATTCCTGACAACTTT+TGG 0.230394 1.3:-28412340 None:intergenic
ACCGAAGATGAAACCGAATT+AGG 0.275613 1.3:+28412316 MS.gene64299:CDS
AACAGAAAAGAAACACTAAT+TGG 0.288536 1.3:-28412401 None:intergenic
CCCTAATTCGGTTTCATCTT+CGG 0.303612 1.3:-28412317 None:intergenic
AGGATGAAGAAGAGTGTTAG+AGG 0.334353 1.3:-28411648 None:intergenic
CATTGTTATACATGTCTTAC+GGG 0.356166 1.3:+28412071 MS.gene64299:CDS
ATTATCATCCACCGTATTGC+TGG 0.360275 1.3:-28412128 None:intergenic
GTACCCTTCTTCAAACCCTT+TGG 0.366898 1.3:-28411872 None:intergenic
TACTTTGACAAGTCAGTTGC+TGG 0.380308 1.3:-28411953 None:intergenic
CCGAAGATGAAACCGAATTA+GGG 0.394408 1.3:+28412317 MS.gene64299:CDS
ACATTGTTATACATGTCTTA+CGG 0.407102 1.3:+28412070 MS.gene64299:CDS
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.3:+28412095 MS.gene64299:CDS
ACATCACATGTATGGTTCTT+CGG 0.407728 1.3:-28411791 None:intergenic
TCATCCAACAACGCTTTGAA+TGG 0.417838 1.3:+28411830 MS.gene64299:CDS
TGTTACAAACATCACATGTA+TGG 0.417941 1.3:-28411799 None:intergenic
CATAATCATGATCATGATGA+TGG 0.425720 1.3:+28411764 MS.gene64299:CDS
AGCAGCAATATGCCTTCTCC+TGG 0.432642 1.3:-28412014 None:intergenic
AGTGTTAGAGGAGCGGTGAA+TGG 0.433506 1.3:-28411636 None:intergenic
GGCTCTGTTCCAAGGAAGAT+GGG 0.441032 1.3:-28411916 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1.3:+28411907 MS.gene64299:CDS
TCTTCTTGCCTTCAATATCA+AGG 0.449412 1.3:-28412288 None:intergenic
TACTCCAAAGGGTTTGAAGA+AGG 0.451848 1.3:+28411868 MS.gene64299:CDS
GTCTCTAACCTTGATATTGA+AGG 0.457506 1.3:+28412280 MS.gene64299:CDS
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.3:-28411559 None:intergenic
TGTCACAAAACATTCACGTC+TGG 0.467517 1.3:+28411590 MS.gene64299:CDS
TCAAACATCACAAGATTCAA+AGG 0.476909 1.3:+28412249 MS.gene64299:CDS
ATGTCCATTCAAAGCGTTGT+TGG 0.483248 1.3:-28411834 None:intergenic
TGGCTCTGTTCCAAGGAAGA+TGG 0.484956 1.3:-28411917 None:intergenic
AATTAGGGCCAAAAGTTGTC+AGG 0.486858 1.3:+28412332 MS.gene64299:CDS
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.3:-28411560 None:intergenic
ATGAGATTTCATACTCCAAA+GGG 0.500060 1.3:+28411857 MS.gene64299:CDS
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.3:-28411529 None:intergenic
TTGCCACAACGAAAAGAACT+TGG 0.525913 1.3:+28412192 MS.gene64299:CDS
CATGACCATGCTGTGAATAA+CGG 0.527833 1.3:+28411689 MS.gene64299:CDS
ATATCAAGGTTAGAGACTGC+AGG 0.538103 1.3:-28412274 None:intergenic
CTCAAGATGGCTCTGTTCCA+AGG 0.539755 1.3:-28411924 None:intergenic
ACTCCAAAGGGTTTGAAGAA+GGG 0.545861 1.3:+28411869 MS.gene64299:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.3:+28412117 MS.gene64299:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1.3:-28411476 None:intergenic
CGTTATTCACAGCATGGTCA+TGG 0.552480 1.3:-28411688 None:intergenic
AACAAGGTGTGATGCTAACA+AGG 0.557593 1.3:+28412164 MS.gene64299:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.3:-28411643 None:intergenic
TCATCTTCAAAATCATCACT+TGG 0.561665 1.3:-28412376 None:intergenic
GGATGATAATGAGAAGATGA+AGG 0.579672 1.3:+28412141 MS.gene64299:CDS
ACGTCTGGTAAATCACTTGG+TGG 0.584140 1.3:+28411605 MS.gene64299:CDS
TTCACGTCTGGTAAATCACT+TGG 0.587605 1.3:+28411602 MS.gene64299:CDS
ATAATCATGATCATGATGAT+GGG 0.591510 1.3:+28411765 MS.gene64299:CDS
TATGAGATTTCATACTCCAA+AGG 0.603569 1.3:+28411856 MS.gene64299:CDS
AATGAGAAGATGAAGGAACA+AGG 0.607433 1.3:+28412148 MS.gene64299:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1.3:-28411908 None:intergenic
GCAGCAATATGCCTTCTCCT+GGG 0.615845 1.3:-28412013 None:intergenic
ACGAAAAGAACTTGGTGCTG+AGG 0.634219 1.3:+28412200 MS.gene64299:CDS
TACCGCCGTTATTCACAGCA+TGG 0.634771 1.3:-28411694 None:intergenic
TATTGCTGCTGATGATGATG+AGG 0.663094 1.3:+28412027 MS.gene64299:CDS
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.3:+28412120 MS.gene64299:CDS
TTGCTGGTAGAAACTCAAGA+TGG 0.666842 1.3:-28411937 None:intergenic
GCTCTGTTCCAAGGAAGATG+GGG 0.667093 1.3:-28411915 None:intergenic
ATTGTTATACATGTCTTACG+GGG 0.683485 1.3:+28412072 MS.gene64299:CDS
TTGTTATACATGTCTTACGG+GGG 0.692006 1.3:+28412073 MS.gene64299:CDS
GACCATGCTGTGAATAACGG+CGG 0.713054 1.3:+28411692 MS.gene64299:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATCGTATAAAACCAAAAAA+CGG + chr1.3:28411987-28412006 MS.gene64299:CDS 20.0%
!!! TTTTTGGTTTTATACGATAT+TGG - chr1.3:28411986-28412005 None:intergenic 20.0%
! ACATTGTTATACATGTCTTA+CGG + chr1.3:28412070-28412089 MS.gene64299:CDS 25.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.3:28411723-28411742 MS.gene64299:CDS 25.0%
! ATAATCATGATCATGATGAT+GGG + chr1.3:28411765-28411784 MS.gene64299:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.3:28411724-28411743 MS.gene64299:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.3:28411720-28411739 None:intergenic 25.0%
!! ATAATGATCATGTCTGTTTT+TGG - chr1.3:28411507-28411526 None:intergenic 25.0%
!! GTTTGAAAAATCACATCTTT+TGG - chr1.3:28412235-28412254 None:intergenic 25.0%
!!! TAATGATCATGTCTGTTTTT+GGG - chr1.3:28411506-28411525 None:intergenic 25.0%
ATGAGATTTCATACTCCAAA+GGG + chr1.3:28411857-28411876 MS.gene64299:CDS 30.0%
ATTGTTATACATGTCTTACG+GGG + chr1.3:28412072-28412091 MS.gene64299:CDS 30.0%
CATAATCATGATCATGATGA+TGG + chr1.3:28411764-28411783 MS.gene64299:CDS 30.0%
CATTGTTATACATGTCTTAC+GGG + chr1.3:28412071-28412090 MS.gene64299:CDS 30.0%
TATGAGATTTCATACTCCAA+AGG + chr1.3:28411856-28411875 MS.gene64299:CDS 30.0%
TCAAACATCACAAGATTCAA+AGG + chr1.3:28412249-28412268 MS.gene64299:CDS 30.0%
TCATCTTCAAAATCATCACT+TGG - chr1.3:28412379-28412398 None:intergenic 30.0%
TGTTACAAACATCACATGTA+TGG - chr1.3:28411802-28411821 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.3:28411671-28411690 None:intergenic 30.0%
!!! TTGGTTTTATACGATATTGG+TGG - chr1.3:28411983-28412002 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.3:28411490-28411509 None:intergenic 30.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.3:28411562-28411581 None:intergenic 35.0%
AATGAGAAGATGAAGGAACA+AGG + chr1.3:28412148-28412167 MS.gene64299:CDS 35.0%
ACATCACATGTATGGTTCTT+CGG - chr1.3:28411794-28411813 None:intergenic 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.3:28411542-28411561 MS.gene64299:CDS 35.0%
GTCTCTAACCTTGATATTGA+AGG + chr1.3:28412280-28412299 MS.gene64299:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.3:28412095-28412114 MS.gene64299:CDS 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.3:28411532-28411551 None:intergenic 35.0%
TCTTCTTGCCTTCAATATCA+AGG - chr1.3:28412291-28412310 None:intergenic 35.0%
TTGTTATACATGTCTTACGG+GGG + chr1.3:28412073-28412092 MS.gene64299:CDS 35.0%
! GGATGATAATGAGAAGATGA+AGG + chr1.3:28412141-28412160 MS.gene64299:CDS 35.0%
! TCGAAATTCCTGACAACTTT+TGG - chr1.3:28412343-28412362 None:intergenic 35.0%
AACAAGGTGTGATGCTAACA+AGG + chr1.3:28412164-28412183 MS.gene64299:CDS 40.0%
AATTAGGGCCAAAAGTTGTC+AGG + chr1.3:28412332-28412351 MS.gene64299:CDS 40.0%
ACCGAAGATGAAACCGAATT+AGG + chr1.3:28412316-28412335 MS.gene64299:CDS 40.0%
ACTCCAAAGGGTTTGAAGAA+GGG + chr1.3:28411869-28411888 MS.gene64299:CDS 40.0%
ATATCAAGGTTAGAGACTGC+AGG - chr1.3:28412277-28412296 None:intergenic 40.0%
ATTATCATCCACCGTATTGC+TGG - chr1.3:28412131-28412150 None:intergenic 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.3:28411563-28411582 None:intergenic 40.0%
CATGACCATGCTGTGAATAA+CGG + chr1.3:28411689-28411708 MS.gene64299:CDS 40.0%
CCCTAATTCGGTTTCATCTT+CGG - chr1.3:28412320-28412339 None:intergenic 40.0%
CCGAAGATGAAACCGAATTA+GGG + chr1.3:28412317-28412336 MS.gene64299:CDS 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.3:28412117-28412136 MS.gene64299:CDS 40.0%
TACTCCAAAGGGTTTGAAGA+AGG + chr1.3:28411868-28411887 MS.gene64299:CDS 40.0%
TACTTTGACAAGTCAGTTGC+TGG - chr1.3:28411956-28411975 None:intergenic 40.0%
TCAAACGAATGGTGAGAAGA+AGG - chr1.3:28411479-28411498 None:intergenic 40.0%
TGTCACAAAACATTCACGTC+TGG + chr1.3:28411590-28411609 MS.gene64299:CDS 40.0%
TTCACGTCTGGTAAATCACT+TGG + chr1.3:28411602-28411621 MS.gene64299:CDS 40.0%
TTGCCACAACGAAAAGAACT+TGG + chr1.3:28412192-28412211 MS.gene64299:CDS 40.0%
TTGCTGGTAGAAACTCAAGA+TGG - chr1.3:28411940-28411959 None:intergenic 40.0%
! GACAACTTTTGGCCCTAATT+CGG - chr1.3:28412332-28412351 None:intergenic 40.0%
! TATTGCTGCTGATGATGATG+AGG + chr1.3:28412027-28412046 MS.gene64299:CDS 40.0%
! TCATCCAACAACGCTTTGAA+TGG + chr1.3:28411830-28411849 MS.gene64299:CDS 40.0%
!! AGGATGAAGAAGAGTGTTAG+AGG - chr1.3:28411651-28411670 None:intergenic 40.0%
!! ATGTCCATTCAAAGCGTTGT+TGG - chr1.3:28411837-28411856 None:intergenic 40.0%
AAACCAAAAAACGGAGTCCC+AGG + chr1.3:28411996-28412015 MS.gene64299:CDS 45.0%
ACGTCTGGTAAATCACTTGG+TGG + chr1.3:28411605-28411624 MS.gene64299:CDS 45.0%
ATGTCTTACGGGGGTTATGA+GGG + chr1.3:28412082-28412101 MS.gene64299:CDS 45.0%
CGTTATTCACAGCATGGTCA+TGG - chr1.3:28411691-28411710 None:intergenic 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.3:28412120-28412139 MS.gene64299:CDS 45.0%
GTACCCTTCTTCAAACCCTT+TGG - chr1.3:28411875-28411894 None:intergenic 45.0%
! GCACCAAGTTCTTTTCGTTG+TGG - chr1.3:28412198-28412217 None:intergenic 45.0%
!! ACGAAAAGAACTTGGTGCTG+AGG + chr1.3:28412200-28412219 MS.gene64299:CDS 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.3:28411646-28411665 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.3:28412002-28412021 MS.gene64299:CDS 50.0%
AGCAGCAATATGCCTTCTCC+TGG - chr1.3:28412017-28412036 None:intergenic 50.0%
AGTGTTAGAGGAGCGGTGAA+TGG - chr1.3:28411639-28411658 None:intergenic 50.0%
CATGTCTTACGGGGGTTATG+AGG + chr1.3:28412081-28412100 MS.gene64299:CDS 50.0%
GACCATGCTGTGAATAACGG+CGG + chr1.3:28411692-28411711 MS.gene64299:CDS 50.0%
GCAGCAATATGCCTTCTCCT+GGG - chr1.3:28412016-28412035 None:intergenic 50.0%
GCTCTGTTCCAAGGAAGATG+GGG - chr1.3:28411918-28411937 None:intergenic 50.0%
GGCTCTGTTCCAAGGAAGAT+GGG - chr1.3:28411919-28411938 None:intergenic 50.0%
TACCGCCGTTATTCACAGCA+TGG - chr1.3:28411697-28411716 None:intergenic 50.0%
! CTCAAGATGGCTCTGTTCCA+AGG - chr1.3:28411927-28411946 None:intergenic 50.0%
! TGGCTCTGTTCCAAGGAAGA+TGG - chr1.3:28411920-28411939 None:intergenic 50.0%
!! AGGAGCGGTGAATGGTTTTG+TGG - chr1.3:28411631-28411650 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.3:28412002-28412021 None:intergenic 50.0%
TCCAAGGAAGATGGGGCAGT+CGG - chr1.3:28411911-28411930 None:intergenic 55.0%
ACCGACTGCCCCATCTTCCT+TGG + chr1.3:28411907-28411926 MS.gene64299:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 28411455 28412408 28411455 ID=MS.gene64299
chr1.3 mRNA 28411455 28412408 28411455 ID=MS.gene64299.t1;Parent=MS.gene64299
chr1.3 exon 28411455 28412408 28411455 ID=MS.gene64299.t1.exon1;Parent=MS.gene64299.t1
chr1.3 CDS 28411455 28412408 28411455 ID=cds.MS.gene64299.t1;Parent=MS.gene64299.t1
Gene Sequence

>MS.gene64299

ATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGACATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACGTCTGGTAAATCACTTGGTGGCCACAAAACCATTCACCGCTCCTCTAACACTCTTCTTCATCCTAAAACAAACAAACAGATCCATGACCATGCTGTGAATAACGGCGGTACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCATAATCATGATCATGATGATGGGAAACCGAAGAACCATACATGTGATGTTTGTAACAAAGTTTTTTCATCCAACAACGCTTTGAATGGACATATGAGATTTCATACTCCAAAGGGTTTGAAGAAGGGTACTATTATTCACTCACCGACTGCCCCATCTTCCTTGGAACAGAGCCATCTTGAGTTTCTACCAGCAACTGACTTGTCAAAGTACTTGCCACCAATATCGTATAAAACCAAAAAACGGAGTCCCAGGAGAAGGCATATTGCTGCTGATGATGATGAGGAAATTACTCTTGCTGCAAAAACATTGTTATACATGTCTTACGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGATGCTAACAAGGTGTGTTTGCCACAACGAAAAGAACTTGGTGCTGAGGTTGAAGATTCCAAAAGATGTGATTTTTCAAACATCACAAGATTCAAAGGAACCTGCAGTCTCTAACCTTGATATTGAAGGCAAGAAGAATGTTACCGAAGATGAAACCGAATTAGGGCCAAAAGTTGTCAGGAATTTCGATTTGAATGAGCTTCCAAGTGATGATTTTGAAGATGAAACCAATTAG
Protein sequence

>MS.gene64299.t1

MNKHYSSPSSHHSFDKPKNRHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLHPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHNHDHDDGKPKNHTCDVCNKVFSSNNALNGHMRFHTPKGLKKGTIIHSPTAPSSLEQSHLEFLPATDLSKYLPPISYKTKKRSPRRRHIAADDDEEITLAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVMLTRCVCHNEKNLVLRLKIPKDVIFQTSQDSKEPAVSNLDIEGKKNVTEDETELGPKVVRNFDLNELPSDDFEDETN