AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53634

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53634.t1 MTR_1g046810 87.066 317 40 1 60 376 1 316 0.0 535
MS.gene53634.t1 MTR_1g052185 36.905 336 120 14 64 376 12 278 2.51e-37 136
MS.gene53634.t1 MTR_1g085590 37.970 266 108 11 137 375 35 270 5.58e-28 111
MS.gene53634.t1 MTR_1g063150 37.156 218 54 7 153 370 36 170 4.23e-26 103
MS.gene53634.t1 MTR_1g053530 41.143 175 79 5 174 341 67 224 6.25e-26 105
MS.gene53634.t1 MTR_1g063140 40.361 166 44 8 207 371 2 113 1.47e-15 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 68 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGAAATTCCTGACAACTTT+TGG 0.230394 1.1:-29696967 None:intergenic
ACCGAAGATGAAACCGAATT+AGG 0.275613 1.1:+29696943 MS.gene53634:CDS
AACAGAAAAGAAACACTAAT+TGG 0.288536 1.1:-29697028 None:intergenic
AGATTGAAGAAGAGTGTTAG+AGG 0.300936 1.1:-29696275 None:intergenic
CCCTAATTCGGTTTCATCTT+CGG 0.303612 1.1:-29696944 None:intergenic
CACTATAGGGTTTGAACTTA+GGG 0.317465 1.1:-29696021 None:intergenic
GATCACTTGAATGATGAAAA+TGG 0.324278 1.1:-29695934 None:intergenic
CATTGTTATACATGTCTTAC+GGG 0.356166 1.1:+29696698 MS.gene53634:CDS
ATTATCATCCACCGTATTGC+TGG 0.360275 1.1:-29696755 None:intergenic
GTACCCTTCTTCAAACCCTT+TGG 0.366898 1.1:-29696499 None:intergenic
ACACTATAGGGTTTGAACTT+AGG 0.369629 1.1:-29696022 None:intergenic
TACTTTGACAAGTCAGTTGC+TGG 0.381007 1.1:-29696580 None:intergenic
TGAATGATGAAAATGGAAAT+AGG 0.384414 1.1:-29695927 None:intergenic
TTCATGATGTTGTGAGTGTT+TGG 0.387952 1.1:-29696064 None:intergenic
ATGTTGTGAGTGTTTGGTTC+AGG 0.392267 1.1:-29696058 None:intergenic
CCGAAGATGAAACCGAATTA+GGG 0.394408 1.1:+29696944 MS.gene53634:CDS
ACATTGTTATACATGTCTTA+CGG 0.407102 1.1:+29696697 MS.gene53634:CDS
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.1:+29696722 MS.gene53634:CDS
ACATCACATGTATGGTTCTT+CGG 0.407728 1.1:-29696418 None:intergenic
TCATCCAACAACGCTTTGAA+TGG 0.417838 1.1:+29696457 MS.gene53634:CDS
TGTTACAAACATCACATGTA+TGG 0.417941 1.1:-29696426 None:intergenic
CATAATCATGATCATGATGA+TGG 0.425720 1.1:+29696391 MS.gene53634:CDS
AGCAGCAATATGCCTTCTCC+TGG 0.432642 1.1:-29696641 None:intergenic
GGCTCTGTTCCAAGGAAGAT+GGG 0.441032 1.1:-29696543 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1.1:+29696534 MS.gene53634:CDS
TCTTCTTGCCTTCAATATCA+AGG 0.449412 1.1:-29696915 None:intergenic
TACTCCAAAGGGTTTGAAGA+AGG 0.451848 1.1:+29696495 MS.gene53634:CDS
GTCTCTAACCTTGATATTGA+AGG 0.457506 1.1:+29696907 MS.gene53634:CDS
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.1:-29696186 None:intergenic
TCAAACATCACAAGATTCAA+AGG 0.476909 1.1:+29696876 MS.gene53634:CDS
ATGTCCATTCAAAGCGTTGT+TGG 0.483248 1.1:-29696461 None:intergenic
TGGCTCTGTTCCAAGGAAGA+TGG 0.484956 1.1:-29696544 None:intergenic
AATTAGGGCCAAAAGTTGTC+AGG 0.486858 1.1:+29696959 MS.gene53634:CDS
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.1:-29696187 None:intergenic
TGTCACAAAACATTCACCTC+TGG 0.499496 1.1:+29696217 MS.gene53634:CDS
ATGAGATTTCATACTCCAAA+GGG 0.500060 1.1:+29696484 MS.gene53634:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1.1:-29696315 None:intergenic
AGTGTTAGAGGAGCCGTGAA+TGG 0.512425 1.1:-29696263 None:intergenic
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.1:-29696156 None:intergenic
CATGATCATGCTGTGAATAA+CGG 0.518528 1.1:+29696316 MS.gene53634:CDS
TTGCCACAACGAAAAGAACT+TGG 0.525913 1.1:+29696819 MS.gene53634:CDS
ATATCAAGGTTAGAGACTGC+AGG 0.538103 1.1:-29696901 None:intergenic
CTCAAGATGGCTCTGTTCCA+AGG 0.539755 1.1:-29696551 None:intergenic
GGTGGTCACAAAACCATTCA+CGG 0.541180 1.1:+29696250 MS.gene53634:CDS
ACTCCAAAGGGTTTGAAGAA+GGG 0.545861 1.1:+29696496 MS.gene53634:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.1:+29696744 MS.gene53634:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1.1:-29696103 None:intergenic
ACCTCTGGTAAATCACTTGG+TGG 0.556710 1.1:+29696232 MS.gene53634:CDS
AACAAGGTGTGATGCTAACA+AGG 0.557593 1.1:+29696791 MS.gene53634:CDS
TCATCTTCAAAATCATCACT+TGG 0.561665 1.1:-29697003 None:intergenic
TTCACCTCTGGTAAATCACT+TGG 0.575760 1.1:+29696229 MS.gene53634:CDS
GGATGATAATGAGAAGATGA+AGG 0.579672 1.1:+29696768 MS.gene53634:CDS
ATAATCATGATCATGATGAT+GGG 0.591510 1.1:+29696392 MS.gene53634:CDS
TATGAGATTTCATACTCCAA+AGG 0.603569 1.1:+29696483 MS.gene53634:CDS
AATGAGAAGATGAAGGAACA+AGG 0.607433 1.1:+29696775 MS.gene53634:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1.1:-29696535 None:intergenic
GCAGCAATATGCCTTCTCCT+GGG 0.615845 1.1:-29696640 None:intergenic
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.1:-29696141 None:intergenic
TTGCTGGTCGAAACTCAAGA+TGG 0.617863 1.1:-29696564 None:intergenic
ACGAAAAGAACTTGGTGCTG+AGG 0.634219 1.1:+29696827 MS.gene53634:CDS
TATTGCTGCTGATGATGATG+AGG 0.663094 1.1:+29696654 MS.gene53634:CDS
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.1:+29696747 MS.gene53634:CDS
GCTCTGTTCCAAGGAAGATG+GGG 0.667093 1.1:-29696542 None:intergenic
ATTGTTATACATGTCTTACG+GGG 0.683485 1.1:+29696699 MS.gene53634:CDS
TTGTTATACATGTCTTACGG+GGG 0.692006 1.1:+29696700 MS.gene53634:CDS
AATGAAATTCAGAAACAACA+AGG 0.709396 1.1:+29695992 MS.gene53634:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.1:-29696233 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1.1:+29696319 MS.gene53634:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATCGTATAAAACCAAAAAA+CGG + chr1.1:29696614-29696633 MS.gene53634:CDS 20.0%
!!! ATGATATTCATAGTTGTTTT+CGG - chr1.1:29695966-29695985 None:intergenic 20.0%
!!! TTTTTGGTTTTATACGATAT+TGG - chr1.1:29696613-29696632 None:intergenic 20.0%
! AATGAAATTCAGAAACAACA+AGG + chr1.1:29695992-29696011 MS.gene53634:CDS 25.0%
! ACATTGTTATACATGTCTTA+CGG + chr1.1:29696697-29696716 MS.gene53634:CDS 25.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.1:29696350-29696369 MS.gene53634:CDS 25.0%
! ATAATCATGATCATGATGAT+GGG + chr1.1:29696392-29696411 MS.gene53634:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.1:29696351-29696370 MS.gene53634:CDS 25.0%
! TGAATGATGAAAATGGAAAT+AGG - chr1.1:29695930-29695949 None:intergenic 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.1:29696347-29696366 None:intergenic 25.0%
!! GTTTGAAAAATCACATCTTT+TGG - chr1.1:29696862-29696881 None:intergenic 25.0%
!!! TGATATTCATAGTTGTTTTC+GGG - chr1.1:29695965-29695984 None:intergenic 25.0%
AGAGTGTACAAAAACACTAT+AGG - chr1.1:29696038-29696057 None:intergenic 30.0%
ATGAGATTTCATACTCCAAA+GGG + chr1.1:29696484-29696503 MS.gene53634:CDS 30.0%
ATTGTTATACATGTCTTACG+GGG + chr1.1:29696699-29696718 MS.gene53634:CDS 30.0%
CATAATCATGATCATGATGA+TGG + chr1.1:29696391-29696410 MS.gene53634:CDS 30.0%
CATTGTTATACATGTCTTAC+GGG + chr1.1:29696698-29696717 MS.gene53634:CDS 30.0%
GAGTGTACAAAAACACTATA+GGG - chr1.1:29696037-29696056 None:intergenic 30.0%
GATCACTTGAATGATGAAAA+TGG - chr1.1:29695937-29695956 None:intergenic 30.0%
TATGAGATTTCATACTCCAA+AGG + chr1.1:29696483-29696502 MS.gene53634:CDS 30.0%
TCAAACATCACAAGATTCAA+AGG + chr1.1:29696876-29696895 MS.gene53634:CDS 30.0%
TCATCTTCAAAATCATCACT+TGG - chr1.1:29697006-29697025 None:intergenic 30.0%
TGTTACAAACATCACATGTA+TGG - chr1.1:29696429-29696448 None:intergenic 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.1:29696134-29696153 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.1:29696133-29696152 None:intergenic 30.0%
!!! TTGGTTTTATACGATATTGG+TGG - chr1.1:29696610-29696629 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.1:29696117-29696136 None:intergenic 30.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.1:29696189-29696208 None:intergenic 35.0%
AATGAGAAGATGAAGGAACA+AGG + chr1.1:29696775-29696794 MS.gene53634:CDS 35.0%
ACACTATAGGGTTTGAACTT+AGG - chr1.1:29696025-29696044 None:intergenic 35.0%
ACATCACATGTATGGTTCTT+CGG - chr1.1:29696421-29696440 None:intergenic 35.0%
CACTATAGGGTTTGAACTTA+GGG - chr1.1:29696024-29696043 None:intergenic 35.0%
CATGATCATGCTGTGAATAA+CGG + chr1.1:29696316-29696335 MS.gene53634:CDS 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.1:29696169-29696188 MS.gene53634:CDS 35.0%
GTCTCTAACCTTGATATTGA+AGG + chr1.1:29696907-29696926 MS.gene53634:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.1:29696722-29696741 MS.gene53634:CDS 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.1:29696159-29696178 None:intergenic 35.0%
TCTTCTTGCCTTCAATATCA+AGG - chr1.1:29696918-29696937 None:intergenic 35.0%
TTCATGATGTTGTGAGTGTT+TGG - chr1.1:29696067-29696086 None:intergenic 35.0%
TTGTTATACATGTCTTACGG+GGG + chr1.1:29696700-29696719 MS.gene53634:CDS 35.0%
! GGATGATAATGAGAAGATGA+AGG + chr1.1:29696768-29696787 MS.gene53634:CDS 35.0%
! TCGAAATTCCTGACAACTTT+TGG - chr1.1:29696970-29696989 None:intergenic 35.0%
!! AGATTGAAGAAGAGTGTTAG+AGG - chr1.1:29696278-29696297 None:intergenic 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.1:29696144-29696163 None:intergenic 35.0%
AACAAGGTGTGATGCTAACA+AGG + chr1.1:29696791-29696810 MS.gene53634:CDS 40.0%
AATTAGGGCCAAAAGTTGTC+AGG + chr1.1:29696959-29696978 MS.gene53634:CDS 40.0%
ACCGAAGATGAAACCGAATT+AGG + chr1.1:29696943-29696962 MS.gene53634:CDS 40.0%
ACTCCAAAGGGTTTGAAGAA+GGG + chr1.1:29696496-29696515 MS.gene53634:CDS 40.0%
ATATCAAGGTTAGAGACTGC+AGG - chr1.1:29696904-29696923 None:intergenic 40.0%
ATTATCATCCACCGTATTGC+TGG - chr1.1:29696758-29696777 None:intergenic 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.1:29696190-29696209 None:intergenic 40.0%
CCCTAATTCGGTTTCATCTT+CGG - chr1.1:29696947-29696966 None:intergenic 40.0%
CCGAAGATGAAACCGAATTA+GGG + chr1.1:29696944-29696963 MS.gene53634:CDS 40.0%
CGTTATTCACAGCATGATCA+TGG - chr1.1:29696318-29696337 None:intergenic 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.1:29696744-29696763 MS.gene53634:CDS 40.0%
TACTCCAAAGGGTTTGAAGA+AGG + chr1.1:29696495-29696514 MS.gene53634:CDS 40.0%
TACTTTGACAAGTCAGTTGC+TGG - chr1.1:29696583-29696602 None:intergenic 40.0%
TCAAACGAATGGTGAGAAGA+AGG - chr1.1:29696106-29696125 None:intergenic 40.0%
TGTCACAAAACATTCACCTC+TGG + chr1.1:29696217-29696236 MS.gene53634:CDS 40.0%
TTCACCTCTGGTAAATCACT+TGG + chr1.1:29696229-29696248 MS.gene53634:CDS 40.0%
TTGCCACAACGAAAAGAACT+TGG + chr1.1:29696819-29696838 MS.gene53634:CDS 40.0%
! ATGTTGTGAGTGTTTGGTTC+AGG - chr1.1:29696061-29696080 None:intergenic 40.0%
! GACAACTTTTGGCCCTAATT+CGG - chr1.1:29696959-29696978 None:intergenic 40.0%
! TATTGCTGCTGATGATGATG+AGG + chr1.1:29696654-29696673 MS.gene53634:CDS 40.0%
! TCATCCAACAACGCTTTGAA+TGG + chr1.1:29696457-29696476 MS.gene53634:CDS 40.0%
!! ATGTCCATTCAAAGCGTTGT+TGG - chr1.1:29696464-29696483 None:intergenic 40.0%
AAACCAAAAAACGGAGTCCC+AGG + chr1.1:29696623-29696642 MS.gene53634:CDS 45.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.1:29696236-29696255 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.1:29696232-29696251 MS.gene53634:CDS 45.0%
ATGTCTTACGGGGGTTATGA+GGG + chr1.1:29696709-29696728 MS.gene53634:CDS 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.1:29696747-29696766 MS.gene53634:CDS 45.0%
GATCATGCTGTGAATAACGG+CGG + chr1.1:29696319-29696338 MS.gene53634:CDS 45.0%
GGTGGTCACAAAACCATTCA+CGG + chr1.1:29696250-29696269 MS.gene53634:CDS 45.0%
GTACCCTTCTTCAAACCCTT+TGG - chr1.1:29696502-29696521 None:intergenic 45.0%
TTGCTGGTCGAAACTCAAGA+TGG - chr1.1:29696567-29696586 None:intergenic 45.0%
! GCACCAAGTTCTTTTCGTTG+TGG - chr1.1:29696825-29696844 None:intergenic 45.0%
!! ACGAAAAGAACTTGGTGCTG+AGG + chr1.1:29696827-29696846 MS.gene53634:CDS 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.1:29696629-29696648 MS.gene53634:CDS 50.0%
AGCAGCAATATGCCTTCTCC+TGG - chr1.1:29696644-29696663 None:intergenic 50.0%
AGTGTTAGAGGAGCCGTGAA+TGG - chr1.1:29696266-29696285 None:intergenic 50.0%
CATGTCTTACGGGGGTTATG+AGG + chr1.1:29696708-29696727 MS.gene53634:CDS 50.0%
GCAGCAATATGCCTTCTCCT+GGG - chr1.1:29696643-29696662 None:intergenic 50.0%
GCTCTGTTCCAAGGAAGATG+GGG - chr1.1:29696545-29696564 None:intergenic 50.0%
GGCTCTGTTCCAAGGAAGAT+GGG - chr1.1:29696546-29696565 None:intergenic 50.0%
! CTCAAGATGGCTCTGTTCCA+AGG - chr1.1:29696554-29696573 None:intergenic 50.0%
! TGGCTCTGTTCCAAGGAAGA+TGG - chr1.1:29696547-29696566 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.1:29696629-29696648 None:intergenic 50.0%
TCCAAGGAAGATGGGGCAGT+CGG - chr1.1:29696538-29696557 None:intergenic 55.0%
ACCGACTGCCCCATCTTCCT+TGG + chr1.1:29696534-29696553 MS.gene53634:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 29695905 29697035 29695905 ID=MS.gene53634
chr1.1 mRNA 29695905 29697035 29695905 ID=MS.gene53634.t1;Parent=MS.gene53634
chr1.1 exon 29695905 29697035 29695905 ID=MS.gene53634.t1.exon1;Parent=MS.gene53634.t1
chr1.1 CDS 29695905 29697035 29695905 ID=cds.MS.gene53634.t1;Parent=MS.gene53634.t1
Gene Sequence

>MS.gene53634

ATGAAGAGTTCTTTCTCATCATCCTATTTCCATTTTCATCATTCAAGTGATCACAAACCCGAAAACAACTATGAATATCATCATGATAATGAAATTCAGAAACAACAAGGTTCAAACCCTAAGTTCAAACCCTATAGTGTTTTTGTACACTCTCCTGAACCAAACACTCACAACATCATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACCTCTGGTAAATCACTTGGTGGTCACAAAACCATTCACGGCTCCTCTAACACTCTTCTTCAATCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCATAATCATGATCATGATGATGGGAAACCGAAGAACCATACATGTGATGTTTGTAACAAAGTTTTTTCATCCAACAACGCTTTGAATGGACATATGAGATTTCATACTCCAAAGGGTTTGAAGAAGGGTACTATTATTCACTCACCGACTGCCCCATCTTCCTTGGAACAGAGCCATCTTGAGTTTCGACCAGCAACTGACTTGTCAAAGTACTTGCCACCAATATCGTATAAAACCAAAAAACGGAGTCCCAGGAGAAGGCATATTGCTGCTGATGATGATGAGGAAATTACTCTTGCTGCAAAAACATTGTTATACATGTCTTACGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGATGCTAACAAGGTGTGTTTGCCACAACGAAAAGAACTTGGTGCTGAGGTTGAAGATTCCAAAAGATGTGATTTTTCAAACATCACAAGATTCAAAGGAACCTGCAGTCTCTAACCTTGATATTGAAGGCAAGAAGAATGTTACCGAAGATGAAACCGAATTAGGGCCAAAAGTTGTCAGGAATTTCGATTTGAATGAGCTTCCAAGTGATGATTTTGAAGATGAAACCAATTAG
Protein sequence

>MS.gene53634.t1

MKSSFSSSYFHFHHSSDHKPENNYEYHHDNEIQKQQGSNPKFKPYSVFVHSPEPNTHNIMNKHYSSPSSHHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHGSSNTLLQSKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHNHDHDDGKPKNHTCDVCNKVFSSNNALNGHMRFHTPKGLKKGTIIHSPTAPSSLEQSHLEFRPATDLSKYLPPISYKTKKRSPRRRHIAADDDEEITLAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVMLTRCVCHNEKNLVLRLKIPKDVIFQTSQDSKEPAVSNLDIEGKKNVTEDETELGPKVVRNFDLNELPSDDFEDETN