AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene061757

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061757.t1 MTR_1g046810 84.810 316 48 0 1 316 1 316 0.0 520
MS.gene061757.t1 MTR_1g052185 37.612 335 118 13 5 316 12 278 2.60e-40 142
MS.gene061757.t1 MTR_1g053530 36.515 241 103 8 63 293 39 239 2.49e-29 112
MS.gene061757.t1 MTR_1g085590 34.444 270 89 9 71 315 16 222 5.35e-27 107
MS.gene061757.t1 MTR_1g063150 35.945 217 57 7 94 310 36 170 1.50e-25 101
MS.gene061757.t1 MTR_1g063140 37.195 164 51 8 147 310 1 112 4.94e-14 69.7
MS.gene061757.t1 MTR_5g098470 29.851 201 95 7 14 210 46 204 4.15e-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 63 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCGAAGATGAAGCCGAATT+AGG 0.257535 1.2:+29657110 MS.gene061757:CDS
AACAGAAAAGAAACACTAAT+TGG 0.288536 1.2:-29657195 None:intergenic
AGGTTGAAGAAGAGTGTTAG+AGG 0.343983 1.2:-29656445 None:intergenic
CTTTGAATGGACATATTAGA+TGG 0.355165 1.2:+29656640 MS.gene061757:CDS
CATTGTTATATATGTCTTAC+GGG 0.356666 1.2:+29656865 MS.gene061757:CDS
ATTATCATCCACCGTATTGC+TGG 0.360275 1.2:-29656922 None:intergenic
GCGAAGATGAAGCCGAATTA+GGG 0.363142 1.2:+29657111 MS.gene061757:CDS
TTTGATTTGAATGAGCTTCC+AGG 0.385067 1.2:+29657152 MS.gene061757:CDS
ATCAGCAATACGCCTTCTCC+TGG 0.390025 1.2:-29656811 None:intergenic
GACAACTCTTGGCCCTAATT+CGG 0.403127 1.2:-29657123 None:intergenic
TCAAAATTCCTGACAACTCT+TGG 0.403974 1.2:-29657134 None:intergenic
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.2:+29656889 MS.gene061757:CDS
GACTTTGTTCCGAGGAAGAT+GGG 0.414040 1.2:-29656713 None:intergenic
ACATTGTTATATATGTCTTA+CGG 0.415793 1.2:+29656864 MS.gene061757:CDS
CACAAGCATAATCATGATGA+TGG 0.420773 1.2:+29656561 MS.gene061757:CDS
TCATCCAACAATGCTTTGAA+TGG 0.423695 1.2:+29656627 MS.gene061757:CDS
AGTGTTAGAGGAGCGGTGAA+TGG 0.433506 1.2:-29656433 None:intergenic
GTTCGAGCATGCAGGTTCCT+TGG 0.449960 1.2:-29657060 None:intergenic
TATTAGATGGCATACTCAAA+AGG 0.453871 1.2:+29656653 MS.gene061757:CDS
TACTTTGACAAGTCAGTAGA+TGG 0.459060 1.2:-29656750 None:intergenic
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.2:-29656356 None:intergenic
TGACTTTGTTCCGAGGAAGA+TGG 0.476518 1.2:-29656714 None:intergenic
ATGTCCATTCAAAGCATTGT+TGG 0.483556 1.2:-29656631 None:intergenic
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.2:-29656357 None:intergenic
TGTCACAAAACATTCACCTC+TGG 0.499496 1.2:+29656387 MS.gene061757:CDS
TACTCAAAAGGGTTCGAAGA+AGG 0.504806 1.2:+29656665 MS.gene061757:CDS
AATTAGGGCCAAGAGTTGTC+AGG 0.505315 1.2:+29657126 MS.gene061757:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1.2:-29656485 None:intergenic
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.2:-29656326 None:intergenic
ACCGACTGCCCCATCTTCCT+CGG 0.517275 1.2:+29656704 MS.gene061757:CDS
CATGATCATGCTGTGAATAA+CGG 0.518528 1.2:+29656486 MS.gene061757:CDS
ATTAGATGGCATACTCAAAA+GGG 0.526510 1.2:+29656654 MS.gene061757:CDS
CACATGTGATGTTTGTAACA+AGG 0.533818 1.2:+29656599 MS.gene061757:CDS
TTGGTCTTATATGATATTGG+CGG 0.539661 1.2:-29656777 None:intergenic
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.2:+29656911 MS.gene061757:CDS
ACTCAAAAGGGTTCGAAGAA+GGG 0.553906 1.2:+29656666 MS.gene061757:CDS
ACCTCTGGTAAATCACTTGG+TGG 0.556710 1.2:+29656402 MS.gene061757:CDS
AACAAGGTGTGATGCTAACA+AGG 0.557593 1.2:+29656958 MS.gene061757:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.2:-29656440 None:intergenic
TCTTCTTGTCTTCAATATCA+CGG 0.570833 1.2:-29657082 None:intergenic
ATATCACGGTTCGAGCATGC+AGG 0.573532 1.2:-29657068 None:intergenic
TTCACCTCTGGTAAATCACT+TGG 0.575760 1.2:+29656399 MS.gene061757:CDS
GGATGATAATGAGAAGATGA+AGG 0.579672 1.2:+29656935 MS.gene061757:CDS
ACAAGCATAATCATGATGAT+GGG 0.583581 1.2:+29656562 MS.gene061757:CDS
TCAAACGAATGGTAAGAAGA+AGG 0.583642 1.2:-29656273 None:intergenic
AACAAGGTGTGTTTGCCACA+AGG 0.586611 1.2:+29656974 MS.gene061757:CDS
AAGATGGGGCAGTCGGTGAG+TGG 0.586640 1.2:-29656698 None:intergenic
TCAGCAATACGCCTTCTCCT+GGG 0.592381 1.2:-29656810 None:intergenic
CTCAAGTTGACTTTGTTCCG+AGG 0.596308 1.2:-29656721 None:intergenic
TCATCTTCAAAATCATCACC+TGG 0.598488 1.2:-29657170 None:intergenic
AATGAGAAGATGAAGGAACA+AGG 0.607433 1.2:+29656942 MS.gene061757:CDS
TCCGAGGAAGATGGGGCAGT+CGG 0.608551 1.2:-29656705 None:intergenic
TTGCCACAAGGAAAAGAACC+TGG 0.615119 1.2:+29656986 MS.gene061757:CDS
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.2:-29656311 None:intergenic
GAATCTTCAACATCAGCACC+AGG 0.621858 1.2:-29657004 None:intergenic
GCGTATTGCTGATAATGATG+AGG 0.644357 1.2:+29656821 MS.gene061757:CDS
ACTTTGTTCCGAGGAAGATG+GGG 0.648774 1.2:-29656712 None:intergenic
TGTTACAAACATCACATGTG+TGG 0.651192 1.2:-29656596 None:intergenic
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.2:+29656914 MS.gene061757:CDS
TTGTTATATATGTCTTACGG+GGG 0.696960 1.2:+29656867 MS.gene061757:CDS
ATTGTTATATATGTCTTACG+GGG 0.706998 1.2:+29656866 MS.gene061757:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.2:-29656403 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1.2:+29656489 MS.gene061757:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTGTTATATATGTCTTA+CGG + chr1.2:29656864-29656883 MS.gene061757:CDS 20.0%
!! TATCATATAAGACCAAAAAA+CGG + chr1.2:29656784-29656803 MS.gene061757:CDS 20.0%
!!! TTTTTGGTCTTATATGATAT+TGG - chr1.2:29656783-29656802 None:intergenic 20.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.2:29656520-29656539 MS.gene061757:CDS 25.0%
! ATTGTTATATATGTCTTACG+GGG + chr1.2:29656866-29656885 MS.gene061757:CDS 25.0%
! CATTGTTATATATGTCTTAC+GGG + chr1.2:29656865-29656884 MS.gene061757:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.2:29656521-29656540 MS.gene061757:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.2:29656517-29656536 None:intergenic 25.0%
ACAAGCATAATCATGATGAT+GGG + chr1.2:29656562-29656581 MS.gene061757:CDS 30.0%
ATTAGATGGCATACTCAAAA+GGG + chr1.2:29656654-29656673 MS.gene061757:CDS 30.0%
CTTTGAATGGACATATTAGA+TGG + chr1.2:29656640-29656659 MS.gene061757:CDS 30.0%
TATTAGATGGCATACTCAAA+AGG + chr1.2:29656653-29656672 MS.gene061757:CDS 30.0%
TCAAAAATCACAAGATTCCA+AGG + chr1.2:29657043-29657062 MS.gene061757:CDS 30.0%
TCTTCTTGTCTTCAATATCA+CGG - chr1.2:29657085-29657104 None:intergenic 30.0%
TTGTTATATATGTCTTACGG+GGG + chr1.2:29656867-29656886 MS.gene061757:CDS 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.2:29656304-29656323 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.2:29656468-29656487 None:intergenic 30.0%
!! TTGGTCTTATATGATATTGG+CGG - chr1.2:29656780-29656799 None:intergenic 30.0%
!! TTTTGAAAAGTCGTGTCTTT+AGG - chr1.2:29657029-29657048 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.2:29656303-29656322 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.2:29656287-29656306 None:intergenic 30.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.2:29656359-29656378 None:intergenic 35.0%
AATGAGAAGATGAAGGAACA+AGG + chr1.2:29656942-29656961 MS.gene061757:CDS 35.0%
CACAAGCATAATCATGATGA+TGG + chr1.2:29656561-29656580 MS.gene061757:CDS 35.0%
CACATGTGATGTTTGTAACA+AGG + chr1.2:29656599-29656618 MS.gene061757:CDS 35.0%
CATGATCATGCTGTGAATAA+CGG + chr1.2:29656486-29656505 MS.gene061757:CDS 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.2:29656339-29656358 MS.gene061757:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.2:29656889-29656908 MS.gene061757:CDS 35.0%
TACTTTGACAAGTCAGTAGA+TGG - chr1.2:29656753-29656772 None:intergenic 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.2:29656329-29656348 None:intergenic 35.0%
TCAAAATTCCTGACAACTCT+TGG - chr1.2:29657137-29657156 None:intergenic 35.0%
TCAAACGAATGGTAAGAAGA+AGG - chr1.2:29656276-29656295 None:intergenic 35.0%
TCATCTTCAAAATCATCACC+TGG - chr1.2:29657173-29657192 None:intergenic 35.0%
TGTTACAAACATCACATGTG+TGG - chr1.2:29656599-29656618 None:intergenic 35.0%
! GGATGATAATGAGAAGATGA+AGG + chr1.2:29656935-29656954 MS.gene061757:CDS 35.0%
! TCATCCAACAATGCTTTGAA+TGG + chr1.2:29656627-29656646 MS.gene061757:CDS 35.0%
!! ATGTCCATTCAAAGCATTGT+TGG - chr1.2:29656634-29656653 None:intergenic 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.2:29656314-29656333 None:intergenic 35.0%
!! TTTGATTTGAATGAGCTTCC+AGG + chr1.2:29657152-29657171 MS.gene061757:CDS 35.0%
AACAAGGTGTGATGCTAACA+AGG + chr1.2:29656958-29656977 MS.gene061757:CDS 40.0%
ACTCAAAAGGGTTCGAAGAA+GGG + chr1.2:29656666-29656685 MS.gene061757:CDS 40.0%
ATTATCATCCACCGTATTGC+TGG - chr1.2:29656925-29656944 None:intergenic 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.2:29656360-29656379 None:intergenic 40.0%
CGTTATTCACAGCATGATCA+TGG - chr1.2:29656488-29656507 None:intergenic 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.2:29656911-29656930 MS.gene061757:CDS 40.0%
TACTCAAAAGGGTTCGAAGA+AGG + chr1.2:29656665-29656684 MS.gene061757:CDS 40.0%
TGTCACAAAACATTCACCTC+TGG + chr1.2:29656387-29656406 MS.gene061757:CDS 40.0%
TTCACCTCTGGTAAATCACT+TGG + chr1.2:29656399-29656418 MS.gene061757:CDS 40.0%
! GCGTATTGCTGATAATGATG+AGG + chr1.2:29656821-29656840 MS.gene061757:CDS 40.0%
!! AGGTTGAAGAAGAGTGTTAG+AGG - chr1.2:29656448-29656467 None:intergenic 40.0%
AACAAGGTGTGTTTGCCACA+AGG + chr1.2:29656974-29656993 MS.gene061757:CDS 45.0%
AATTAGGGCCAAGAGTTGTC+AGG + chr1.2:29657126-29657145 MS.gene061757:CDS 45.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.2:29656406-29656425 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.2:29656402-29656421 MS.gene061757:CDS 45.0%
ACTTTGTTCCGAGGAAGATG+GGG - chr1.2:29656715-29656734 None:intergenic 45.0%
AGCGAAGATGAAGCCGAATT+AGG + chr1.2:29657110-29657129 MS.gene061757:CDS 45.0%
ATGTCTTACGGGGGTTATGA+GGG + chr1.2:29656876-29656895 MS.gene061757:CDS 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.2:29656914-29656933 MS.gene061757:CDS 45.0%
GAATCTTCAACATCAGCACC+AGG - chr1.2:29657007-29657026 None:intergenic 45.0%
GACAACTCTTGGCCCTAATT+CGG - chr1.2:29657126-29657145 None:intergenic 45.0%
GACTTTGTTCCGAGGAAGAT+GGG - chr1.2:29656716-29656735 None:intergenic 45.0%
GATCATGCTGTGAATAACGG+CGG + chr1.2:29656489-29656508 MS.gene061757:CDS 45.0%
GCGAAGATGAAGCCGAATTA+GGG + chr1.2:29657111-29657130 MS.gene061757:CDS 45.0%
TATGTCTTACGGGGGTTATG+AGG + chr1.2:29656875-29656894 MS.gene061757:CDS 45.0%
TGACTTTGTTCCGAGGAAGA+TGG - chr1.2:29656717-29656736 None:intergenic 45.0%
TTGCCACAAGGAAAAGAACC+TGG + chr1.2:29656986-29657005 MS.gene061757:CDS 45.0%
!! CTCAAGTTGACTTTGTTCCG+AGG - chr1.2:29656724-29656743 None:intergenic 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.2:29656443-29656462 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.2:29656799-29656818 MS.gene061757:CDS 50.0%
AGACCAAAAAACGGAGTCCC+AGG + chr1.2:29656793-29656812 MS.gene061757:CDS 50.0%
AGTGTTAGAGGAGCGGTGAA+TGG - chr1.2:29656436-29656455 None:intergenic 50.0%
ATATCACGGTTCGAGCATGC+AGG - chr1.2:29657071-29657090 None:intergenic 50.0%
ATCAGCAATACGCCTTCTCC+TGG - chr1.2:29656814-29656833 None:intergenic 50.0%
TCAGCAATACGCCTTCTCCT+GGG - chr1.2:29656813-29656832 None:intergenic 50.0%
! GCACCAGGTTCTTTTCCTTG+TGG - chr1.2:29656992-29657011 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.2:29656799-29656818 None:intergenic 50.0%
GTTCGAGCATGCAGGTTCCT+TGG - chr1.2:29657063-29657082 None:intergenic 55.0%
AAGATGGGGCAGTCGGTGAG+TGG - chr1.2:29656701-29656720 None:intergenic 60.0%
ACCGACTGCCCCATCTTCCT+CGG + chr1.2:29656704-29656723 MS.gene061757:CDS 60.0%
TCCGAGGAAGATGGGGCAGT+CGG - chr1.2:29656708-29656727 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 29656252 29657202 29656252 ID=MS.gene061757
chr1.2 mRNA 29656252 29657202 29656252 ID=MS.gene061757.t1;Parent=MS.gene061757
chr1.2 exon 29656252 29657202 29656252 ID=MS.gene061757.t1.exon1;Parent=MS.gene061757.t1
chr1.2 CDS 29656252 29657202 29656252 ID=cds.MS.gene061757.t1;Parent=MS.gene061757.t1
Gene Sequence

>MS.gene061757

ATGAACAAACACTATTCTTCACCTTCTTCTTACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTTTGTCACAAAACATTCACCTCTGGTAAATCACTTGGTGGTCACAAAACCATTCACCGCTCCTCTAACACTCTTCTTCAACCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCACAAGCATAATCATGATGATGGGAAACTGAAGAACCACACATGTGATGTTTGTAACAAGGTTTTTTCATCCAACAATGCTTTGAATGGACATATTAGATGGCATACTCAAAAGGGTTCGAAGAAGGGTGTTATTATCCACTCACCGACTGCCCCATCTTCCTCGGAACAAAGTCAACTTGAGTTTCTACCATCTACTGACTTGTCAAAGTACTTGCCGCCAATATCATATAAGACCAAAAAACGGAGTCCCAGGAGAAGGCGTATTGCTGATAATGATGAGGAAATTACTATTGCTGCAAAAACATTGTTATATATGTCTTACGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGATGCTAACAAGGTGTGTTTGCCACAAGGAAAAGAACCTGGTGCTGATGTTGAAGATTCCTAAAGACACGACTTTTCAAAAATCACAAGATTCCAAGGAACCTGCATGCTCGAACCGTGATATTGAAGACAAGAAGAATGTTAGCGAAGATGAAGCCGAATTAGGGCCAAGAGTTGTCAGGAATTTTGATTTGAATGAGCTTCCAGGTGATGATTTTGAAGATGAAACCAATTAG
Protein sequence

>MS.gene061757.t1

MNKHYSSPSSYHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHKHNHDDGKLKNHTCDVCNKVFSSNNALNGHIRWHTQKGSKKGVIIHSPTAPSSSEQSQLEFLPSTDLSKYLPPISYKTKKRSPRRRRIADNDEEITIAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVMLTRCVCHKEKNLVLMLKIPKDTTFQKSQDSKEPACSNRDIEDKKNVSEDEAELGPRVVRNFDLNELPGDDFEDETN