AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054935

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054935.t1 MTR_8g012210 95.601 341 15 0 2 342 30 370 0.0 677
MS.gene054935.t1 MTR_2g437260 20.130 308 233 9 35 335 80 381 5.11e-12 66.6
MS.gene054935.t1 MTR_4g120380 21.498 307 226 8 19 319 72 369 5.70e-12 66.6
MS.gene054935.t1 MTR_2g436460 21.212 297 218 9 30 319 86 373 1.54e-11 65.1
MS.gene054935.t1 MTR_6g083110 56.364 55 20 1 244 298 1 51 2.31e-11 62.0
MS.gene054935.t1 MTR_4g120380 20.521 307 230 7 19 319 72 370 2.86e-11 64.7
MS.gene054935.t1 MTR_2g019810 22.727 308 170 11 30 323 107 360 8.75e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054935.t1 AT1G79220 48.485 330 165 3 16 342 72 399 1.16e-105 315
MS.gene054935.t1 AT1G21150 22.047 254 194 4 20 269 47 300 4.02e-11 63.9
MS.gene054935.t1 AT1G21150 22.047 254 194 4 20 269 83 336 4.19e-11 63.9
MS.gene054935.t1 AT1G21150 22.047 254 194 4 20 269 147 400 6.35e-11 63.5

Find 58 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCGCTTGCTTAGTGATT+TGG 0.257285 8.3:-77065975 MS.gene054935:CDS
GTTGACAATGTCAAAATATT+AGG 0.276459 8.3:+77065494 None:intergenic
CTTCGCTTGCTTAGTGATTT+GGG 0.280618 8.3:-77065974 MS.gene054935:CDS
GGAAATTGCTGATGAGTTAA+TGG 0.297355 8.3:-77065234 MS.gene054935:CDS
TTGCTTAGTGATTTGGGTTT+AGG 0.299185 8.3:-77065968 MS.gene054935:CDS
AAATATGTGGTGACATTAAT+AGG 0.301744 8.3:-77065611 MS.gene054935:CDS
TAGCAGTTTCATCAAGGAAT+TGG 0.311012 8.3:-77065178 MS.gene054935:CDS
CAAGCCTCTCGTCGAAATTA+TGG 0.312035 8.3:+77065885 None:intergenic
AGCAATGAAGGTACAGAATA+TGG 0.327499 8.3:-77065345 MS.gene054935:CDS
GTTAAACAATATGAAGAGTT+AGG 0.347136 8.3:-77065761 MS.gene054935:CDS
ATATTTGAAAACAACAGATA+TGG 0.357754 8.3:+77065398 None:intergenic
TTTGACATTGTCAACTGATA+AGG 0.368653 8.3:-77065486 MS.gene054935:CDS
TGCAAAATGTTGAAGACAAA+TGG 0.380077 8.3:-77066111 MS.gene054935:CDS
TTCATTGCTAGAAGCACTCT+TGG 0.407140 8.3:+77065359 None:intergenic
GCGCAATGCGGATCCTTCTC+AGG 0.407457 8.3:-77066008 MS.gene054935:CDS
TATGTCATTGTTTGAGTCAA+AGG 0.408420 8.3:-77065855 MS.gene054935:CDS
TTGTAAAGATTATCAATTGT+AGG 0.408436 8.3:-77065934 MS.gene054935:CDS
CATCAGCAATTTCCTTATCA+TGG 0.411377 8.3:+77065243 None:intergenic
TTGTCGGATGATGAGATATT+CGG 0.417333 8.3:-77065533 MS.gene054935:CDS
CGTGGAAACAATTCGCGAAA+AGG 0.422845 8.3:-77065579 MS.gene054935:CDS
AGCTGGGACTTTCGTCGAAT+AGG 0.432888 8.3:+77066150 None:intergenic
CCTCAATGCTCTAAGTATTG+AGG 0.451275 8.3:+77065304 None:intergenic
CTCAATGCTCTAAGTATTGA+GGG 0.456627 8.3:+77065305 None:intergenic
TTCCTTTGACGATGAGAAGA+TGG 0.459653 8.3:-77065678 MS.gene054935:CDS
ATGGAATATATAAGTAGGAC+TGG 0.464288 8.3:-77065659 MS.gene054935:CDS
AAGAGTTAGGTATACCGAAA+AGG 0.464523 8.3:-77065748 MS.gene054935:CDS
GTCAAAGGAAATGCTTCATA+AGG 0.473131 8.3:-77065840 MS.gene054935:CDS
GATCCGCATTGCGCAAAGAC+GGG 0.492040 8.3:+77066017 None:intergenic
GGGTTGTGGTGATGACGATT+TGG 0.493364 8.3:-77066059 MS.gene054935:CDS
ATATAAAAGTAGTTCAGAAA+GGG 0.499107 8.3:+77065141 None:intergenic
AGAGTTAGGTATACCGAAAA+GGG 0.502937 8.3:-77065747 MS.gene054935:CDS
TTCAAAATTGTACAAATATG+TGG 0.504006 8.3:-77065624 MS.gene054935:CDS
GTTTGTCAGATGCCATGATA+AGG 0.508257 8.3:-77065255 MS.gene054935:CDS
AGGTATACCGAAAAGGGACT+TGG 0.508376 8.3:-77065741 MS.gene054935:CDS
TATTTGAAAACAACAGATAT+GGG 0.512551 8.3:+77065399 None:intergenic
AATATAAAAGTAGTTCAGAA+AGG 0.519070 8.3:+77065140 None:intergenic
GGATCCGCATTGCGCAAAGA+CGG 0.525836 8.3:+77066016 None:intergenic
AGAGATTAGCAGTTTCATCA+AGG 0.527319 8.3:-77065184 MS.gene054935:CDS
AAGAGTGCTTCTAGCAATGA+AGG 0.527541 8.3:-77065357 MS.gene054935:CDS
CAATGAAGGGTTTCTTGCAA+TGG 0.534493 8.3:+77065817 None:intergenic
AGAAGATGGAATATATAAGT+AGG 0.535407 8.3:-77065664 MS.gene054935:CDS
TTCCATCTTCTCATCGTCAA+AGG 0.562047 8.3:+77065676 None:intergenic
AAGTAGGACTGGGCTTTCCA+AGG 0.567180 8.3:-77065648 MS.gene054935:CDS
TCAAGGAATTGGACTACTAG+AGG 0.573509 8.3:-77065167 MS.gene054935:CDS
CATTGAGGATGTCCGAGGAG+AGG 0.582695 8.3:-77065289 MS.gene054935:CDS
ACTTTCGTCGAATAGGTGGC+AGG 0.582772 8.3:+77066157 None:intergenic
ATTAATAGGCATCTCTCGCG+TGG 0.592649 8.3:-77065597 MS.gene054935:CDS
TGTCAACTGATAAGGTTCAA+AGG 0.601835 8.3:-77065478 MS.gene054935:CDS
GAAAGTCCCAGCTCAAAATG+AGG 0.604863 8.3:-77066140 MS.gene054935:CDS
CCTCAATACTTAGAGCATTG+AGG 0.607754 8.3:-77065304 MS.gene054935:CDS
TGGAATATATAAGTAGGACT+GGG 0.608434 8.3:-77065658 MS.gene054935:CDS
TGGGACTTTCGTCGAATAGG+TGG 0.610226 8.3:+77066153 None:intergenic
TTAACCATAATTTCGACGAG+AGG 0.625796 8.3:-77065889 MS.gene054935:CDS
AGTTTCGACTGAACCTGAGA+AGG 0.646506 8.3:+77065995 None:intergenic
AAATGTTGAAGACAAATGGA+AGG 0.655802 8.3:-77066107 MS.gene054935:CDS
GAAGTTCTTGAAATAACCGT+CGG 0.665623 8.3:+77065698 None:intergenic
TAGAGCATTGAGGATGTCCG+AGG 0.681763 8.3:-77065294 MS.gene054935:CDS
TTGCCCGTCTTTGCGCAATG+CGG 0.689638 8.3:-77066020 MS.gene054935:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTAATGGAATTTTATAAA+AGG - chr8.3:77066094-77066113 MS.gene054935:CDS 15.0%
!! ATATTTGAAAACAACAGATA+TGG + chr8.3:77065919-77065938 None:intergenic 20.0%
!! TATTTGAAAACAACAGATAT+GGG + chr8.3:77065918-77065937 None:intergenic 20.0%
!! TTCAAAATTGTACAAATATG+TGG - chr8.3:77065690-77065709 MS.gene054935:CDS 20.0%
!! TTGTAAAGATTATCAATTGT+AGG - chr8.3:77065380-77065399 MS.gene054935:CDS 20.0%
!!! ATATCTGTTGTTTTCAAATA+TGG - chr8.3:77065918-77065937 MS.gene054935:CDS 20.0%
!!! ATTTTATAAAAGGACAAAAC+AGG - chr8.3:77066104-77066123 MS.gene054935:CDS 20.0%
! AAATATGTGGTGACATTAAT+AGG - chr8.3:77065703-77065722 MS.gene054935:CDS 25.0%
! AGAAGATGGAATATATAAGT+AGG - chr8.3:77065650-77065669 MS.gene054935:CDS 25.0%
! GTTAAACAATATGAAGAGTT+AGG - chr8.3:77065553-77065572 MS.gene054935:CDS 25.0%
! GTTGACAATGTCAAAATATT+AGG + chr8.3:77065823-77065842 None:intergenic 25.0%
!! GTGTTGAATTTTACAAAGTA+TGG - chr8.3:77065757-77065776 MS.gene054935:CDS 25.0%
!! TTTGTACAATTTTGAATCCT+TGG + chr8.3:77065686-77065705 None:intergenic 25.0%
!!! TACTGAAGTTTTGAGTAAAT+GGG - chr8.3:77065234-77065253 MS.gene054935:CDS 25.0%
!!! TTTTACAAAGTATGGTTTGT+CGG - chr8.3:77065765-77065784 MS.gene054935:CDS 25.0%
AAATGTTGAAGACAAATGGA+AGG - chr8.3:77065207-77065226 MS.gene054935:CDS 30.0%
ATGGAATATATAAGTAGGAC+TGG - chr8.3:77065655-77065674 MS.gene054935:CDS 30.0%
TATGTCATTGTTTGAGTCAA+AGG - chr8.3:77065459-77065478 MS.gene054935:CDS 30.0%
TGCAAAATGTTGAAGACAAA+TGG - chr8.3:77065203-77065222 MS.gene054935:CDS 30.0%
TGGAATATATAAGTAGGACT+GGG - chr8.3:77065656-77065675 MS.gene054935:CDS 30.0%
TTTGACATTGTCAACTGATA+AGG - chr8.3:77065828-77065847 MS.gene054935:CDS 30.0%
! AGGAACATGACTTTCATTTT+AGG - chr8.3:77065856-77065875 MS.gene054935:CDS 30.0%
! ATGAGATATTCGGTCTTTTT+GGG - chr8.3:77065791-77065810 MS.gene054935:CDS 30.0%
! TATTTTCACACAGCAATGAA+GGG + chr8.3:77065513-77065532 None:intergenic 30.0%
! TGGTTCAAATGATGATTTTG+CGG - chr8.3:77065593-77065612 MS.gene054935:CDS 30.0%
! TTATTTTCACACAGCAATGA+AGG + chr8.3:77065514-77065533 None:intergenic 30.0%
!!! ACTGAAGTTTTGAGTAAATG+GGG - chr8.3:77065235-77065254 MS.gene054935:CDS 30.0%
!!! ATTGAGGGTGTTTTCATATT+AGG + chr8.3:77065997-77066016 None:intergenic 30.0%
!!! CTACTGAAGTTTTGAGTAAA+TGG - chr8.3:77065233-77065252 MS.gene054935:CDS 30.0%
AAGAGTTAGGTATACCGAAA+AGG - chr8.3:77065566-77065585 MS.gene054935:CDS 35.0%
AGAGATTAGCAGTTTCATCA+AGG - chr8.3:77066130-77066149 MS.gene054935:CDS 35.0%
AGAGTTAGGTATACCGAAAA+GGG - chr8.3:77065567-77065586 MS.gene054935:CDS 35.0%
CATCAGCAATTTCCTTATCA+TGG + chr8.3:77066074-77066093 None:intergenic 35.0%
GAAGTTCTTGAAATAACCGT+CGG + chr8.3:77065619-77065638 None:intergenic 35.0%
GGAAATTGCTGATGAGTTAA+TGG - chr8.3:77066080-77066099 MS.gene054935:CDS 35.0%
GTCAAAGGAAATGCTTCATA+AGG - chr8.3:77065474-77065493 MS.gene054935:CDS 35.0%
TAGCAGTTTCATCAAGGAAT+TGG - chr8.3:77066136-77066155 MS.gene054935:CDS 35.0%
TGTCAACTGATAAGGTTCAA+AGG - chr8.3:77065836-77065855 MS.gene054935:CDS 35.0%
TTAACCATAATTTCGACGAG+AGG - chr8.3:77065425-77065444 MS.gene054935:CDS 35.0%
TTGTCGGATGATGAGATATT+CGG - chr8.3:77065781-77065800 MS.gene054935:CDS 35.0%
! AGCAATGAAGGTACAGAATA+TGG - chr8.3:77065969-77065988 MS.gene054935:CDS 35.0%
! ATTTCAACCTCATTTTGAGC+TGG + chr8.3:77065184-77065203 None:intergenic 35.0%
! ATTTGAACCAAGTCCCTTTT+CGG + chr8.3:77065583-77065602 None:intergenic 35.0%
! GATGAGATATTCGGTCTTTT+TGG - chr8.3:77065790-77065809 MS.gene054935:CDS 35.0%
! TTGCTTAGTGATTTGGGTTT+AGG - chr8.3:77065346-77065365 MS.gene054935:CDS 35.0%
! TTTCAACCTCATTTTGAGCT+GGG + chr8.3:77065183-77065202 None:intergenic 35.0%
!! CTCAATGCTCTAAGTATTGA+GGG + chr8.3:77066012-77066031 None:intergenic 35.0%
ACTTCGCTTGCTTAGTGATT+TGG - chr8.3:77065339-77065358 MS.gene054935:CDS 40.0%
CAATGAAGGGTTTCTTGCAA+TGG + chr8.3:77065500-77065519 None:intergenic 40.0%
CGTATTGAAAAACCTCTCCT+CGG + chr8.3:77066040-77066059 None:intergenic 40.0%
CTTCGCTTGCTTAGTGATTT+GGG - chr8.3:77065340-77065359 MS.gene054935:CDS 40.0%
GTTTGTCAGATGCCATGATA+AGG - chr8.3:77066059-77066078 MS.gene054935:CDS 40.0%
TCAAGGAATTGGACTACTAG+AGG - chr8.3:77066147-77066166 MS.gene054935:CDS 40.0%
TTCCATCTTCTCATCGTCAA+AGG + chr8.3:77065641-77065660 None:intergenic 40.0%
TTCCTTTGACGATGAGAAGA+TGG - chr8.3:77065636-77065655 MS.gene054935:CDS 40.0%
! ATTGTAGGCCTCGATTTTTC+AGG - chr8.3:77065395-77065414 MS.gene054935:CDS 40.0%
! CCTCAATGCTCTAAGTATTG+AGG + chr8.3:77066013-77066032 None:intergenic 40.0%
!! AAGAGTGCTTCTAGCAATGA+AGG - chr8.3:77065957-77065976 MS.gene054935:CDS 40.0%
!! CCTCAATACTTAGAGCATTG+AGG - chr8.3:77066010-77066029 MS.gene054935:CDS 40.0%
!! GTTTTGAGTAAATGGGGTTG+TGG - chr8.3:77065241-77065260 MS.gene054935:CDS 40.0%
!! TTCATTGCTAGAAGCACTCT+TGG + chr8.3:77065958-77065977 None:intergenic 40.0%
AGGTATACCGAAAAGGGACT+TGG - chr8.3:77065573-77065592 MS.gene054935:CDS 45.0%
AGTCGAGTCCTGAAAAATCG+AGG + chr8.3:77065406-77065425 None:intergenic 45.0%
AGTTTCGACTGAACCTGAGA+AGG + chr8.3:77065322-77065341 None:intergenic 45.0%
ATTAATAGGCATCTCTCGCG+TGG - chr8.3:77065717-77065736 MS.gene054935:CDS 45.0%
CAAGCCTCTCGTCGAAATTA+TGG + chr8.3:77065432-77065451 None:intergenic 45.0%
CGTGGAAACAATTCGCGAAA+AGG - chr8.3:77065735-77065754 MS.gene054935:CDS 45.0%
GAAAGTCCCAGCTCAAAATG+AGG - chr8.3:77065174-77065193 MS.gene054935:CDS 45.0%
! AATGATGATTTTGCGGCCGA+CGG - chr8.3:77065600-77065619 MS.gene054935:CDS 45.0%
AAGTAGGACTGGGCTTTCCA+AGG - chr8.3:77065666-77065685 MS.gene054935:CDS 50.0%
ACTTTCGTCGAATAGGTGGC+AGG + chr8.3:77065160-77065179 None:intergenic 50.0%
AGCTGGGACTTTCGTCGAAT+AGG + chr8.3:77065167-77065186 None:intergenic 50.0%
TGGGACTTTCGTCGAATAGG+TGG + chr8.3:77065164-77065183 None:intergenic 50.0%
! GGGTTGTGGTGATGACGATT+TGG - chr8.3:77065255-77065274 MS.gene054935:CDS 50.0%
!! TAGAGCATTGAGGATGTCCG+AGG - chr8.3:77066020-77066039 MS.gene054935:CDS 50.0%
CATTGAGGATGTCCGAGGAG+AGG - chr8.3:77066025-77066044 MS.gene054935:CDS 55.0%
GATCCGCATTGCGCAAAGAC+GGG + chr8.3:77065300-77065319 None:intergenic 55.0%
GGATCCGCATTGCGCAAAGA+CGG + chr8.3:77065301-77065320 None:intergenic 55.0%
TTGCCCGTCTTTGCGCAATG+CGG - chr8.3:77065294-77065313 MS.gene054935:CDS 55.0%
GCGCAATGCGGATCCTTCTC+AGG - chr8.3:77065306-77065325 MS.gene054935:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 77065154 77066182 77065154 ID=MS.gene054935
chr8.3 mRNA 77065154 77066182 77065154 ID=MS.gene054935.t1;Parent=MS.gene054935
chr8.3 exon 77065154 77066182 77065154 ID=MS.gene054935.t1.exon1;Parent=MS.gene054935.t1
chr8.3 CDS 77065154 77066182 77065154 ID=cds.MS.gene054935.t1;Parent=MS.gene054935.t1
Gene Sequence

>MS.gene054935

ATGCCTGCCACCTATTCGACGAAAGTCCCAGCTCAAAATGAGGTTGAAATGCAAAATGTTGAAGACAAATGGAAGGATGCTACTGAAGTTTTGAGTAAATGGGGTTGTGGTGATGACGATTTGGCAAGAATATTCACTCGTTGCCCGTCTTTGCGCAATGCGGATCCTTCTCAGGTTCAGTCGAAACTTCGCTTGCTTAGTGATTTGGGTTTAGGCTCAGCTGAGCTTGTAAAGATTATCAATTGTAGGCCTCGATTTTTCAGGACTCGACTTAACCATAATTTCGACGAGAGGCTTGACTCTCTTATGTCATTGTTTGAGTCAAAGGAAATGCTTCATAAGGCCATTGCAAGAAACCCTTCATTGCTGTGTGAAAATAATTATGACATTGAACGTATTGTTAAACAATATGAAGAGTTAGGTATACCGAAAAGGGACTTGGTTCAAATGATGATTTTGCGGCCGACGGTTATTTCAAGAACTTCCTTTGACGATGAGAAGATGGAATATATAAGTAGGACTGGGCTTTCCAAGGATTCAAAATTGTACAAATATGTGGTGACATTAATAGGCATCTCTCGCGTGGAAACAATTCGCGAAAAGGTGTTGAATTTTACAAAGTATGGTTTGTCGGATGATGAGATATTCGGTCTTTTTGGGAAGTCTCCTAATATTTTGACATTGTCAACTGATAAGGTTCAAAGGAACATGACTTTCATTTTAGGCACAATGAAGCTTGAAGCTAACATAATCTTTACGTACCCATATCTGTTGTTTTCAAATATGGAGACTGTTTTGAAGCCAAGAGTGCTTCTAGCAATGAAGGTACAGAATATGGTTCCTAATATGAAAACACCCTCAATACTTAGAGCATTGAGGATGTCCGAGGAGAGGTTTTTCAATACGTTTGTCAGATGCCATGATAAGGAAATTGCTGATGAGTTAATGGAATTTTATAAAAGGACAAAACAGGTTAAGAGATTAGCAGTTTCATCAAGGAATTGGACTACTAGAGGATTCCCTTTCTGA
Protein sequence

>MS.gene054935.t1

MPATYSTKVPAQNEVEMQNVEDKWKDATEVLSKWGCGDDDLARIFTRCPSLRNADPSQVQSKLRLLSDLGLGSAELVKIINCRPRFFRTRLNHNFDERLDSLMSLFESKEMLHKAIARNPSLLCENNYDIERIVKQYEELGIPKRDLVQMMILRPTVISRTSFDDEKMEYISRTGLSKDSKLYKYVVTLIGISRVETIREKVLNFTKYGLSDDEIFGLFGKSPNILTLSTDKVQRNMTFILGTMKLEANIIFTYPYLLFSNMETVLKPRVLLAMKVQNMVPNMKTPSILRALRMSEERFFNTFVRCHDKEIADELMEFYKRTKQVKRLAVSSRNWTTRGFPF