AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028266

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028266.t1 MTR_4g094720 98.624 218 3 0 1 218 1 218 1.85e-163 449
MS.gene028266.t1 MTR_7g105830 31.111 180 114 3 6 180 74 248 5.35e-23 94.0
MS.gene028266.t1 MTR_1g105090 30.000 180 116 3 6 180 76 250 4.76e-22 91.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028266.t1 AT1G48130 72.273 220 54 2 1 218 1 215 3.08e-116 330
MS.gene028266.t1 AT5G06290 31.667 180 113 3 6 180 82 256 2.45e-24 97.4
MS.gene028266.t1 AT3G11630 32.222 180 112 3 6 180 75 249 1.69e-23 95.1
MS.gene028266.t1 AT5G06290 29.448 163 106 2 6 164 82 239 6.20e-20 85.1

Find 62 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTAATGATTTCTCTTT+TGG 0.116285 4.2:-16940515 None:intergenic
GATATTTGTACCTTCTTATC+TGG 0.262678 4.2:-16940610 None:intergenic
TCCCCTGGCTTCCAGTTAGC+AGG 0.316622 4.2:-16940809 None:intergenic
ATGTTCCTCCCAGTTGTTGC+AGG 0.342538 4.2:-16940725 None:intergenic
CCATTGGAATCTTTCTCATC+AGG 0.347454 4.2:-16940553 None:intergenic
CCAAGCTCAGTGGTACAAAC+TGG 0.350619 4.2:-16940209 None:intergenic
TTTCTGTACCCTGCAACAAC+TGG 0.357498 4.2:+16940716 MS.gene028266:CDS
CATATCCTTAGCTTGTTCAT+TGG 0.360719 4.2:-16940858 None:intergenic
AAATTGCAACCCCTGCTAAC+TGG 0.361486 4.2:+16940798 MS.gene028266:CDS
TGCAGATCTTCCATCCAAAA+AGG 0.376713 4.2:+16940901 MS.gene028266:CDS
CTTGTGTAGTATCAACTTCA+AGG 0.408006 4.2:-16940115 None:intergenic
GCTTGTTCATTGGTAACATC+AGG 0.425824 4.2:-16940848 None:intergenic
ACAATATGAAGAGCCCTTGA+TGG 0.428726 4.2:-16940583 None:intergenic
ACCCCTGCTAACTGGAAGCC+AGG 0.430708 4.2:+16940806 MS.gene028266:CDS
TACCACTGAGCTTGGTAAGA+TGG 0.430872 4.2:+16940217 MS.gene028266:CDS
CCCCTGGCTTCCAGTTAGCA+GGG 0.440132 4.2:-16940808 None:intergenic
AAACGAGGAGTTATGCTGTT+AGG 0.461288 4.2:+16940263 MS.gene028266:CDS
CAATGGAAATTTACCATCAA+GGG 0.465608 4.2:+16940570 MS.gene028266:CDS
GGATAGTTCACCTTTGCACC+TGG 0.476765 4.2:-16940478 None:intergenic
AATATGCCAGGCCTTACTAT+AGG 0.481380 4.2:+16940077 None:intergenic
CCAATGGAAATTTACCATCA+AGG 0.485151 4.2:+16940569 MS.gene028266:CDS
CCTTGATGGTAAATTTCCAT+TGG 0.485846 4.2:-16940569 None:intergenic
ACCATTCTCTTCTCTCATCC+AGG 0.497155 4.2:+16940176 MS.gene028266:CDS
ATCACTTCTGTTCTGATACA+TGG 0.498086 4.2:+16940153 MS.gene028266:CDS
GTAGTATCAACTTCAAGGTC+AGG 0.507580 4.2:-16940110 None:intergenic
ATCAAGGGCTCTTCATATTG+TGG 0.511782 4.2:+16940585 MS.gene028266:CDS
CTGCAGTCTTAAAACCTTGA+GGG 0.516211 4.2:-16940883 None:intergenic
ACATCAGGAGAAATGACAAC+AGG 0.519996 4.2:-16940833 None:intergenic
CAAGCTCAGTGGTACAAACT+GGG 0.522401 4.2:-16940208 None:intergenic
TCAAGGGCTCTTCATATTGT+GGG 0.523725 4.2:+16940586 MS.gene028266:CDS
TGTTCCTCCCAGTTGTTGCA+GGG 0.527210 4.2:-16940724 None:intergenic
TTCTGTACCCTGCAACAACT+GGG 0.528210 4.2:+16940717 MS.gene028266:CDS
GAATTGTGTCACCTATAGTA+AGG 0.528944 4.2:-16940088 None:intergenic
CCAGTTTGTACCACTGAGCT+TGG 0.529958 4.2:+16940209 MS.gene028266:CDS
TCAAAACTAGAAAATATGCC+AGG 0.532876 4.2:+16940065 None:intergenic
CAAACTGGGGTGAAATCACC+TGG 0.538828 4.2:-16940194 None:intergenic
ATCTAGAATCTCACAAGGAG+TGG 0.546589 4.2:+16940300 MS.gene028266:CDS
CCCCTGCTAACTGGAAGCCA+GGG 0.547614 4.2:+16940807 MS.gene028266:CDS
GTGTCACCTATAGTAAGGCC+TGG 0.556059 4.2:-16940083 None:intergenic
CCCTGGCTTCCAGTTAGCAG+GGG 0.564511 4.2:-16940807 None:intergenic
ATGTATCAGAACAGAAGTGA+TGG 0.570051 4.2:-16940151 None:intergenic
TGTTACCAATGAACAAGCTA+AGG 0.572171 4.2:+16940853 MS.gene028266:CDS
TATTGTGGGACCAGATAAGA+AGG 0.572882 4.2:+16940600 MS.gene028266:CDS
GAAATGACAACAGGTTCCCC+TGG 0.579339 4.2:-16940824 None:intergenic
GTAAATGCAGCCAGGTGCAA+AGG 0.582844 4.2:+16940468 MS.gene028266:intron
TGCAACAACTGGGAGGAACA+TGG 0.585961 4.2:+16940727 MS.gene028266:CDS
CCTGATGAGAAAGATTCCAA+TGG 0.589101 4.2:+16940553 MS.gene028266:CDS
TCTGCAGTCTTAAAACCTTG+AGG 0.590174 4.2:-16940884 None:intergenic
GCTAAGGATATGTTCCCTCA+AGG 0.596047 4.2:+16940869 MS.gene028266:CDS
ACCTGGATGAGAGAAGAGAA+TGG 0.604374 4.2:-16940177 None:intergenic
GCAGGCACATTATCAAACAT+TGG 0.624118 4.2:-16940939 None:intergenic
GAACATGGATGAAGTGCTGA+GGG 0.626828 4.2:+16940742 MS.gene028266:CDS
AATCATTAAGCAACTCAACA+TGG 0.634966 4.2:+16940525 MS.gene028266:CDS
GGAACATGGATGAAGTGCTG+AGG 0.641851 4.2:+16940741 MS.gene028266:CDS
CTTGAAGTTGATACTACACA+AGG 0.656492 4.2:+16940116 MS.gene028266:CDS
GCTTCTGAGTTTAACAAACG+AGG 0.664933 4.2:+16940248 MS.gene028266:CDS
AGCCATCTTACCAAGCTCAG+TGG 0.696126 4.2:-16940219 None:intergenic
CCCTGCTAACTGGAAGCCAG+GGG 0.697213 4.2:+16940808 MS.gene028266:CDS
CATGGATGAAGTGCTGAGGG+TGG 0.707751 4.2:+16940745 MS.gene028266:CDS
TGATGATCTAGAATCTCACA+AGG 0.709676 4.2:+16940295 MS.gene028266:CDS
AAGCTCAGTGGTACAAACTG+GGG 0.712192 4.2:-16940207 None:intergenic
TGTACCCTGCAACAACTGGG+AGG 0.722121 4.2:+16940720 MS.gene028266:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGAAAATAGGAAAACTTA+CGG - chr4.2:16940348-16940367 None:intergenic 20.0%
!! ACAAATTAAACCATCATTTA+TGG - chr4.2:16940679-16940698 None:intergenic 20.0%
!! GAAACATGCATAGAAAATTT+TGG - chr4.2:16940387-16940406 None:intergenic 25.0%
!! TAAGAAGGTACAAATATCTA+TGG + chr4.2:16940615-16940634 MS.gene028266:intron 25.0%
!! TGCTTAATGATTTCTCTTTT+GGG - chr4.2:16940517-16940536 None:intergenic 25.0%
!! TTGCTTAATGATTTCTCTTT+TGG - chr4.2:16940518-16940537 None:intergenic 25.0%
!!! CTTTTTTCTTCCATAAATGA+TGG + chr4.2:16940666-16940685 MS.gene028266:intron 25.0%
AATCATTAAGCAACTCAACA+TGG + chr4.2:16940525-16940544 MS.gene028266:CDS 30.0%
ATGCATGTGGAAAAGAAAAT+AGG - chr4.2:16940359-16940378 None:intergenic 30.0%
CAATGGAAATTTACCATCAA+GGG + chr4.2:16940570-16940589 MS.gene028266:CDS 30.0%
GATATTTGTACCTTCTTATC+TGG - chr4.2:16940613-16940632 None:intergenic 30.0%
!!! CTTTTGGGATCACTAATTAT+TGG - chr4.2:16940502-16940521 None:intergenic 30.0%
!!! TTTTTTATGTAAATGCAGCC+AGG + chr4.2:16940460-16940479 MS.gene028266:intron 30.0%
ATCACTTCTGTTCTGATACA+TGG + chr4.2:16940153-16940172 MS.gene028266:CDS 35.0%
ATGTATCAGAACAGAAGTGA+TGG - chr4.2:16940154-16940173 None:intergenic 35.0%
CCAATGGAAATTTACCATCA+AGG + chr4.2:16940569-16940588 MS.gene028266:CDS 35.0%
CTTGTGTAGTATCAACTTCA+AGG - chr4.2:16940118-16940137 None:intergenic 35.0%
GAATTGTGTCACCTATAGTA+AGG - chr4.2:16940091-16940110 None:intergenic 35.0%
TGTTACCAATGAACAAGCTA+AGG + chr4.2:16940853-16940872 MS.gene028266:CDS 35.0%
! CCTTGATGGTAAATTTCCAT+TGG - chr4.2:16940572-16940591 None:intergenic 35.0%
! CTAAGATACTCCTTTTTGGA+TGG - chr4.2:16940914-16940933 None:intergenic 35.0%
! GAACCTAAGATACTCCTTTT+TGG - chr4.2:16940918-16940937 None:intergenic 35.0%
! TGATGATCTAGAATCTCACA+AGG + chr4.2:16940295-16940314 MS.gene028266:CDS 35.0%
!! AATTTTGGTATGCATGCATG+TGG - chr4.2:16940372-16940391 None:intergenic 35.0%
!! CATATCCTTAGCTTGTTCAT+TGG - chr4.2:16940861-16940880 None:intergenic 35.0%
!! CATCCAAAAAGGAGTATCTT+AGG + chr4.2:16940912-16940931 MS.gene028266:CDS 35.0%
!! CTTGAAGTTGATACTACACA+AGG + chr4.2:16940116-16940135 MS.gene028266:CDS 35.0%
AAACGAGGAGTTATGCTGTT+AGG + chr4.2:16940263-16940282 MS.gene028266:CDS 40.0%
ACAATATGAAGAGCCCTTGA+TGG - chr4.2:16940586-16940605 None:intergenic 40.0%
ACATCAGGAGAAATGACAAC+AGG - chr4.2:16940836-16940855 None:intergenic 40.0%
ATCAAGGGCTCTTCATATTG+TGG + chr4.2:16940585-16940604 MS.gene028266:CDS 40.0%
CCATTGGAATCTTTCTCATC+AGG - chr4.2:16940556-16940575 None:intergenic 40.0%
CCTGATGAGAAAGATTCCAA+TGG + chr4.2:16940553-16940572 MS.gene028266:CDS 40.0%
CTGCAGTCTTAAAACCTTGA+GGG - chr4.2:16940886-16940905 None:intergenic 40.0%
GCTTCTGAGTTTAACAAACG+AGG + chr4.2:16940248-16940267 MS.gene028266:CDS 40.0%
GTAGTATCAACTTCAAGGTC+AGG - chr4.2:16940113-16940132 None:intergenic 40.0%
TATTGTGGGACCAGATAAGA+AGG + chr4.2:16940600-16940619 MS.gene028266:CDS 40.0%
TCAAGGGCTCTTCATATTGT+GGG + chr4.2:16940586-16940605 MS.gene028266:CDS 40.0%
TCTGCAGTCTTAAAACCTTG+AGG - chr4.2:16940887-16940906 None:intergenic 40.0%
TGCAGATCTTCCATCCAAAA+AGG + chr4.2:16940901-16940920 MS.gene028266:CDS 40.0%
! ATCTAGAATCTCACAAGGAG+TGG + chr4.2:16940300-16940319 MS.gene028266:CDS 40.0%
! GCTTGTTCATTGGTAACATC+AGG - chr4.2:16940851-16940870 None:intergenic 40.0%
AAATTGCAACCCCTGCTAAC+TGG + chr4.2:16940798-16940817 MS.gene028266:CDS 45.0%
AAGCTCAGTGGTACAAACTG+GGG - chr4.2:16940210-16940229 None:intergenic 45.0%
ACCATTCTCTTCTCTCATCC+AGG + chr4.2:16940176-16940195 MS.gene028266:CDS 45.0%
ACCTGGATGAGAGAAGAGAA+TGG - chr4.2:16940180-16940199 None:intergenic 45.0%
CAAGCTCAGTGGTACAAACT+GGG - chr4.2:16940211-16940230 None:intergenic 45.0%
GCTAAGGATATGTTCCCTCA+AGG + chr4.2:16940869-16940888 MS.gene028266:CDS 45.0%
TACCACTGAGCTTGGTAAGA+TGG + chr4.2:16940217-16940236 MS.gene028266:CDS 45.0%
TTCTGTACCCTGCAACAACT+GGG + chr4.2:16940717-16940736 MS.gene028266:CDS 45.0%
TTTCTGTACCCTGCAACAAC+TGG + chr4.2:16940716-16940735 MS.gene028266:CDS 45.0%
!! GAACATGGATGAAGTGCTGA+GGG + chr4.2:16940742-16940761 MS.gene028266:CDS 45.0%
!!! ATTGATAATATTAATTAATT+AGG + chr4.2:16940430-16940449 MS.gene028266:intron 5.0%
AGCCATCTTACCAAGCTCAG+TGG - chr4.2:16940222-16940241 None:intergenic 50.0%
ATGTTCCTCCCAGTTGTTGC+AGG - chr4.2:16940728-16940747 None:intergenic 50.0%
CAAACTGGGGTGAAATCACC+TGG - chr4.2:16940197-16940216 None:intergenic 50.0%
CCAAGCTCAGTGGTACAAAC+TGG - chr4.2:16940212-16940231 None:intergenic 50.0%
CCAGTTTGTACCACTGAGCT+TGG + chr4.2:16940209-16940228 MS.gene028266:CDS 50.0%
GAAATGACAACAGGTTCCCC+TGG - chr4.2:16940827-16940846 None:intergenic 50.0%
GGATAGTTCACCTTTGCACC+TGG - chr4.2:16940481-16940500 None:intergenic 50.0%
GTAAATGCAGCCAGGTGCAA+AGG + chr4.2:16940468-16940487 MS.gene028266:intron 50.0%
GTGTCACCTATAGTAAGGCC+TGG - chr4.2:16940086-16940105 None:intergenic 50.0%
TGCAACAACTGGGAGGAACA+TGG + chr4.2:16940727-16940746 MS.gene028266:CDS 50.0%
TGTTCCTCCCAGTTGTTGCA+GGG - chr4.2:16940727-16940746 None:intergenic 50.0%
!! GGAACATGGATGAAGTGCTG+AGG + chr4.2:16940741-16940760 MS.gene028266:CDS 50.0%
TGTACCCTGCAACAACTGGG+AGG + chr4.2:16940720-16940739 MS.gene028266:CDS 55.0%
!! CATGGATGAAGTGCTGAGGG+TGG + chr4.2:16940745-16940764 MS.gene028266:CDS 55.0%
ACCCCTGCTAACTGGAAGCC+AGG + chr4.2:16940806-16940825 MS.gene028266:CDS 60.0%
CCCCTGCTAACTGGAAGCCA+GGG + chr4.2:16940807-16940826 MS.gene028266:CDS 60.0%
CCCCTGGCTTCCAGTTAGCA+GGG - chr4.2:16940811-16940830 None:intergenic 60.0%
CCCTGCTAACTGGAAGCCAG+GGG + chr4.2:16940808-16940827 MS.gene028266:CDS 60.0%
CCCTGGCTTCCAGTTAGCAG+GGG - chr4.2:16940810-16940829 None:intergenic 60.0%
TCCCCTGGCTTCCAGTTAGC+AGG - chr4.2:16940812-16940831 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 16940080 16940949 16940080 ID=MS.gene028266
chr4.2 mRNA 16940080 16940949 16940080 ID=MS.gene028266.t1;Parent=MS.gene028266
chr4.2 exon 16940080 16940346 16940080 ID=MS.gene028266.t1.exon1;Parent=MS.gene028266.t1
chr4.2 CDS 16940080 16940346 16940080 ID=cds.MS.gene028266.t1;Parent=MS.gene028266.t1
chr4.2 exon 16940478 16940621 16940478 ID=MS.gene028266.t1.exon2;Parent=MS.gene028266.t1
chr4.2 CDS 16940478 16940621 16940478 ID=cds.MS.gene028266.t1;Parent=MS.gene028266.t1
chr4.2 exon 16940704 16940949 16940704 ID=MS.gene028266.t1.exon3;Parent=MS.gene028266.t1
chr4.2 CDS 16940704 16940949 16940704 ID=cds.MS.gene028266.t1;Parent=MS.gene028266.t1
Gene Sequence

>MS.gene028266

ATGCCAGGCCTTACTATAGGTGACACAATTCCTGACCTTGAAGTTGATACTACACAAGGCAAGATCAAACTCCATCACTTCTGTTCTGATACATGGACCATTCTCTTCTCTCATCCAGGTGATTTCACCCCAGTTTGTACCACTGAGCTTGGTAAGATGGCTCAATATGCTTCTGAGTTTAACAAACGAGGAGTTATGCTGTTAGGTATGTCTTGTGATGATCTAGAATCTCACAAGGAGTGGATCAAAGACATTGAAGCACACACCGTAAGTTTTCCTATTTTCTTTTCCACATGCATGCATACCAAAATTTTCTATGCATGTTTCTATATAAACTTTTTCATATTCTTATTGATAATATTAATTAATTAGGATGTGTTTTTTTTATGTAAATGCAGCCAGGTGCAAAGGTGAACTATCCAATAATTAGTGATCCCAAAAGAGAAATCATTAAGCAACTCAACATGGTTGATCCTGATGAGAAAGATTCCAATGGAAATTTACCATCAAGGGCTCTTCATATTGTGGGACCAGATAAGAAGGTACAAATATCTATGGACTAAATTAATTTTATAAAATTTGTAGTCTTTTTTCTTCCATAAATGATGGTTTAATTTGTTGCAGATTAAGTTGAGTTTTCTGTACCCTGCAACAACTGGGAGGAACATGGATGAAGTGCTGAGGGTGGTAGAGTCACTACAGAAAGCTTCGAAGTACAAAATTGCAACCCCTGCTAACTGGAAGCCAGGGGAACCTGTTGTCATTTCTCCTGATGTTACCAATGAACAAGCTAAGGATATGTTCCCTCAAGGTTTTAAGACTGCAGATCTTCCATCCAAAAAGGAGTATCTTAGGTTCACCAATGTTTGA
Protein sequence

>MS.gene028266.t1

MPGLTIGDTIPDLEVDTTQGKIKLHHFCSDTWTILFSHPGDFTPVCTTELGKMAQYASEFNKRGVMLLGMSCDDLESHKEWIKDIEAHTPGAKVNYPIISDPKREIIKQLNMVDPDEKDSNGNLPSRALHIVGPDKKIKLSFLYPATTGRNMDEVLRVVESLQKASKYKIATPANWKPGEPVVISPDVTNEQAKDMFPQGFKTADLPSKKEYLRFTNV