AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24173

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24173.t1 MTR_1g023400 75.314 239 56 2 1 239 117 352 1.82e-126 362
MS.gene24173.t1 MTR_1g022200 64.202 257 77 7 3 247 127 380 8.28e-104 306
MS.gene24173.t1 MTR_1g024125 91.525 118 9 1 110 226 38 155 3.85e-77 230
MS.gene24173.t1 MTR_1g023430 69.032 155 44 2 94 247 29 180 3.36e-71 216
MS.gene24173.t1 MTR_4g080200 48.400 250 109 8 1 239 109 349 3.00e-63 201
MS.gene24173.t1 MTR_1g009110 46.063 254 112 9 1 240 137 379 4.35e-60 194
MS.gene24173.t1 MTR_1g037540 43.511 262 116 12 1 239 148 400 1.53e-46 159
MS.gene24173.t1 MTR_1g022105 48.750 160 74 4 62 221 169 320 8.99e-42 145
MS.gene24173.t1 MTR_1g008000 36.937 222 93 8 26 240 88 269 4.09e-25 100
MS.gene24173.t1 MTR_8g064890 26.872 227 124 11 1 202 140 349 5.98e-12 65.1
MS.gene24173.t1 MTR_5g027330 29.730 222 120 13 3 214 175 370 8.44e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 70 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGATGATGTTGCCGAGATTA+AGG 0.171278 1.2:-1061907 MS.gene24173:CDS
TATGAACATCAATTTGAAAT+TGG 0.236488 1.2:+1061670 None:intergenic
CTTCTGTCGTTTCGAACATT+TGG 0.245236 1.2:-1061848 MS.gene24173:CDS
TAAGACTAAATATTGGATTC+AGG 0.310121 1.2:-1061649 MS.gene24173:CDS
GAACTCCTTGGAGGAAAGTT+TGG 0.311876 1.2:-1061735 MS.gene24173:CDS
ATATAAGTTATGATGGAATT+AGG 0.312979 1.2:-1062187 MS.gene24173:CDS
GTTTGGTGTCCTAGCTATCT+TGG 0.313901 1.2:+1061596 None:intergenic
AACTCATGCTTGCATGGTTT+TGG 0.318057 1.2:-1062254 MS.gene24173:CDS
TCACTCTACTATAGCAATAA+TGG 0.344231 1.2:-1062023 MS.gene24173:CDS
ATGTTCATAAGACTAAATAT+TGG 0.349506 1.2:-1061656 MS.gene24173:CDS
CAAATATATTGATCCTAGTT+TGG 0.355534 1.2:+1061579 None:intergenic
AGGCGTCTGATCTTGGTAAA+AGG 0.359916 1.2:+1062104 None:intergenic
GATGATGTTGCCGAGATTAA+GGG 0.361061 1.2:-1061906 MS.gene24173:CDS
TTCTGTCGTTTCGAACATTT+GGG 0.378895 1.2:-1061847 MS.gene24173:CDS
AGATATAACACTCTTGTTAA+CGG 0.387900 1.2:-1062071 MS.gene24173:CDS
CGTTTCGAACATTTGGGTAA+TGG 0.394618 1.2:-1061841 MS.gene24173:CDS
TTGTTAACGGCGTTTATCAT+TGG 0.397348 1.2:-1062058 MS.gene24173:CDS
TGTCTCGTATGCTCGGCCTT+TGG 0.408788 1.2:-1061770 MS.gene24173:CDS
AATCAGTTTCACGAACTTAG+AGG 0.414322 1.2:-1061966 MS.gene24173:CDS
GGCAAAGTGAGTTGCCTTGA+TGG 0.414472 1.2:+1061691 None:intergenic
ATAATCTAAGTACCAACTCT+TGG 0.426515 1.2:-1062148 MS.gene24173:CDS
GTTGTTGTCAAGGCAGAGAC+TGG 0.428676 1.2:+1062274 None:intergenic
GACAACAACTCATGCTTGCA+TGG 0.438461 1.2:-1062260 MS.gene24173:CDS
AGGACACAGGCGTCTGATCT+TGG 0.439056 1.2:+1062097 None:intergenic
GATTCTGTGTAACATAAGTA+AGG 0.458247 1.2:+1061880 None:intergenic
ACAAGAGTGTTATATCTAGA+AGG 0.467432 1.2:+1062077 None:intergenic
AAACTCTATATAAGTTATGA+TGG 0.468261 1.2:-1062194 MS.gene24173:CDS
GGTGGACCTCACTAGTTGTT+GGG 0.481841 1.2:+1062306 None:intergenic
AAGGAGGAGGATGTTCAGTT+GGG 0.484768 1.2:+1062123 None:intergenic
CCTAGCTATCTTGGTTGACA+AGG 0.485062 1.2:+1061605 None:intergenic
CGGTGGACCTCACTAGTTGT+TGG 0.487614 1.2:+1062305 None:intergenic
ATGCTCGGCCTTTGGAAGAA+TGG 0.492025 1.2:-1061762 MS.gene24173:CDS
AACTTTGAAGCTGATGTTGT+TGG 0.493018 1.2:+1062220 None:intergenic
AAAGGAGGAGGATGTTCAGT+TGG 0.498063 1.2:+1062122 None:intergenic
ACTTTGAAGCTGATGTTGTT+GGG 0.507643 1.2:+1062221 None:intergenic
GTATCAATGTCTCGTATGCT+CGG 0.516361 1.2:-1061777 MS.gene24173:CDS
AAGAATGGCGATGAACTCCT+TGG 0.520103 1.2:-1061747 MS.gene24173:CDS
CTAGCTATCTTGGTTGACAA+GGG 0.528799 1.2:+1061606 None:intergenic
CCTTGTCAACCAAGATAGCT+AGG 0.532417 1.2:-1061605 MS.gene24173:CDS
AGCATACGAGACATTGATAC+AGG 0.533749 1.2:+1061780 None:intergenic
TTCAGTTGGGGTCCAAGAGT+TGG 0.536792 1.2:+1062136 None:intergenic
GTTGTGGTCTTCAACTGAGA+AGG 0.546090 1.2:+1061938 None:intergenic
GATAGCTAGGACACCAAACT+AGG 0.547828 1.2:-1061592 None:intergenic
AGTAAGGGAACCCTTAATCT+CGG 0.554521 1.2:+1061896 None:intergenic
CTGATCTTGGTAAAAGGAGG+AGG 0.555515 1.2:+1062110 None:intergenic
TGGTCTTCAACTGAGAAGGT+TGG 0.561774 1.2:+1061942 None:intergenic
ATCAGTTTCACGAACTTAGA+GGG 0.563965 1.2:-1061965 MS.gene24173:CDS
GTTCATCGCCATTCTTCCAA+AGG 0.565148 1.2:+1061754 None:intergenic
AATGGCGATGAACTCCTTGG+AGG 0.569060 1.2:-1061744 MS.gene24173:CDS
GTTCTCCAAACTTTCCTCCA+AGG 0.571961 1.2:+1061730 None:intergenic
CTCAAATCATATGACCATCA+AGG 0.583706 1.2:-1061705 MS.gene24173:CDS
TAGCTATCTTGGTTGACAAG+GGG 0.591109 1.2:+1061607 None:intergenic
AGCTATCTTGGTTGACAAGG+GGG 0.593652 1.2:+1061608 None:intergenic
TGATGGTCATATGATTTGAG+CGG 0.609744 1.2:+1061708 None:intergenic
TTGTTGTCAAGGCAGAGACT+GGG 0.611099 1.2:+1062275 None:intergenic
ATTCTGTGTAACATAAGTAA+GGG 0.613076 1.2:+1061881 None:intergenic
GGGTAATGGATCAAAGTGGA+TGG 0.622462 1.2:-1061827 MS.gene24173:CDS
GCAAGCATGAGTTGTTGTCA+AGG 0.624082 1.2:+1062264 None:intergenic
CGTCTGATCTTGGTAAAAGG+AGG 0.635316 1.2:+1062107 None:intergenic
CATCATCGCGTAGAAAGTTG+TGG 0.640683 1.2:+1061922 None:intergenic
TACGAGACATTGATACAGGT+GGG 0.641469 1.2:+1061784 None:intergenic
TGTTATATCTAGAAGGACAC+AGG 0.641742 1.2:+1062084 None:intergenic
ATACGAGACATTGATACAGG+TGG 0.649476 1.2:+1061783 None:intergenic
GGCAGAGACTGGGAGGAACA+CGG 0.658353 1.2:+1062285 None:intergenic
ATTTGGGTAATGGATCAAAG+TGG 0.662912 1.2:-1061831 MS.gene24173:CDS
AGGAGGAGGATGTTCAGTTG+GGG 0.674344 1.2:+1062124 None:intergenic
TGATGGAATTAGGAGATCAG+CGG 0.680423 1.2:-1062177 MS.gene24173:CDS
GTGGAACCCAACAACTAGTG+AGG 0.684553 1.2:-1062312 MS.gene24173:CDS
TTGTCAAGGCAGAGACTGGG+AGG 0.684585 1.2:+1062278 None:intergenic
AGAGACTGGGAGGAACACGG+TGG 0.807268 1.2:+1062288 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACTCTATATAAGTTATGA+TGG - chr1.2:1061713-1061732 MS.gene24173:CDS 20.0%
!! ATGTTCATAAGACTAAATAT+TGG - chr1.2:1062251-1062270 MS.gene24173:CDS 20.0%
!!! ATATAAGTTATGATGGAATT+AGG - chr1.2:1061720-1061739 MS.gene24173:CDS 20.0%
!!! TATGAACATCAATTTGAAAT+TGG + chr1.2:1062240-1062259 None:intergenic 20.0%
! AGATATAACACTCTTGTTAA+CGG - chr1.2:1061836-1061855 MS.gene24173:CDS 25.0%
! ATTCTGTGTAACATAAGTAA+GGG + chr1.2:1062029-1062048 None:intergenic 25.0%
! TAAGACTAAATATTGGATTC+AGG - chr1.2:1062258-1062277 MS.gene24173:CDS 25.0%
ATAATCTAAGTACCAACTCT+TGG - chr1.2:1061759-1061778 MS.gene24173:CDS 30.0%
GATTCTGTGTAACATAAGTA+AGG + chr1.2:1062030-1062049 None:intergenic 30.0%
TCACTCTACTATAGCAATAA+TGG - chr1.2:1061884-1061903 MS.gene24173:CDS 30.0%
!! ACAAGAGTGTTATATCTAGA+AGG + chr1.2:1061833-1061852 None:intergenic 30.0%
AATCAGTTTCACGAACTTAG+AGG - chr1.2:1061941-1061960 MS.gene24173:CDS 35.0%
ATCAGTTTCACGAACTTAGA+GGG - chr1.2:1061942-1061961 MS.gene24173:CDS 35.0%
CTCAAATCATATGACCATCA+AGG - chr1.2:1062202-1062221 MS.gene24173:CDS 35.0%
TGATGGTCATATGATTTGAG+CGG + chr1.2:1062202-1062221 None:intergenic 35.0%
TGTTATATCTAGAAGGACAC+AGG + chr1.2:1061826-1061845 None:intergenic 35.0%
TTGTTAACGGCGTTTATCAT+TGG - chr1.2:1061849-1061868 MS.gene24173:CDS 35.0%
! TGGCACAAAAAGTACAACAT+TGG - chr1.2:1062100-1062119 MS.gene24173:CDS 35.0%
! TTCTGTCGTTTCGAACATTT+GGG - chr1.2:1062060-1062079 MS.gene24173:CDS 35.0%
!! AACTTTGAAGCTGATGTTGT+TGG + chr1.2:1061690-1061709 None:intergenic 35.0%
!! ACTTTGAAGCTGATGTTGTT+GGG + chr1.2:1061689-1061708 None:intergenic 35.0%
!! ATTTGGGTAATGGATCAAAG+TGG - chr1.2:1062076-1062095 MS.gene24173:CDS 35.0%
AGCATACGAGACATTGATAC+AGG + chr1.2:1062130-1062149 None:intergenic 40.0%
AGTAAGGGAACCCTTAATCT+CGG + chr1.2:1062014-1062033 None:intergenic 40.0%
ATACGAGACATTGATACAGG+TGG + chr1.2:1062127-1062146 None:intergenic 40.0%
CGTTTCGAACATTTGGGTAA+TGG - chr1.2:1062066-1062085 MS.gene24173:CDS 40.0%
CTAGCTATCTTGGTTGACAA+GGG + chr1.2:1062304-1062323 None:intergenic 40.0%
GATGATGTTGCCGAGATTAA+GGG - chr1.2:1062001-1062020 MS.gene24173:CDS 40.0%
GTATCAATGTCTCGTATGCT+CGG - chr1.2:1062130-1062149 MS.gene24173:CDS 40.0%
TACGAGACATTGATACAGGT+GGG + chr1.2:1062126-1062145 None:intergenic 40.0%
TAGCTATCTTGGTTGACAAG+GGG + chr1.2:1062303-1062322 None:intergenic 40.0%
TGATGGAATTAGGAGATCAG+CGG - chr1.2:1061730-1061749 MS.gene24173:CDS 40.0%
! AACTCATGCTTGCATGGTTT+TGG - chr1.2:1061653-1061672 MS.gene24173:CDS 40.0%
! CTTCTGTCGTTTCGAACATT+TGG - chr1.2:1062059-1062078 MS.gene24173:CDS 40.0%
AAAGGAGGAGGATGTTCAGT+TGG + chr1.2:1061788-1061807 None:intergenic 45.0%
AAGAATGGCGATGAACTCCT+TGG - chr1.2:1062160-1062179 MS.gene24173:CDS 45.0%
AAGGAGGAGGATGTTCAGTT+GGG + chr1.2:1061787-1061806 None:intergenic 45.0%
AGCTATCTTGGTTGACAAGG+GGG + chr1.2:1062302-1062321 None:intergenic 45.0%
AGGCGTCTGATCTTGGTAAA+AGG + chr1.2:1061806-1061825 None:intergenic 45.0%
CATCATCGCGTAGAAAGTTG+TGG + chr1.2:1061988-1062007 None:intergenic 45.0%
CCTAGCTATCTTGGTTGACA+AGG + chr1.2:1062305-1062324 None:intergenic 45.0%
CCTTGTCAACCAAGATAGCT+AGG - chr1.2:1062302-1062321 MS.gene24173:CDS 45.0%
CGATGATGTTGCCGAGATTA+AGG - chr1.2:1062000-1062019 MS.gene24173:CDS 45.0%
CGTCTGATCTTGGTAAAAGG+AGG + chr1.2:1061803-1061822 None:intergenic 45.0%
CTGATCTTGGTAAAAGGAGG+AGG + chr1.2:1061800-1061819 None:intergenic 45.0%
GAACTCCTTGGAGGAAAGTT+TGG - chr1.2:1062172-1062191 MS.gene24173:CDS 45.0%
GACAACAACTCATGCTTGCA+TGG - chr1.2:1061647-1061666 MS.gene24173:CDS 45.0%
GCAAGCATGAGTTGTTGTCA+AGG + chr1.2:1061646-1061665 None:intergenic 45.0%
GTTCATCGCCATTCTTCCAA+AGG + chr1.2:1062156-1062175 None:intergenic 45.0%
GTTCTCCAAACTTTCCTCCA+AGG + chr1.2:1062180-1062199 None:intergenic 45.0%
GTTGTGGTCTTCAACTGAGA+AGG + chr1.2:1061972-1061991 None:intergenic 45.0%
TGGTCTTCAACTGAGAAGGT+TGG + chr1.2:1061968-1061987 None:intergenic 45.0%
TTGTTGTCAAGGCAGAGACT+GGG + chr1.2:1061635-1061654 None:intergenic 45.0%
!! GGGTAATGGATCAAAGTGGA+TGG - chr1.2:1062080-1062099 MS.gene24173:CDS 45.0%
!! GTTTGGTGTCCTAGCTATCT+TGG + chr1.2:1062314-1062333 None:intergenic 45.0%
AATGGCGATGAACTCCTTGG+AGG - chr1.2:1062163-1062182 MS.gene24173:CDS 50.0%
AGGAGGAGGATGTTCAGTTG+GGG + chr1.2:1061786-1061805 None:intergenic 50.0%
GGCAAAGTGAGTTGCCTTGA+TGG + chr1.2:1062219-1062238 None:intergenic 50.0%
GGTGGACCTCACTAGTTGTT+GGG + chr1.2:1061604-1061623 None:intergenic 50.0%
GTGGAACCCAACAACTAGTG+AGG - chr1.2:1061595-1061614 MS.gene24173:CDS 50.0%
GTTGTTGTCAAGGCAGAGAC+TGG + chr1.2:1061636-1061655 None:intergenic 50.0%
TTCAGTTGGGGTCCAAGAGT+TGG + chr1.2:1061774-1061793 None:intergenic 50.0%
! ATGCTCGGCCTTTGGAAGAA+TGG - chr1.2:1062145-1062164 MS.gene24173:CDS 50.0%
AGGACACAGGCGTCTGATCT+TGG + chr1.2:1061813-1061832 None:intergenic 55.0%
CGGTGGACCTCACTAGTTGT+TGG + chr1.2:1061605-1061624 None:intergenic 55.0%
GTTGACAAGGGGGCTATGCT+TGG + chr1.2:1062292-1062311 None:intergenic 55.0%
TGTCTCGTATGCTCGGCCTT+TGG - chr1.2:1062137-1062156 MS.gene24173:CDS 55.0%
TTGTCAAGGCAGAGACTGGG+AGG + chr1.2:1061632-1061651 None:intergenic 55.0%
AGAGACTGGGAGGAACACGG+TGG + chr1.2:1061622-1061641 None:intergenic 60.0%
GGCAGAGACTGGGAGGAACA+CGG + chr1.2:1061625-1061644 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 1061593 1062336 1061593 ID=MS.gene24173
chr1.2 mRNA 1061593 1062336 1061593 ID=MS.gene24173.t1;Parent=MS.gene24173
chr1.2 exon 1061593 1062336 1061593 ID=MS.gene24173.t1.exon1;Parent=MS.gene24173.t1
chr1.2 CDS 1061593 1062336 1061593 ID=cds.MS.gene24173.t1;Parent=MS.gene24173.t1
Gene Sequence

>MS.gene24173

ATGTGGAACCCAACAACTAGTGAGGTCCACCGTGTTCCTCCCAGTCTCTGCCTTGACAACAACTCATGCTTGCATGGTTTTGGTGCTGATGATCCCAACAACATCAGCTTCAAAGTTGTGAAACTCTATATAAGTTATGATGGAATTAGGAGATCAGCGGAAGTTTATAATCTAAGTACCAACTCTTGGACCCCAACTGAACATCCTCCTCCTTTTACCAAGATCAGACGCCTGTGTCCTTCTAGATATAACACTCTTGTTAACGGCGTTTATCATTGGATTACAAACAATTCACTCTACTATAGCAATAATGGTGTTGCAAATATTCTATGCTTTGACTTTCGCAACAATCAGTTTCACGAACTTAGAGGGCCAACCTTCTCAGTTGAAGACCACAACTTTCTACGCGATGATGTTGCCGAGATTAAGGGTTCCCTTACTTATGTTACACAGAATCGCTTCGATTCTTCTGTCGTTTCGAACATTTGGGTAATGGATCAAAGTGGATGGCACAAAAAGTACAACATTGGCCCACCTGTATCAATGTCTCGTATGCTCGGCCTTTGGAAGAATGGCGATGAACTCCTTGGAGGAAAGTTTGGAGAACCGCTCAAATCATATGACCATCAAGGCAACTCACTTTGCCAATTTCAAATTGATGTTCATAAGACTAAATATTGGATTCAGGAGTATGTGCCAAGCATAGCCCCCTTGTCAACCAAGATAGCTAGGACACCAAACTAG
Protein sequence

>MS.gene24173.t1

MWNPTTSEVHRVPPSLCLDNNSCLHGFGADDPNNISFKVVKLYISYDGIRRSAEVYNLSTNSWTPTEHPPPFTKIRRLCPSRYNTLVNGVYHWITNNSLYYSNNGVANILCFDFRNNQFHELRGPTFSVEDHNFLRDDVAEIKGSLTYVTQNRFDSSVVSNIWVMDQSGWHKKYNIGPPVSMSRMLGLWKNGDELLGGKFGEPLKSYDHQGNSLCQFQIDVHKTKYWIQEYVPSIAPLSTKIARTPN