AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90744

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90744.t1 MTR_1g023400 71.293 317 78 5 1 313 45 352 5.46e-158 446
MS.gene90744.t1 MTR_1g022200 61.818 330 111 7 1 321 57 380 1.52e-130 377
MS.gene90744.t1 MTR_1g023430 92.105 152 12 0 170 321 29 180 9.51e-103 299
MS.gene90744.t1 MTR_1g009110 46.914 324 149 10 6 314 64 379 3.50e-80 248
MS.gene90744.t1 MTR_4g080200 45.455 319 144 11 10 313 46 349 2.61e-79 245
MS.gene90744.t1 MTR_1g037540 45.277 307 128 15 30 313 111 400 4.76e-59 195
MS.gene90744.t1 MTR_1g022105 38.538 301 124 7 6 295 71 321 3.52e-56 185
MS.gene90744.t1 MTR_1g024125 69.492 118 32 2 186 299 38 155 7.30e-53 171
MS.gene90744.t1 MTR_1g008000 34.194 310 137 16 19 314 13 269 1.06e-32 122
MS.gene90744.t1 MTR_4g133170 22.772 303 193 11 1 281 43 326 1.49e-12 68.2
MS.gene90744.t1 MTR_6g080680 24.900 249 145 10 43 266 116 347 9.32e-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

Find 69 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAACATCAATTTGAAAT+TGG 0.185453 1.4:-1327352 None:intergenic
AAATACAACACTCTTGTTAA+TGG 0.207720 1.4:+1326960 MS.gene90744:CDS
CTCCTGTCGTCTTGCACATT+TGG 0.210715 1.4:+1327174 MS.gene90744:CDS
ATAATCTAAGTACTAAATTA+TGG 0.229738 1.4:+1326883 MS.gene90744:CDS
ACATGAAAGAAGGGTTAAAT+AGG 0.250391 1.4:-1326538 None:intergenic
TCCTGTCGTCTTGCACATTT+GGG 0.292237 1.4:+1327175 MS.gene90744:CDS
CAACTCCTTGGAGGAAAGTT+TGG 0.295354 1.4:+1327287 MS.gene90744:CDS
GTTTGGTGTCCTAGCTATCT+TGG 0.313901 1.4:-1327429 None:intergenic
ACAAGAGTGTTGTATTTAGA+AGG 0.319163 1.4:-1326954 None:intergenic
TCTTCTCTCGCAACTTTCAA+TGG 0.354491 1.4:+1327093 MS.gene90744:CDS
ATATATAATATATCCTAGTT+TGG 0.355918 1.4:-1327446 None:intergenic
TGACGTGTGATGATAGTTAA+AGG 0.366005 1.4:-1326927 None:intergenic
GGCAAAATGAGTTGCCTTGA+TGG 0.369019 1.4:-1327331 None:intergenic
TTGTTAATGGCGTTTATCAT+TGG 0.379442 1.4:+1326973 MS.gene90744:CDS
TATAAAGAATCATGAGACTA+TGG 0.393080 1.4:-1326506 None:intergenic
GACTCATGCATGTATGGTTT+TGG 0.395961 1.4:+1326762 MS.gene90744:CDS
ATGTTTGGCCTTTGGAAGAA+TGG 0.411360 1.4:+1327260 MS.gene90744:CDS
GACAACGACTCATGCATGTA+TGG 0.419933 1.4:+1326756 MS.gene90744:CDS
AAAGGAGGAGGATGTTGAGT+AGG 0.426239 1.4:-1326909 None:intergenic
TGTTTCGTATGTTTGGCCTT+TGG 0.429988 1.4:+1327252 MS.gene90744:CDS
AAGGAGGAGGATGTTGAGTA+GGG 0.432055 1.4:-1326908 None:intergenic
CTTCTCTCGCAACTTTCAAT+GGG 0.434082 1.4:+1327094 MS.gene90744:CDS
GCTTTGAAGTTGATGTTGTC+GGG 0.441312 1.4:-1326795 None:intergenic
GGAAAATGTTGCCGAGATCA+AGG 0.444536 1.4:+1327115 MS.gene90744:CDS
TGAAAGTTGCGAGAGAAGAT+TGG 0.450386 1.4:-1327089 None:intergenic
AGCTTTGAAGTTGATGTTGT+CGG 0.460508 1.4:-1326796 None:intergenic
CGGTGAACCTCTCTAGTTGT+TGG 0.473040 1.4:-1326711 None:intergenic
GGTGAACCTCTCTAGTTGTT+GGG 0.479668 1.4:-1326710 None:intergenic
AAAGACGTTGTTGGAAAAGA+GGG 0.491814 1.4:-1326583 None:intergenic
CCATAAGATTCTATTCGTAC+AGG 0.495381 1.4:-1326609 None:intergenic
CGTCTTGCACATTTGGGCAA+TGG 0.495898 1.4:+1327181 MS.gene90744:CDS
GCCCAAATGTGCAAGACGAC+AGG 0.509229 1.4:-1327176 None:intergenic
CTTTGTCAACCAAGATAGCT+AGG 0.511992 1.4:+1327420 MS.gene90744:CDS
AAGAATGGCGATCAACTCCT+TGG 0.512877 1.4:+1327275 MS.gene90744:CDS
CCTGTACGAATAGAATCTTA+TGG 0.516975 1.4:+1326609 MS.gene90744:CDS
TACAGGGTGAAAGACGTTGT+TGG 0.517337 1.4:-1326592 None:intergenic
CATGAAAGAAGGGTTAAATA+GGG 0.524259 1.4:-1326537 None:intergenic
GAAAGACGTTGTTGGAAAAG+AGG 0.525259 1.4:-1326584 None:intergenic
TCTGTCTCAAACGTTTATGT+CGG 0.526472 1.4:+1326649 MS.gene90744:CDS
AGCAAGGGAACCCTTGATCT+CGG 0.527450 1.4:-1327126 None:intergenic
CTACGTTGTCACATGAAAGA+AGG 0.527676 1.4:-1326548 None:intergenic
GTTGACAAAGGAGCTATGCT+TGG 0.537962 1.4:-1327407 None:intergenic
GTGATGATAGTTAAAGGAGG+AGG 0.543019 1.4:-1326921 None:intergenic
AACAAGTTTCACACACTCAG+AGG 0.544907 1.4:+1327065 MS.gene90744:CDS
GATAGCTAGGACACCAAACT+AGG 0.547828 1.4:+1327433 MS.gene90744:CDS
AATGGCGATCAACTCCTTGG+AGG 0.570585 1.4:+1327278 MS.gene90744:CDS
GTTGATCGCCATTCTTCCAA+AGG 0.574741 1.4:-1327268 None:intergenic
GTCTCGATGAGTTAATTATG+TGG 0.576563 1.4:+1326685 MS.gene90744:CDS
TCAATTATTGTTCTGTGACA+AGG 0.579061 1.4:+1326832 MS.gene90744:CDS
AAGACGTTGTTGGAAAAGAG+GGG 0.584987 1.4:-1326582 None:intergenic
GAAAATGTTGCCGAGATCAA+GGG 0.586335 1.4:+1327116 MS.gene90744:CDS
GAATCTTATGGTAGTTGCAA+CGG 0.589540 1.4:+1326621 MS.gene90744:CDS
CTAGCTATCTTGGTTGACAA+AGG 0.595687 1.4:-1327419 None:intergenic
ACATGCATGAGTCGTTGTCA+AGG 0.608520 1.4:-1326752 None:intergenic
CTCACATCATATGACCATCA+AGG 0.608996 1.4:+1327317 MS.gene90744:CDS
GGGCAATGGATCAAAGTGGA+TGG 0.609401 1.4:+1327195 MS.gene90744:CDS
CGTGTGATGATAGTTAAAGG+AGG 0.609950 1.4:-1326924 None:intergenic
GATTCTGCACAACATAAGCA+AGG 0.613750 1.4:-1327142 None:intergenic
CATAAGATTCTATTCGTACA+GGG 0.614653 1.4:-1326608 None:intergenic
TCGTTGTCAAGGCAGAGACT+CGG 0.619869 1.4:-1326741 None:intergenic
TGATGGTCATATGATGTGAG+TGG 0.624286 1.4:-1327314 None:intergenic
TACGTTGTCACATGAAAGAA+GGG 0.624496 1.4:-1326547 None:intergenic
ACAAGTTTCACACACTCAGA+GGG 0.630363 1.4:+1327066 MS.gene90744:CDS
GGCAGAGACTCGGAGGAACA+CGG 0.631574 1.4:-1326731 None:intergenic
GTGGAACCCAACAACTAGAG+AGG 0.665628 1.4:+1326704 MS.gene90744:CDS
ATTTGGGCAATGGATCAAAG+TGG 0.667392 1.4:+1327191 MS.gene90744:CDS
ATTCTGCACAACATAAGCAA+GGG 0.674457 1.4:-1327141 None:intergenic
TTGTCAAGGCAGAGACTCGG+AGG 0.701974 1.4:-1326738 None:intergenic
AGGAGGAGGATGTTGAGTAG+GGG 0.705269 1.4:-1326907 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCTAAGTACTAAATTA+TGG + chr1.4:1326883-1326902 MS.gene90744:CDS 15.0%
!!! GAAACATTATATTTCATTTT+CGG + chr1.4:1326854-1326873 MS.gene90744:CDS 15.0%
!!! TTGATGATAATGAATATTTT+TGG + chr1.4:1327369-1327388 MS.gene90744:CDS 15.0%
! AAATACAACACTCTTGTTAA+TGG + chr1.4:1326960-1326979 MS.gene90744:CDS 25.0%
! ATACGAAACATTGAAAAAAC+TGG - chr1.4:1327242-1327261 None:intergenic 25.0%
! TACGAAACATTGAAAAAACT+GGG - chr1.4:1327241-1327260 None:intergenic 25.0%
! TATAAAGAATCATGAGACTA+TGG - chr1.4:1326509-1326528 None:intergenic 25.0%
!! CATCAACATCAATTTGAAAT+TGG - chr1.4:1327355-1327374 None:intergenic 25.0%
!! TTTTCAATGTTTCGTATGTT+TGG + chr1.4:1327245-1327264 MS.gene90744:CDS 25.0%
ACATGAAAGAAGGGTTAAAT+AGG - chr1.4:1326541-1326560 None:intergenic 30.0%
CATAAGATTCTATTCGTACA+GGG - chr1.4:1326611-1326630 None:intergenic 30.0%
CATGAAAGAAGGGTTAAATA+GGG - chr1.4:1326540-1326559 None:intergenic 30.0%
TCAATTATTGTTCTGTGACA+AGG + chr1.4:1326832-1326851 MS.gene90744:CDS 30.0%
TGGAGAAAAATGTACAACAT+TGG + chr1.4:1327215-1327234 MS.gene90744:CDS 30.0%
TTGTTAATGGCGTTTATCAT+TGG + chr1.4:1326973-1326992 MS.gene90744:CDS 30.0%
!! ACAAGAGTGTTGTATTTAGA+AGG - chr1.4:1326957-1326976 None:intergenic 30.0%
AAAGACGTTGTTGGAAAAGA+GGG - chr1.4:1326586-1326605 None:intergenic 35.0%
ATTCTGCACAACATAAGCAA+GGG - chr1.4:1327144-1327163 None:intergenic 35.0%
CCATAAGATTCTATTCGTAC+AGG - chr1.4:1326612-1326631 None:intergenic 35.0%
CCTGTACGAATAGAATCTTA+TGG + chr1.4:1326609-1326628 MS.gene90744:CDS 35.0%
GAATCTTATGGTAGTTGCAA+CGG + chr1.4:1326621-1326640 MS.gene90744:CDS 35.0%
GTCTCGATGAGTTAATTATG+TGG + chr1.4:1326685-1326704 MS.gene90744:CDS 35.0%
TACGTTGTCACATGAAAGAA+GGG - chr1.4:1326550-1326569 None:intergenic 35.0%
TCTGTCTCAAACGTTTATGT+CGG + chr1.4:1326649-1326668 MS.gene90744:CDS 35.0%
TGACGTGTGATGATAGTTAA+AGG - chr1.4:1326930-1326949 None:intergenic 35.0%
!! AGCTTTGAAGTTGATGTTGT+CGG - chr1.4:1326799-1326818 None:intergenic 35.0%
AACAAGTTTCACACACTCAG+AGG + chr1.4:1327065-1327084 MS.gene90744:CDS 40.0%
AAGACGTTGTTGGAAAAGAG+GGG - chr1.4:1326585-1326604 None:intergenic 40.0%
ACAAGTTTCACACACTCAGA+GGG + chr1.4:1327066-1327085 MS.gene90744:CDS 40.0%
ATTTGGGCAATGGATCAAAG+TGG + chr1.4:1327191-1327210 MS.gene90744:CDS 40.0%
CGTGTGATGATAGTTAAAGG+AGG - chr1.4:1326927-1326946 None:intergenic 40.0%
CTACGTTGTCACATGAAAGA+AGG - chr1.4:1326551-1326570 None:intergenic 40.0%
CTAGCTATCTTGGTTGACAA+AGG - chr1.4:1327422-1327441 None:intergenic 40.0%
CTCACATCATATGACCATCA+AGG + chr1.4:1327317-1327336 MS.gene90744:CDS 40.0%
CTTCTCTCGCAACTTTCAAT+GGG + chr1.4:1327094-1327113 MS.gene90744:CDS 40.0%
CTTTGTCAACCAAGATAGCT+AGG + chr1.4:1327420-1327439 MS.gene90744:CDS 40.0%
GAAAATGTTGCCGAGATCAA+GGG + chr1.4:1327116-1327135 MS.gene90744:CDS 40.0%
GAAAGACGTTGTTGGAAAAG+AGG - chr1.4:1326587-1326606 None:intergenic 40.0%
GATTCTGCACAACATAAGCA+AGG - chr1.4:1327145-1327164 None:intergenic 40.0%
GTGATGATAGTTAAAGGAGG+AGG - chr1.4:1326924-1326943 None:intergenic 40.0%
TCTTCTCTCGCAACTTTCAA+TGG + chr1.4:1327093-1327112 MS.gene90744:CDS 40.0%
TGAAAGTTGCGAGAGAAGAT+TGG - chr1.4:1327092-1327111 None:intergenic 40.0%
TGATGGTCATATGATGTGAG+TGG - chr1.4:1327317-1327336 None:intergenic 40.0%
! ATGTTTGGCCTTTGGAAGAA+TGG + chr1.4:1327260-1327279 MS.gene90744:CDS 40.0%
! GACTCATGCATGTATGGTTT+TGG + chr1.4:1326762-1326781 MS.gene90744:CDS 40.0%
! GTTTTCCAAACTTTCCTCCA+AGG - chr1.4:1327295-1327314 None:intergenic 40.0%
! TGTTTCGTATGTTTGGCCTT+TGG + chr1.4:1327252-1327271 MS.gene90744:CDS 40.0%
!! GCTTTGAAGTTGATGTTGTC+GGG - chr1.4:1326798-1326817 None:intergenic 40.0%
AAAGGAGGAGGATGTTGAGT+AGG - chr1.4:1326912-1326931 None:intergenic 45.0%
AAGAATGGCGATCAACTCCT+TGG + chr1.4:1327275-1327294 MS.gene90744:CDS 45.0%
AAGGAGGAGGATGTTGAGTA+GGG - chr1.4:1326911-1326930 None:intergenic 45.0%
ACATGCATGAGTCGTTGTCA+AGG - chr1.4:1326755-1326774 None:intergenic 45.0%
CAACTCCTTGGAGGAAAGTT+TGG + chr1.4:1327287-1327306 MS.gene90744:CDS 45.0%
GACAACGACTCATGCATGTA+TGG + chr1.4:1326756-1326775 MS.gene90744:CDS 45.0%
GGAAAATGTTGCCGAGATCA+AGG + chr1.4:1327115-1327134 MS.gene90744:CDS 45.0%
GGCAAAATGAGTTGCCTTGA+TGG - chr1.4:1327334-1327353 None:intergenic 45.0%
GGTGAACCTCTCTAGTTGTT+GGG - chr1.4:1326713-1326732 None:intergenic 45.0%
GTTGACAAAGGAGCTATGCT+TGG - chr1.4:1327410-1327429 None:intergenic 45.0%
GTTGATCGCCATTCTTCCAA+AGG - chr1.4:1327271-1327290 None:intergenic 45.0%
TACAGGGTGAAAGACGTTGT+TGG - chr1.4:1326595-1326614 None:intergenic 45.0%
TCCTGTCGTCTTGCACATTT+GGG + chr1.4:1327175-1327194 MS.gene90744:CDS 45.0%
!! GTTTGGTGTCCTAGCTATCT+TGG - chr1.4:1327432-1327451 None:intergenic 45.0%
AATGGCGATCAACTCCTTGG+AGG + chr1.4:1327278-1327297 MS.gene90744:CDS 50.0%
AGCAAGGGAACCCTTGATCT+CGG - chr1.4:1327129-1327148 None:intergenic 50.0%
AGGAGGAGGATGTTGAGTAG+GGG - chr1.4:1326910-1326929 None:intergenic 50.0%
CGGTGAACCTCTCTAGTTGT+TGG - chr1.4:1326714-1326733 None:intergenic 50.0%
CGTCTTGCACATTTGGGCAA+TGG + chr1.4:1327181-1327200 MS.gene90744:CDS 50.0%
CTCCTGTCGTCTTGCACATT+TGG + chr1.4:1327174-1327193 MS.gene90744:CDS 50.0%
GGGCAATGGATCAAAGTGGA+TGG + chr1.4:1327195-1327214 MS.gene90744:CDS 50.0%
GTGGAACCCAACAACTAGAG+AGG + chr1.4:1326704-1326723 MS.gene90744:CDS 50.0%
TCGTTGTCAAGGCAGAGACT+CGG - chr1.4:1326744-1326763 None:intergenic 50.0%
GCCCAAATGTGCAAGACGAC+AGG - chr1.4:1327179-1327198 None:intergenic 55.0%
TTGTCAAGGCAGAGACTCGG+AGG - chr1.4:1326741-1326760 None:intergenic 55.0%
GGCAGAGACTCGGAGGAACA+CGG - chr1.4:1326734-1326753 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 1326489 1327454 1326489 ID=MS.gene90744
chr1.4 mRNA 1326489 1327454 1326489 ID=MS.gene90744.t1;Parent=MS.gene90744
chr1.4 exon 1326489 1327454 1326489 ID=MS.gene90744.t1.exon1;Parent=MS.gene90744.t1
chr1.4 CDS 1326489 1327454 1326489 ID=cds.MS.gene90744.t1;Parent=MS.gene90744.t1
Gene Sequence

>MS.gene90744

ATGAACATGTCTGATAGCCATAGTCTCATGATTCTTTATAAAACAATACCCTATTTAACCCTTCTTTCATGTGACAACGTAGCACACATCAAACCCCTCTTTTCCAACAACGTCTTTCACCCTGTACGAATAGAATCTTATGGTAGTTGCAACGGTGTTTTCTGTCTCAAACGTTTATGTCGGTTTCATAAAAGTTGTCTCGATGAGTTAATTATGTGGAACCCAACAACTAGAGAGGTTCACCGTGTTCCTCCGAGTCTCTGCCTTGACAACGACTCATGCATGTATGGTTTTGGTGCTGATGATCCCGACAACATCAACTTCAAAGCTGTGAAACTTCATATCAATTATTGTTCTGTGACAAGGAAACATTATATTTCATTTTCGGAAGTTTATAATCTAAGTACTAAATTATGGACCCCTACTCAACATCCTCCTCCTTTAACTATCATCACACGTCAATGTCCTTCTAAATACAACACTCTTGTTAATGGCGTTTATCATTGGATTACAGAGAATACATACTACTATCACAATGATTATGCTGCAAATATTCTATGTTTTGACTTTCACAGCAACAAGTTTCACACACTCAGAGGGCCAATCTTCTCTCGCAACTTTCAATGGGAAAATGTTGCCGAGATCAAGGGTTCCCTTGCTTATGTTGTGCAGAATCACTTCAATGCTCCTGTCGTCTTGCACATTTGGGCAATGGATCAAAGTGGATGGAGAAAAATGTACAACATTGGCCCAGTTTTTTCAATGTTTCGTATGTTTGGCCTTTGGAAGAATGGCGATCAACTCCTTGGAGGAAAGTTTGGAAAACCACTCACATCATATGACCATCAAGGCAACTCATTTTGCCAATTTCAAATTGATGTTGATGATAATGAATATTTTTGGATTCATGAGTATGTGCCAAGCATAGCTCCTTTGTCAACCAAGATAGCTAGGACACCAAACTAG
Protein sequence

>MS.gene90744.t1

MNMSDSHSLMILYKTIPYLTLLSCDNVAHIKPLFSNNVFHPVRIESYGSCNGVFCLKRLCRFHKSCLDELIMWNPTTREVHRVPPSLCLDNDSCMYGFGADDPDNINFKAVKLHINYCSVTRKHYISFSEVYNLSTKLWTPTQHPPPLTIITRQCPSKYNTLVNGVYHWITENTYYYHNDYAANILCFDFHSNKFHTLRGPIFSRNFQWENVAEIKGSLAYVVQNHFNAPVVLHIWAMDQSGWRKMYNIGPVFSMFRMFGLWKNGDQLLGGKFGKPLTSYDHQGNSFCQFQIDVDDNEYFWIHEYVPSIAPLSTKIARTPN