AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0689180

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0689180 MtrunA17_Chr5g0397601 100.000 261 0 0 1 261 747 1007 0.0 543
Msa0689180 MtrunA17_Chr7g0258331 74.713 261 66 0 1 261 515 775 1.47e-145 426
Msa0689180 MtrunA17_Chr1g0174761 73.946 261 68 0 1 261 514 774 3.55e-144 422
Msa0689180 MtrunA17_Chr8g0349231 72.414 261 72 0 1 261 743 1003 3.78e-142 423
Msa0689180 MtrunA17_Chr1g0174581 71.264 261 75 0 1 261 537 797 5.29e-142 417
Msa0689180 MtrunA17_Chr4g0033151 70.498 261 77 0 1 261 510 770 4.61e-135 399
Msa0689180 MtrunA17_Chr3g0087501 68.966 261 81 0 1 261 562 822 9.00e-135 399
Msa0689180 MtrunA17_Chr4g0010751 68.199 261 83 0 1 261 934 1194 6.72e-132 401
Msa0689180 MtrunA17_Chr4g0014711 67.433 261 85 0 1 261 784 1044 2.28e-131 396
Msa0689180 MtrunA17_Chr7g0247271 66.667 261 87 0 1 261 706 966 1.09e-129 390
Msa0689180 MtrunA17_Chr4g0060191 58.238 261 109 0 1 261 778 1038 7.55e-107 332
Msa0689180 MtrunA17_Chr6g0460791 54.406 261 119 0 1 261 749 1009 1.28e-95 301
Msa0689180 MtrunA17_Chr6g0461151 51.527 262 126 1 1 261 765 1026 1.37e-94 299
Msa0689180 MtrunA17_Chr4g0028371 46.360 261 140 0 1 261 523 783 1.76e-73 238
Msa0689180 MtrunA17_Chr1g0151051 42.023 257 148 1 1 256 537 793 1.40e-65 218
Msa0689180 MtrunA17_Chr4g0035961 37.931 261 111 1 1 261 523 732 3.60e-58 197
Msa0689180 MtrunA17_Chr4g0010641 60.000 130 50 1 131 260 1 128 3.56e-52 166
Msa0689180 MtrunA17_Chr5g0447321 36.782 261 163 2 2 261 504 763 2.39e-51 178
Msa0689180 MtrunA17_Chr4g0010701 44.231 104 36 2 134 237 16 97 2.16e-21 85.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0689180 AT4G11610.3 80.843 261 50 0 1 261 614 874 1.10e-160 468
Msa0689180 AT4G11610.1 80.843 261 50 0 1 261 751 1011 1.28e-159 469
Msa0689180 AT4G11610.2 80.843 261 50 0 1 261 747 1007 1.59e-159 469
Msa0689180 AT5G12970.1 74.713 261 66 0 1 261 509 769 4.40e-149 435
Msa0689180 AT3G57880.4 73.563 261 69 0 1 261 513 773 2.25e-142 418
Msa0689180 AT3G57880.2 73.563 261 69 0 1 261 513 773 2.25e-142 418
Msa0689180 AT3G57880.3 73.563 261 69 0 1 261 513 773 2.25e-142 418
Msa0689180 AT3G57880.1 73.563 261 69 0 1 261 513 773 2.25e-142 418
Msa0689180 AT1G51570.1 73.180 261 70 0 1 261 516 776 3.07e-142 417
Msa0689180 AT5G06850.1 69.732 261 79 0 1 261 534 794 9.63e-140 412
Msa0689180 AT5G48060.1 70.498 261 77 0 1 261 776 1036 9.45e-134 403
Msa0689180 AT1G22610.1 69.349 261 80 0 1 261 769 1029 2.58e-132 399
Msa0689180 AT4G00700.1 63.985 261 94 0 1 261 746 1006 1.99e-127 385
Msa0689180 AT4G00700.2 63.985 261 94 0 1 261 746 1006 1.99e-127 385
Msa0689180 AT3G61300.1 63.740 262 94 1 1 261 711 972 2.38e-123 374
Msa0689180 AT1G74720.1 57.088 261 112 0 1 261 821 1081 2.91e-105 328
Msa0689180 AT3G03680.1 54.962 262 117 1 1 261 756 1017 8.48e-105 326
Msa0689180 AT1G04150.1 60.920 261 102 0 1 261 752 1012 1.09e-101 318
Msa0689180 AT4G20080.1 52.290 262 124 1 1 261 513 774 9.12e-97 300
Msa0689180 AT5G17980.1 51.527 262 126 1 1 261 788 1049 5.82e-96 303
Msa0689180 AT3G61720.1 32.313 294 160 8 2 261 507 795 7.87e-33 127
Msa0689180 AT5G03435.1 34.483 261 149 8 2 256 497 741 1.22e-30 120
Msa0689180 AT5G44760.1 29.927 137 47 1 27 163 364 451 3.43e-15 75.1

Find 63 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTGTTTGTTAGCTGCTT+TGG 0.314831 4_4:-56136622 Msa0689180:CDS
GTGTGTTTGCAGTTGGAAAA+TGG 0.332879 4_4:-56137205 Msa0689180:CDS
TTTCTCTACCTATTCTTGAT+AGG 0.343636 4_4:-56137080 Msa0689180:CDS
TGATAGGTGTATGGAACTTC+AGG 0.347349 4_4:-56137064 Msa0689180:intron
TGAACAAGGACTGTTGTAAT+AGG 0.354570 4_4:+56137155 None:intergenic
CAGATGTTGACTCACATCTA+TGG 0.373205 4_4:-56137280 Msa0689180:CDS
ACAAACGGTTGTAGGTGATT+TGG 0.383411 4_4:-56136715 Msa0689180:CDS
CAAATGGTGGCTGGTTTAGC+AGG 0.392665 4_4:-56136579 Msa0689180:CDS
TGTAGGTGATTTGGCTAGCC+AGG 0.412061 4_4:-56136706 Msa0689180:CDS
TACCGCATTCTTACAAGGTC+AGG 0.427894 4_4:+56136768 None:intergenic
AATTCCTCATCCATTTCATC+GGG 0.432095 4_4:+56136816 None:intergenic
AACATACTATCAGTTCTTGC+AGG 0.433599 4_4:+56136483 None:intergenic
TCATGTGTTGTTTCTCATGT+TGG 0.437544 4_4:-56137135 Msa0689180:CDS
TTCATGTGTGGAGGGTATCT+TGG 0.447757 4_4:+56136870 None:intergenic
TTCTCTGGTGTGTTTGCAGT+TGG 0.450907 4_4:-56137212 Msa0689180:CDS
ACCTATTCTTGATAGGTGTA+TGG 0.457302 4_4:-56137073 Msa0689180:CDS
GGATTCATGCACTGTTGAGC+TGG 0.468052 4_4:-56136677 Msa0689180:CDS
AGTGTAGGCAAAATCAACTC+TGG 0.470324 4_4:+56137104 None:intergenic
GGAAGCCTGTGTCGAAATCT+CGG 0.473709 4_4:+56136537 None:intergenic
TGTAGTACACCCCGATGAAA+TGG 0.494237 4_4:-56136826 Msa0689180:CDS
GGTAGAATACAAACGGTTGT+AGG 0.496800 4_4:-56136723 Msa0689180:CDS
GATCGTTTGAGGAGCGTGGC+TGG 0.499227 4_4:-56136744 Msa0689180:CDS
CTGCCACTATGTTTACTGCT+TGG 0.501177 4_4:+56137357 None:intergenic
AAATTCCTCATCCATTTCAT+CGG 0.503321 4_4:+56136815 None:intergenic
AACATAGTGGCAGCGCGGCT+CGG 0.511333 4_4:-56137347 Msa0689180:CDS
TTTGCAGTTGGAAAATGGTT+AGG 0.514024 4_4:-56137200 Msa0689180:CDS
GAAAGAAGTTTGCCTTGCTA+CGG 0.518974 4_4:+56137249 None:intergenic
AAACCAGCCACCATTTGAAA+AGG 0.520236 4_4:+56136585 None:intergenic
TCCCGAAAATGCATTACGTT+AGG 0.522411 4_4:-56137415 None:intergenic
GAATGCGGTATGATCGTTTG+AGG 0.538021 4_4:-56136755 Msa0689180:CDS
TCCATACACCTATCAAGAAT+AGG 0.544412 4_4:+56137072 None:intergenic
ACCACTTCTTTACGAAGTGG+TGG 0.550403 4_4:+56137314 None:intergenic
AAGAAGTTGATCGGTGCAGA+CGG 0.553790 4_4:+56136516 None:intergenic
GATCATACCGCATTCTTACA+AGG 0.554571 4_4:+56136763 None:intergenic
GTAGGTGATTTGGCTAGCCA+GGG 0.554831 4_4:-56136705 Msa0689180:CDS
GTGTAGGCAAAATCAACTCT+GGG 0.561083 4_4:+56137105 None:intergenic
ATGGAGCATGCGCCGTAGCA+AGG 0.566672 4_4:-56137261 Msa0689180:CDS
TTCTTGTGTTCATGTGTGGA+GGG 0.569126 4_4:+56136862 None:intergenic
ATTCTTGTGTTCATGTGTGG+AGG 0.569293 4_4:+56136861 None:intergenic
ATTTGGCTAGCCAGGGTGAG+AGG 0.571757 4_4:-56136698 Msa0689180:CDS
GGCATCCGAGATTTCGACAC+AGG 0.577334 4_4:-56136542 Msa0689180:CDS
CGTGGCTGGTAGAATACAAA+CGG 0.577843 4_4:-56136730 Msa0689180:CDS
TAGCAGGTTTCTATTTCATG+AGG 0.582086 4_4:-56136563 Msa0689180:CDS
CAGTTCTTGCAGGAAGTCGA+CGG 0.588288 4_4:+56136493 None:intergenic
GAGATTCTTGTGTTCATGTG+TGG 0.591639 4_4:+56136858 None:intergenic
TCCACCACTTCTTTACGAAG+TGG 0.596303 4_4:+56137311 None:intergenic
TCGAGTTGCATCACTGCGAA+TGG 0.597451 4_4:+56137392 None:intergenic
GTGCATGAATCCTCTCACCC+TGG 0.601936 4_4:+56136688 None:intergenic
ACACCCCGATGAAATGGATG+AGG 0.606414 4_4:-56136820 Msa0689180:CDS
TGTGTGGAGGGTATCTTGGT+CGG 0.608323 4_4:+56136874 None:intergenic
ACCACTTCGTAAAGAAGTGG+TGG 0.616825 4_4:-56137312 Msa0689180:CDS
CATGAACACAAGAATCTCAC+AGG 0.619367 4_4:-56136853 Msa0689180:CDS
GCCACCACTTCGTAAAGAAG+TGG 0.629915 4_4:-56137315 Msa0689180:CDS
ATCCTGACCTTGTAAGAATG+CGG 0.634955 4_4:-56136770 Msa0689180:CDS
AGTCGACGGAAGAAGTTGAT+CGG 0.641660 4_4:+56136507 None:intergenic
TCACCAAGCAGTAAACATAG+TGG 0.653759 4_4:-56137360 Msa0689180:CDS
TGAGAAACAACACATGAACA+AGG 0.662150 4_4:+56137141 None:intergenic
CACCAGAGAAAACTGTCATG+AGG 0.672325 4_4:+56137225 None:intergenic
GTATGATCGTTTGAGGAGCG+TGG 0.680386 4_4:-56136748 Msa0689180:CDS
ATGAATAAAGAAGTAGCACG+CGG 0.714106 4_4:+56136648 None:intergenic
CAGTAAACATAGTGGCAGCG+CGG 0.720769 4_4:-56137352 Msa0689180:CDS
ATTCCTCATCCATTTCATCG+GGG 0.747292 4_4:+56136817 None:intergenic
GGTTAGGTGATATCTGCATG+TGG 0.750592 4_4:-56137184 Msa0689180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGCAATCATGTATAAATA+GGG + chr4_4:56136909-56136928 None:intergenic 20.0%
!! ATATGCAATCATGTATAAAT+AGG + chr4_4:56136910-56136929 None:intergenic 20.0%
! CCTGATATTGAAAATAAAGT+TGG + chr4_4:56136990-56137009 None:intergenic 25.0%
!!! CCAACTTTATTTTCAATATC+AGG - chr4_4:56136987-56137006 Msa0689180:intron 25.0%
!! ATATGTTACTCCTTTTCAAA+TGG - chr4_4:56137291-56137310 Msa0689180:CDS 25.0%
! AATAGGTAGAGAAAAAGTGT+AGG + chr4_4:56136800-56136819 None:intergenic 30.0%
TTTCTCTACCTATTCTTGAT+AGG - chr4_4:56136806-56136825 Msa0689180:CDS 30.0%
AAATTCCTCATCCATTTCAT+CGG + chr4_4:56137074-56137093 None:intergenic 30.0%
TTTGCAGTTGGAAAATGGTT+AGG - chr4_4:56136686-56136705 Msa0689180:CDS 35.0%
TGAACAAGGACTGTTGTAAT+AGG + chr4_4:56136734-56136753 None:intergenic 35.0%
TGAGAAACAACACATGAACA+AGG + chr4_4:56136748-56136767 None:intergenic 35.0%
!! TCATGTGTTGTTTCTCATGT+TGG - chr4_4:56136751-56136770 Msa0689180:CDS 35.0%
ACCTATTCTTGATAGGTGTA+TGG - chr4_4:56136813-56136832 Msa0689180:CDS 35.0%
TCCATACACCTATCAAGAAT+AGG + chr4_4:56136817-56136836 None:intergenic 35.0%
AATTCCTCATCCATTTCATC+GGG + chr4_4:56137073-56137092 None:intergenic 35.0%
ATGAATAAAGAAGTAGCACG+CGG + chr4_4:56137241-56137260 None:intergenic 35.0%
! TTTCTGTTTGTTAGCTGCTT+TGG - chr4_4:56137264-56137283 Msa0689180:CDS 35.0%
! TGTTACTCCTTTTCAAATGG+TGG - chr4_4:56137294-56137313 Msa0689180:CDS 35.0%
TAGCAGGTTTCTATTTCATG+AGG - chr4_4:56137323-56137342 Msa0689180:CDS 35.0%
AACATACTATCAGTTCTTGC+AGG + chr4_4:56137406-56137425 None:intergenic 35.0%
TCACCAAGCAGTAAACATAG+TGG - chr4_4:56136526-56136545 Msa0689180:CDS 40.0%
!! CAGATGTTGACTCACATCTA+TGG - chr4_4:56136606-56136625 Msa0689180:CDS 40.0%
GAAAGAAGTTTGCCTTGCTA+CGG + chr4_4:56136640-56136659 None:intergenic 40.0%
GTGTGTTTGCAGTTGGAAAA+TGG - chr4_4:56136681-56136700 Msa0689180:CDS 40.0%
GTGTAGGCAAAATCAACTCT+GGG + chr4_4:56136784-56136803 None:intergenic 40.0%
AGTGTAGGCAAAATCAACTC+TGG + chr4_4:56136785-56136804 None:intergenic 40.0%
TGATAGGTGTATGGAACTTC+AGG - chr4_4:56136822-56136841 Msa0689180:CDS 40.0%
TTCTTGTGTTCATGTGTGGA+GGG + chr4_4:56137027-56137046 None:intergenic 40.0%
ATTCTTGTGTTCATGTGTGG+AGG + chr4_4:56137028-56137047 None:intergenic 40.0%
GAGATTCTTGTGTTCATGTG+TGG + chr4_4:56137031-56137050 None:intergenic 40.0%
CATGAACACAAGAATCTCAC+AGG - chr4_4:56137033-56137052 Msa0689180:intron 40.0%
ATTCCTCATCCATTTCATCG+GGG + chr4_4:56137072-56137091 None:intergenic 40.0%
! AGGTCAGGATTTTTGCTTGT+TGG + chr4_4:56137106-56137125 None:intergenic 40.0%
ATCCTGACCTTGTAAGAATG+CGG - chr4_4:56137116-56137135 Msa0689180:CDS 40.0%
GATCATACCGCATTCTTACA+AGG + chr4_4:56137126-56137145 None:intergenic 40.0%
GGTAGAATACAAACGGTTGT+AGG - chr4_4:56137163-56137182 Msa0689180:CDS 40.0%
ACAAACGGTTGTAGGTGATT+TGG - chr4_4:56137171-56137190 Msa0689180:CDS 40.0%
AAACCAGCCACCATTTGAAA+AGG + chr4_4:56137304-56137323 None:intergenic 40.0%
CTGCCACTATGTTTACTGCT+TGG + chr4_4:56136532-56136551 None:intergenic 45.0%
ACCACTTCTTTACGAAGTGG+TGG + chr4_4:56136575-56136594 None:intergenic 45.0%
ACCACTTCGTAAAGAAGTGG+TGG - chr4_4:56136574-56136593 Msa0689180:CDS 45.0%
TCCACCACTTCTTTACGAAG+TGG + chr4_4:56136578-56136597 None:intergenic 45.0%
CACCAGAGAAAACTGTCATG+AGG + chr4_4:56136664-56136683 None:intergenic 45.0%
TTCTCTGGTGTGTTTGCAGT+TGG - chr4_4:56136674-56136693 Msa0689180:CDS 45.0%
GGTTAGGTGATATCTGCATG+TGG - chr4_4:56136702-56136721 Msa0689180:CDS 45.0%
!! TTCATGTGTGGAGGGTATCT+TGG + chr4_4:56137019-56137038 None:intergenic 45.0%
TGTAGTACACCCCGATGAAA+TGG - chr4_4:56137060-56137079 Msa0689180:intron 45.0%
TACCGCATTCTTACAAGGTC+AGG + chr4_4:56137121-56137140 None:intergenic 45.0%
GAATGCGGTATGATCGTTTG+AGG - chr4_4:56137131-56137150 Msa0689180:CDS 45.0%
CGTGGCTGGTAGAATACAAA+CGG - chr4_4:56137156-56137175 Msa0689180:CDS 45.0%
! ACTCCTTTTCAAATGGTGGC+TGG - chr4_4:56137298-56137317 Msa0689180:CDS 45.0%
! AAGAAGTTGATCGGTGCAGA+CGG + chr4_4:56137373-56137392 None:intergenic 45.0%
! AGTCGACGGAAGAAGTTGAT+CGG + chr4_4:56137382-56137401 None:intergenic 45.0%
! TCGAGTTGCATCACTGCGAA+TGG + chr4_4:56136497-56136516 None:intergenic 50.0%
CAGTAAACATAGTGGCAGCG+CGG - chr4_4:56136534-56136553 Msa0689180:CDS 50.0%
GCCACCACTTCGTAAAGAAG+TGG - chr4_4:56136571-56136590 Msa0689180:CDS 50.0%
! CGCCTCATGACAGTTTTCTC+TGG - chr4_4:56136659-56136678 Msa0689180:CDS 50.0%
!! TGTGTGGAGGGTATCTTGGT+CGG + chr4_4:56137015-56137034 None:intergenic 50.0%
ACACCCCGATGAAATGGATG+AGG - chr4_4:56137066-56137085 Msa0689180:CDS 50.0%
GTATGATCGTTTGAGGAGCG+TGG - chr4_4:56137138-56137157 Msa0689180:CDS 50.0%
! TGTAGGTGATTTGGCTAGCC+AGG - chr4_4:56137180-56137199 Msa0689180:CDS 50.0%
! GTAGGTGATTTGGCTAGCCA+GGG - chr4_4:56137181-56137200 Msa0689180:CDS 50.0%
GGATTCATGCACTGTTGAGC+TGG - chr4_4:56137209-56137228 Msa0689180:CDS 50.0%
!! CAAATGGTGGCTGGTTTAGC+AGG - chr4_4:56137307-56137326 Msa0689180:CDS 50.0%
GGAAGCCTGTGTCGAAATCT+CGG + chr4_4:56137352-56137371 None:intergenic 50.0%
CAGTTCTTGCAGGAAGTCGA+CGG + chr4_4:56137396-56137415 None:intergenic 50.0%
! ATTTGGCTAGCCAGGGTGAG+AGG - chr4_4:56137188-56137207 Msa0689180:CDS 55.0%
GTGCATGAATCCTCTCACCC+TGG + chr4_4:56137201-56137220 None:intergenic 55.0%
GGCATCCGAGATTTCGACAC+AGG - chr4_4:56137344-56137363 Msa0689180:CDS 55.0%
AACATAGTGGCAGCGCGGCT+CGG - chr4_4:56136539-56136558 Msa0689180:CDS 60.0%
ATGGAGCATGCGCCGTAGCA+AGG - chr4_4:56136625-56136644 Msa0689180:CDS 60.0%
! GATCGTTTGAGGAGCGTGGC+TGG - chr4_4:56137142-56137161 Msa0689180:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 56136479 56137429 56136479 ID=Msa0689180;Name=Msa0689180
chr4_4 mRNA 56136479 56137429 56136479 ID=Msa0689180-mRNA-1;Parent=Msa0689180;Name=Msa0689180-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|261
chr4_4 exon 56137065 56137429 56137065 ID=Msa0689180-mRNA-1:exon:14731;Parent=Msa0689180-mRNA-1
chr4_4 exon 56136479 56136899 56136479 ID=Msa0689180-mRNA-1:exon:14730;Parent=Msa0689180-mRNA-1
chr4_4 CDS 56137065 56137429 56137065 ID=Msa0689180-mRNA-1:cds;Parent=Msa0689180-mRNA-1
chr4_4 CDS 56136479 56136899 56136479 ID=Msa0689180-mRNA-1:cds;Parent=Msa0689180-mRNA-1
Gene Sequence

>Msa0689180

ATGCATTACGTTAGGCCATTCGCAGTGATGCAACTCGATATGCTACGTCACCAAGCAGTAAACATAGTGGCAGCGCGGCTCGGTCGAGCAGAGCCACCACTTCGTAAAGAAGTGGTGGAATACATGTCAGATGTTGACTCACATCTATGGAGCATGCGCCGTAGCAAGGCAAACTTCTTTCGCCTCATGACAGTTTTCTCTGGTGTGTTTGCAGTTGGAAAATGGTTAGGTGATATCTGCATGTGGTTAAATCCTATTACAACAGTCCTTGTTCATGTGTTGTTTCTCATGTTGGTTTGCTTCCCAGAGTTGATTTTGCCTACACTTTTTCTCTACCTATTCTTGATAGGTGTATGGAACTTCAGGTACCGACCAAGATACCCTCCACACATGAACACAAGAATCTCACAGGCTGATGTAGTACACCCCGATGAAATGGATGAGGAATTTGATACTTTTCCAACAAGCAAAAATCCTGACCTTGTAAGAATGCGGTATGATCGTTTGAGGAGCGTGGCTGGTAGAATACAAACGGTTGTAGGTGATTTGGCTAGCCAGGGTGAGAGGATTCATGCACTGTTGAGCTGGAGAGATCCGCGTGCTACTTCTTTATTCATTACTTTCTGTTTGTTAGCTGCTTTGGTGTTATATGTTACTCCTTTTCAAATGGTGGCTGGTTTAGCAGGTTTCTATTTCATGAGGCATCCGAGATTTCGACACAGGCTTCCGTCTGCACCGATCAACTTCTTCCGTCGACTTCCTGCAAGAACTGATAGTATGTTGTAG
Protein sequence

>Msa0689180

MHYVRPFAVMQLDMLRHQAVNIVAARLGRAEPPLRKEVVEYMSDVDSHLWSMRRSKANFFRLMTVFSGVFAVGKWLGDICMWLNPITTVLVHVLFLMLVCFPELILPTLFLYLFLIGVWNFRYRPRYPPHMNTRISQADVVHPDEMDEEFDTFPTSKNPDLVRMRYDRLRSVAGRIQTVVGDLASQGERIHALLSWRDPRATSLFITFCLLAALVLYVTPFQMVAGLAGFYFMRHPRFRHRLPSAPINFFRRLPARTDSML*