AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010515

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010515.t1 MTR_5g020510 92.459 305 14 4 1 304 1 297 0.0 526
MS.gene010515.t1 MTR_4g134580 41.152 243 93 7 105 304 113 348 5.11e-52 176
MS.gene010515.t1 MTR_1g077020 41.000 200 98 2 105 304 9 188 3.64e-50 165
MS.gene010515.t1 MTR_5g032600 42.000 200 108 2 105 302 78 271 2.71e-47 160
MS.gene010515.t1 MTR_3g100650 41.284 218 104 4 95 302 70 273 3.36e-45 155
MS.gene010515.t1 MTR_7g010300 39.437 213 102 7 103 303 86 283 2.88e-44 155
MS.gene010515.t1 MTR_5g065440 39.623 212 112 5 105 302 58 267 1.26e-41 145
MS.gene010515.t1 MTR_2g076780 34.263 251 132 7 69 303 4 237 3.73e-40 141
MS.gene010515.t1 MTR_6g012280 38.208 212 107 5 105 306 91 288 5.89e-39 140
MS.gene010515.t1 MTR_8g069080 37.321 209 100 6 105 297 69 262 8.24e-39 138
MS.gene010515.t1 MTR_8g467340 61.404 57 22 0 240 296 271 327 4.72e-19 87.4
MS.gene010515.t1 MTR_8g467340 52.113 71 25 2 98 166 57 120 4.51e-18 84.3
MS.gene010515.t1 MTR_3g039810 53.846 65 30 0 94 158 9 73 1.29e-18 79.7
MS.gene010515.t1 MTR_6g073013 55.000 60 26 1 240 298 101 160 1.86e-18 82.0
MS.gene010515.t1 MTR_6g073013 62.000 50 18 1 105 153 19 68 4.29e-15 72.8
MS.gene010515.t1 MTR_8g442330 28.659 164 79 3 114 277 14 139 4.65e-18 79.7
MS.gene010515.t1 MTR_8g051480 48.387 62 31 1 241 302 68 128 2.29e-15 72.0
MS.gene010515.t1 MTR_8g069380 46.032 63 34 0 240 302 52 114 5.87e-15 70.5
MS.gene010515.t1 MTR_6g012220 57.143 49 17 1 105 153 21 65 1.14e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010515.t1 AT2G18350 47.639 233 86 8 81 304 57 262 1.60e-58 189
MS.gene010515.t1 AT3G50890 37.313 268 126 7 43 301 8 242 9.80e-50 166
MS.gene010515.t1 AT2G02540 39.013 223 90 6 103 302 85 284 1.57e-48 165
MS.gene010515.t1 AT2G02540 39.013 223 90 6 103 302 85 284 1.57e-48 165
MS.gene010515.t1 AT4G24660 39.070 215 86 4 101 306 45 223 3.86e-48 161
MS.gene010515.t1 AT4G24660 39.810 211 82 4 101 302 45 219 9.11e-48 160
MS.gene010515.t1 AT1G14440 40.191 209 100 5 103 302 88 280 8.76e-45 155
MS.gene010515.t1 AT1G14440 40.191 209 100 5 103 302 88 280 8.76e-45 155
MS.gene010515.t1 AT1G69600 36.475 244 115 6 86 315 12 229 1.04e-43 150
MS.gene010515.t1 AT5G65410 38.389 211 103 4 95 301 65 252 1.49e-40 143
MS.gene010515.t1 AT3G28920 37.379 206 120 3 102 300 49 252 5.00e-40 143
MS.gene010515.t1 AT5G15210 34.137 249 124 6 73 296 2 235 3.13e-39 139
MS.gene010515.t1 AT5G60480 35.814 215 95 6 91 296 23 203 5.83e-36 130
MS.gene010515.t1 AT5G42780 30.457 197 113 5 105 299 64 238 1.13e-26 105
MS.gene010515.t1 AT1G75240 76.471 51 12 0 105 155 76 126 5.91e-23 97.4
MS.gene010515.t1 AT5G39760 55.385 65 29 0 240 304 200 264 3.52e-20 90.1
MS.gene010515.t1 AT1G74660 53.448 58 27 0 101 158 35 92 1.32e-18 80.1
MS.gene010515.t1 AT1G74660 53.448 58 27 0 101 158 35 92 1.23e-17 77.4
MS.gene010515.t1 AT3G28917 54.098 61 27 1 99 158 27 87 1.40e-16 74.7
MS.gene010515.t1 AT1G18835 51.852 54 23 1 105 158 26 76 1.60e-13 65.9

Find 57 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATGTCACAAACAACTTT+AGG 0.291725 5.2:+11751834 MS.gene010515:CDS
CCGTCCATGATGATGACTTT+TGG 0.355768 5.2:+11752434 MS.gene010515:CDS
AGAGTTTCACAACCTAGTTC+TGG 0.368324 5.2:+11752401 MS.gene010515:CDS
AAGATGGTGTTGGAAGATTA+AGG 0.378783 5.2:-11752367 None:intergenic
TAGTAGTAGTAGTATGGTTA+GGG 0.404916 5.2:-11751947 None:intergenic
GTTGTTGCAGCCGTTAGATC+TGG 0.406325 5.2:-11752038 None:intergenic
CTTACCCTCTTCTTCAAAAC+CGG 0.408989 5.2:-11752533 None:intergenic
GCTTAAAAGTGGATAATTGC+AGG 0.412519 5.2:+11752815 MS.gene010515:CDS
CGGTTGCTGCGGCGTCTGTA+TGG 0.433418 5.2:-11752513 None:intergenic
ATGGAGTTTGCTGAAAAGAT+TGG 0.437625 5.2:+11752590 MS.gene010515:CDS
CATACAGACGCCGCAGCAAC+CGG 0.441402 5.2:+11752514 MS.gene010515:CDS
GAGGAATACTATGTTGTTGT+TGG 0.445811 5.2:-11752289 None:intergenic
AGTGAAGATCTCAACATGTT+TGG 0.446843 5.2:+11752479 MS.gene010515:CDS
ATGGGAAGCCACGTGGTAGA+TGG 0.447420 5.2:+11752170 MS.gene010515:CDS
GTTGATGATGTTATTTGTTG+TGG 0.461191 5.2:-11752098 None:intergenic
GATGTTATTTGTTGTGGCTG+AGG 0.462310 5.2:-11752092 None:intergenic
CGTGGTTTCTCAGACATTCT+CGG 0.464493 5.2:-11752139 None:intergenic
TCAAGTTGGTATCAAGAGAC+AGG 0.468371 5.2:+11752661 MS.gene010515:CDS
GGGGTACCTTCTTCACCGCT+TGG 0.472411 5.2:-11752209 None:intergenic
ACTTGAGGTGGTGGTGGAGT+TGG 0.474110 5.2:-11751885 None:intergenic
GAGAAACCACGCGGCAAGCA+TGG 0.475746 5.2:+11752151 MS.gene010515:CDS
CAGCACATTTGAAATATTGT+GGG 0.475954 5.2:-11752229 None:intergenic
GCAGCACATTTGAAATATTG+TGG 0.476946 5.2:-11752230 None:intergenic
TCTTCACTTGATGATTCAGC+TGG 0.479858 5.2:-11752464 None:intergenic
GTGTGAACTTGAGGTGGTGG+TGG 0.490980 5.2:-11751891 None:intergenic
TTCACAACCTAGTTCTGGAC+AGG 0.499932 5.2:+11752406 MS.gene010515:CDS
ATGACAGGTCTTTGAGAAGA+AGG 0.512659 5.2:-11752011 None:intergenic
TTCATGCCAAGCGGTGAAGA+AGG 0.514566 5.2:+11752203 MS.gene010515:CDS
TGGAGTTTGCTGAAAAGATT+GGG 0.549528 5.2:+11752591 MS.gene010515:CDS
AGAAACCACGCGGCAAGCAT+GGG 0.549901 5.2:+11752152 MS.gene010515:CDS
GGTGGAACCTGTCCAGAACT+AGG 0.552234 5.2:-11752413 None:intergenic
ATACACTTGGTGCTTAAAAG+TGG 0.558616 5.2:+11752804 MS.gene010515:CDS
GTTAGATCTGGATCTATGAC+AGG 0.562020 5.2:-11752026 None:intergenic
AGGCGAAACTCGCATACACT+TGG 0.566495 5.2:+11752791 MS.gene010515:CDS
GAAGGTGCAAGATGTGGTGG+TGG 0.572439 5.2:-11751993 None:intergenic
TGAGATGAAGAAGATGGTGT+TGG 0.575563 5.2:-11752377 None:intergenic
TGATCCAAAAGTCATCATCA+TGG 0.575663 5.2:-11752438 None:intergenic
TTCTTCAAAACCGGTTGCTG+CGG 0.576173 5.2:-11752524 None:intergenic
AATGTGTGAACTTGAGGTGG+TGG 0.602598 5.2:-11751894 None:intergenic
TGTCATAGATCCAGATCTAA+CGG 0.606727 5.2:+11752028 MS.gene010515:CDS
AAGACTAATGTGTGAACTTG+AGG 0.616691 5.2:-11751900 None:intergenic
CCAAAAGTCATCATCATGGA+CGG 0.622115 5.2:-11752434 None:intergenic
AGCCACGTGGTAGATGGATG+TGG 0.625991 5.2:+11752176 MS.gene010515:CDS
ACTCTTTGAGATGAAGAAGA+TGG 0.637378 5.2:-11752383 None:intergenic
GGCTTCCCATGCTTGCCGCG+TGG 0.643184 5.2:-11752157 None:intergenic
GAAGAAGGTGCAAGATGTGG+TGG 0.651537 5.2:-11751996 None:intergenic
AGCACATTTGAAATATTGTG+GGG 0.654466 5.2:-11752228 None:intergenic
ACATGCTGAACATGTTGTTG+AGG 0.672696 5.2:-11752308 None:intergenic
AGTTTGCTGAAAAGATTGGG+TGG 0.678186 5.2:+11752594 MS.gene010515:CDS
CATCATCAAAACAACAACAA+CGG 0.680341 5.2:+11752341 MS.gene010515:CDS
AAAGTCATCATCATGGACGG+TGG 0.680716 5.2:-11752431 None:intergenic
TGAGAAGAAGGTGCAAGATG+TGG 0.685772 5.2:-11751999 None:intergenic
GGCAAGCATGGGAAGCCACG+TGG 0.697743 5.2:+11752163 MS.gene010515:CDS
ACTAATGTGTGAACTTGAGG+TGG 0.703165 5.2:-11751897 None:intergenic
CACCACATCCATCTACCACG+TGG 0.722647 5.2:-11752178 None:intergenic
TGTGGTGAATTCATGCCAAG+CGG 0.769326 5.2:+11752194 MS.gene010515:CDS
AGAATGTCTGAGAAACCACG+CGG 0.882510 5.2:+11752142 MS.gene010515:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTTTGATGATGATAATT+AGG - chr5.2:11752335-11752354 None:intergenic 20.0%
!!! TTTTTTTCAAAAAAGCTTAG+AGG + chr5.2:11752771-11752790 MS.gene010515:intron 20.0%
!! TATGTTTTCGATGGAAATTA+CGG - chr5.2:11752268-11752287 None:intergenic 25.0%
AAGATGTCACAAACAACTTT+AGG + chr5.2:11751834-11751853 MS.gene010515:CDS 30.0%
CATCATCAAAACAACAACAA+CGG + chr5.2:11752341-11752360 MS.gene010515:CDS 30.0%
TAGTAGTAGTAGTAGTAGTA+TGG - chr5.2:11751956-11751975 None:intergenic 30.0%
TAGTAGTAGTAGTATGGTTA+GGG - chr5.2:11751950-11751969 None:intergenic 30.0%
! AGCACATTTGAAATATTGTG+GGG - chr5.2:11752231-11752250 None:intergenic 30.0%
! CAGCACATTTGAAATATTGT+GGG - chr5.2:11752232-11752251 None:intergenic 30.0%
!! GTTGATGATGTTATTTGTTG+TGG - chr5.2:11752101-11752120 None:intergenic 30.0%
AAGACTAATGTGTGAACTTG+AGG - chr5.2:11751903-11751922 None:intergenic 35.0%
AGTGAAGATCTCAACATGTT+TGG + chr5.2:11752479-11752498 MS.gene010515:CDS 35.0%
GAGGAATACTATGTTGTTGT+TGG - chr5.2:11752292-11752311 None:intergenic 35.0%
GCAACAAAAAGATAGGATGA+TGG + chr5.2:11752571-11752590 MS.gene010515:CDS 35.0%
GCTTAAAAGTGGATAATTGC+AGG + chr5.2:11752815-11752834 MS.gene010515:CDS 35.0%
GTAGTAGTAGTAGTATGGTT+AGG - chr5.2:11751951-11751970 None:intergenic 35.0%
TCTCACAGCAACAAAAAGAT+AGG + chr5.2:11752564-11752583 MS.gene010515:CDS 35.0%
TGATCCAAAAGTCATCATCA+TGG - chr5.2:11752441-11752460 None:intergenic 35.0%
TGTCATAGATCCAGATCTAA+CGG + chr5.2:11752028-11752047 MS.gene010515:CDS 35.0%
! AAGATGGTGTTGGAAGATTA+AGG - chr5.2:11752370-11752389 None:intergenic 35.0%
! GCAGCACATTTGAAATATTG+TGG - chr5.2:11752233-11752252 None:intergenic 35.0%
! GTTGTTGGATATGTTTTCGA+TGG - chr5.2:11752277-11752296 None:intergenic 35.0%
!! ACTCTTTGAGATGAAGAAGA+TGG - chr5.2:11752386-11752405 None:intergenic 35.0%
!! ATACACTTGGTGCTTAAAAG+TGG + chr5.2:11752804-11752823 MS.gene010515:CDS 35.0%
!! ATGGAGTTTGCTGAAAAGAT+TGG + chr5.2:11752590-11752609 MS.gene010515:CDS 35.0%
!! TGGAGTTTGCTGAAAAGATT+GGG + chr5.2:11752591-11752610 MS.gene010515:CDS 35.0%
!!! CAACAGTTTTGTTCTCAAGT+TGG + chr5.2:11752647-11752666 MS.gene010515:CDS 35.0%
ACATGCTGAACATGTTGTTG+AGG - chr5.2:11752311-11752330 None:intergenic 40.0%
ACTAATGTGTGAACTTGAGG+TGG - chr5.2:11751900-11751919 None:intergenic 40.0%
AGAGTTTCACAACCTAGTTC+TGG + chr5.2:11752401-11752420 MS.gene010515:CDS 40.0%
CCAAAAGTCATCATCATGGA+CGG - chr5.2:11752437-11752456 None:intergenic 40.0%
CTTACCCTCTTCTTCAAAAC+CGG - chr5.2:11752536-11752555 None:intergenic 40.0%
GTTAGATCTGGATCTATGAC+AGG - chr5.2:11752029-11752048 None:intergenic 40.0%
TGAGATGAAGAAGATGGTGT+TGG - chr5.2:11752380-11752399 None:intergenic 40.0%
! ATGACAGGTCTTTGAGAAGA+AGG - chr5.2:11752014-11752033 None:intergenic 40.0%
! TCTTCACTTGATGATTCAGC+TGG - chr5.2:11752467-11752486 None:intergenic 40.0%
! TGGTTAGGGTGTGAATTTTG+AGG - chr5.2:11751936-11751955 None:intergenic 40.0%
!! AGTTTGCTGAAAAGATTGGG+TGG + chr5.2:11752594-11752613 MS.gene010515:CDS 40.0%
!! GATGTTATTTGTTGTGGCTG+AGG - chr5.2:11752095-11752114 None:intergenic 40.0%
!! TCAAGTTGGTATCAAGAGAC+AGG + chr5.2:11752661-11752680 MS.gene010515:CDS 40.0%
!! TTAGGGTGTGAATTTTGAGG+TGG - chr5.2:11751933-11751952 None:intergenic 40.0%
!!! TAGGGTGTGAATTTTGAGGT+GGG - chr5.2:11751932-11751951 None:intergenic 40.0%
AAAGTCATCATCATGGACGG+TGG - chr5.2:11752434-11752453 None:intergenic 45.0%
AATGTGTGAACTTGAGGTGG+TGG - chr5.2:11751897-11751916 None:intergenic 45.0%
AGAATGTCTGAGAAACCACG+CGG + chr5.2:11752142-11752161 MS.gene010515:CDS 45.0%
CGTGGTTTCTCAGACATTCT+CGG - chr5.2:11752142-11752161 None:intergenic 45.0%
TGTGGTGAATTCATGCCAAG+CGG + chr5.2:11752194-11752213 MS.gene010515:CDS 45.0%
TTCTTCAAAACCGGTTGCTG+CGG - chr5.2:11752527-11752546 None:intergenic 45.0%
! TGAGAAGAAGGTGCAAGATG+TGG - chr5.2:11752002-11752021 None:intergenic 45.0%
!! CCGTCCATGATGATGACTTT+TGG + chr5.2:11752434-11752453 MS.gene010515:CDS 45.0%
!! TTCACAACCTAGTTCTGGAC+AGG + chr5.2:11752406-11752425 MS.gene010515:CDS 45.0%
!!! AGCAACCGGTTTTGAAGAAG+AGG + chr5.2:11752528-11752547 MS.gene010515:CDS 45.0%
!!! CGGTTTTGAAGAAGAGGGTA+AGG + chr5.2:11752534-11752553 MS.gene010515:CDS 45.0%
!!! GCAACCGGTTTTGAAGAAGA+GGG + chr5.2:11752529-11752548 MS.gene010515:CDS 45.0%
AGGCGAAACTCGCATACACT+TGG + chr5.2:11752791-11752810 MS.gene010515:CDS 50.0%
GTTGTTGCAGCCGTTAGATC+TGG - chr5.2:11752041-11752060 None:intergenic 50.0%
TTCATGCCAAGCGGTGAAGA+AGG + chr5.2:11752203-11752222 MS.gene010515:CDS 50.0%
! GAAGAAGGTGCAAGATGTGG+TGG - chr5.2:11751999-11752018 None:intergenic 50.0%
AGAAACCACGCGGCAAGCAT+GGG + chr5.2:11752152-11752171 MS.gene010515:CDS 55.0%
AGCCACGTGGTAGATGGATG+TGG + chr5.2:11752176-11752195 MS.gene010515:CDS 55.0%
ATGGGAAGCCACGTGGTAGA+TGG + chr5.2:11752170-11752189 MS.gene010515:CDS 55.0%
CACCACATCCATCTACCACG+TGG - chr5.2:11752181-11752200 None:intergenic 55.0%
GGTGGAACCTGTCCAGAACT+AGG - chr5.2:11752416-11752435 None:intergenic 55.0%
! GAAGGTGCAAGATGTGGTGG+TGG - chr5.2:11751996-11752015 None:intergenic 55.0%
! GTGTGAACTTGAGGTGGTGG+TGG - chr5.2:11751894-11751913 None:intergenic 55.0%
!! ACTTGAGGTGGTGGTGGAGT+TGG - chr5.2:11751888-11751907 None:intergenic 55.0%
CATACAGACGCCGCAGCAAC+CGG + chr5.2:11752514-11752533 MS.gene010515:CDS 60.0%
GAGAAACCACGCGGCAAGCA+TGG + chr5.2:11752151-11752170 MS.gene010515:CDS 60.0%
! GGGGTACCTTCTTCACCGCT+TGG - chr5.2:11752212-11752231 None:intergenic 60.0%
CGGTTGCTGCGGCGTCTGTA+TGG - chr5.2:11752516-11752535 None:intergenic 65.0%
GGCAAGCATGGGAAGCCACG+TGG + chr5.2:11752163-11752182 MS.gene010515:CDS 65.0%
GGCTTCCCATGCTTGCCGCG+TGG - chr5.2:11752160-11752179 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 11751825 11752855 11751825 ID=MS.gene010515
chr5.2 mRNA 11751825 11752855 11751825 ID=MS.gene010515.t1;Parent=MS.gene010515
chr5.2 exon 11751825 11752735 11751825 ID=MS.gene010515.t1.exon1;Parent=MS.gene010515.t1
chr5.2 CDS 11751825 11752735 11751825 ID=cds.MS.gene010515.t1;Parent=MS.gene010515.t1
chr5.2 exon 11752786 11752855 11752786 ID=MS.gene010515.t1.exon2;Parent=MS.gene010515.t1
chr5.2 CDS 11752786 11752855 11752786 ID=cds.MS.gene010515.t1;Parent=MS.gene010515.t1
Gene Sequence

>MS.gene010515

ATGGAAACAAAGATGTCACAAACAACTTTAGGTTACAATAGAGATTCTTCTTCTTCTTCACCAACTCCACCACCACCTCAAGTTCACACATTAGTCTTCAATAACCCACCTCAAAATTCACACCCTAACCATACTACTACTACTACTACTACTACTACTAATCTTTATCCACCACCACATCTTGCACCTTCTTCTCAAAGACCTGTCATAGATCCAGATCTAACGGCTGCAACAACAACAACAAACACTTCTACAATAACAACACAACCTCAGCCACAACAAATAACATCATCAACAACAACAAAAATATGTTACCGAGAATGTCTGAGAAACCACGCGGCAAGCATGGGAAGCCACGTGGTAGATGGATGTGGTGAATTCATGCCAAGCGGTGAAGAAGGTACCCCACAATATTTCAAATGTGCTGCTTGTGATTGTCACCGTAATTTCCATCGAAAACATATCCAACAACAACATAGTATTCCTCAACAACATGTTCAGCATGTTCCTAATTATCATCATCAAAACAACAACAACGGTCACCTTAATCTTCCAACACCATCTTCTTCATCTCAAAGAGTTTCACAACCTAGTTCTGGACAGGTTCCACCGTCCATGATGATGACTTTTGGATCAGTTCCAGCTGAATCATCAAGTGAAGATCTCAACATGTTTGGTGCACAATTTTCCATACAGACGCCGCAGCAACCGGTTTTGAAGAAGAGGGTAAGGACGAAATTCTCACAGCAACAAAAAGATAGGATGATGGAGTTTGCTGAAAAGATTGGGTGGAAGATTCAGAAACATGATGAACAAGAAGTGCAACAGTTTTGTTCTCAAGTTGGTATCAAGAGACAGGTTTTTAAAGTTTTTATGCATAATAACAAACAAGCTATGAAGAAACAGCAAATGTAAGCTTAGTTATAATAAACTAATTTCATTATTATTTTTTTCAAAAAAGCTTAGAGGCGAAACTCGCATACACTTGGTGCTTAAAAGTGGATAATTGCAGGTTCAAACTCGCACTCTAG
Protein sequence

>MS.gene010515.t1

METKMSQTTLGYNRDSSSSSPTPPPPQVHTLVFNNPPQNSHPNHTTTTTTTTTNLYPPPHLAPSSQRPVIDPDLTAATTTTNTSTITTQPQPQQITSSTTTKICYRECLRNHAASMGSHVVDGCGEFMPSGEEGTPQYFKCAACDCHRNFHRKHIQQQHSIPQQHVQHVPNYHHQNNNNGHLNLPTPSSSSQRVSQPSSGQVPPSMMMTFGSVPAESSSEDLNMFGAQFSIQTPQQPVLKKRVRTKFSQQQKDRMMEFAEKIGWKIQKHDEQEVQQFCSQVGIKRQVFKVFMHNNKQAMKKQQILEAKLAYTWCLKVDNCRFKLAL