AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene063599

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063599.t1 MTR_1g046650 61.624 271 67 3 2 236 46 315 6.62e-107 311
MS.gene063599.t1 MTR_1g046650 61.624 271 67 3 2 236 46 315 1.45e-106 310
MS.gene063599.t1 MTR_1g046650 61.624 271 67 3 2 236 77 346 3.72e-106 310
MS.gene063599.t1 MTR_7g024290 62.362 271 65 4 2 235 46 316 5.58e-106 309
MS.gene063599.t1 MTR_1g046640 61.993 271 66 5 2 236 46 315 2.14e-103 302
MS.gene063599.t1 MTR_5g067400 60.741 270 70 2 2 235 46 315 2.84e-103 302
MS.gene063599.t1 MTR_5g076810 60.223 269 70 3 5 236 2 270 5.16e-101 294
MS.gene063599.t1 MTR_5g076720 57.875 273 76 2 2 235 117 389 8.76e-100 295
MS.gene063599.t1 MTR_5g076505 57.509 273 77 3 2 235 42 314 1.58e-99 292
MS.gene063599.t1 MTR_2g038430 57.244 283 72 4 2 235 60 342 2.55e-98 290
MS.gene063599.t1 MTR_7g094390 57.407 270 79 2 2 235 207 476 1.81e-97 293
MS.gene063599.t1 MTR_5g076520 57.836 268 73 2 2 229 46 313 4.16e-97 286
MS.gene063599.t1 MTR_5g076820 70.558 197 57 1 5 200 56 252 7.23e-95 280
MS.gene063599.t1 MTR_1g046650 60.324 247 61 3 26 236 1 246 9.87e-95 278
MS.gene063599.t1 MTR_5g076660 55.351 271 82 3 2 233 68 338 8.84e-93 276
MS.gene063599.t1 MTR_5g076370 53.137 271 88 2 2 233 69 339 5.22e-91 271
MS.gene063599.t1 MTR_2g038420 55.636 275 81 4 2 235 60 334 1.64e-89 268
MS.gene063599.t1 MTR_5g061290 53.623 276 84 6 2 235 53 326 7.96e-89 265
MS.gene063599.t1 MTR_5g076540 70.000 180 54 0 4 183 48 227 5.97e-84 250
MS.gene063599.t1 MTR_5g077020 63.590 195 57 4 9 193 17 207 9.45e-76 229
MS.gene063599.t1 MTR_4g058025 76.522 115 26 1 37 150 14 128 8.49e-55 174
MS.gene063599.t1 MTR_4g094468 44.792 192 102 2 2 190 132 322 6.47e-48 160
MS.gene063599.t1 MTR_7g085590 28.931 159 108 2 24 178 109 266 9.08e-17 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063599.t1 AT5G37930 32.323 198 129 2 2 194 145 342 2.04e-27 107
MS.gene063599.t1 AT5G37870 31.351 185 120 6 2 180 77 260 2.12e-21 90.5
MS.gene063599.t1 AT1G66650 31.527 203 127 6 2 192 118 320 6.21e-21 89.7
MS.gene063599.t1 AT1G66620 27.861 201 133 5 2 192 76 274 3.46e-20 87.8
MS.gene063599.t1 AT5G37890 30.055 183 124 4 2 180 83 265 9.75e-19 83.2
MS.gene063599.t1 AT5G37910 28.108 185 127 3 2 180 70 254 1.23e-17 80.1
MS.gene063599.t1 AT5G62800 33.562 146 93 3 5 146 80 225 4.46e-17 79.3
MS.gene063599.t1 AT5G62800 34.028 144 91 3 5 144 80 223 5.69e-17 78.6
MS.gene063599.t1 AT1G66630 28.704 216 129 6 2 192 81 296 1.85e-15 74.3
MS.gene063599.t1 AT1G66660 27.805 205 135 6 2 194 138 341 2.31e-14 71.6
MS.gene063599.t1 AT1G66660 27.273 198 131 6 9 194 21 217 6.84e-14 68.9
MS.gene063599.t1 AT5G37900 26.842 190 130 4 15 195 48 237 9.52e-13 65.9
MS.gene063599.t1 AT1G66610 26.667 150 107 3 34 180 185 334 3.97e-12 65.5

Find 46 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATAATAGTACTATGCTTT+TGG 0.189283 5.2:+65434719 MS.gene063599:CDS
ACCTCGTTCACCGTCTCGTT+GGG 0.259864 5.2:+65435388 MS.gene063599:CDS
GCCGTCCTCTAGTCGCTTCT+TGG 0.293410 5.2:-65435322 None:intergenic
CTTATCTTTGATGTTGTAAT+CGG 0.318108 5.2:-65435355 None:intergenic
TACTCAGATTCGGAAGAGTT+TGG 0.344645 5.2:-65434771 None:intergenic
GTTCTTCAAGAGGAAAATTA+CGG 0.361161 5.2:+65434681 MS.gene063599:CDS
TGAGTATAGTTATGATATAT+TGG 0.366607 5.2:+65434788 MS.gene063599:CDS
AAATGCCTAGACACCACTTT+TGG 0.388797 5.2:-65434573 None:intergenic
GAGTTCCTTGTGATTCCATT+TGG 0.395774 5.2:+65434891 MS.gene063599:CDS
TCATGTCGCAATGAAATATA+TGG 0.427208 5.2:+65434447 MS.gene063599:CDS
AACATAGTCACAACCTGAAA+GGG 0.454084 5.2:-65434544 None:intergenic
GGTTTCATCAGTAGACTTCA+AGG 0.454847 5.2:-65434655 None:intergenic
ATCATAACTATACTCAGATT+CGG 0.470039 5.2:-65434781 None:intergenic
TGTTGTAATCGGCAAGGGTC+CGG 0.474032 5.2:-65435344 None:intergenic
GACCTCGTTCACCGTCTCGT+TGG 0.481105 5.2:+65435387 MS.gene063599:CDS
TATTGCGAAGAGTGTCCAAC+AGG 0.510924 5.2:+65434845 MS.gene063599:CDS
GCTGTTAATATTTATTGTGT+TGG 0.514058 5.2:+65434747 MS.gene063599:CDS
ATGCAAATTTCTAGCTTGAG+AGG 0.524126 5.2:-65434921 None:intergenic
CTTTGATGTTGTAATCGGCA+AGG 0.528531 5.2:-65435350 None:intergenic
CATGAAGAAGAATGCATCCA+TGG 0.530214 5.2:+65434507 MS.gene063599:CDS
CATCACCAAAAGTGGTGTCT+AGG 0.532139 5.2:+65434568 MS.gene063599:CDS
GAGACGGTGAACGAGGTCAA+TGG 0.532925 5.2:-65435382 None:intergenic
AAATAAGTTACACTAGAAAG+AGG 0.535076 5.2:+65434481 MS.gene063599:CDS
TGAAACCATTGTTCTTCAAG+AGG 0.536422 5.2:+65434671 MS.gene063599:CDS
GGCATTTCAGCTATAGACAC+GGG 0.540766 5.2:+65434589 MS.gene063599:CDS
CCTCGTTCACCGTCTCGTTG+GGG 0.544443 5.2:+65435389 MS.gene063599:CDS
TTTGATGTTGTAATCGGCAA+GGG 0.545339 5.2:-65435349 None:intergenic
CAACATAGTCACAACCTGAA+AGG 0.551176 5.2:-65434545 None:intergenic
AGAAGCGACTAGAGGACGGC+CGG 0.565813 5.2:+65435325 MS.gene063599:CDS
GAGGTTCTAAAGTAACCTGT+TGG 0.565954 5.2:-65434860 None:intergenic
ACAAGGAACTCTGACGAAAG+AGG 0.566768 5.2:-65434879 None:intergenic
TTGAGAGGTTCAGAACCAAA+TGG 0.575969 5.2:-65434906 None:intergenic
CTATGTTGCATCACCAAAAG+TGG 0.577380 5.2:+65434560 MS.gene063599:CDS
CAATGAAATATATGGTTGCA+AGG 0.591729 5.2:+65434455 MS.gene063599:CDS
ATAGTTATGATATATTGGCT+AGG 0.603327 5.2:+65434793 MS.gene063599:CDS
GCCAAGAAGCGACTAGAGGA+CGG 0.613812 5.2:+65435321 MS.gene063599:CDS
CATAACTTATACAATCCCAA+TGG 0.629912 5.2:+65434941 MS.gene063599:CDS
CCCCAACGAGACGGTGAACG+AGG 0.637975 5.2:-65435389 None:intergenic
CTTTGCCAAGAAGCGACTAG+AGG 0.639703 5.2:+65435317 MS.gene063599:CDS
CAGAACCAAATGGAATCACA+AGG 0.644146 5.2:-65434896 None:intergenic
ACATAGTCACAACCTGAAAG+GGG 0.647074 5.2:-65434543 None:intergenic
CTCGTTCACCGTCTCGTTGG+GGG 0.647230 5.2:+65435390 MS.gene063599:CDS
AGGCATTTCAGCTATAGACA+CGG 0.665779 5.2:+65434588 MS.gene063599:CDS
CATAGTCACAACCTGAAAGG+GGG 0.680591 5.2:-65434542 None:intergenic
AGACTTCAAGGAGACAACGA+AGG 0.709831 5.2:-65434643 None:intergenic
GCATTTCAGCTATAGACACG+GGG 0.728700 5.2:+65434590 MS.gene063599:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATAATAAGACTATAATA+GGG - chr5.2:65435003-65435022 None:intergenic 10.0%
!! GAAAATAATAAGACTATAAT+AGG - chr5.2:65435004-65435023 None:intergenic 15.0%
!!! TCTCAAATAAAATTTTCTTA+TGG + chr5.2:65434615-65434634 MS.gene063599:CDS 15.0%
!! TGAGTATAGTTATGATATAT+TGG + chr5.2:65434788-65434807 MS.gene063599:CDS 20.0%
!!! AATAATAGTACTATGCTTTT+GGG + chr5.2:65434720-65434739 MS.gene063599:CDS 20.0%
!!! GTTTTTTAAATGCCAAAAAA+AGG + chr5.2:65435071-65435090 MS.gene063599:intron 20.0%
! AAATAAGTTACACTAGAAAG+AGG + chr5.2:65434481-65434500 MS.gene063599:CDS 25.0%
! AACAAACCAAAGTAAAGAAT+TGG - chr5.2:65434979-65434998 None:intergenic 25.0%
! ATCATAACTATACTCAGATT+CGG - chr5.2:65434784-65434803 None:intergenic 25.0%
! CTTATCTTTGATGTTGTAAT+CGG - chr5.2:65435358-65435377 None:intergenic 25.0%
! GCTGTTAATATTTATTGTGT+TGG + chr5.2:65434747-65434766 MS.gene063599:CDS 25.0%
!! ATAGTTATGATATATTGGCT+AGG + chr5.2:65434793-65434812 MS.gene063599:CDS 25.0%
!! ATTATCATTGGTTAATGAGT+TGG + chr5.2:65435234-65435253 MS.gene063599:intron 25.0%
!! CAATAATAGTACTATGCTTT+TGG + chr5.2:65434719-65434738 MS.gene063599:CDS 25.0%
!! GGTTTAGTGTTTTCTATTTT+TGG + chr5.2:65435092-65435111 MS.gene063599:intron 25.0%
!!! GAAAACACTAAACCTTTTTT+TGG - chr5.2:65435086-65435105 None:intergenic 25.0%
CAAAGTAAAGAATTGGAGAT+TGG - chr5.2:65434972-65434991 None:intergenic 30.0%
CAATCTCCAATTCTTTACTT+TGG + chr5.2:65434970-65434989 MS.gene063599:intron 30.0%
CAATGAAATATATGGTTGCA+AGG + chr5.2:65434455-65434474 MS.gene063599:CDS 30.0%
CATAACTTATACAATCCCAA+TGG + chr5.2:65434941-65434960 MS.gene063599:CDS 30.0%
GTTCTTCAAGAGGAAAATTA+CGG + chr5.2:65434681-65434700 MS.gene063599:CDS 30.0%
TCATGTCGCAATGAAATATA+TGG + chr5.2:65434447-65434466 MS.gene063599:CDS 30.0%
TTATAATGACCTTGACTAGA+AGG + chr5.2:65435281-65435300 MS.gene063599:intron 30.0%
! ATTTTCCTCTTGAAGAACAA+TGG - chr5.2:65434679-65434698 None:intergenic 30.0%
! TGACTGCTTTGAATTATCAT+TGG + chr5.2:65435222-65435241 MS.gene063599:intron 30.0%
!!! CTACAACGTTTTGAGTTAAT+GGG - chr5.2:65434393-65434412 None:intergenic 30.0%
!!! TCTACAACGTTTTGAGTTAA+TGG - chr5.2:65434394-65434413 None:intergenic 30.0%
AAATCTTCTCCTTCTAGTCA+AGG - chr5.2:65435293-65435312 None:intergenic 35.0%
AACATAGTCACAACCTGAAA+GGG - chr5.2:65434547-65434566 None:intergenic 35.0%
ACTATTATCACAGCACAACT+AGG - chr5.2:65435180-65435199 None:intergenic 35.0%
AGTAAAGAATTGGAGATTGG+AGG - chr5.2:65434969-65434988 None:intergenic 35.0%
TGAAACCATTGTTCTTCAAG+AGG + chr5.2:65434671-65434690 MS.gene063599:CDS 35.0%
TGCTGTGATAATAGTTGCAA+GGG + chr5.2:65435185-65435204 MS.gene063599:intron 35.0%
TTTGATGTTGTAATCGGCAA+GGG - chr5.2:65435352-65435371 None:intergenic 35.0%
! ATAATAGTTGCAAGGGGTTT+TGG + chr5.2:65435192-65435211 MS.gene063599:intron 35.0%
!! ATGCAAATTTCTAGCTTGAG+AGG - chr5.2:65434924-65434943 None:intergenic 35.0%
ACATAGTCACAACCTGAAAG+GGG - chr5.2:65434546-65434565 None:intergenic 40.0%
AGGCATTTCAGCTATAGACA+CGG + chr5.2:65434588-65434607 MS.gene063599:CDS 40.0%
CAACATAGTCACAACCTGAA+AGG - chr5.2:65434548-65434567 None:intergenic 40.0%
CAGAACCAAATGGAATCACA+AGG - chr5.2:65434899-65434918 None:intergenic 40.0%
CATGAAGAAGAATGCATCCA+TGG + chr5.2:65434507-65434526 MS.gene063599:CDS 40.0%
CTATGTTGCATCACCAAAAG+TGG + chr5.2:65434560-65434579 MS.gene063599:CDS 40.0%
CTTTGATGTTGTAATCGGCA+AGG - chr5.2:65435353-65435372 None:intergenic 40.0%
GAGTTCCTTGTGATTCCATT+TGG + chr5.2:65434891-65434910 MS.gene063599:CDS 40.0%
GCTGTGATAATAGTTGCAAG+GGG + chr5.2:65435186-65435205 MS.gene063599:intron 40.0%
GGTTTCATCAGTAGACTTCA+AGG - chr5.2:65434658-65434677 None:intergenic 40.0%
GTGCTGTGATAATAGTTGCA+AGG + chr5.2:65435184-65435203 MS.gene063599:intron 40.0%
TACTCAGATTCGGAAGAGTT+TGG - chr5.2:65434774-65434793 None:intergenic 40.0%
TTGAGAGGTTCAGAACCAAA+TGG - chr5.2:65434909-65434928 None:intergenic 40.0%
! AAATGCCTAGACACCACTTT+TGG - chr5.2:65434576-65434595 None:intergenic 40.0%
! GGTTAATGAGTTGGCAATTG+CGG + chr5.2:65435243-65435262 MS.gene063599:intron 40.0%
!! GAGGTTCTAAAGTAACCTGT+TGG - chr5.2:65434863-65434882 None:intergenic 40.0%
AAATGTTACTGCCCCCTTTC+AGG + chr5.2:65434531-65434550 MS.gene063599:CDS 45.0%
ACAAGGAACTCTGACGAAAG+AGG - chr5.2:65434882-65434901 None:intergenic 45.0%
AGACTTCAAGGAGACAACGA+AGG - chr5.2:65434646-65434665 None:intergenic 45.0%
CATAGTCACAACCTGAAAGG+GGG - chr5.2:65434545-65434564 None:intergenic 45.0%
CATCACCAAAAGTGGTGTCT+AGG + chr5.2:65434568-65434587 MS.gene063599:CDS 45.0%
GCATTTCAGCTATAGACACG+GGG + chr5.2:65434590-65434609 MS.gene063599:CDS 45.0%
GGCATTTCAGCTATAGACAC+GGG + chr5.2:65434589-65434608 MS.gene063599:CDS 45.0%
!! TATTGCGAAGAGTGTCCAAC+AGG + chr5.2:65434845-65434864 MS.gene063599:CDS 45.0%
!! TGGAGATTGGAGGTACCATT+GGG - chr5.2:65434959-65434978 None:intergenic 45.0%
!! TTGGAGATTGGAGGTACCAT+TGG - chr5.2:65434960-65434979 None:intergenic 45.0%
CTTTGCCAAGAAGCGACTAG+AGG + chr5.2:65435317-65435336 MS.gene063599:CDS 50.0%
TGTTGTAATCGGCAAGGGTC+CGG - chr5.2:65435347-65435366 None:intergenic 50.0%
! GGGGGCAGTAACATTTTCCA+TGG - chr5.2:65434527-65434546 None:intergenic 50.0%
ACCTCGTTCACCGTCTCGTT+GGG + chr5.2:65435388-65435407 MS.gene063599:CDS 55.0%
GAGACGGTGAACGAGGTCAA+TGG - chr5.2:65435385-65435404 None:intergenic 55.0%
GCCAAGAAGCGACTAGAGGA+CGG + chr5.2:65435321-65435340 MS.gene063599:CDS 55.0%
GTTGGCAATTGCGGTGCAGA+TGG + chr5.2:65435252-65435271 MS.gene063599:intron 55.0%
AGAAGCGACTAGAGGACGGC+CGG + chr5.2:65435325-65435344 MS.gene063599:CDS 60.0%
CCTCGTTCACCGTCTCGTTG+GGG + chr5.2:65435389-65435408 MS.gene063599:CDS 60.0%
CTCGTTCACCGTCTCGTTGG+GGG + chr5.2:65435390-65435409 MS.gene063599:CDS 60.0%
GACCTCGTTCACCGTCTCGT+TGG + chr5.2:65435387-65435406 MS.gene063599:CDS 60.0%
GCCGTCCTCTAGTCGCTTCT+TGG - chr5.2:65435325-65435344 None:intergenic 60.0%
CCCCAACGAGACGGTGAACG+AGG - chr5.2:65435392-65435411 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 65434369 65435416 65434369 ID=MS.gene063599
chr5.2 mRNA 65434369 65435416 65434369 ID=MS.gene063599.t1;Parent=MS.gene063599
chr5.2 exon 65434369 65434962 65434369 ID=MS.gene063599.t1.exon1;Parent=MS.gene063599.t1
chr5.2 CDS 65434369 65434962 65434369 ID=cds.MS.gene063599.t1;Parent=MS.gene063599.t1
chr5.2 exon 65435300 65435416 65435300 ID=MS.gene063599.t1.exon2;Parent=MS.gene063599.t1
chr5.2 CDS 65435300 65435416 65435300 ID=cds.MS.gene063599.t1;Parent=MS.gene063599.t1
Gene Sequence

>MS.gene063599

ATGTGTAGCAAGTGCTTATTGCCCATTAACTCAAAACGTTGTAGAGCGATTGAGAATCTATTGCTATCTATCAAAGTGTCATGTCGCAATGAAATATATGGTTGCAAGGAGAAAATAAGTTACACTAGAAAGAGGAAGCATGAAGAAGAATGCATCCATGGAAAATGTTACTGCCCCCTTTCAGGTTGTGACTATGTTGCATCACCAAAAGTGGTGTCTAGGCATTTCAGCTATAGACACGGGGATTCTCAAATAAAATTTTCTTATGGTCACTCCTTCGTTGTCTCCTTGAAGTCTACTGATGAAACCATTGTTCTTCAAGAGGAAAATTACGGCAAACTATTTATTCTCAATAATAGTACTATGCTTTTGGGAAATGCTGTTAATATTTATTGTGTTGGTCCAAACTCTTCCGAATCTGAGTATAGTTATGATATATTGGCTAGGTCTCAGACATGCAAACTGAAATTACAGTCTATTGCGAAGAGTGTCCAACAGGTTACTTTAGAACCTCTTTCGTCAGAGTTCCTTGTGATTCCATTTGGTTCTGAACCTCTCAAGCTAGAAATTTGCATAACTTATACAATCCCAATGGTACCTCCAATCTCCAATTCTTTACTTTGGTTTGTTTCCCTATTATAGTCTTATTATTTTCTTATATGTTTTTAATTTGTGTTCTAGCATTTTATCTCAAATTCATCAGTTTTTTAAATGCCAAAAAAAGGTTTAGTGTTTTCTATTTTTGGATCACTTTTTGAAATACGAGTCTCAATATTTCTTTTGTTAATTTGATCATAACTTTATTGTGCCTAGTTGTGCTGTGATAATAGTTGCAAGGGGTTTTGGTTTCTTTTGACTGCTTTGAATTATCATTGGTTAATGAGTTGGCAATTGCGGTGCAGATGGATATTATTATAATGACCTTGACTAGAAGGAGAAGATTTTGCTCTTTGCCAAGAAGCGACTAGAGGACGGCCGGACCCTTGCCGATTACAACATCAAAGATAAGTCAACCATTGACCTCGTTCACCGTCTCGTTGGGGGCTAG
Protein sequence

>MS.gene063599.t1

MCSKCLLPINSKRCRAIENLLLSIKVSCRNEIYGCKEKISYTRKRKHEEECIHGKCYCPLSGCDYVASPKVVSRHFSYRHGDSQIKFSYGHSFVVSLKSTDETIVLQEENYGKLFILNNSTMLLGNAVNIYCVGPNSSESEYSYDILARSQTCKLKLQSIAKSVQQVTLEPLSSEFLVIPFGSEPLKLEICITYTIPMKEKILLFAKKRLEDGRTLADYNIKDKSTIDLVHRLVGG