AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene012171

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene012171.t1 MTR_8g074450 92.414 290 22 0 1 290 1 290 0.0 546
MS.gene012171.t1 MTR_8g074510 85.517 290 40 1 1 290 1 288 0.0 504
MS.gene012171.t1 MTR_8g074420 84.138 290 46 0 1 290 1 290 4.77e-171 475
MS.gene012171.t1 MTR_5g023600 70.629 286 78 2 2 287 3 282 4.58e-135 384
MS.gene012171.t1 MTR_5g023520 67.586 290 89 1 1 290 1 285 7.48e-135 383
MS.gene012171.t1 MTR_5g023550 69.338 287 82 2 1 287 1 281 9.18e-135 383
MS.gene012171.t1 MTR_5g023370 69.930 286 80 2 2 287 3 282 1.68e-134 382
MS.gene012171.t1 MTR_5g023350 69.930 286 80 2 2 287 3 282 2.70e-134 382
MS.gene012171.t1 MTR_5g023340 69.580 286 81 2 2 287 3 282 3.43e-134 381
MS.gene012171.t1 MTR_5g023390 69.231 286 82 2 2 287 3 282 1.52e-133 380
MS.gene012171.t1 MTR_5g023320 69.310 290 79 4 2 290 3 283 2.68e-132 376
MS.gene012171.t1 MTR_5g023530 68.512 289 83 4 1 287 1 283 1.69e-130 372
MS.gene012171.t1 MTR_5g023470 67.820 289 85 4 1 287 1 283 1.02e-128 367
MS.gene012171.t1 MTR_5g023580 66.551 287 94 1 2 288 3 287 2.47e-124 359
MS.gene012171.t1 MTR_8g074530 47.241 290 149 3 2 289 17 304 2.59e-79 243
MS.gene012171.t1 MTR_5g023460 63.021 192 61 3 99 290 11 192 3.64e-77 233
MS.gene012171.t1 MTR_5g023290 42.953 298 158 4 4 289 11 308 9.88e-71 221
MS.gene012171.t1 MTR_4g070530 34.843 287 176 4 6 287 13 293 4.05e-44 152
MS.gene012171.t1 MTR_5g023650 32.990 291 183 4 7 287 14 302 4.45e-43 149
MS.gene012171.t1 MTR_5g023410 73.000 100 27 0 1 100 1 100 4.50e-43 147
MS.gene012171.t1 MTR_8g074380 33.793 290 160 5 7 287 14 280 4.56e-43 150
MS.gene012171.t1 MTR_4g070540 32.632 285 185 4 6 287 13 293 6.58e-38 135
MS.gene012171.t1 MTR_3g116950 35.986 289 172 9 5 287 12 293 4.41e-37 134
MS.gene012171.t1 MTR_3g116920 33.564 289 181 6 5 287 12 295 4.42e-37 134
MS.gene012171.t1 MTR_4g070570 31.034 290 189 5 5 287 15 300 1.29e-36 132
MS.gene012171.t1 MTR_4g070590 34.364 291 176 7 6 287 14 298 2.82e-35 129
MS.gene012171.t1 MTR_3g115150 28.571 301 181 9 5 286 27 312 9.24e-25 101
MS.gene012171.t1 MTR_1g037820 29.707 239 142 5 51 287 9 223 3.04e-24 98.2
MS.gene012171.t1 MTR_5g023540 50.746 67 29 1 165 231 4 66 1.84e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene012171.t1 AT4G35690 40.000 295 156 8 1 289 4 283 4.28e-55 180
MS.gene012171.t1 AT2G17680 40.328 305 151 10 1 290 4 292 2.70e-49 165
MS.gene012171.t1 AT4G35710 38.255 298 159 9 1 289 1 282 2.12e-47 160
MS.gene012171.t1 AT2G17080 36.458 288 154 6 1 287 1 260 1.38e-42 147
MS.gene012171.t1 AT4G35200 35.540 287 151 9 1 287 1 253 5.05e-39 137
MS.gene012171.t1 AT2G17070 35.986 289 152 8 1 286 1 259 1.64e-38 136
MS.gene012171.t1 AT4G35210 33.798 287 153 8 1 287 1 250 1.21e-35 129
MS.gene012171.t1 AT4G35660 34.228 298 155 10 7 289 16 287 3.09e-30 115
MS.gene012171.t1 AT4G35720 32.492 317 176 9 5 289 14 324 2.42e-28 111
MS.gene012171.t1 AT4G35680 29.293 297 191 7 7 289 18 309 3.54e-23 97.1
MS.gene012171.t1 AT1G76240 30.584 291 178 8 5 286 29 304 5.34e-23 96.7
MS.gene012171.t1 AT3G51400 30.847 295 177 10 1 289 1 274 4.52e-21 90.9
MS.gene012171.t1 AT1G76210 26.906 223 140 4 65 287 24 223 9.23e-17 77.8
MS.gene012171.t1 AT3G51410 30.851 282 151 7 7 287 39 277 5.21e-16 76.6
MS.gene012171.t1 AT1G20520 25.620 242 153 6 47 287 8 223 8.07e-11 61.2

Find 45 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGGCATGTCTTCAATTT+TGG 0.093147 8.4:-30283414 MS.gene012171:CDS
AAGCAAATGGATAGTAAATT+TGG 0.146612 8.4:-30283431 MS.gene012171:CDS
CATTAGTACCTTCACTTAAA+AGG 0.153684 8.4:+30283165 None:intergenic
GGATGGTTCTATGAGAATTT+TGG 0.227811 8.4:-30283627 MS.gene012171:CDS
TTGTTTGATTAGAGTGTTTA+GGG 0.289236 8.4:-30283372 MS.gene012171:CDS
TGAAACTATTGAGAATGATT+TGG 0.295462 8.4:-30283090 MS.gene012171:CDS
ATGATTTGGAGAATTTATTT+AGG 0.300645 8.4:-30283076 MS.gene012171:CDS
CTTGTTTGATTAGAGTGTTT+AGG 0.307790 8.4:-30283373 MS.gene012171:CDS
TACTAATGGAGAAAACTTGC+AGG 0.379519 8.4:-30283150 MS.gene012171:CDS
AAGCCCTTCACTCTTCTCTA+AGG 0.389201 8.4:-30283553 MS.gene012171:CDS
CAAAGTCAAAGACAACAAAA+TGG 0.396471 8.4:-30283286 MS.gene012171:CDS
ATTAGTACCTTCACTTAAAA+GGG 0.427283 8.4:+30283166 None:intergenic
ACATGAAAGATTAGAGGCTT+TGG 0.438324 8.4:-30283123 MS.gene012171:CDS
GATCACATCTTTGAAGCAAA+TGG 0.443039 8.4:-30283444 MS.gene012171:CDS
GGAACATCCACATCCACATC+AGG 0.453856 8.4:-30283776 MS.gene012171:CDS
GGCTGCACATGAAAGATTAG+AGG 0.456678 8.4:-30283129 MS.gene012171:CDS
TATAGGTCTTTCCTTGCTTG+AGG 0.469013 8.4:-30283744 MS.gene012171:CDS
ATGGTGAGAAATCACTTGTT+GGG 0.481727 8.4:+30283679 None:intergenic
TGAGGATTTGTATATGTCAA+TGG 0.487266 8.4:-30283726 MS.gene012171:CDS
ACATCAGGGTCTATTCATAT+AGG 0.495133 8.4:-30283761 MS.gene012171:CDS
GATGGTGAGAAATCACTTGT+TGG 0.504782 8.4:+30283678 None:intergenic
TCTTCTCTAAGGAGAAGAAA+AGG 0.505857 8.4:-30283542 MS.gene012171:CDS
GTACTAGGATGAGATCTAGA+AGG 0.509536 8.4:+30283842 None:intergenic
TCTTCTACTCTAATAGTACT+AGG 0.512252 8.4:+30283827 None:intergenic
TTCTCCTTAGAGAAGAGTGA+AGG 0.531189 8.4:+30283549 None:intergenic
ACACTCTAATCAAACAAGAA+AGG 0.532051 8.4:+30283378 None:intergenic
GTTGAACAAGCTCAAGACTT+GGG 0.547472 8.4:-30283801 MS.gene012171:CDS
AGTTGAACAAGCTCAAGACT+TGG 0.550757 8.4:-30283802 MS.gene012171:CDS
AAAATGTGTGGAAGAGGTGT+TGG 0.559008 8.4:-30283648 MS.gene012171:CDS
ATTGGGAAGTTATATTCAAG+AGG 0.571012 8.4:+30283030 None:intergenic
TGGATATATGTGGTATCACA+AGG 0.577239 8.4:-30283607 MS.gene012171:CDS
AATAGACCCTGATGTGGATG+TGG 0.577845 8.4:+30283769 None:intergenic
AACAAGCTCAAGACTTGGGA+AGG 0.577984 8.4:-30283797 MS.gene012171:CDS
TCTCCTTAGAGAAGAGTGAA+GGG 0.582594 8.4:+30283550 None:intergenic
CAAGTGATTTCTCACCATCA+AGG 0.601182 8.4:-30283674 MS.gene012171:CDS
CATATACAAATCCTCAAGCA+AGG 0.603637 8.4:+30283733 None:intergenic
TTGGGAAGTTATATTCAAGA+GGG 0.624126 8.4:+30283031 None:intergenic
AACATGATACTTGTTTGCCA+TGG 0.636180 8.4:+30283880 None:intergenic
TGTGTGGAAGAGGTGTTGGA+TGG 0.647133 8.4:-30283644 MS.gene012171:CDS
AATGGAAGATCTTCTTAACA+TGG 0.647281 8.4:-30283708 MS.gene012171:CDS
GAACATCCACATCCACATCA+GGG 0.664398 8.4:-30283775 MS.gene012171:CDS
TATATGAATAGACCCTGATG+TGG 0.674746 8.4:+30283763 None:intergenic
GTGACTAAACTGATGCACAA+AGG 0.685825 8.4:-30283257 MS.gene012171:CDS
GGATATATGTGGTATCACAA+GGG 0.686332 8.4:-30283606 MS.gene012171:CDS
TTCAAGTGTTGAAAGAAGTG+TGG 0.711991 8.4:-30283516 MS.gene012171:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGATTTGGAGAATTTATTT+AGG - chr8.4:30283830-30283849 MS.gene012171:CDS 20.0%
! AAGCAAATGGATAGTAAATT+TGG - chr8.4:30283475-30283494 MS.gene012171:CDS 25.0%
! ATTAGTACCTTCACTTAAAA+GGG + chr8.4:30283743-30283762 None:intergenic 25.0%
! TGAAACTATTGAGAATGATT+TGG - chr8.4:30283816-30283835 MS.gene012171:CDS 25.0%
!! ATGAGAATTTTGGATATATG+TGG - chr8.4:30283289-30283308 MS.gene012171:CDS 25.0%
!! TTGTTTGATTAGAGTGTTTA+GGG - chr8.4:30283534-30283553 MS.gene012171:CDS 25.0%
!!! ATTTTCCTTGATTTGCAAAA+TGG + chr8.4:30283329-30283348 None:intergenic 25.0%
AATGGAAGATCTTCTTAACA+TGG - chr8.4:30283198-30283217 MS.gene012171:CDS 30.0%
ACACTCTAATCAAACAAGAA+AGG + chr8.4:30283531-30283550 None:intergenic 30.0%
ATTGGGAAGTTATATTCAAG+AGG + chr8.4:30283879-30283898 None:intergenic 30.0%
CAAAGTCAAAGACAACAAAA+TGG - chr8.4:30283620-30283639 MS.gene012171:CDS 30.0%
CATTAGTACCTTCACTTAAA+AGG + chr8.4:30283744-30283763 None:intergenic 30.0%
TCTTCTACTCTAATAGTACT+AGG + chr8.4:30283082-30283101 None:intergenic 30.0%
TGAGGATTTGTATATGTCAA+TGG - chr8.4:30283180-30283199 MS.gene012171:CDS 30.0%
TTGGGAAGTTATATTCAAGA+GGG + chr8.4:30283878-30283897 None:intergenic 30.0%
! ATTTGGCATGTCTTCAATTT+TGG - chr8.4:30283492-30283511 MS.gene012171:CDS 30.0%
! CTTGTTTGATTAGAGTGTTT+AGG - chr8.4:30283533-30283552 MS.gene012171:CDS 30.0%
!! TTAAACACCCTTTTAAGTGA+AGG - chr8.4:30283733-30283752 MS.gene012171:CDS 30.0%
!!! CTTTTAAGTGAAGGTACTAA+TGG - chr8.4:30283742-30283761 MS.gene012171:CDS 30.0%
ACATCAGGGTCTATTCATAT+AGG - chr8.4:30283145-30283164 MS.gene012171:CDS 35.0%
ACATGAAAGATTAGAGGCTT+TGG - chr8.4:30283783-30283802 MS.gene012171:CDS 35.0%
ATGGTGAGAAATCACTTGTT+GGG + chr8.4:30283230-30283249 None:intergenic 35.0%
CATATACAAATCCTCAAGCA+AGG + chr8.4:30283176-30283195 None:intergenic 35.0%
GGATATATGTGGTATCACAA+GGG - chr8.4:30283300-30283319 MS.gene012171:CDS 35.0%
TACTAATGGAGAAAACTTGC+AGG - chr8.4:30283756-30283775 MS.gene012171:CDS 35.0%
TATATGAATAGACCCTGATG+TGG + chr8.4:30283146-30283165 None:intergenic 35.0%
TGGATATATGTGGTATCACA+AGG - chr8.4:30283299-30283318 MS.gene012171:CDS 35.0%
! TCTTCTCTAAGGAGAAGAAA+AGG - chr8.4:30283364-30283383 MS.gene012171:CDS 35.0%
!! GATCACATCTTTGAAGCAAA+TGG - chr8.4:30283462-30283481 MS.gene012171:CDS 35.0%
!! GGATGGTTCTATGAGAATTT+TGG - chr8.4:30283279-30283298 MS.gene012171:CDS 35.0%
!! TTCAAGTGTTGAAAGAAGTG+TGG - chr8.4:30283390-30283409 MS.gene012171:CDS 35.0%
AGGTGAAAAATGTGTGGAAG+AGG - chr8.4:30283252-30283271 MS.gene012171:CDS 40.0%
AGTTGAACAAGCTCAAGACT+TGG - chr8.4:30283104-30283123 MS.gene012171:CDS 40.0%
CAAGTGATTTCTCACCATCA+AGG - chr8.4:30283232-30283251 MS.gene012171:CDS 40.0%
CCATCAAGGTGAAAAATGTG+TGG - chr8.4:30283246-30283265 MS.gene012171:CDS 40.0%
GATGGTGAGAAATCACTTGT+TGG + chr8.4:30283231-30283250 None:intergenic 40.0%
GTACTAGGATGAGATCTAGA+AGG + chr8.4:30283067-30283086 None:intergenic 40.0%
GTGACTAAACTGATGCACAA+AGG - chr8.4:30283649-30283668 MS.gene012171:CDS 40.0%
GTTGAACAAGCTCAAGACTT+GGG - chr8.4:30283105-30283124 MS.gene012171:CDS 40.0%
TATAGGTCTTTCCTTGCTTG+AGG - chr8.4:30283162-30283181 MS.gene012171:CDS 40.0%
TCTCCTTAGAGAAGAGTGAA+GGG + chr8.4:30283359-30283378 None:intergenic 40.0%
TTCTCCTTAGAGAAGAGTGA+AGG + chr8.4:30283360-30283379 None:intergenic 40.0%
! AAAATGTGTGGAAGAGGTGT+TGG - chr8.4:30283258-30283277 MS.gene012171:CDS 40.0%
! CCACACATTTTTCACCTTGA+TGG + chr8.4:30283249-30283268 None:intergenic 40.0%
! GGACACCATTTTGCAAATCA+AGG - chr8.4:30283321-30283340 MS.gene012171:CDS 40.0%
AACAAGCTCAAGACTTGGGA+AGG - chr8.4:30283109-30283128 MS.gene012171:CDS 45.0%
AAGCCCTTCACTCTTCTCTA+AGG - chr8.4:30283353-30283372 MS.gene012171:CDS 45.0%
AATAGACCCTGATGTGGATG+TGG + chr8.4:30283140-30283159 None:intergenic 45.0%
GAACATCCACATCCACATCA+GGG - chr8.4:30283131-30283150 MS.gene012171:CDS 45.0%
GGCTGCACATGAAAGATTAG+AGG - chr8.4:30283777-30283796 MS.gene012171:CDS 45.0%
GGAACATCCACATCCACATC+AGG - chr8.4:30283130-30283149 MS.gene012171:CDS 50.0%
!! TGTGTGGAAGAGGTGTTGGA+TGG - chr8.4:30283262-30283281 MS.gene012171:CDS 50.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 30283028 30283900 30283028 ID=MS.gene012171
chr8.4 mRNA 30283028 30283900 30283028 ID=MS.gene012171.t1;Parent=MS.gene012171
chr8.4 exon 30283028 30283900 30283028 ID=MS.gene012171.t1.exon1;Parent=MS.gene012171.t1
chr8.4 CDS 30283028 30283900 30283028 ID=cds.MS.gene012171.t1;Parent=MS.gene012171.t1
Gene Sequence

>MS.gene012171

ATGGCAAACAAGTATCATGTTCGTTCAATTAGTTTGCCTTCTAGATCTCATCCTAGTACTATTAGAGTAGAAGAAGAGTTGAACAAGCTCAAGACTTGGGAAGGAACATCCACATCCACATCAGGGTCTATTCATATAGGTCTTTCCTTGCTTGAGGATTTGTATATGTCAATGGAAGATCTTCTTAACATGGCATCAACCCAACAAGTGATTTCTCACCATCAAGGTGAAAAATGTGTGGAAGAGGTGTTGGATGGTTCTATGAGAATTTTGGATATATGTGGTATCACAAGGGACACCATTTTGCAAATCAAGGAAAATGTTCAAGCCCTTCACTCTTCTCTAAGGAGAAGAAAAGGTGATTCAAGTGTTGAAAGAAGTGTGGCAGAATACAAATTCTTCACAAAAAAGATGAAGAAAAATGTCAACAAGTTGATCACATCTTTGAAGCAAATGGATAGTAAATTTGGCATGTCTTCAATTTTGGAACTTGATCATCACCTTTCTTGTTTGATTAGAGTGTTTAGGGAAGTCATAGTAATGAACTTATCTGTTTTTCAATTCATTTTGTCATTCTTGACTTTGTCTTCATCAAAGTCAAAGACAACAAAATGGAAGTTTGTGACTAAACTGATGCACAAAGGAGTCATAACATGTGAAGATAACTCAGATAGTATTAATGAGTTGCAGTGTGTCAAAGTTACTTTAAACACCCTTTTAAGTGAAGGTACTAATGGAGAAAACTTGCAGGCTGCACATGAAAGATTAGAGGCTTTGGAGAATGCAATTGAAACTATTGAGAATGATTTGGAGAATTTATTTAGGCGCTTGATTAAATCTAGAGCTTCCCTCTTGAATATAACTTCCCAATAG
Protein sequence

>MS.gene012171.t1

MANKYHVRSISLPSRSHPSTIRVEEELNKLKTWEGTSTSTSGSIHIGLSLLEDLYMSMEDLLNMASTQQVISHHQGEKCVEEVLDGSMRILDICGITRDTILQIKENVQALHSSLRRRKGDSSVERSVAEYKFFTKKMKKNVNKLITSLKQMDSKFGMSSILELDHHLSCLIRVFREVIVMNLSVFQFILSFLTLSSSKSKTTKWKFVTKLMHKGVITCEDNSDSINELQCVKVTLNTLLSEGTNGENLQAAHERLEALENAIETIENDLENLFRRLIKSRASLLNITSQ