AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062571


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062571.t1 MTR_4g059780 98.214 280 5 0 1 280 24 303 0.0 548
MS.gene062571.t1 MTR_2g093980 60.616 292 95 9 1 280 1 284 5.79e-101 296
MS.gene062571.t1 MTR_2g017960 52.669 281 121 5 1 277 1 273 6.77e-77 235
MS.gene062571.t1 MTR_8g087450 49.458 277 118 5 16 278 16 284 3.17e-75 231
MS.gene062571.t1 MTR_2g017970 51.071 280 124 5 1 275 1 272 2.05e-74 229
MS.gene062571.t1 MTR_4g059840 52.874 261 105 8 14 262 18 272 1.15e-73 227
MS.gene062571.t1 MTR_4g059790 52.232 224 92 5 50 262 53 272 1.68e-71 222
MS.gene062571.t1 MTR_4g053380 54.505 222 88 4 14 224 20 239 2.65e-69 216
MS.gene062571.t1 MTR_4g059720 51.835 218 76 4 1 218 4 192 5.39e-66 206
MS.gene062571.t1 MTR_8g087470 52.361 233 96 7 36 254 51 282 3.90e-63 201
MS.gene062571.t1 MTR_8g087460 52.402 229 96 6 38 254 55 282 5.94e-63 201
MS.gene062571.t1 MTR_2g017950 45.926 270 116 7 1 250 2 261 1.27e-62 199
MS.gene062571.t1 MTR_2g093970 51.220 205 96 2 13 214 13 216 5.79e-62 197
MS.gene062571.t1 MTR_2g093990 59.732 149 59 1 67 215 41 188 5.85e-57 183
MS.gene062571.t1 MTR_7g101080 49.032 155 77 2 63 216 36 189 1.30e-42 146
MS.gene062571.t1 MTR_2g090765 38.509 161 98 1 56 216 27 186 1.37e-28 110
MS.gene062571.t1 MTR_5g098060 32.184 174 107 4 67 233 48 217 5.62e-18 81.6
MS.gene062571.t1 MTR_7g075453 30.808 198 114 6 50 237 169 353 2.11e-15 75.9
MS.gene062571.t1 MTR_5g098420 32.743 113 75 1 103 215 227 338 6.64e-13 68.6
MS.gene062571.t1 MTR_2g437700 31.169 154 99 4 67 216 195 345 1.08e-11 65.1
MS.gene062571.t1 MTR_3g460780 33.913 115 75 1 101 215 223 336 1.23e-11 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.gene062571.t1 AT5G03170 44.693 179 97 2 53 229 22 200 9.36e-48 159
MS.gene062571.t1 AT5G60490 50.000 150 73 2 67 215 39 187 1.90e-45 154
MS.gene062571.t1 AT2G20520 38.542 192 109 4 60 243 31 221 4.92e-30 114
MS.gene062571.t1 AT5G44130 35.533 197 119 5 67 259 36 228 2.01e-29 112
MS.gene062571.t1 AT1G03870 32.195 205 134 4 67 270 39 239 8.19e-26 102
MS.gene062571.t1 AT3G46550 31.169 154 98 5 67 215 207 357 4.73e-15 75.1
MS.gene062571.t1 AT4G12730 34.862 218 126 8 49 259 171 379 1.77e-14 73.2
MS.gene062571.t1 AT3G60900 28.125 192 123 5 50 233 173 357 3.96e-12 66.2
MS.gene062571.t1 AT2G45470 30.968 155 92 3 67 216 189 333 1.01e-11 65.1
MS.gene062571.t1 AT5G55730 32.759 116 77 1 104 219 219 333 9.37e-11 62.4
MS.gene062571.t1 AT5G55730 32.759 116 77 1 104 219 219 333 9.37e-11 62.4

Find 50 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGATGGTGCTGTTGCTTT+TGG 0.250966 4.3:+42205882 None:intergenic
TACCTTGATCCTGATCATTT+TGG 0.263017 4.3:+42205259 None:intergenic
GGCTCCTAAAGCTGCTAATA+AGG 0.272377 4.3:-42205307 MS.gene062571:CDS
CAAGCTCGCGATTTATCATT+TGG 0.291478 4.3:-42205406 MS.gene062571:CDS
TCTGTTGAGTCTGGTGATTC+AGG 0.294510 4.3:+42205837 None:intergenic
CGCTACTAAGGCACCTGCTT+TGG 0.312281 4.3:-42205355 MS.gene062571:CDS
CCACTTAATGTTTATGCATC+AGG 0.321174 4.3:-42205495 MS.gene062571:CDS
TTCTCCTTATTAGCAGCTTT+AGG 0.349370 4.3:+42205303 None:intergenic
TTACCAGCTATTGTTTGAAC+AGG 0.356173 4.3:+42205534 None:intergenic
CATCACAACAATCCTCAAAA+AGG 0.364595 4.3:-42205799 MS.gene062571:CDS
GTGAGATTGTGTGGAATTCT+TGG 0.371931 4.3:-42205225 MS.gene062571:CDS
TTGTTGCTGTAGCATTGATA+TGG 0.375247 4.3:-42205185 MS.gene062571:CDS
GATCAGGATCAAGGTAAATC+TGG 0.376467 4.3:-42205252 MS.gene062571:CDS
AGGATTGTTGTGATGTCGTC+AGG 0.395586 4.3:+42205807 None:intergenic
AACAATGTCAGTCTTTCAAC+CGG 0.416183 4.3:-42205471 MS.gene062571:CDS
ACATTAAGTGGAAGCCTTGT+TGG 0.417673 4.3:+42205507 None:intergenic
GTTGTTACTGCTTCCGTTGT+GGG 0.419419 4.3:-42205447 MS.gene062571:CDS
CTTGAAAATGCTGAATCGTC+TGG 0.426953 4.3:+42205669 None:intergenic
CATTAAGTGGAAGCCTTGTT+GGG 0.430758 4.3:+42205508 None:intergenic
CCTGATGCATAAACATTAAG+TGG 0.445735 4.3:+42205495 None:intergenic
AACTCGTGCTGCTGCTGCTA+AGG 0.446593 4.3:-42205328 MS.gene062571:CDS
GGGACGGAGTCTGTTGAGTC+TGG 0.453003 4.3:+42205828 None:intergenic
AATGTGGGGACTAATGATTT+TGG 0.458446 4.3:+42205861 None:intergenic
TTAGCAGCAGCAGCACGAGT+TGG 0.460626 4.3:+42205330 None:intergenic
GCACGAGTTGGAGCCAAAGC+AGG 0.464102 4.3:+42205342 None:intergenic
TTTGAGCTCGCTACATATTG+AGG 0.476279 4.3:+42205576 None:intergenic
TCGTGATTTCTTCGCTACTA+AGG 0.488348 4.3:-42205367 MS.gene062571:CDS
TGATCAAGACCAAAATGATC+AGG 0.490187 4.3:-42205268 MS.gene062571:CDS
AACCCTGTTCAAACAATAGC+TGG 0.497527 4.3:-42205537 MS.gene062571:CDS
ATGATTCAGGTGCTTGTGAA+AGG 0.511644 4.3:+42205937 None:intergenic
GACCAAAATGATCAGGATCA+AGG 0.527131 4.3:-42205261 MS.gene062571:CDS
GGTTGTTACTGCTTCCGTTG+TGG 0.541810 4.3:-42205448 MS.gene062571:CDS
AGTTAAGAAACCCTGCTTTG+AGG 0.544708 4.3:+42205646 None:intergenic
TGTTGTGATGTCGTCAGGGA+CGG 0.571744 4.3:+42205812 None:intergenic
GTCTGGTGATTCAGGTAATG+TGG 0.576222 4.3:+42205845 None:intergenic
CTACATATTGAGGTAAGATG+TGG 0.578300 4.3:+42205586 None:intergenic
TGATTCAGGTGCTTGTGAAA+GGG 0.580955 4.3:+42205938 None:intergenic
TCTGGTGATTCAGGTAATGT+GGG 0.585032 4.3:+42205846 None:intergenic
ACAATGTCAGTCTTTCAACC+GGG 0.598947 4.3:-42205470 MS.gene062571:CDS
TACCAGCTATTGTTTGAACA+GGG 0.607680 4.3:+42205535 None:intergenic
TGCTTGTGAAAGGGATAATG+TGG 0.613574 4.3:+42205947 None:intergenic
ATGCTGAATCGTCTGGCGCG+AGG 0.616806 4.3:+42205676 None:intergenic
TCTGGAGCAGTGAGATTGTG+TGG 0.636283 4.3:-42205234 MS.gene062571:CDS
TAGCTGGTAAAGACCCAACA+AGG 0.652326 4.3:-42205521 MS.gene062571:CDS
CAATGTCAGTCTTTCAACCG+GGG 0.675430 4.3:-42205469 MS.gene062571:CDS
AGTGTACACAACACCCACAA+CGG 0.678067 4.3:+42205434 None:intergenic
CTGGTGATTCAGGTAATGTG+GGG 0.679078 4.3:+42205847 None:intergenic
GGATTGTTGTGATGTCGTCA+GGG 0.683685 4.3:+42205808 None:intergenic
AACGGAAGCAGTAACAACCC+CGG 0.701266 4.3:+42205452 None:intergenic
TTAGTAGCGAAGAAATCACG+AGG 0.758452 4.3:+42205369 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTTTTTTGTTTTCGTCTA+AGG + chr4.3:42205558-42205577 None:intergenic 25.0%
!!! GTGTTTTTTTTGGAGATTTT+GGG + chr4.3:42205268-42205287 None:intergenic 25.0%
!!! TCATGATTTCTGTTGTTTTT+AGG + chr4.3:42205433-42205452 None:intergenic 25.0%
!!! TGTTTTTTTTGGAGATTTTG+GGG + chr4.3:42205267-42205286 None:intergenic 25.0%
!!! GGTGTTTTTTTTGGAGATTT+TGG + chr4.3:42205269-42205288 None:intergenic 30.0%
!!! TTTCTGTTGTTTTTAGGAGA+CGG + chr4.3:42205427-42205446 None:intergenic 30.0%
AACAATGTCAGTCTTTCAAC+CGG - chr4.3:42205707-42205726 MS.gene062571:CDS 35.0%
CATCACAACAATCCTCAAAA+AGG - chr4.3:42205379-42205398 MS.gene062571:CDS 35.0%
CCACTTAATGTTTATGCATC+AGG - chr4.3:42205683-42205702 MS.gene062571:CDS 35.0%
CCTGATGCATAAACATTAAG+TGG + chr4.3:42205686-42205705 None:intergenic 35.0%
CTACATATTGAGGTAAGATG+TGG + chr4.3:42205595-42205614 None:intergenic 35.0%
TACCAGCTATTGTTTGAACA+GGG + chr4.3:42205646-42205665 None:intergenic 35.0%
TGATCAAGACCAAAATGATC+AGG - chr4.3:42205910-42205929 MS.gene062571:CDS 35.0%
TTACCAGCTATTGTTTGAAC+AGG + chr4.3:42205647-42205666 None:intergenic 35.0%
TTCTCCTTATTAGCAGCTTT+AGG + chr4.3:42205878-42205897 None:intergenic 35.0%
! AATGTGGGGACTAATGATTT+TGG + chr4.3:42205320-42205339 None:intergenic 35.0%
! AGAATGTTTTCGCCTTTTTG+AGG + chr4.3:42205394-42205413 None:intergenic 35.0%
! TACCTTGATCCTGATCATTT+TGG + chr4.3:42205922-42205941 None:intergenic 35.0%
!! TTGTTGCTGTAGCATTGATA+TGG - chr4.3:42205993-42206012 MS.gene062571:CDS 35.0%
!!! TTGTTTTTAGGAGACGGATT+AGG + chr4.3:42205421-42205440 None:intergenic 35.0%
AACCCTGTTCAAACAATAGC+TGG - chr4.3:42205641-42205660 MS.gene062571:CDS 40.0%
ACAATGTCAGTCTTTCAACC+GGG - chr4.3:42205708-42205727 MS.gene062571:CDS 40.0%
AGTTAAGAAACCCTGCTTTG+AGG + chr4.3:42205535-42205554 None:intergenic 40.0%
ATGATTCAGGTGCTTGTGAA+AGG + chr4.3:42205244-42205263 None:intergenic 40.0%
CAAGCTCGCGATTTATCATT+TGG - chr4.3:42205772-42205791 MS.gene062571:CDS 40.0%
CTTGAAAATGCTGAATCGTC+TGG + chr4.3:42205512-42205531 None:intergenic 40.0%
GACCAAAATGATCAGGATCA+AGG - chr4.3:42205917-42205936 MS.gene062571:CDS 40.0%
GATCAGGATCAAGGTAAATC+TGG - chr4.3:42205926-42205945 MS.gene062571:CDS 40.0%
GTGAGATTGTGTGGAATTCT+TGG - chr4.3:42205953-42205972 MS.gene062571:CDS 40.0%
TCGTGATTTCTTCGCTACTA+AGG - chr4.3:42205811-42205830 MS.gene062571:CDS 40.0%
TCTGGTGATTCAGGTAATGT+GGG + chr4.3:42205335-42205354 None:intergenic 40.0%
TGATTCAGGTGCTTGTGAAA+GGG + chr4.3:42205243-42205262 None:intergenic 40.0%
TGCTTGTGAAAGGGATAATG+TGG + chr4.3:42205234-42205253 None:intergenic 40.0%
TTAGTAGCGAAGAAATCACG+AGG + chr4.3:42205812-42205831 None:intergenic 40.0%
TTTGAGCTCGCTACATATTG+AGG + chr4.3:42205605-42205624 None:intergenic 40.0%
! ACATTAAGTGGAAGCCTTGT+TGG + chr4.3:42205674-42205693 None:intergenic 40.0%
!! CATTAAGTGGAAGCCTTGTT+GGG + chr4.3:42205673-42205692 None:intergenic 40.0%
!! CATTTTCAAGCCTCAAAGCA+GGG - chr4.3:42205522-42205541 MS.gene062571:CDS 40.0%
!! GGGACTAATGATTTTGGTGA+TGG + chr4.3:42205314-42205333 None:intergenic 40.0%
!!! TTTTAGGAGACGGATTAGGA+CGG + chr4.3:42205417-42205436 None:intergenic 40.0%
AGGATTGTTGTGATGTCGTC+AGG + chr4.3:42205374-42205393 None:intergenic 45.0%
AGTGTACACAACACCCACAA+CGG + chr4.3:42205747-42205766 None:intergenic 45.0%
CAATGTCAGTCTTTCAACCG+GGG - chr4.3:42205709-42205728 MS.gene062571:CDS 45.0%
CAGCTCATCACAGCCAAAAA+CGG - chr4.3:42205467-42205486 MS.gene062571:CDS 45.0%
CTGGTGATTCAGGTAATGTG+GGG + chr4.3:42205334-42205353 None:intergenic 45.0%
GGATTGTTGTGATGTCGTCA+GGG + chr4.3:42205373-42205392 None:intergenic 45.0%
GGCTCCTAAAGCTGCTAATA+AGG - chr4.3:42205871-42205890 MS.gene062571:CDS 45.0%
GTCTGGTGATTCAGGTAATG+TGG + chr4.3:42205336-42205355 None:intergenic 45.0%
GTTGTTACTGCTTCCGTTGT+GGG - chr4.3:42205731-42205750 MS.gene062571:CDS 45.0%
TAGCTGGTAAAGACCCAACA+AGG - chr4.3:42205657-42205676 MS.gene062571:CDS 45.0%
TCTGTTGAGTCTGGTGATTC+AGG + chr4.3:42205344-42205363 None:intergenic 45.0%
!! GATTGTTAAGCCGCCGTTTT+TGG + chr4.3:42205483-42205502 None:intergenic 45.0%
!! GCATTTTCAAGCCTCAAAGC+AGG - chr4.3:42205521-42205540 MS.gene062571:CDS 45.0%
!! GGAGATTTTGGGGATGATTC+AGG + chr4.3:42205257-42205276 None:intergenic 45.0%
!!! GTGATGGTGCTGTTGCTTTT+GGG + chr4.3:42205298-42205317 None:intergenic 45.0%
!!! TGATGGTGCTGTTGCTTTTG+GGG + chr4.3:42205297-42205316 None:intergenic 45.0%
AACGGAAGCAGTAACAACCC+CGG + chr4.3:42205729-42205748 None:intergenic 50.0%
CTCATCACAGCCAAAAACGG+CGG - chr4.3:42205470-42205489 MS.gene062571:CDS 50.0%
GGTTGTTACTGCTTCCGTTG+TGG - chr4.3:42205730-42205749 MS.gene062571:CDS 50.0%
TGTTGTGATGTCGTCAGGGA+CGG + chr4.3:42205369-42205388 None:intergenic 50.0%
! TCTGGAGCAGTGAGATTGTG+TGG - chr4.3:42205944-42205963 MS.gene062571:CDS 50.0%
!!! GGGGTAGGGGGTGTTTTTTT+TGG + chr4.3:42205278-42205297 None:intergenic 50.0%
!!! GGTGATGGTGCTGTTGCTTT+TGG + chr4.3:42205299-42205318 None:intergenic 50.0%
!!! GTGCTGTTGCTTTTGGGGTA+GGG + chr4.3:42205292-42205311 None:intergenic 50.0%
!!! TGCTGTTGCTTTTGGGGTAG+GGG + chr4.3:42205291-42205310 None:intergenic 50.0%
TTAGCAGCAGCAGCACGAGT+TGG + chr4.3:42205851-42205870 None:intergenic 55.0%
! AACTCGTGCTGCTGCTGCTA+AGG - chr4.3:42205850-42205869 MS.gene062571:CDS 55.0%
! CGCTACTAAGGCACCTGCTT+TGG - chr4.3:42205823-42205842 MS.gene062571:CDS 55.0%
!!! GCTGTTGCTTTTGGGGTAGG+GGG + chr4.3:42205290-42205309 None:intergenic 55.0%
!!! GGTGCTGTTGCTTTTGGGGT+AGG + chr4.3:42205293-42205312 None:intergenic 55.0%
ATGCTGAATCGTCTGGCGCG+AGG + chr4.3:42205505-42205524 None:intergenic 60.0%
GGGACGGAGTCTGTTGAGTC+TGG + chr4.3:42205353-42205372 None:intergenic 60.0%
! GCACGAGTTGGAGCCAAAGC+AGG + chr4.3:42205839-42205858 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 42205179 42206021 42205179 ID=MS.gene062571
chr4.3 mRNA 42205179 42206021 42205179 ID=MS.gene062571.t1;Parent=MS.gene062571
chr4.3 exon 42205179 42206021 42205179 ID=MS.gene062571.t1.exon1;Parent=MS.gene062571.t1
chr4.3 CDS 42205179 42206021 42205179 ID=cds.MS.gene062571.t1;Parent=MS.gene062571.t1
Gene Sequence

>MS.gene062571

ATGAAACAAGTAACTTTATTCTTTTTCTTTTCACTCTTACTTCTCTTTTCATCCACATTATCCCTTTCACAAGCACCTGAATCATCCCCAAAATCTCCAAAAAAAACACCCCCTACCCCAAAAGCAACAGCACCATCACCAAAATCATTAGTCCCCACATTACCTGAATCACCAGACTCAACAGACTCCGTCCCTGACGACATCACAACAATCCTCAAAAAGGCGAAAACATTCTCCGTCCTAATCCGTCTCCTAAAAACAACAGAAATCATGAGCAGCGTAAACTCACAGCTCATCACAGCCAAAAACGGCGGCTTAACAATCCTCGCGCCAGACGATTCAGCATTTTCAAGCCTCAAAGCAGGGTTTCTTAACTCCTTAGACGAAAACAAAAAAATCGAACTTTTACAATTCCACATCTTACCTCAATATGTAGCGAGCTCAAACTTCGATTCTTTAAGCAACCCTGTTCAAACAATAGCTGGTAAAGACCCAACAAGGCTTCCACTTAATGTTTATGCATCAGGTAACAATGTCAGTCTTTCAACCGGGGTTGTTACTGCTTCCGTTGTGGGTGTTGTGTACACTGATAACAAGCTCGCGATTTATCATTTGGATAAAGTGCTTCTTCCTCGTGATTTCTTCGCTACTAAGGCACCTGCTTTGGCTCCAACTCGTGCTGCTGCTGCTAAGGCTCCTAAAGCTGCTAATAAGGAGAATTCTTCTGCTGATGATCAAGACCAAAATGATCAGGATCAAGGTAAATCTGGAGCAGTGAGATTGTGTGGAATTCTTGGAACAACGTTGATGTCTTTTGTTGCTGTAGCATTGATATGGAGTTGA

Protein sequence

>MS.gene062571.t1

MKQVTLFFFFSLLLLFSSTLSLSQAPESSPKSPKKTPPTPKATAPSPKSLVPTLPESPDSTDSVPDDITTILKKAKTFSVLIRLLKTTEIMSSVNSQLITAKNGGLTILAPDDSAFSSLKAGFLNSLDENKKIELLQFHILPQYVASSNFDSLSNPVQTIAGKDPTRLPLNVYASGNNVSLSTGVVTASVVGVVYTDNKLAIYHLDKVLLPRDFFATKAPALAPTRAAAAKAPKAANKENSSADDQDQNDQDQGKSGAVRLCGILGTTLMSFVAVALIWS