AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene82996

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82996.t1 MTR_1g033340 93.385 257 11 1 1 257 1 251 0.0 498
MS.gene82996.t1 MTR_3g065020 41.897 253 130 7 5 257 3 238 4.11e-57 182
MS.gene82996.t1 MTR_5g077370 43.561 264 107 10 6 257 4 237 8.01e-56 179
MS.gene82996.t1 MTR_2g104900 66.234 77 21 2 97 168 81 157 2.79e-27 105
MS.gene82996.t1 MTR_1g013130 39.726 146 68 2 43 168 35 180 2.83e-24 98.2
MS.gene82996.t1 MTR_1g107055 34.595 185 96 8 42 218 8 175 1.24e-20 87.0
MS.gene82996.t1 MTR_3g106230 44.828 116 42 6 69 168 49 158 7.22e-20 85.5
MS.gene82996.t1 MTR_4g006575 55.556 72 24 2 97 168 67 130 5.36e-18 80.5
MS.gene82996.t1 MTR_4g006600 55.556 72 24 2 97 168 67 130 5.36e-18 80.5
MS.gene82996.t1 MTR_4g128340 52.632 76 32 2 97 170 45 118 2.11e-16 75.1
MS.gene82996.t1 MTR_7g086860 51.923 52 24 1 82 133 16 66 4.68e-12 62.8
MS.gene82996.t1 MTR_7g083210 69.697 33 10 0 97 129 39 71 2.86e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82996.t1 AT1G66140 41.758 182 81 6 97 257 83 260 4.70e-37 131
MS.gene82996.t1 AT1G24625 39.381 226 95 11 39 257 19 209 8.29e-32 116
MS.gene82996.t1 AT1G80730 55.682 88 23 2 97 168 66 153 1.26e-23 95.9
MS.gene82996.t1 AT5G10970 45.378 119 59 4 55 168 58 175 7.39e-21 89.4
MS.gene82996.t1 AT5G25160 51.163 86 36 3 88 168 50 134 8.71e-20 85.5
MS.gene82996.t1 AT5G57520 51.515 66 32 0 97 162 50 115 1.53e-15 72.0
MS.gene82996.t1 AT5G14010 46.575 73 28 1 93 154 32 104 1.00e-14 70.1
MS.gene82996.t1 AT5G01860 57.500 40 17 0 97 136 65 104 2.25e-11 62.0

Find 46 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGCTTCCAAGTTCAAATT+TGG 0.203450 1.4:-18148257 None:intergenic
ATGAAGATGTCGGCGTATTT+TGG 0.224650 1.4:+18148855 MS.gene82996:CDS
GACATCAGAATGCTCATAAA+AGG 0.253068 1.4:+18148591 MS.gene82996:CDS
TTAGCTTCTTTACCTCTTCA+TGG 0.299313 1.4:+18148674 MS.gene82996:CDS
TTTATCTGCCTGAAACTTCC+AGG 0.347691 1.4:-18148878 None:intergenic
ACGACGATGGCATATGGTTT+TGG 0.357563 1.4:-18148745 None:intergenic
AAATTCGAGAAAGATTGTTT+TGG 0.369690 1.4:+18148809 MS.gene82996:CDS
AGCTAAGCTTGTATACCTTT+CGG 0.370401 1.4:-18148657 None:intergenic
TCCTTCAAATCTTCATTGCT+CGG 0.385585 1.4:-18148437 None:intergenic
CCTATCCTGATCTTACTTTG+AGG 0.413927 1.4:+18148990 MS.gene82996:CDS
TCCGAGCAATGAAGATTTGA+AGG 0.432984 1.4:+18148436 MS.gene82996:CDS
AACTTCTTCTTGTCTTACTA+AGG 0.451364 1.4:+18148364 MS.gene82996:CDS
TTCTTTAGCTCACAAGCGTT+AGG 0.463186 1.4:+18148566 MS.gene82996:CDS
GTAGTAGATGTTTGTTGAGG+AGG 0.483825 1.4:-18148968 None:intergenic
ACTAAGGCAGACATTAATCC+AGG 0.488717 1.4:+18148380 MS.gene82996:CDS
TCTTTCTCGAATTTCGCTGC+AGG 0.490019 1.4:-18148800 None:intergenic
TCGGATCGAAGTTGAGAGTC+AGG 0.491506 1.4:-18148418 None:intergenic
TCGACGACGACGATGGCATA+TGG 0.495080 1.4:-18148751 None:intergenic
GAAGACTCCAAATTTGAACT+TGG 0.507535 1.4:+18148250 MS.gene82996:CDS
CAAAGCGCGCTATGCAAGTA+GGG 0.513002 1.4:+18148627 MS.gene82996:CDS
TAAAGCCTCAAAGTAAGATC+AGG 0.515851 1.4:-18148995 None:intergenic
TCTCTTGTAATTATTGTAGG+AGG 0.522769 1.4:+18148540 MS.gene82996:CDS
TGATTCTTGTAAGTATATGT+TGG 0.525252 1.4:-18148312 None:intergenic
GCAAAGCGCGCTATGCAAGT+AGG 0.525984 1.4:+18148626 MS.gene82996:CDS
ACATCAGAATGCTCATAAAA+GGG 0.526603 1.4:+18148592 MS.gene82996:CDS
CCTCAAAGTAAGATCAGGAT+AGG 0.529476 1.4:-18148990 None:intergenic
GAGAAAACTCTATGAATCGT+TGG 0.530449 1.4:-18148521 None:intergenic
CGTCGTCGTCGATGCTGATG+AGG 0.540974 1.4:+18148762 MS.gene82996:CDS
AGGTCAAGGGAAATAGAACC+TGG 0.542650 1.4:-18148398 None:intergenic
AGTATATGTTGGAACCTACT+TGG 0.544787 1.4:-18148301 None:intergenic
CGAAGTTGAGAGTCAGGTCA+AGG 0.567959 1.4:-18148412 None:intergenic
TTTAGCTCACAAGCGTTAGG+AGG 0.570693 1.4:+18148569 MS.gene82996:CDS
TAGGTAGTAGATGTTTGTTG+AGG 0.576261 1.4:-18148971 None:intergenic
AACTCTATGAATCGTTGGTG+CGG 0.596598 1.4:-18148516 None:intergenic
TTAGAAGTAAGCAGCCAAGT+AGG 0.598009 1.4:+18148287 MS.gene82996:CDS
GTCGTCGTCGATGCTGATGA+GGG 0.606346 1.4:+18148763 MS.gene82996:CDS
GACACTAACAGTGAAGTACT+AGG 0.613028 1.4:+18148467 MS.gene82996:CDS
AAAGAAGAAGAACCATGAAG+AGG 0.622542 1.4:-18148686 None:intergenic
AAGTAGGGATGTTTACCGAA+AGG 0.636930 1.4:+18148642 MS.gene82996:CDS
GAAGTTGAGAGTCAGGTCAA+GGG 0.642054 1.4:-18148411 None:intergenic
TTTATGCATAATGAAGATGT+CGG 0.651635 1.4:+18148845 MS.gene82996:CDS
AGTAAGACAAGAAGAAGTTG+TGG 0.657771 1.4:-18148360 None:intergenic
ATCAGCATCGACGACGACGA+TGG 0.667792 1.4:-18148758 None:intergenic
TCTTCATTATGCATAAACAT+CGG 0.674163 1.4:-18148839 None:intergenic
TCATAAAAGGGAGAGAACGA+TGG 0.677286 1.4:+18148604 MS.gene82996:CDS
GCATGAGCTTGAATCCCAAG+AGG 0.685243 1.4:-18148713 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTCTCTTGTAATTATTGT+AGG + chr1.4:18148537-18148556 MS.gene82996:CDS 20.0%
! TCTTCATTATGCATAAACAT+CGG - chr1.4:18148842-18148861 None:intergenic 25.0%
! TGATTCTTGTAAGTATATGT+TGG - chr1.4:18148315-18148334 None:intergenic 25.0%
! TTTATGCATAATGAAGATGT+CGG + chr1.4:18148845-18148864 MS.gene82996:CDS 25.0%
!! AAATTCGAGAAAGATTGTTT+TGG + chr1.4:18148809-18148828 MS.gene82996:CDS 25.0%
AACTTCTTCTTGTCTTACTA+AGG + chr1.4:18148364-18148383 MS.gene82996:CDS 30.0%
ACATCAGAATGCTCATAAAA+GGG + chr1.4:18148592-18148611 MS.gene82996:CDS 30.0%
TCTCTTGTAATTATTGTAGG+AGG + chr1.4:18148540-18148559 MS.gene82996:CDS 30.0%
AAAGAAGAAGAACCATGAAG+AGG - chr1.4:18148689-18148708 None:intergenic 35.0%
AGCTAAGCTTGTATACCTTT+CGG - chr1.4:18148660-18148679 None:intergenic 35.0%
AGTAAGACAAGAAGAAGTTG+TGG - chr1.4:18148363-18148382 None:intergenic 35.0%
AGTATATGTTGGAACCTACT+TGG - chr1.4:18148304-18148323 None:intergenic 35.0%
GAAGACTCCAAATTTGAACT+TGG + chr1.4:18148250-18148269 MS.gene82996:CDS 35.0%
GACATCAGAATGCTCATAAA+AGG + chr1.4:18148591-18148610 MS.gene82996:CDS 35.0%
GAGAAAACTCTATGAATCGT+TGG - chr1.4:18148524-18148543 None:intergenic 35.0%
TAAAGCCTCAAAGTAAGATC+AGG - chr1.4:18148998-18149017 None:intergenic 35.0%
TCAGCTTCCAAGTTCAAATT+TGG - chr1.4:18148260-18148279 None:intergenic 35.0%
TCCTTCAAATCTTCATTGCT+CGG - chr1.4:18148440-18148459 None:intergenic 35.0%
TTAGCTTCTTTACCTCTTCA+TGG + chr1.4:18148674-18148693 MS.gene82996:CDS 35.0%
! CTTCTTCTTTTCATCCTCTT+GGG + chr1.4:18148699-18148718 MS.gene82996:CDS 35.0%
! TAGGTAGTAGATGTTTGTTG+AGG - chr1.4:18148974-18148993 None:intergenic 35.0%
! TCTTCTTCTTTTCATCCTCT+TGG + chr1.4:18148698-18148717 MS.gene82996:CDS 35.0%
AACTCTATGAATCGTTGGTG+CGG - chr1.4:18148519-18148538 None:intergenic 40.0%
AAGTAGGGATGTTTACCGAA+AGG + chr1.4:18148642-18148661 MS.gene82996:CDS 40.0%
ACTAAGGCAGACATTAATCC+AGG + chr1.4:18148380-18148399 MS.gene82996:CDS 40.0%
CCTATCCTGATCTTACTTTG+AGG + chr1.4:18148990-18149009 MS.gene82996:CDS 40.0%
CCTCAAAGTAAGATCAGGAT+AGG - chr1.4:18148993-18149012 None:intergenic 40.0%
TCATAAAAGGGAGAGAACGA+TGG + chr1.4:18148604-18148623 MS.gene82996:CDS 40.0%
TCCGAGCAATGAAGATTTGA+AGG + chr1.4:18148436-18148455 MS.gene82996:CDS 40.0%
TTAGAAGTAAGCAGCCAAGT+AGG + chr1.4:18148287-18148306 MS.gene82996:CDS 40.0%
TTTATCTGCCTGAAACTTCC+AGG - chr1.4:18148881-18148900 None:intergenic 40.0%
! ATGAAGATGTCGGCGTATTT+TGG + chr1.4:18148855-18148874 MS.gene82996:CDS 40.0%
! GACACTAACAGTGAAGTACT+AGG + chr1.4:18148467-18148486 MS.gene82996:CDS 40.0%
! GTAGTAGATGTTTGTTGAGG+AGG - chr1.4:18148971-18148990 None:intergenic 40.0%
! TTCTTTAGCTCACAAGCGTT+AGG + chr1.4:18148566-18148585 MS.gene82996:CDS 40.0%
!!! TATTTTGGCCTGGAAGTTTC+AGG + chr1.4:18148870-18148889 MS.gene82996:CDS 40.0%
AGGTCAAGGGAAATAGAACC+TGG - chr1.4:18148401-18148420 None:intergenic 45.0%
GAAGTTGAGAGTCAGGTCAA+GGG - chr1.4:18148414-18148433 None:intergenic 45.0%
TCTTTCTCGAATTTCGCTGC+AGG - chr1.4:18148803-18148822 None:intergenic 45.0%
! ACGACGATGGCATATGGTTT+TGG - chr1.4:18148748-18148767 None:intergenic 45.0%
! TTTAGCTCACAAGCGTTAGG+AGG + chr1.4:18148569-18148588 MS.gene82996:CDS 45.0%
CAAAGCGCGCTATGCAAGTA+GGG + chr1.4:18148627-18148646 MS.gene82996:CDS 50.0%
CGAAGTTGAGAGTCAGGTCA+AGG - chr1.4:18148415-18148434 None:intergenic 50.0%
GCATGAGCTTGAATCCCAAG+AGG - chr1.4:18148716-18148735 None:intergenic 50.0%
TCGGATCGAAGTTGAGAGTC+AGG - chr1.4:18148421-18148440 None:intergenic 50.0%
GCAAAGCGCGCTATGCAAGT+AGG + chr1.4:18148626-18148645 MS.gene82996:CDS 55.0%
GTCGTCGTCGATGCTGATGA+GGG + chr1.4:18148763-18148782 MS.gene82996:CDS 55.0%
TCGACGACGACGATGGCATA+TGG - chr1.4:18148754-18148773 None:intergenic 55.0%
!! ATCAGCATCGACGACGACGA+TGG - chr1.4:18148761-18148780 None:intergenic 55.0%
!!! GATGTCGGCGTATTTTGGCC+TGG + chr1.4:18148860-18148879 MS.gene82996:CDS 55.0%
CGTCGTCGTCGATGCTGATG+AGG + chr1.4:18148762-18148781 MS.gene82996:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 18148245 18149018 18148245 ID=MS.gene82996
chr1.4 mRNA 18148245 18149018 18148245 ID=MS.gene82996.t1;Parent=MS.gene82996
chr1.4 exon 18148245 18149018 18148245 ID=MS.gene82996.t1.exon1;Parent=MS.gene82996.t1
chr1.4 CDS 18148245 18149018 18148245 ID=cds.MS.gene82996.t1;Parent=MS.gene82996.t1
Gene Sequence

>MS.gene82996

ATGATGAAGACTCCAAATTTGAACTTGGAAGCTGAAAATAGTTTAGAAGTAAGCAGCCAAGTAGGTTCCAACATATACTTACAAGAATCATCTCATGATCTTACAAAAGACAGTGCCACAACTTCTTCTTGTCTTACTAAGGCAGACATTAATCCAGGTTCTATTTCCCTTGACCTGACTCTCAACTTCGATCCGAGCAATGAAGATTTGAAGGAAACAAGCGACACTAACAGTGAAGTACTAGGAGCTAATCAAGCTCATAATACTGTTTCCGCACCAACGATTCATAGAGTTTTCTCTTGTAATTATTGTAGGAGGAAATTCTTTAGCTCACAAGCGTTAGGAGGACATCAGAATGCTCATAAAAGGGAGAGAACGATGGCAAAGCGCGCTATGCAAGTAGGGATGTTTACCGAAAGGTATACAAGCTTAGCTTCTTTACCTCTTCATGGTTCTTCTTCTTTTCATCCTCTTGGGATTCAAGCTCATGCTGCAATGCACCAAAACCATATGCCATCGTCGTCGTCGATGCTGATGAGGGCTCAAAATATGAGACCTGCAGCGAAATTCGAGAAAGATTGTTTTGGAGCAGCACCGATGTTTATGCATAATGAAGATGTCGGCGTATTTTGGCCTGGAAGTTTCAGGCAGATAAATCAAAGTGTTCATAATTCAAATTTGAATCATAACTCAAATTTAAATACTAGTTTTGTAGCAACTGAACCTCCTCAACAAACATCTACTACCTATCCTGATCTTACTTTGAGGCTTTAA
Protein sequence

>MS.gene82996.t1

MMKTPNLNLEAENSLEVSSQVGSNIYLQESSHDLTKDSATTSSCLTKADINPGSISLDLTLNFDPSNEDLKETSDTNSEVLGANQAHNTVSAPTIHRVFSCNYCRRKFFSSQALGGHQNAHKRERTMAKRAMQVGMFTERYTSLASLPLHGSSSFHPLGIQAHAAMHQNHMPSSSSMLMRAQNMRPAAKFEKDCFGAAPMFMHNEDVGVFWPGSFRQINQSVHNSNLNHNSNLNTSFVATEPPQQTSTTYPDLTLRL