AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073991

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073991.t1 MTR_1g060700 90.852 317 15 8 1 310 178 487 0.0 556
MS.gene073991.t1 MTR_2g067000 85.443 316 22 6 1 310 1 298 6.30e-178 493
MS.gene073991.t1 MTR_8g093500 58.491 53 22 0 180 232 125 177 1.06e-12 67.4
MS.gene073991.t1 MTR_3g101810 58.491 53 22 0 180 232 182 234 3.96e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073991.t1 AT1G30670 38.596 228 123 6 87 303 41 262 3.36e-33 123
MS.gene073991.t1 AT2G34820 40.336 238 107 8 87 303 66 289 7.57e-28 109
MS.gene073991.t1 AT3G21330 60.377 53 21 0 180 232 280 332 5.05e-13 69.3
MS.gene073991.t1 AT5G01305 50.000 58 29 0 180 237 48 105 5.06e-12 63.9

Find 47 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATTATGATTGCTCAATT+TGG 0.191234 2.1:+30066024 None:intergenic
AGTTGGAATGCTTCAACTTA+TGG 0.195386 2.1:-30066933 MS.gene073991:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 2.1:+30066998 None:intergenic
AAAATGAAATCTTCCTCATT+TGG 0.263570 2.1:+30067325 None:intergenic
AATTTGGTGACAAACTCTTT+TGG 0.289383 2.1:+30066040 None:intergenic
CCTCATAATATAGCAGCTTT+TGG 0.311729 2.1:+30067272 None:intergenic
GTTCAATGTGAGAAGAAAAT+TGG 0.315720 2.1:-30067118 MS.gene073991:CDS
AAATGAAATCTTCCTCATTT+GGG 0.325640 2.1:+30067326 None:intergenic
TACAATTTCTCTTGAACAAA+TGG 0.348402 2.1:+30066085 None:intergenic
GAGAAGCTTCATTGAAATAG+TGG 0.359894 2.1:+30067488 None:intergenic
ATCAAAACCTACCATCCTTA+AGG 0.361760 2.1:-30065996 MS.gene073991:CDS
AAATAACACTATTCTTGCTT+TGG 0.365183 2.1:+30065935 None:intergenic
TCAAAGGAAGCAAAAGGGTT+AGG 0.369513 2.1:+30067178 None:intergenic
GCAGTTTGAATAGGTTGATA+AGG 0.385279 2.1:+30067574 None:intergenic
GAGCTTGGGAAGTTGGTTCC+TGG 0.392352 2.1:-30067025 MS.gene073991:CDS
GACACAAGAGCTTGGGAAGT+TGG 0.397999 2.1:-30067032 MS.gene073991:CDS
TTGATTATTTCAGGAAGAAA+AGG 0.418378 2.1:-30066149 MS.gene073991:intron
CAAGCTGTTTCAGACCCTTA+AGG 0.427556 2.1:+30065981 None:intergenic
CCAAAAGCTGCTATATTATG+AGG 0.434506 2.1:-30067272 MS.gene073991:CDS
TCTGCCTCAAAGGAAGCAAA+AGG 0.449981 2.1:+30067172 None:intergenic
TCAAAACCTACCATCCTTAA+GGG 0.456430 2.1:-30065995 MS.gene073991:CDS
AAGGGTCTGAAACAGCTTGT+TGG 0.460418 2.1:-30065977 MS.gene073991:CDS
CAAAGGAAGCAAAAGGGTTA+GGG 0.461232 2.1:+30067179 None:intergenic
TTGTGTAGATCTTCACTTGG+AGG 0.465635 2.1:+30066121 None:intergenic
AGAGTATCGCGGCGAGAGAA+AGG 0.466876 2.1:-30067075 MS.gene073991:CDS
AGTGGTGATTTCTGAGTTGT+TGG 0.472171 2.1:+30067549 None:intergenic
CAGTTTGAATAGGTTGATAA+GGG 0.475268 2.1:+30067575 None:intergenic
TTGTTGGTAGCAGTTTGAAT+AGG 0.476845 2.1:+30067565 None:intergenic
TGTAGATCTTCACTTGGAGG+AGG 0.494574 2.1:+30066124 None:intergenic
GTGTTCATCTTTGGTCCACC+AGG 0.499817 2.1:+30067007 None:intergenic
ACTGAGAAGACACAAGAGCT+TGG 0.499993 2.1:-30067040 MS.gene073991:CDS
CTGAGAAGACACAAGAGCTT+GGG 0.500383 2.1:-30067039 MS.gene073991:CDS
AGCAAAGGTTTCTGCCTCAA+AGG 0.518713 2.1:+30067162 None:intergenic
CTTGGGAAGTTGGTTCCTGG+TGG 0.551828 2.1:-30067022 MS.gene073991:CDS
AGTTTGTGTAGATCTTCACT+TGG 0.558027 2.1:+30066118 None:intergenic
TTGTTCATGATGTTGAAAAG+TGG 0.560071 2.1:+30067531 None:intergenic
GTGAGAAGAAAATTGGTGAA+AGG 0.563717 2.1:-30067111 MS.gene073991:CDS
AAGTTTCTTCAAGCTCAAGT+TGG 0.567049 2.1:-30066950 MS.gene073991:CDS
GAGTTCAAAAGCTCTTGTTG+TGG 0.567814 2.1:+30067235 None:intergenic
ACTTATGGAAACATTTAGCA+AGG 0.569731 2.1:-30066918 MS.gene073991:intron
TTCAGACCCTTAAGGATGGT+AGG 0.578594 2.1:+30065989 None:intergenic
CTGCCTCAAAGGAAGCAAAA+GGG 0.580071 2.1:+30067173 None:intergenic
TCGCGGCGAGAGAAAGGAGA+AGG 0.587504 2.1:-30067069 MS.gene073991:CDS
CTGTTTCAGACCCTTAAGGA+TGG 0.616344 2.1:+30065985 None:intergenic
AGTAGTTGATCATCTTGACA+AGG 0.655107 2.1:+30067406 None:intergenic
TATCTCGTCGCAGAGTATCG+CGG 0.686396 2.1:-30067086 MS.gene073991:CDS
GTAGTTGATCATCTTGACAA+GGG 0.704443 2.1:+30067407 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTTTGTAAATATCTAAAA+TGG - chr2.1:30066839-30066858 MS.gene073991:intron 15.0%
!!! CACTATTAATTTTATTTTCT+AGG + chr2.1:30067289-30067308 None:intergenic 15.0%
!! ACTAACTAAATCTACAATAA+TGG + chr2.1:30066874-30066893 None:intergenic 20.0%
!! GAATATTTAAAAACAAAGAG+TGG + chr2.1:30067179-30067198 None:intergenic 20.0%
!! TCATTTGAGTAAAAACAATT+AGG + chr2.1:30066123-30066142 None:intergenic 20.0%
!! TTATTGTATAAAGTTACACT+AGG + chr2.1:30067336-30067355 None:intergenic 20.0%
!!! AATATTTTCAGAGTAAAAGT+AGG + chr2.1:30066968-30066987 None:intergenic 20.0%
!!! ATATGATCATTGATTATTTC+AGG - chr2.1:30067398-30067417 MS.gene073991:CDS 20.0%
!!! CTTTTACTCTGAAAATATTT+AGG - chr2.1:30066969-30066988 MS.gene073991:CDS 20.0%
! AAAATGAAATCTTCCTCATT+TGG + chr2.1:30066234-30066253 None:intergenic 25.0%
! AAACTCATCCACAAAAAAAT+TGG + chr2.1:30066349-30066368 None:intergenic 25.0%
! AAATGAAATCTTCCTCATTT+GGG + chr2.1:30066233-30066252 None:intergenic 25.0%
! ATCATTATGATTGCTCAATT+TGG + chr2.1:30067535-30067554 None:intergenic 25.0%
! TACAATTTCTCTTGAACAAA+TGG + chr2.1:30067474-30067493 None:intergenic 25.0%
! TTAGGAACAACAATTGTATA+TGG - chr2.1:30067116-30067135 MS.gene073991:CDS 25.0%
! TTGATTATTTCAGGAAGAAA+AGG - chr2.1:30067407-30067426 MS.gene073991:CDS 25.0%
!! TTTTATCAACATAAGACCTA+AGG + chr2.1:30066776-30066795 None:intergenic 25.0%
!!! CAATAAACAAGAGAGTATTT+AGG - chr2.1:30067098-30067117 MS.gene073991:CDS 25.0%
ACTTATGGAAACATTTAGCA+AGG - chr2.1:30066638-30066657 MS.gene073991:intron 30.0%
GTTCAATGTGAGAAGAAAAT+TGG - chr2.1:30066438-30066457 MS.gene073991:intron 30.0%
TAATATCCTTCCAAGTGTTT+GGG + chr2.1:30067234-30067253 None:intergenic 30.0%
TTAATATCCTTCCAAGTGTT+TGG + chr2.1:30067235-30067254 None:intergenic 30.0%
TTGTTCATGATGTTGAAAAG+TGG + chr2.1:30066028-30066047 None:intergenic 30.0%
! GAATGAAATTTTCCCAAATG+AGG - chr2.1:30066218-30066237 MS.gene073991:intron 30.0%
! TATTTAGTTTCCCAAACACT+TGG - chr2.1:30067221-30067240 MS.gene073991:CDS 30.0%
!! AATTTGGTGACAAACTCTTT+TGG + chr2.1:30067519-30067538 None:intergenic 30.0%
!! ACTTTTTCTTCTCAAAACGA+TGG - chr2.1:30066183-30066202 MS.gene073991:intron 30.0%
!! CAGTTTGAATAGGTTGATAA+GGG + chr2.1:30065984-30066003 None:intergenic 30.0%
!!! AACAATTTTTGAAGCAGCAA+AGG + chr2.1:30066412-30066431 None:intergenic 30.0%
!!! ATCGTTTTGAGAAGAAAAAG+TGG + chr2.1:30066184-30066203 None:intergenic 30.0%
!!! GAACTCAACCAATTTTTTTG+TGG - chr2.1:30066338-30066357 MS.gene073991:intron 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG - chr2.1:30066606-30066625 MS.gene073991:intron 35.0%
AGTAGTTGATCATCTTGACA+AGG + chr2.1:30066153-30066172 None:intergenic 35.0%
AGTTGGAATGCTTCAACTTA+TGG - chr2.1:30066623-30066642 MS.gene073991:intron 35.0%
AGTTTGTGTAGATCTTCACT+TGG + chr2.1:30067441-30067460 None:intergenic 35.0%
ATCAAAACCTACCATCCTTA+AGG - chr2.1:30067560-30067579 MS.gene073991:CDS 35.0%
ATCAACATAAGACCTAAGGA+AGG + chr2.1:30066772-30066791 None:intergenic 35.0%
CAATTGTATATGGAATGAGC+TGG - chr2.1:30067126-30067145 MS.gene073991:CDS 35.0%
CCAAAAGCTGCTATATTATG+AGG - chr2.1:30066284-30066303 MS.gene073991:intron 35.0%
CGGTTAATAAGAAGAGGAAA+TGG - chr2.1:30067074-30067093 MS.gene073991:CDS 35.0%
GAGAAGCTTCATTGAAATAG+TGG + chr2.1:30066071-30066090 None:intergenic 35.0%
GTAGTTGATCATCTTGACAA+GGG + chr2.1:30066152-30066171 None:intergenic 35.0%
GTGAGAAGAAAATTGGTGAA+AGG - chr2.1:30066445-30066464 MS.gene073991:intron 35.0%
TCAAAACCTACCATCCTTAA+GGG - chr2.1:30067561-30067580 MS.gene073991:CDS 35.0%
! CCTCATAATATAGCAGCTTT+TGG + chr2.1:30066287-30066306 None:intergenic 35.0%
! TTTTCAGAGTAAAAGTAGGC+AGG + chr2.1:30066964-30066983 None:intergenic 35.0%
!! GCAGTTTGAATAGGTTGATA+AGG + chr2.1:30065985-30066004 None:intergenic 35.0%
!! TTGTTGGTAGCAGTTTGAAT+AGG + chr2.1:30065994-30066013 None:intergenic 35.0%
AGTGGTGATTTCTGAGTTGT+TGG + chr2.1:30066010-30066029 None:intergenic 40.0%
ATCTCTGCTGTGTTCATCTT+TGG + chr2.1:30066561-30066580 None:intergenic 40.0%
CAAAGGAAGCAAAAGGGTTA+GGG + chr2.1:30066380-30066399 None:intergenic 40.0%
GAGTTCAAAAGCTCTTGTTG+TGG + chr2.1:30066324-30066343 None:intergenic 40.0%
GGCTATGTAACTGTTCAACA+AGG - chr2.1:30067147-30067166 MS.gene073991:CDS 40.0%
GGGAAACGGTTAATAAGAAG+AGG - chr2.1:30067068-30067087 MS.gene073991:CDS 40.0%
TAGTTTCCCAAACACTTGGA+AGG - chr2.1:30067225-30067244 MS.gene073991:CDS 40.0%
TCAAAGGAAGCAAAAGGGTT+AGG + chr2.1:30066381-30066400 None:intergenic 40.0%
TTGTGTAGATCTTCACTTGG+AGG + chr2.1:30067438-30067457 None:intergenic 40.0%
! ACTGTTTTGTGTCCTTCCTT+AGG - chr2.1:30066757-30066776 MS.gene073991:intron 40.0%
! TAACCCTTTTGCTTCCTTTG+AGG - chr2.1:30066380-30066399 MS.gene073991:intron 40.0%
! TATAGCAGCTTTTGGCGTTT+TGG + chr2.1:30066279-30066298 None:intergenic 40.0%
!! TAGGTGCTGAATCATGTCAT+GGG + chr2.1:30067270-30067289 None:intergenic 40.0%
ACTGAGAAGACACAAGAGCT+TGG - chr2.1:30066516-30066535 MS.gene073991:intron 45.0%
AGAGAGAAGGGTTAGGGAAA+CGG - chr2.1:30067054-30067073 MS.gene073991:CDS 45.0%
AGAGAGAGAGAGAAGGGTTA+GGG - chr2.1:30067048-30067067 MS.gene073991:CDS 45.0%
AGAGAGAGAGAGAGAGAGAA+GGG - chr2.1:30067042-30067061 MS.gene073991:CDS 45.0%
AGCAAAGGTTTCTGCCTCAA+AGG + chr2.1:30066397-30066416 None:intergenic 45.0%
CTGAGAAGACACAAGAGCTT+GGG - chr2.1:30066517-30066536 MS.gene073991:intron 45.0%
CTGCCTCAAAGGAAGCAAAA+GGG + chr2.1:30066386-30066405 None:intergenic 45.0%
CTGTTTCAGACCCTTAAGGA+TGG + chr2.1:30067574-30067593 None:intergenic 45.0%
TCTGCCTCAAAGGAAGCAAA+AGG + chr2.1:30066387-30066406 None:intergenic 45.0%
TGTAGATCTTCACTTGGAGG+AGG + chr2.1:30067435-30067454 None:intergenic 45.0%
TTCAGACCCTTAAGGATGGT+AGG + chr2.1:30067570-30067589 None:intergenic 45.0%
! AAGGGTCTGAAACAGCTTGT+TGG - chr2.1:30067579-30067598 MS.gene073991:CDS 45.0%
! CAAGCTGTTTCAGACCCTTA+AGG + chr2.1:30067578-30067597 None:intergenic 45.0%
!! CTAGGTGCTGAATCATGTCA+TGG + chr2.1:30067271-30067290 None:intergenic 45.0%
GACACAAGAGCTTGGGAAGT+TGG - chr2.1:30066524-30066543 MS.gene073991:intron 50.0%
GAGAGAGAGAGAGAAGGGTT+AGG - chr2.1:30067047-30067066 MS.gene073991:CDS 50.0%
GAGAGAGAGAGAGAGAGAGA+AGG - chr2.1:30067023-30067042 MS.gene073991:CDS 50.0%
GTGTTCATCTTTGGTCCACC+AGG + chr2.1:30066552-30066571 None:intergenic 50.0%
!! GGCGTTTTGGACAATGAAGC+TGG + chr2.1:30066266-30066285 None:intergenic 50.0%
!! TATCTCGTCGCAGAGTATCG+CGG - chr2.1:30066470-30066489 MS.gene073991:intron 50.0%
! CTTGGGAAGTTGGTTCCTGG+TGG - chr2.1:30066534-30066553 MS.gene073991:intron 55.0%
! GAGCTTGGGAAGTTGGTTCC+TGG - chr2.1:30066531-30066550 MS.gene073991:intron 55.0%
!! AGAGTATCGCGGCGAGAGAA+AGG - chr2.1:30066481-30066500 MS.gene073991:intron 55.0%
TCGCGGCGAGAGAAAGGAGA+AGG - chr2.1:30066487-30066506 MS.gene073991:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 30065943 30067635 30065943 ID=MS.gene073991
chr2.1 mRNA 30065943 30067635 30065943 ID=MS.gene073991.t1;Parent=MS.gene073991
chr2.1 exon 30066919 30067635 30066919 ID=MS.gene073991.t1.exon1;Parent=MS.gene073991.t1
chr2.1 CDS 30066919 30067635 30066919 ID=cds.MS.gene073991.t1;Parent=MS.gene073991.t1
chr2.1 exon 30065943 30066158 30065943 ID=MS.gene073991.t1.exon2;Parent=MS.gene073991.t1
chr2.1 CDS 30065943 30066158 30065943 ID=cds.MS.gene073991.t1;Parent=MS.gene073991.t1
Gene Sequence

>MS.gene073991

ATGGGAGCACTTAGCACATACTTTAACTATAATTGTTACCCTTATCAACCTATTCAAACTGCTACCAACAACTCAGAAATCACCACTTTTCAACATCATGAACAAGAACAACTTGTGCAACAAAACCACTATTTCAATGAAGCTTCTCTTTTAGATGAAAGCTTCATTTTTCAAACTCCTAATTGTTTTTACTCAAATGAGACTTACCCTTGTCAAGATGATCAACTACTTGTTGACTCCACTTTTTCTTCTCAAAACGATGGCTTCGTTTCGATGAATGAAATTTTCCCAAATGAGGAAGATTTCATTTTCAACAACTACCAGCTTCATTGTCCAAAACGCCAAAAGCTGCTATATTATGAGGAGAAAAGAGAAGAGCCACAACAAGAGCTTTTGAACTCAACCAATTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTTTTGCTTCCTTTGAGGCAGAAACCTTTGCTGCTTCAAAAATTGTTGATGTTGTTCAATGTGAGAAGAAAATTGGTGAAAGGACTATCTCGTCGCAGAGTATCGCGGCGAGAGAAAGGAGAAGGAAGATAACTGAGAAGACACAAGAGCTTGGGAAGTTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTCATGCTGCTGCTAATTATGTCAAGTTTCTTCAAGCTCAAGTTGGAATGCTTCAACTTATGGAAACATTTAGCAAGGTAACTGTTTTTGCTTTTTTATTGTTGCAATGTTCTTATATATATTAGAGCTCATAATTGAAGTTAATTACTTGTCTTCACTTGAGTTTCGATTTCAACTGTTTTGTGTCCTTCCTTAGGTCTTATGTTGATAAAAAAAAATGATTATATGTCATTTTTCGTAGTGTGATTATGTATGTATCTTTGTAAATATCTAAAATGGATATTAATGCCATTATTGTAGATTTAGTTAGTTTTCTCATTTATGTGTGTAAAATAATAACTATTGTCTCAATGTTGTCTTTTTTACATTTATTTTTTTCCTGCCTACTTTTACTCTGAAAATATTTAGGAATTGTTAAAAAAAAAATTGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAGGGTTAGGGAAACGGTTAATAAGAAGAGGAAATGGTCAATAAACAAGAGAGTATTTAGGAACAACAATTGTATATGGAATGAGCTGGCTATGTAACTGTTCAACAAGGAATTATCCACTCTTTGTTTTTAAATATTCATTATTTTTACTTTCTTTATTATATTTAGTTTCCCAAACACTTGGAAGGATATTAAAAAATTTATAATCCCATGACATGATTCAGCACCTAGAAAATAAAATTAATAGTGTAACATTTTTGTAAAAGCTAAATTCCTAGTGTAACTTTATACAATAAAATTAATTAATGCTTAGAGTATTCATTCTCTTTTGTTTATATATATGATCATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATCTACACAAACTAGTTGTTTCTCCATTTGTTCAAGAGAAATTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCAAATTGAGCAATCATAATGATGTTCAATCAAAACCTACCATCCTTAAGGGTCTGAAACAGCTTGTTGGAACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene073991.t1

MGALSTYFNYNCYPYQPIQTATNNSEITTFQHHEQEQLVQQNHYFNEASLLDESFIFQTPNCFYSNETYPCQDDQLLVDSTFSSQNDGFVSMNEIFPNEEDFIFNNYQLHCPKRQKLLYYEEKREEPQQELLNSTNFFVDEFMTNPNPFASFEAETFAASKIVDVVQCEKKIGERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLHAAANYVKFLQAQVGMLQLMETFSKEEKEPPPSEDLHKLVVSPFVQEKLYSEEKCFVPKEFVTKLSNHNDVQSKPTILKGLKQLVGTEIEKKPKQE