AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene45036

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene45036.t1 MTR_1g066530 93.243 222 15 0 1 222 1 222 4.79e-158 436
MS.gene45036.t1 MTR_6g073540 50.000 230 106 2 1 221 1 230 2.96e-75 227
MS.gene45036.t1 MTR_6g072470 52.000 200 90 1 1 194 1 200 4.70e-69 211
MS.gene45036.t1 MTR_6g048620 49.099 222 106 5 6 220 5 226 3.29e-66 204
MS.gene45036.t1 MTR_6g045077 45.000 220 116 3 4 220 3 220 2.55e-64 199
MS.gene45036.t1 MTR_6g048910 45.455 220 113 4 6 220 5 222 8.35e-64 197
MS.gene45036.t1 MTR_0695s0030 44.091 220 118 4 6 220 65 284 2.83e-62 197
MS.gene45036.t1 MTR_8g038100 44.545 220 117 4 6 220 281 500 4.91e-60 197
MS.gene45036.t1 MTR_8g038070 44.091 220 118 4 6 220 219 438 5.46e-60 195
MS.gene45036.t1 MTR_0057s0100 40.909 220 125 5 6 220 7 226 1.67e-53 172
MS.gene45036.t1 MTR_0057s0170 40.909 220 125 5 6 220 7 226 5.23e-53 170
MS.gene45036.t1 MTR_7g103990 41.704 223 120 8 6 220 7 227 9.58e-51 164
MS.gene45036.t1 MTR_6g040290 39.910 223 126 6 6 220 7 229 3.96e-46 153
MS.gene45036.t1 MTR_0807s0020 37.054 224 131 5 1 220 1 218 9.06e-46 151
MS.gene45036.t1 MTR_0216s0030 38.889 198 113 3 4 197 1 194 1.05e-44 148
MS.gene45036.t1 MTR_6g048880 41.011 178 95 5 50 220 4 178 1.69e-40 137
MS.gene45036.t1 MTR_7g012000 39.423 208 96 5 6 209 7 188 1.70e-39 135
MS.gene45036.t1 MTR_6g048810 31.699 306 108 9 6 220 5 300 4.12e-37 131
MS.gene45036.t1 MTR_4g102470 41.111 180 83 5 6 182 7 166 2.03e-34 122
MS.gene45036.t1 MTR_6g049040 40.876 137 64 3 1 135 1 122 5.56e-27 100
MS.gene45036.t1 MTR_6g049040 34.188 117 66 2 72 187 16 122 5.99e-16 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCGGTACGGTCTTTGAAAA+TGG 0.203555 1.2:+49970849 MS.gene45036:CDS
ATCCGGAGAGAAATCTATTT+TGG 0.256716 1.2:-49970616 None:intergenic
TTTAACAACACGATCCTTCT+TGG 0.279901 1.2:-49970472 None:intergenic
ATTAGATCTAGAAGTTTAAT+AGG 0.298795 1.2:-49971022 None:intergenic
ACTCATTACTCCATTCGTTC+TGG 0.346885 1.2:+49970813 MS.gene45036:CDS
AATGGTGTTTCATCAAGAAA+TGG 0.395080 1.2:-49970522 None:intergenic
AACATGGTAGTGATTGGAAC+AGG 0.421529 1.2:-49970663 None:intergenic
GTTACGTGTTCAAGAAGAAA+AGG 0.446425 1.2:+49970421 MS.gene45036:CDS
CAATGGAACATGGTAGTGAT+TGG 0.462327 1.2:-49970669 None:intergenic
GAATAAGAAAACATTATGTC+CGG 0.469058 1.2:-49970742 None:intergenic
ACCGAAGCAATCATCTTCTC+TGG 0.471293 1.2:+49970582 MS.gene45036:CDS
TGCAGTTGTGAATTATGCTC+CGG 0.478704 1.2:+49970446 MS.gene45036:CDS
TGATGAAACACCATTTGAAA+AGG 0.482259 1.2:+49970530 MS.gene45036:CDS
GACAATACAATCACCTTCGT+TGG 0.494467 1.2:-49970952 None:intergenic
AGAAGTTTAATAGGCTCTGA+AGG 0.499900 1.2:-49971013 None:intergenic
TTTAATAGGCTCTGAAGGGC+AGG 0.501025 1.2:-49971008 None:intergenic
GCCAGAGAAGATGATTGCTT+CGG 0.505795 1.2:-49970583 None:intergenic
AACAGGGCCATCGAGTAAAT+CGG 0.507747 1.2:-49970646 None:intergenic
AGTAAATCGGTATCTGAATC+CGG 0.514277 1.2:-49970633 None:intergenic
GAAGGGCAGGCCATTCCTCA+TGG 0.517980 1.2:-49970995 None:intergenic
ACACGATCCTTCTTGGCTCC+CGG 0.519674 1.2:-49970465 None:intergenic
TGTCAATGGTAGAGTAAAGT+TGG 0.520266 1.2:+49970971 MS.gene45036:CDS
AAACCATCGGAAGTATGAAT+CGG 0.529141 1.2:-49970498 None:intergenic
TTCGGTGCCTTCTGTCTCAA+AGG 0.532520 1.2:-49970565 None:intergenic
AGGAAATGAGTATGTTCGTA+TGG 0.536361 1.2:+49970767 MS.gene45036:CDS
GAAGGTGATTGTATTGTCAA+TGG 0.538827 1.2:+49970957 MS.gene45036:CDS
TACCATGTTCCATTGTCTCA+AGG 0.539896 1.2:+49970677 MS.gene45036:CDS
TGCCAAAATAGATTTCTCTC+CGG 0.543347 1.2:+49970614 MS.gene45036:CDS
GAATTGACGCTGCAATTAAG+TGG 0.544957 1.2:+49970718 MS.gene45036:CDS
AAGCCGATTCATACTTCCGA+TGG 0.550807 1.2:+49970495 MS.gene45036:CDS
TTATGCTCCGGGAGCCAAGA+AGG 0.560419 1.2:+49970458 MS.gene45036:CDS
AAAACGTTCCCTTGAGACAA+TGG 0.561335 1.2:-49970686 None:intergenic
ATCAAGAAATGGAAAACCAT+CGG 0.570603 1.2:-49970511 None:intergenic
GATTGTGCCTTTGAGACAGA+AGG 0.572261 1.2:+49970558 MS.gene45036:CDS
GCAGTTGTGAATTATGCTCC+GGG 0.572517 1.2:+49970447 MS.gene45036:CDS
ACCATGTTCCATTGTCTCAA+GGG 0.576700 1.2:+49970678 MS.gene45036:CDS
GACGCTGCAATTAAGTGGAC+CGG 0.578299 1.2:+49970723 MS.gene45036:CDS
GAAATGCAGTATCAATGACT+TGG 0.591249 1.2:-49970377 None:intergenic
TAAAGTTGGTCCATGAGGAA+TGG 0.593058 1.2:+49970985 MS.gene45036:CDS
TCAGATACCGATTTACTCGA+TGG 0.596226 1.2:+49970639 MS.gene45036:CDS
CGTATTGATATTTCCAACGA+AGG 0.604655 1.2:+49970939 MS.gene45036:CDS
GAAGTTTAATAGGCTCTGAA+GGG 0.628949 1.2:-49971012 None:intergenic
TAGAGTAAAGTTGGTCCATG+AGG 0.649165 1.2:+49970980 MS.gene45036:CDS
TCCCTTGAGACAATGGAACA+TGG 0.652701 1.2:-49970679 None:intergenic
ACATGGTAGTGATTGGAACA+GGG 0.671114 1.2:-49970662 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATAATGTTTTCTTATTCAA+AGG + chr1.2:49970747-49970766 MS.gene45036:CDS 20.0%
! GAATAAGAAAACATTATGTC+CGG - chr1.2:49970745-49970764 None:intergenic 25.0%
AATGGTGTTTCATCAAGAAA+TGG - chr1.2:49970525-49970544 None:intergenic 30.0%
ATCAAGAAATGGAAAACCAT+CGG - chr1.2:49970514-49970533 None:intergenic 30.0%
TGATGAAACACCATTTGAAA+AGG + chr1.2:49970530-49970549 MS.gene45036:CDS 30.0%
! AATCAAGCTTACGTTTTCAA+AGG + chr1.2:49970903-49970922 MS.gene45036:CDS 30.0%
! CAATCTACTTCCTTTTCAAA+TGG - chr1.2:49970543-49970562 None:intergenic 30.0%
!! AAGGGAACGTTTTTAGAAAA+TGG + chr1.2:49970696-49970715 MS.gene45036:CDS 30.0%
!! TTTTAAAAGTTTGCTCGGTA+CGG + chr1.2:49970836-49970855 MS.gene45036:CDS 30.0%
!!! ACTTTTAAAACCAGAACGAA+TGG - chr1.2:49970826-49970845 None:intergenic 30.0%
!!! TCTGGTTTTAAAAGTTTGCT+CGG + chr1.2:49970831-49970850 MS.gene45036:CDS 30.0%
AGGAAATGAGTATGTTCGTA+TGG + chr1.2:49970767-49970786 MS.gene45036:CDS 35.0%
AGTAAATCGGTATCTGAATC+CGG - chr1.2:49970636-49970655 None:intergenic 35.0%
GAAATGCAGTATCAATGACT+TGG - chr1.2:49970380-49970399 None:intergenic 35.0%
GAAGGTGATTGTATTGTCAA+TGG + chr1.2:49970957-49970976 MS.gene45036:CDS 35.0%
GTTACGTGTTCAAGAAGAAA+AGG + chr1.2:49970421-49970440 MS.gene45036:CDS 35.0%
TGCCAAAATAGATTTCTCTC+CGG + chr1.2:49970614-49970633 MS.gene45036:CDS 35.0%
TGTCAATGGTAGAGTAAAGT+TGG + chr1.2:49970971-49970990 MS.gene45036:CDS 35.0%
TTTAACAACACGATCCTTCT+TGG - chr1.2:49970475-49970494 None:intergenic 35.0%
! AAACCATCGGAAGTATGAAT+CGG - chr1.2:49970501-49970520 None:intergenic 35.0%
! AGAAGTTTAATAGGCTCTGA+AGG - chr1.2:49971016-49971035 None:intergenic 35.0%
! ATCCGGAGAGAAATCTATTT+TGG - chr1.2:49970619-49970638 None:intergenic 35.0%
! CGTATTGATATTTCCAACGA+AGG + chr1.2:49970939-49970958 MS.gene45036:CDS 35.0%
!! GAAGTTTAATAGGCTCTGAA+GGG - chr1.2:49971015-49971034 None:intergenic 35.0%
AAAACGTTCCCTTGAGACAA+TGG - chr1.2:49970689-49970708 None:intergenic 40.0%
ACCATGTTCCATTGTCTCAA+GGG + chr1.2:49970678-49970697 MS.gene45036:CDS 40.0%
ACTCATTACTCCATTCGTTC+TGG + chr1.2:49970813-49970832 MS.gene45036:CDS 40.0%
GAATTGACGCTGCAATTAAG+TGG + chr1.2:49970718-49970737 MS.gene45036:CDS 40.0%
GACAATACAATCACCTTCGT+TGG - chr1.2:49970955-49970974 None:intergenic 40.0%
TACCATGTTCCATTGTCTCA+AGG + chr1.2:49970677-49970696 MS.gene45036:CDS 40.0%
TGCAGTTGTGAATTATGCTC+CGG + chr1.2:49970446-49970465 MS.gene45036:CDS 40.0%
! AACATGGTAGTGATTGGAAC+AGG - chr1.2:49970666-49970685 None:intergenic 40.0%
! ACATGGTAGTGATTGGAACA+GGG - chr1.2:49970665-49970684 None:intergenic 40.0%
! CAATGGAACATGGTAGTGAT+TGG - chr1.2:49970672-49970691 None:intergenic 40.0%
! TAAAGTTGGTCCATGAGGAA+TGG + chr1.2:49970985-49971004 MS.gene45036:CDS 40.0%
! TAGAGTAAAGTTGGTCCATG+AGG + chr1.2:49970980-49970999 MS.gene45036:CDS 40.0%
!! TCAGATACCGATTTACTCGA+TGG + chr1.2:49970639-49970658 MS.gene45036:CDS 40.0%
AACAGGGCCATCGAGTAAAT+CGG - chr1.2:49970649-49970668 None:intergenic 45.0%
ACCGAAGCAATCATCTTCTC+TGG + chr1.2:49970582-49970601 MS.gene45036:CDS 45.0%
GCAGTTGTGAATTATGCTCC+GGG + chr1.2:49970447-49970466 MS.gene45036:CDS 45.0%
GCCAGAGAAGATGATTGCTT+CGG - chr1.2:49970586-49970605 None:intergenic 45.0%
TCCCTTGAGACAATGGAACA+TGG - chr1.2:49970682-49970701 None:intergenic 45.0%
! AAGCCGATTCATACTTCCGA+TGG + chr1.2:49970495-49970514 MS.gene45036:CDS 45.0%
! CTCGGTACGGTCTTTGAAAA+TGG + chr1.2:49970849-49970868 MS.gene45036:CDS 45.0%
!! GATTGTGCCTTTGAGACAGA+AGG + chr1.2:49970558-49970577 MS.gene45036:CDS 45.0%
!! TTTAATAGGCTCTGAAGGGC+AGG - chr1.2:49971011-49971030 None:intergenic 45.0%
GACGCTGCAATTAAGTGGAC+CGG + chr1.2:49970723-49970742 MS.gene45036:CDS 50.0%
!! TTCGGTGCCTTCTGTCTCAA+AGG - chr1.2:49970568-49970587 None:intergenic 50.0%
ACACGATCCTTCTTGGCTCC+CGG - chr1.2:49970468-49970487 None:intergenic 55.0%
TTATGCTCCGGGAGCCAAGA+AGG + chr1.2:49970458-49970477 MS.gene45036:CDS 55.0%
GAAGGGCAGGCCATTCCTCA+TGG - chr1.2:49970998-49971017 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 49970369 49971037 49970369 ID=MS.gene45036
chr1.2 mRNA 49970369 49971037 49970369 ID=MS.gene45036.t1;Parent=MS.gene45036
chr1.2 exon 49970369 49971037 49970369 ID=MS.gene45036.t1.exon1;Parent=MS.gene45036.t1
chr1.2 CDS 49970369 49971037 49970369 ID=cds.MS.gene45036.t1;Parent=MS.gene45036.t1
Gene Sequence

>MS.gene45036

ATGTCAATCCAAGTCATTGATACTGCATTTCGTTCATCTAAGCTCAATGAGTGTTACGTGTTCAAGAAGAAAAGGTTTGCAGTTGTGAATTATGCTCCGGGAGCCAAGAAGGATCGTGTTGTTAAAAAGCCGATTCATACTTCCGATGGTTTTCCATTTCTTGATGAAACACCATTTGAAAAGGAAGTAGATTGTGCCTTTGAGACAGAAGGCACCGAAGCAATCATCTTCTCTGGCAAGCAATGTGCCAAAATAGATTTCTCTCCGGATTCAGATACCGATTTACTCGATGGCCCTGTTCCAATCACTACCATGTTCCATTGTCTCAAGGGAACGTTTTTAGAAAATGGAATTGACGCTGCAATTAAGTGGACCGGACATAATGTTTTCTTATTCAAAGGAAATGAGTATGTTCGTATGGACTATCACAAGAAGACTATTGTGACTCATTACTCCATTCGTTCTGGTTTTAAAAGTTTGCTCGGTACGGTCTTTGAAAATGGAATTGATGCAGCATTTTCTTCTCATGTTGCGAATCAAGCTTACGTTTTCAAAGGAGAATACTATGCACGTATTGATATTTCCAACGAAGGTGATTGTATTGTCAATGGTAGAGTAAAGTTGGTCCATGAGGAATGGCCTGCCCTTCAGAGCCTATTAAACTTCTAG
Protein sequence

>MS.gene45036.t1

MSIQVIDTAFRSSKLNECYVFKKKRFAVVNYAPGAKKDRVVKKPIHTSDGFPFLDETPFEKEVDCAFETEGTEAIIFSGKQCAKIDFSPDSDTDLLDGPVPITTMFHCLKGTFLENGIDAAIKWTGHNVFLFKGNEYVRMDYHKKTIVTHYSIRSGFKSLLGTVFENGIDAAFSSHVANQAYVFKGEYYARIDISNEGDCIVNGRVKLVHEEWPALQSLLNF