AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene97645

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97645.t1 MTR_1g053530 71.713 251 42 5 20 261 16 246 4.08e-116 334
MS.gene97645.t1 MTR_1g046810 35.235 298 133 9 29 278 30 315 6.87e-39 139
MS.gene97645.t1 MTR_1g052185 31.522 276 135 12 29 273 23 275 5.86e-24 98.2
MS.gene97645.t1 MTR_4g073310 30.677 251 128 8 28 277 22 227 3.41e-18 81.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGGTCCCGTATCTTAT+TGG 0.216824 1.1:+39936301 None:intergenic
AGCACCAACAACTTTCTTAA+AGG 0.236987 1.1:-39936526 MS.gene97645:CDS
TACCCTTCTTCGAACCATTT+TGG 0.254107 1.1:+39936380 None:intergenic
ATAATCCCAGCTCCGTTTCT+TGG 0.289051 1.1:+39936285 None:intergenic
ATGAAATGGCACAGCCAAAA+TGG 0.332105 1.1:-39936394 MS.gene97645:CDS
GTTCTCTACATTGTCATCAT+TGG 0.335954 1.1:+39936015 None:intergenic
GTTTGAGTAATAAGTCCTTT+TGG 0.343516 1.1:+39936064 None:intergenic
TGAATCACCGTGACTGTAAA+AGG 0.346155 1.1:-39936186 MS.gene97645:CDS
CAAATTTAAACGCTAAATAG+TGG 0.394892 1.1:+39935880 None:intergenic
CAATGGATGAAAACTGATCT+AGG 0.404461 1.1:+39936344 None:intergenic
TTTACCTTTAAGAAAGTTGT+TGG 0.419418 1.1:+39936522 None:intergenic
TAAGAAAGTTGTTGGTGCTA+TGG 0.440297 1.1:+39936530 None:intergenic
CTTTGAATGGACACATGAAA+TGG 0.459517 1.1:-39936408 MS.gene97645:CDS
CTCTACATTGTCATCATTGG+AGG 0.472478 1.1:+39936018 None:intergenic
ACGGTGATTCACATTAAGAT+TGG 0.473501 1.1:+39936198 None:intergenic
TTGGTCCCGTATCTTATTGG+TGG 0.478295 1.1:+39936304 None:intergenic
ATCCGTTTCATCACCTTCAT+CGG 0.483860 1.1:+39935988 None:intergenic
TGGTGCTATGGAATTGTTTG+TGG 0.484496 1.1:+39936542 None:intergenic
CAGCCAAAATGGTTCGAAGA+AGG 0.488255 1.1:-39936383 MS.gene97645:CDS
TGTGCTAGAGAATTCACAAC+TGG 0.492819 1.1:-39936580 MS.gene97645:CDS
CAAATACTTTGTCAGATCAA+TGG 0.494617 1.1:+39936327 None:intergenic
GAATTGTTTGTGGCCGCCGA+GGG 0.497780 1.1:+39936552 None:intergenic
TACCGATGAAGGTGATGAAA+CGG 0.519602 1.1:-39935990 MS.gene97645:CDS
GTGAGATTAAAGATTCCAAA+AGG 0.530313 1.1:-39936079 MS.gene97645:CDS
AAAGACAAACATGCTGATGA+TGG 0.542758 1.1:-39936493 MS.gene97645:CDS
ACATTGTCATCATTGGAGGC+AGG 0.544139 1.1:+39936022 None:intergenic
TTCATGTGTTCTTTGCAGCA+AGG 0.551012 1.1:-39936449 MS.gene97645:CDS
TGTTAACATTGCTGAAACAA+TGG 0.555726 1.1:-39936245 MS.gene97645:CDS
TAAGATACGGGACCAAGAAA+CGG 0.556029 1.1:-39936297 MS.gene97645:CDS
GGAATTGTTTGTGGCCGCCG+AGG 0.556033 1.1:+39936551 None:intergenic
TATTTGCCACCAATAAGATA+CGG 0.556242 1.1:-39936310 MS.gene97645:CDS
TTCACAACTGGTAATGCCCT+CGG 0.558819 1.1:-39936568 MS.gene97645:CDS
AGCCAAAATGGTTCGAAGAA+GGG 0.561339 1.1:-39936382 MS.gene97645:CDS
ATGAAGGTGATGAAACGGAT+GGG 0.561647 1.1:-39935985 MS.gene97645:CDS
TGAATAGAATGATGAGAAGA+AGG 0.561791 1.1:+39936682 None:intergenic
GCTGATGATGGTATTAAGAT+CGG 0.564146 1.1:-39936481 MS.gene97645:CDS
GTAGAGAACAATACCGATGA+AGG 0.568109 1.1:-39936001 MS.gene97645:CDS
ACGGGACCAAGAAACGGAGC+TGG 0.570799 1.1:-39936291 MS.gene97645:CDS
CAATGAAAAGAACAGGTTGG+TGG 0.599420 1.1:-39936101 MS.gene97645:CDS
CGGGACCAAGAAACGGAGCT+GGG 0.599731 1.1:-39936290 MS.gene97645:CDS
TGAAGGTGATGAAACGGATG+GGG 0.603593 1.1:-39935984 MS.gene97645:CDS
ATTTGCCACCAATAAGATAC+GGG 0.609267 1.1:-39936309 MS.gene97645:CDS
GCAAAGAACACATGAATGGT+TGG 0.610812 1.1:+39936456 None:intergenic
GATGAAGGTGATGAAACGGA+TGG 0.616100 1.1:-39935986 MS.gene97645:CDS
AAACAATGAAAAGAACAGGT+TGG 0.620052 1.1:-39936104 MS.gene97645:CDS
TAACATTGCTGAAACAATGG+TGG 0.675593 1.1:-39936242 MS.gene97645:CDS
TGCTGCAAAGAACACATGAA+TGG 0.688075 1.1:+39936452 None:intergenic
ACAACTGGTAATGCCCTCGG+CGG 0.704742 1.1:-39936565 MS.gene97645:CDS
GAAAATGAGAAACATCAACA+AGG 0.726705 1.1:-39936628 MS.gene97645:CDS
GATGTGAAGATCAATGAACA+AGG 0.760498 1.1:-39936133 MS.gene97645:CDS
GTGAAGATCAATGAACAAGG+TGG 0.773369 1.1:-39936130 MS.gene97645:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTAAAAACAATGAAAAGAAC+AGG - chr1.1:39936496-39936515 MS.gene97645:CDS 25.0%
!! ATTTTCATGATCAACAACAT+TGG + chr1.1:39935962-39935981 None:intergenic 25.0%
!! TTTACCTTTAAGAAAGTTGT+TGG + chr1.1:39936085-39936104 None:intergenic 25.0%
AAACAATGAAAAGAACAGGT+TGG - chr1.1:39936500-39936519 MS.gene97645:CDS 30.0%
CAAATACTTTGTCAGATCAA+TGG + chr1.1:39936280-39936299 None:intergenic 30.0%
GAAAATGAGAAACATCAACA+AGG - chr1.1:39935976-39935995 MS.gene97645:CDS 30.0%
GTGAGATTAAAGATTCCAAA+AGG - chr1.1:39936525-39936544 MS.gene97645:CDS 30.0%
TATTTGCCACCAATAAGATA+CGG - chr1.1:39936294-39936313 MS.gene97645:CDS 30.0%
TGAATAGAATGATGAGAAGA+AGG + chr1.1:39935925-39935944 None:intergenic 30.0%
TGTTAACATTGCTGAAACAA+TGG - chr1.1:39936359-39936378 MS.gene97645:CDS 30.0%
! ATTCGAGTCAAACATTTTTC+AGG - chr1.1:39936656-39936675 MS.gene97645:CDS 30.0%
! GTTTGAGTAATAAGTCCTTT+TGG + chr1.1:39936543-39936562 None:intergenic 30.0%
!! TCATCGAAAAAAGCTTTGAA+TGG - chr1.1:39936183-39936202 MS.gene97645:CDS 30.0%
!!! TGATCAACAACATTGGTTTT+TGG + chr1.1:39935955-39935974 None:intergenic 30.0%
!!! TTTTGATTTGAATGAGCTAC+AGG - chr1.1:39936680-39936699 MS.gene97645:CDS 30.0%
AAAGACAAACATGCTGATGA+TGG - chr1.1:39936111-39936130 MS.gene97645:CDS 35.0%
ACGGTGATTCACATTAAGAT+TGG + chr1.1:39936409-39936428 None:intergenic 35.0%
AGCACCAACAACTTTCTTAA+AGG - chr1.1:39936078-39936097 MS.gene97645:CDS 35.0%
ATTTGCCACCAATAAGATAC+GGG - chr1.1:39936295-39936314 MS.gene97645:CDS 35.0%
CAATGGATGAAAACTGATCT+AGG + chr1.1:39936263-39936282 None:intergenic 35.0%
CTTTGAATGGACACATGAAA+TGG - chr1.1:39936196-39936215 MS.gene97645:CDS 35.0%
GATGTGAAGATCAATGAACA+AGG - chr1.1:39936471-39936490 MS.gene97645:CDS 35.0%
GTTCTCTACATTGTCATCAT+TGG + chr1.1:39936592-39936611 None:intergenic 35.0%
TAACATTGCTGAAACAATGG+TGG - chr1.1:39936362-39936381 MS.gene97645:CDS 35.0%
! GTTTCATCCTTTTACAGTCA+CGG + chr1.1:39936428-39936447 None:intergenic 35.0%
!! GCTGATGATGGTATTAAGAT+CGG - chr1.1:39936123-39936142 MS.gene97645:CDS 35.0%
!! TAAGAAAGTTGTTGGTGCTA+TGG + chr1.1:39936077-39936096 None:intergenic 35.0%
AGCCAAAATGGTTCGAAGAA+GGG - chr1.1:39936222-39936241 MS.gene97645:CDS 40.0%
ATCCGTTTCATCACCTTCAT+CGG + chr1.1:39936619-39936638 None:intergenic 40.0%
ATGAAATGGCACAGCCAAAA+TGG - chr1.1:39936210-39936229 MS.gene97645:CDS 40.0%
ATGAAGGTGATGAAACGGAT+GGG - chr1.1:39936619-39936638 MS.gene97645:CDS 40.0%
CTCTACATTGTCATCATTGG+AGG + chr1.1:39936589-39936608 None:intergenic 40.0%
GCAAAGAACACATGAATGGT+TGG + chr1.1:39936151-39936170 None:intergenic 40.0%
GTAGAGAACAATACCGATGA+AGG - chr1.1:39936603-39936622 MS.gene97645:CDS 40.0%
GTGAAGATCAATGAACAAGG+TGG - chr1.1:39936474-39936493 MS.gene97645:CDS 40.0%
TAAGATACGGGACCAAGAAA+CGG - chr1.1:39936307-39936326 MS.gene97645:CDS 40.0%
TACCGATGAAGGTGATGAAA+CGG - chr1.1:39936614-39936633 MS.gene97645:CDS 40.0%
TGAATCACCGTGACTGTAAA+AGG - chr1.1:39936418-39936437 MS.gene97645:CDS 40.0%
TGCTGCAAAGAACACATGAA+TGG + chr1.1:39936155-39936174 None:intergenic 40.0%
TGTGCTAGAGAATTCACAAC+TGG - chr1.1:39936024-39936043 MS.gene97645:CDS 40.0%
TTCATGTGTTCTTTGCAGCA+AGG - chr1.1:39936155-39936174 MS.gene97645:CDS 40.0%
TTCTTGGTCCCGTATCTTAT+TGG + chr1.1:39936306-39936325 None:intergenic 40.0%
! CAATGAAAAGAACAGGTTGG+TGG - chr1.1:39936503-39936522 MS.gene97645:CDS 40.0%
! TACCCTTCTTCGAACCATTT+TGG + chr1.1:39936227-39936246 None:intergenic 40.0%
!! TGGTGCTATGGAATTGTTTG+TGG + chr1.1:39936065-39936084 None:intergenic 40.0%
ACATTGTCATCATTGGAGGC+AGG + chr1.1:39936585-39936604 None:intergenic 45.0%
ATAATCCCAGCTCCGTTTCT+TGG + chr1.1:39936322-39936341 None:intergenic 45.0%
CAGCCAAAATGGTTCGAAGA+AGG - chr1.1:39936221-39936240 MS.gene97645:CDS 45.0%
GATGAAGGTGATGAAACGGA+TGG - chr1.1:39936618-39936637 MS.gene97645:CDS 45.0%
TGAAGGTGATGAAACGGATG+GGG - chr1.1:39936620-39936639 MS.gene97645:CDS 45.0%
TTGGTCCCGTATCTTATTGG+TGG + chr1.1:39936303-39936322 None:intergenic 45.0%
! TTCACAACTGGTAATGCCCT+CGG - chr1.1:39936036-39936055 MS.gene97645:CDS 45.0%
GAATTGTTTGTGGCCGCCGA+GGG + chr1.1:39936055-39936074 None:intergenic 55.0%
! ACAACTGGTAATGCCCTCGG+CGG - chr1.1:39936039-39936058 MS.gene97645:CDS 55.0%
ACGGGACCAAGAAACGGAGC+TGG - chr1.1:39936313-39936332 MS.gene97645:CDS 60.0%
CGGGACCAAGAAACGGAGCT+GGG - chr1.1:39936314-39936333 MS.gene97645:CDS 60.0%
GGAATTGTTTGTGGCCGCCG+AGG + chr1.1:39936056-39936075 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 39935892 39936734 39935892 ID=MS.gene97645
chr1.1 mRNA 39935892 39936734 39935892 ID=MS.gene97645.t1;Parent=MS.gene97645
chr1.1 exon 39935892 39936734 39935892 ID=MS.gene97645.t1.exon1;Parent=MS.gene97645.t1
chr1.1 CDS 39935892 39936734 39935892 ID=cds.MS.gene97645.t1;Parent=MS.gene97645.t1
Gene Sequence

>MS.gene97645

ATGATGAAGAATTCTTTTTCTTCTTCTTCACCTTCTTCTCATCATTCTATTCATCATAAGCCAAAAACCAATGTTGTTGATCATGAAAATGAGAAACATCAACAAGGTGCAAGACTTCACAAATGTGATTTGTGTGCTAGAGAATTCACAACTGGTAATGCCCTCGGCGGCCACAAACAATTCCATAGCACCAACAACTTTCTTAAAGGTAAAATCAACAAAGACAAACATGCTGATGATGGTATTAAGATCGGAACCAACCATTCATGTGTTCTTTGCAGCAAGGCTTTTTCATCGAAAAAAGCTTTGAATGGACACATGAAATGGCACAGCCAAAATGGTTCGAAGAAGGGTAGTAACAATTATGACCTAGATCAGTTTTCATCCATTGATCTGACAAAGTATTTGCCACCAATAAGATACGGGACCAAGAAACGGAGCTGGGATTATATTCTTGATGTTGAAACTGTTAACATTGCTGAAACAATGGTGGAAATGTCTCAGCTATCATCTGCCAATCTTAATGTGAATCACCGTGACTGTAAAAGGATGAAACTTTGCAGCAATGTTGATGATGATGATGTGAAGATCAATGAACAAGGTGGTAAAAACAATGAAAAGAACAGGTTGGTGGTGAGATTAAAGATTCCAAAAGGACTTATTACTCAAACATCTCAAGCTAGCAAGCAACCTGCCTCCAATGATGACAATGTAGAGAACAATACCGATGAAGGTGATGAAACGGATGGGGAATCAACTCTTGAATTCGAGTCAAACATTTTTCAGGATTTTGATTTGAATGAGCTACAGGCAAATGATGTTGTAGATGAAACCACTATTTAG
Protein sequence

>MS.gene97645.t1

MMKNSFSSSSPSSHHSIHHKPKTNVVDHENEKHQQGARLHKCDLCAREFTTGNALGGHKQFHSTNNFLKGKINKDKHADDGIKIGTNHSCVLCSKAFSSKKALNGHMKWHSQNGSKKGSNNYDLDQFSSIDLTKYLPPIRYGTKKRSWDYILDVETVNIAETMVEMSQLSSANLNVNHRDCKRMKLCSNVDDDDVKINEQGGKNNEKNRLVVRLKIPKGLITQTSQASKQPASNDDNVENNTDEGDETDGESTLEFESNIFQDFDLNELQANDVVDETTI