AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene97641

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97641.t1 MTR_1g053530 54.065 246 83 8 18 258 16 236 3.18e-68 213
MS.gene97641.t1 MTR_1g046810 30.581 327 137 11 27 311 37 315 2.21e-30 117
MS.gene97641.t1 MTR_1g052185 28.621 290 158 10 28 309 30 278 4.64e-20 88.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 65 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAATTCCAGCTCCGTTTCT+TGG 0.269877 1.1:+39963582 None:intergenic
GAAGAAAGTTGTTGCCTCTA+TGG 0.295075 1.1:+39963824 None:intergenic
AGAGGCAACAACTTTCTTCT+AGG 0.323367 1.1:-39963820 MS.gene97641:CDS
GTTCTCTTCATTATCATCAT+TGG 0.330696 1.1:+39963267 None:intergenic
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.1:+39963166 None:intergenic
TACCCTTCTTCGAACCATAT+TGG 0.347145 1.1:+39963677 None:intergenic
TGAGGAACCAACTCATGAAT+TGG 0.350528 1.1:-39963134 MS.gene97641:CDS
ATCATTGGAGGCAGGTTGAT+TGG 0.359527 1.1:+39963282 None:intergenic
ATGAAATCGCACAGCCAATA+TGG 0.368027 1.1:-39963691 MS.gene97641:CDS
ACTCTCATATCAAACCAAAA+AGG 0.373200 1.1:-39963939 MS.gene97641:CDS
TCATCTTCACCAGTGTTGTT+TGG 0.374435 1.1:+39963205 None:intergenic
GAGGAACCAACTCATGAATT+GGG 0.382420 1.1:-39963133 MS.gene97641:CDS
CGATTCCCAACAAGGTTGTT+AGG 0.383944 1.1:+39963502 None:intergenic
AAATACTTTCTCAAATCAAT+TGG 0.400225 1.1:+39963625 None:intergenic
TTCTTGGTCACATACCTCAT+TGG 0.415556 1.1:+39963598 None:intergenic
TGCAGAAATGTGGGTGGGAA+TGG 0.425504 1.1:-39963454 MS.gene97641:CDS
CGATCACCTAACAACCTTGT+TGG 0.429642 1.1:-39963508 MS.gene97641:CDS
TGCCTCTATGGAATGCTTTG+TGG 0.438332 1.1:+39963836 None:intergenic
GATCACCTAACAACCTTGTT+GGG 0.460149 1.1:-39963507 MS.gene97641:CDS
CAATTGGTGGAAATTGATCT+AGG 0.480999 1.1:+39963641 None:intergenic
TACTTTCTCAAATCAATTGG+TGG 0.486384 1.1:+39963628 None:intergenic
TCATGTTGCTGAAGCAATGC+TGG 0.487886 1.1:-39963542 MS.gene97641:CDS
GCAGAAATGTGGGTGGGAAT+GGG 0.488317 1.1:-39963453 MS.gene97641:CDS
CAGCCAATATGGTTCGAAGA+AGG 0.491443 1.1:-39963680 MS.gene97641:CDS
TCATTATCATCATTGGAGGC+AGG 0.491925 1.1:+39963274 None:intergenic
TGTGACAGAGAATTCACAAC+TGG 0.492142 1.1:-39963874 MS.gene97641:CDS
GAATGCTTTGTGGCCGCCGA+GGG 0.493083 1.1:+39963846 None:intergenic
TTTGCTTCATCATCTTCACC+AGG 0.497903 1.1:+39963157 None:intergenic
CTCTTCATTATCATCATTGG+AGG 0.501703 1.1:+39963270 None:intergenic
TTTAACCCCAATTCATGAGT+TGG 0.505846 1.1:+39963127 None:intergenic
GGAATCGCCGTGTCATGAAA+AGG 0.511189 1.1:-39963486 MS.gene97641:CDS
TTGGTCACATACCTCATTGG+TGG 0.513533 1.1:+39963601 None:intergenic
GATCAAACTTTGCAGAAATG+TGG 0.524856 1.1:-39963464 MS.gene97641:CDS
ATCAAACTTTGCAGAAATGT+GGG 0.554714 1.1:-39963463 MS.gene97641:CDS
AAAAGGAGTGTTGTTGATCA+TGG 0.562216 1.1:-39963922 MS.gene97641:CDS
TTCACAACTGGTAACGCCCT+CGG 0.563147 1.1:-39963862 MS.gene97641:CDS
TGAGGTATGTGACCAAGAAA+CGG 0.563267 1.1:-39963594 MS.gene97641:CDS
AGCCAATATGGTTCGAAGAA+GGG 0.568160 1.1:-39963679 MS.gene97641:CDS
GAAGATCAGAGAGCAAGGTA+TGG 0.572806 1.1:-39963425 MS.gene97641:CDS
TCATCTGTCAATGCTCTCAA+CGG 0.575258 1.1:-39963718 MS.gene97641:CDS
ATGTGACCAAGAAACGGAGC+TGG 0.575391 1.1:-39963588 MS.gene97641:CDS
TCATCTGCATCATCATCCAC+TGG 0.575486 1.1:+39963073 None:intergenic
AATCAATGAGAAGAACAAGT+TGG 0.575910 1.1:-39963356 MS.gene97641:CDS
AGAAGAACAAGTTGGTGGTG+AGG 0.577583 1.1:-39963348 MS.gene97641:CDS
AACTTTGCAGAAATGTGGGT+GGG 0.585412 1.1:-39963459 MS.gene97641:CDS
GGAATGCTTTGTGGCCGCCG+AGG 0.588007 1.1:+39963845 None:intergenic
CAATGAGAAGAACAAGTTGG+TGG 0.592690 1.1:-39963353 MS.gene97641:CDS
TGAAGATGATGAAGCAAATG+AGG 0.593094 1.1:-39963152 MS.gene97641:CDS
CGATTTGAATGAGCTGCCAG+TGG 0.597243 1.1:-39963089 MS.gene97641:CDS
GATCAGAGAGCAAGGTATGG+TGG 0.597334 1.1:-39963422 MS.gene97641:CDS
AAGATGAAGATCAGAGAGCA+AGG 0.598147 1.1:-39963430 MS.gene97641:CDS
TTGCTTCATCATCTTCACCA+GGG 0.604583 1.1:+39963158 None:intergenic
TGACACGGCGATTCCCAACA+AGG 0.609535 1.1:+39963494 None:intergenic
AAACTTTGCAGAAATGTGGG+TGG 0.628923 1.1:-39963460 MS.gene97641:CDS
AGGAACCAACTCATGAATTG+GGG 0.629510 1.1:-39963132 MS.gene97641:CDS
GAAGAGAACAACAACAACAC+TGG 0.637064 1.1:-39963253 MS.gene97641:CDS
GAAAGTATTTGCCACCAATG+AGG 0.638748 1.1:-39963612 MS.gene97641:CDS
GGCCACAAAGCATTCCATAG+AGG 0.645608 1.1:-39963838 MS.gene97641:CDS
TGCTGCAACGAACACATGAA+TGG 0.655011 1.1:+39963749 None:intergenic
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.1:-39963230 MS.gene97641:CDS
GTGAGGTTAAAGATTCCGAA+TGG 0.667579 1.1:-39963331 MS.gene97641:CDS
GATGAGGAACCAAACAACAC+TGG 0.670709 1.1:-39963214 MS.gene97641:CDS
GATGAGGAACCAAACAACCC+TGG 0.677497 1.1:-39963175 MS.gene97641:CDS
TGAAGATGATGAAACAGATG+AGG 0.705240 1.1:-39963191 MS.gene97641:CDS
ACAACTGGTAACGCCCTCGG+CGG 0.717230 1.1:-39963859 MS.gene97641:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACTTTCTCAAATCAAT+TGG + chr1.1:39963417-39963436 None:intergenic 20.0%
AACAAAGAAAAACAAGCTGA+TGG - chr1.1:39963249-39963268 MS.gene97641:CDS 30.0%
AATCAATGAGAAGAACAAGT+TGG - chr1.1:39963683-39963702 MS.gene97641:CDS 30.0%
ACTCTCATATCAAACCAAAA+AGG - chr1.1:39963100-39963119 MS.gene97641:CDS 30.0%
ATCAAACTTTGCAGAAATGT+GGG - chr1.1:39963576-39963595 MS.gene97641:CDS 30.0%
GTTCTCTTCATTATCATCAT+TGG + chr1.1:39963775-39963794 None:intergenic 30.0%
TACTTTCTCAAATCAATTGG+TGG + chr1.1:39963414-39963433 None:intergenic 30.0%
! CTTCTGATTTTTGAATGACT+AGG + chr1.1:39963734-39963753 None:intergenic 30.0%
CAATTGGTGGAAATTGATCT+AGG + chr1.1:39963401-39963420 None:intergenic 35.0%
CTCTTCATTATCATCATTGG+AGG + chr1.1:39963772-39963791 None:intergenic 35.0%
GATCAAACTTTGCAGAAATG+TGG - chr1.1:39963575-39963594 MS.gene97641:CDS 35.0%
TGAAGATGATGAAACAGATG+AGG - chr1.1:39963848-39963867 MS.gene97641:CDS 35.0%
TGAAGATGATGAAGCAAATG+AGG - chr1.1:39963887-39963906 MS.gene97641:CDS 35.0%
TTTAACCCCAATTCATGAGT+TGG + chr1.1:39963915-39963934 None:intergenic 35.0%
! GTTTGATCCTTTTCATGACA+CGG + chr1.1:39963563-39963582 None:intergenic 35.0%
! TGATCAACAACACTCCTTTT+TGG + chr1.1:39963117-39963136 None:intergenic 35.0%
! TTTTGAATGACTAGGCCATT+CGG + chr1.1:39963726-39963745 None:intergenic 35.0%
!! AAAAGGAGTGTTGTTGATCA+TGG - chr1.1:39963117-39963136 MS.gene97641:CDS 35.0%
AAACTTTGCAGAAATGTGGG+TGG - chr1.1:39963579-39963598 MS.gene97641:CDS 40.0%
AACTTTGCAGAAATGTGGGT+GGG - chr1.1:39963580-39963599 MS.gene97641:CDS 40.0%
AAGATGAAGATCAGAGAGCA+AGG - chr1.1:39963609-39963628 MS.gene97641:CDS 40.0%
AGAGGCAACAACTTTCTTCT+AGG - chr1.1:39963219-39963238 MS.gene97641:CDS 40.0%
AGCCAATATGGTTCGAAGAA+GGG - chr1.1:39963360-39963379 MS.gene97641:CDS 40.0%
AGGAACCAACTCATGAATTG+GGG - chr1.1:39963907-39963926 MS.gene97641:CDS 40.0%
ATAATTCCAGCTCCGTTTCT+TGG + chr1.1:39963460-39963479 None:intergenic 40.0%
ATGAAATCGCACAGCCAATA+TGG - chr1.1:39963348-39963367 MS.gene97641:CDS 40.0%
GAAGAAAGTTGTTGCCTCTA+TGG + chr1.1:39963218-39963237 None:intergenic 40.0%
GAAGAGAACAACAACAACAC+TGG - chr1.1:39963786-39963805 MS.gene97641:CDS 40.0%
GAGGAACCAACTCATGAATT+GGG - chr1.1:39963906-39963925 MS.gene97641:CDS 40.0%
GATCACCTAACAACCTTGTT+GGG - chr1.1:39963532-39963551 MS.gene97641:CDS 40.0%
GTGAGGTTAAAGATTCCGAA+TGG - chr1.1:39963708-39963727 MS.gene97641:CDS 40.0%
TACCCTTCTTCGAACCATAT+TGG + chr1.1:39963365-39963384 None:intergenic 40.0%
TCATCTGTCAATGCTCTCAA+CGG - chr1.1:39963321-39963340 MS.gene97641:CDS 40.0%
TCATTATCATCATTGGAGGC+AGG + chr1.1:39963768-39963787 None:intergenic 40.0%
TGAAGATGATGAAGCAGATG+AGG - chr1.1:39963809-39963828 MS.gene97641:CDS 40.0%
TGAGGAACCAACTCATGAAT+TGG - chr1.1:39963905-39963924 MS.gene97641:CDS 40.0%
TGAGGTATGTGACCAAGAAA+CGG - chr1.1:39963445-39963464 MS.gene97641:CDS 40.0%
TGTGACAGAGAATTCACAAC+TGG - chr1.1:39963165-39963184 MS.gene97641:CDS 40.0%
TTCTTGGTCACATACCTCAT+TGG + chr1.1:39963444-39963463 None:intergenic 40.0%
TTGCTTCATCATCTTCACCA+GGG + chr1.1:39963884-39963903 None:intergenic 40.0%
TTTGCTTCATCATCTTCACC+AGG + chr1.1:39963885-39963904 None:intergenic 40.0%
! CAATGAGAAGAACAAGTTGG+TGG - chr1.1:39963686-39963705 MS.gene97641:CDS 40.0%
! TCATCTTCACCAGTGTTGTT+TGG + chr1.1:39963798-39963817 None:intergenic 40.0%
!! GAAAGTATTTGCCACCAATG+AGG - chr1.1:39963427-39963446 MS.gene97641:CDS 40.0%
CAGCCAATATGGTTCGAAGA+AGG - chr1.1:39963359-39963378 MS.gene97641:CDS 45.0%
CGATCACCTAACAACCTTGT+TGG - chr1.1:39963531-39963550 MS.gene97641:CDS 45.0%
CGATTCCCAACAAGGTTGTT+AGG + chr1.1:39963540-39963559 None:intergenic 45.0%
GAAGATCAGAGAGCAAGGTA+TGG - chr1.1:39963614-39963633 MS.gene97641:CDS 45.0%
GATGAGGAACCAAACAACAC+TGG - chr1.1:39963825-39963844 MS.gene97641:CDS 45.0%
TCATCTGCATCATCATCCAC+TGG + chr1.1:39963969-39963988 None:intergenic 45.0%
TCATCTTCACCAGGGTTGTT+TGG + chr1.1:39963876-39963895 None:intergenic 45.0%
TCATGTTGCTGAAGCAATGC+TGG - chr1.1:39963497-39963516 MS.gene97641:CDS 45.0%
TGCCTCTATGGAATGCTTTG+TGG + chr1.1:39963206-39963225 None:intergenic 45.0%
TGCTGCAACGAACACATGAA+TGG + chr1.1:39963293-39963312 None:intergenic 45.0%
TTGGTCACATACCTCATTGG+TGG + chr1.1:39963441-39963460 None:intergenic 45.0%
!! AGAAGAACAAGTTGGTGGTG+AGG - chr1.1:39963691-39963710 MS.gene97641:CDS 45.0%
!! ATCATTGGAGGCAGGTTGAT+TGG + chr1.1:39963760-39963779 None:intergenic 45.0%
ATGTGACCAAGAAACGGAGC+TGG - chr1.1:39963451-39963470 MS.gene97641:CDS 50.0%
CGATTTGAATGAGCTGCCAG+TGG - chr1.1:39963950-39963969 MS.gene97641:CDS 50.0%
GATCAGAGAGCAAGGTATGG+TGG - chr1.1:39963617-39963636 MS.gene97641:CDS 50.0%
GATGAGGAACCAAACAACCC+TGG - chr1.1:39963864-39963883 MS.gene97641:CDS 50.0%
GCAGAAATGTGGGTGGGAAT+GGG - chr1.1:39963586-39963605 MS.gene97641:CDS 50.0%
GGAATCGCCGTGTCATGAAA+AGG - chr1.1:39963553-39963572 MS.gene97641:CDS 50.0%
TGCAGAAATGTGGGTGGGAA+TGG - chr1.1:39963585-39963604 MS.gene97641:CDS 50.0%
! GGCCACAAAGCATTCCATAG+AGG - chr1.1:39963201-39963220 MS.gene97641:CDS 50.0%
! TTCACAACTGGTAACGCCCT+CGG - chr1.1:39963177-39963196 MS.gene97641:CDS 50.0%
TGACACGGCGATTCCCAACA+AGG + chr1.1:39963548-39963567 None:intergenic 55.0%
GAATGCTTTGTGGCCGCCGA+GGG + chr1.1:39963196-39963215 None:intergenic 60.0%
! ACAACTGGTAACGCCCTCGG+CGG - chr1.1:39963180-39963199 MS.gene97641:CDS 60.0%
GGAATGCTTTGTGGCCGCCG+AGG + chr1.1:39963197-39963216 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 39963060 39964001 39963060 ID=MS.gene97641
chr1.1 mRNA 39963060 39964001 39963060 ID=MS.gene97641.t1;Parent=MS.gene97641
chr1.1 exon 39963060 39964001 39963060 ID=MS.gene97641.t1.exon1;Parent=MS.gene97641.t1
chr1.1 CDS 39963060 39964001 39963060 ID=cds.MS.gene97641.t1;Parent=MS.gene97641.t1
Gene Sequence

>MS.gene97641

ATGAAGCATTTGTTTTCTTCTGCTTCTTCTTCTTCTTCTCACTCTCATATCAAACCAAAAAGGAGTGTTGTTGATCATGGTGCAAAACTTCACAAATGTGATTTGTGTGACAGAGAATTCACAACTGGTAACGCCCTCGGCGGCCACAAAGCATTCCATAGAGGCAACAACTTTCTTCTAGGAAAAATCAACAAAGAAAAACAAGCTGATGGTATTAAGATCGAAAACAACCATTCATGTGTTCGTTGCAGCAAGACTTTTTCATCTGTCAATGCTCTCAACGGACACATGAAATCGCACAGCCAATATGGTTCGAAGAAGGGTAGTAAGATGTATGACCTAGATCAATTTCCACCAATTGATTTGAGAAAGTATTTGCCACCAATGAGGTATGTGACCAAGAAACGGAGCTGGAATTATGTTATTAATGTTGAAGCTCATGTTGCTGAAGCAATGCTGGATATGTCACAGCGATCACCTAACAACCTTGTTGGGAATCGCCGTGTCATGAAAAGGATCAAACTTTGCAGAAATGTGGGTGGGAATGGGAAGATGAAGATCAGAGAGCAAGGTATGGTGGTAAAACATTGTGTTGATGAAACAATTGTGAGAGAGACTGATCGAATCAATGAGAAGAACAAGTTGGTGGTGAGGTTAAAGATTCCGAATGGCCTAGTCATTCAAAAATCAGAAGCTTCCAATCAACCTGCCTCCAATGATGATAATGAAGAGAACAACAACAACACTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACACTGGTGAAGATGATGAAACAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAAATGAGGAACCAACTCATGAATTGGGGTTAAATGTTGTTCGAGATTTCGATTTGAATGAGCTGCCAGTGGATGATGATGCAGATGAAACCGCCCATTAG
Protein sequence

>MS.gene97641.t1

MKHLFSSASSSSSHSHIKPKRSVVDHGAKLHKCDLCDREFTTGNALGGHKAFHRGNNFLLGKINKEKQADGIKIENNHSCVRCSKTFSSVNALNGHMKSHSQYGSKKGSKMYDLDQFPPIDLRKYLPPMRYVTKKRSWNYVINVEAHVAEAMLDMSQRSPNNLVGNRRVMKRIKLCRNVGGNGKMKIREQGMVVKHCVDETIVRETDRINEKNKLVVRLKIPNGLVIQKSEASNQPASNDDNEENNNNTGEDDEADEEPNNTGEDDETDEEPNNPGEDDEANEEPTHELGLNVVRDFDLNELPVDDDADETAH