AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38515

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38515.t1 MTR_3g466150 93.038 158 10 1 1 157 1 158 1.81e-105 298
MS.gene38515.t1 MTR_5g083810 49.020 153 77 1 1 153 25 176 1.09e-43 142
MS.gene38515.t1 MTR_7g072470 51.200 125 55 3 28 150 7 127 2.42e-33 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38515.t1 AT3G56220 45.455 154 82 2 1 153 1 153 1.47e-42 139
MS.gene38515.t1 AT2G40435 44.872 156 81 3 1 154 1 153 8.22e-39 129
MS.gene38515.t1 AT3G56220 48.462 130 66 1 1 129 1 130 5.05e-36 122
MS.gene38515.t1 AT2G40435 46.825 126 64 2 1 124 1 125 3.29e-32 112
MS.gene38515.t1 AT2G40435 46.825 126 64 2 1 124 1 125 3.57e-32 112
MS.gene38515.t1 AT1G29270 32.374 139 90 3 1 136 1 138 8.76e-11 57.4

Find 32 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGATAACTTCTCCTTAG+AGG 0.288364 3.4:+61791187 MS.gene38515:CDS
ATTACAAAGCCCTCTTCTTT+TGG 0.297287 3.4:-61791065 None:intergenic
AGTTGCAACATCAACTAAAA+TGG 0.297879 3.4:+61790783 MS.gene38515:CDS
TAGTAAAACCTCCGTAATAT+TGG 0.370604 3.4:+61790702 MS.gene38515:CDS
TTTGTTCCCAACAGCCTCTA+AGG 0.392325 3.4:-61791201 None:intergenic
TGTCTCAAGCTATTCAAAAC+TGG 0.409559 3.4:+61791481 MS.gene38515:CDS
CTATCATTCATCATCATTGT+TGG 0.432815 3.4:-61791515 None:intergenic
TATCATTCATCATCATTGTT+GGG 0.439214 3.4:-61791514 None:intergenic
AGGATTGCTAGTGTTCATAT+TGG 0.440392 3.4:+61791115 MS.gene38515:CDS
TTCAAGACCCAGCTCTTCAA+TGG 0.441356 3.4:-61791141 None:intergenic
TTGATGTTGCAACTTGTAAC+GGG 0.455870 3.4:-61790774 None:intergenic
ACTTCTCCTTAGAGGCTGTT+GGG 0.466579 3.4:+61791195 MS.gene38515:CDS
AACTTCTCCTTAGAGGCTGT+TGG 0.470602 3.4:+61791194 MS.gene38515:CDS
GTCTTGAAGTGCTCGACGCT+AGG 0.471261 3.4:+61791156 MS.gene38515:CDS
ATTGGAAGCCATTGAAGAGC+TGG 0.474257 3.4:+61791133 MS.gene38515:CDS
AGCTGTTCTCTTGTGAACCT+TGG 0.501707 3.4:-61790486 None:intergenic
GTTGATGTTGCAACTTGTAA+CGG 0.518123 3.4:-61790775 None:intergenic
TCTTGAAGTGCTCGACGCTA+GGG 0.524120 3.4:+61791157 MS.gene38515:CDS
TCAACTAATTGTGCATTCAA+AGG 0.526427 3.4:-61791450 None:intergenic
GAGAGTGAGAATGGTTTCCA+AGG 0.528898 3.4:+61790469 None:intergenic
ATGAGTGAAAAGAGATGTCA+AGG 0.549501 3.4:+61791095 MS.gene38515:CDS
TAAAGTTGAACCAAAAGAAG+AGG 0.570672 3.4:+61791055 MS.gene38515:CDS
CTCAAGCTATTCAAAACTGG+AGG 0.571158 3.4:+61791484 MS.gene38515:CDS
TGACAATGATGCTACGCCTA+AGG 0.573738 3.4:+61790807 MS.gene38515:CDS
TGATTGAACGTAGAAGATGT+AGG 0.579806 3.4:-61790520 None:intergenic
AAAGTTGAACCAAAAGAAGA+GGG 0.591604 3.4:+61791056 MS.gene38515:CDS
TATGAGAATAATCACCGAAG+TGG 0.596934 3.4:-61790549 None:intergenic
TTGGAAGCCATTGAAGAGCT+GGG 0.599149 3.4:+61791134 MS.gene38515:CDS
AGAAGAGGGCTTTGTAATCG+AGG 0.630502 3.4:+61791070 MS.gene38515:CDS
TCAAGCTATTCAAAACTGGA+GGG 0.633417 3.4:+61791485 MS.gene38515:CDS
TTCAATCATACACTCCACTT+CGG 0.634345 3.4:+61790535 MS.gene38515:CDS
TGTTGCATCCAATATTACGG+AGG 0.660873 3.4:-61790710 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATCAATAAAAACAAAAA+AGG + chr3.4:61790961-61790980 MS.gene38515:intron 10.0%
!!! ATCTTTGAAACATATTTTTA+AGG + chr3.4:61791370-61791389 MS.gene38515:intron 15.0%
!! ATAATTTCATGTTTATGTCA+AGG - chr3.4:61790995-61791014 None:intergenic 20.0%
!! TTAAACTAGGATGAAAAAAA+TGG - chr3.4:61790601-61790620 None:intergenic 20.0%
!! TTAAGTTTAAGAGATAACAA+GGG + chr3.4:61790906-61790925 MS.gene38515:intron 20.0%
!!! GTAATTTTATATATTGTAGC+AGG + chr3.4:61791407-61791426 MS.gene38515:intron 20.0%
!!! TTTAAGTTTAAGAGATAACA+AGG + chr3.4:61790905-61790924 MS.gene38515:intron 20.0%
!!! TTTTGTATTGTGTCAAATAT+TGG - chr3.4:61790937-61790956 None:intergenic 20.0%
! AACAAAAGATGAGTTAAACT+AGG - chr3.4:61790614-61790633 None:intergenic 25.0%
! ATGATGCAAAGTAAATATAG+AGG - chr3.4:61790654-61790673 None:intergenic 25.0%
! ATTTATGAACATGTTACCTT+AGG - chr3.4:61790826-61790845 None:intergenic 25.0%
! TAAGTTTAAGAGATAACAAG+GGG + chr3.4:61790907-61790926 MS.gene38515:intron 25.0%
! TCTATATTTACTTTGCATCA+TGG + chr3.4:61790653-61790672 MS.gene38515:intron 25.0%
!! TTTTGTTGCATCCAATATTA+CGG - chr3.4:61790716-61790735 None:intergenic 25.0%
!!! AGTTCTAAATTGCAATTTGA+AGG - chr3.4:61791320-61791339 None:intergenic 25.0%
!!! TTGCAATTTGAAGGTTTTAT+AGG - chr3.4:61791311-61791330 None:intergenic 25.0%
AAAGTTGAACCAAAAGAAGA+GGG + chr3.4:61791056-61791075 MS.gene38515:CDS 30.0%
ACGAAACAATTCATATGATG+CGG + chr3.4:61790860-61790879 MS.gene38515:intron 30.0%
AGTTGCAACATCAACTAAAA+TGG + chr3.4:61790783-61790802 MS.gene38515:CDS 30.0%
TAAAGTTGAACCAAAAGAAG+AGG + chr3.4:61791055-61791074 MS.gene38515:CDS 30.0%
TAGTAAAACCTCCGTAATAT+TGG + chr3.4:61790702-61790721 MS.gene38515:CDS 30.0%
TCAACTAATTGTGCATTCAA+AGG - chr3.4:61791453-61791472 None:intergenic 30.0%
AGGATTGCTAGTGTTCATAT+TGG + chr3.4:61791115-61791134 MS.gene38515:CDS 35.0%
ATGAGTGAAAAGAGATGTCA+AGG + chr3.4:61791095-61791114 MS.gene38515:CDS 35.0%
GTTGATGTTGCAACTTGTAA+CGG - chr3.4:61790778-61790797 None:intergenic 35.0%
TATGAGAATAATCACCGAAG+TGG - chr3.4:61790552-61790571 None:intergenic 35.0%
TCAAGCTATTCAAAACTGGA+GGG + chr3.4:61791485-61791504 MS.gene38515:CDS 35.0%
TGATTGAACGTAGAAGATGT+AGG - chr3.4:61790523-61790542 None:intergenic 35.0%
TGTCTCAAGCTATTCAAAAC+TGG + chr3.4:61791481-61791500 MS.gene38515:CDS 35.0%
TTCAATCATACACTCCACTT+CGG + chr3.4:61790535-61790554 MS.gene38515:CDS 35.0%
TTGATGTTGCAACTTGTAAC+GGG - chr3.4:61790777-61790796 None:intergenic 35.0%
! ATTACAAAGCCCTCTTCTTT+TGG - chr3.4:61791068-61791087 None:intergenic 35.0%
!! TGTTGATAACTTCTCCTTAG+AGG + chr3.4:61791187-61791206 MS.gene38515:CDS 35.0%
CTCAAGCTATTCAAAACTGG+AGG + chr3.4:61791484-61791503 MS.gene38515:CDS 40.0%
TGTTGCATCCAATATTACGG+AGG - chr3.4:61790713-61790732 None:intergenic 40.0%
!!! TTTTAAGGTATCACTGACGC+AGG + chr3.4:61791385-61791404 MS.gene38515:intron 40.0%
AACTTCTCCTTAGAGGCTGT+TGG + chr3.4:61791194-61791213 MS.gene38515:CDS 45.0%
ACTTCTCCTTAGAGGCTGTT+GGG + chr3.4:61791195-61791214 MS.gene38515:CDS 45.0%
AGCTGTTCTCTTGTGAACCT+TGG - chr3.4:61790489-61790508 None:intergenic 45.0%
ATTGGAAGCCATTGAAGAGC+TGG + chr3.4:61791133-61791152 MS.gene38515:CDS 45.0%
TGACAATGATGCTACGCCTA+AGG + chr3.4:61790807-61790826 MS.gene38515:CDS 45.0%
TTCAAGACCCAGCTCTTCAA+TGG - chr3.4:61791144-61791163 None:intergenic 45.0%
TTGGAAGCCATTGAAGAGCT+GGG + chr3.4:61791134-61791153 MS.gene38515:CDS 45.0%
TTTGTTCCCAACAGCCTCTA+AGG - chr3.4:61791204-61791223 None:intergenic 45.0%
! AGAAGAGGGCTTTGTAATCG+AGG + chr3.4:61791070-61791089 MS.gene38515:CDS 45.0%
! TCTTGAAGTGCTCGACGCTA+GGG + chr3.4:61791157-61791176 MS.gene38515:CDS 50.0%
! GTCTTGAAGTGCTCGACGCT+AGG + chr3.4:61791156-61791175 MS.gene38515:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 61790479 61791524 61790479 ID=MS.gene38515
chr3.4 mRNA 61790479 61791524 61790479 ID=MS.gene38515.t1;Parent=MS.gene38515
chr3.4 exon 61790479 61790556 61790479 ID=MS.gene38515.t1.exon1;Parent=MS.gene38515.t1
chr3.4 CDS 61790479 61790556 61790479 ID=cds.MS.gene38515.t1;Parent=MS.gene38515.t1
chr3.4 exon 61790700 61790828 61790700 ID=MS.gene38515.t1.exon2;Parent=MS.gene38515.t1
chr3.4 CDS 61790700 61790828 61790700 ID=cds.MS.gene38515.t1;Parent=MS.gene38515.t1
chr3.4 exon 61791053 61791223 61791053 ID=MS.gene38515.t1.exon3;Parent=MS.gene38515.t1
chr3.4 CDS 61791053 61791223 61791053 ID=cds.MS.gene38515.t1;Parent=MS.gene38515.t1
chr3.4 exon 61791429 61791524 61791429 ID=MS.gene38515.t1.exon4;Parent=MS.gene38515.t1
chr3.4 CDS 61791429 61791524 61791429 ID=cds.MS.gene38515.t1;Parent=MS.gene38515.t1
Gene Sequence

>MS.gene38515

ATGGTTTCCAAGGTTCACAAGAGAACAGCTATGTACAGAAACCTACATCTTCTACGTTCAATCATACACTCCACTTCGGTGATTATTCTCATACATCTCTTTCTATAATTCAAATAACTCCATTTTTTTCATCCTAGTTTAACTCATCTTTTGTTTATTAATTATGTTTATGCCTCTATATTTACTTTGCATCATGGAATGTTTTGTGTTTGTTAATGCAGCGTAGTAAAACCTCCGTAATATTGGATGCAACAAAATATATACGAGATTTAAAGCAAAAACTTGAAGAACTAAACCCGTTACAAGTTGCAACATCAACTAAAATGGTTGACAATGATGCTACGCCTAAGGTAACATGTTCATAAATCTGATTATTAATCAACGAAACAATTCATATGATGCGGACTTATTTTTTCAAGCAAAAGATTTAAGTTTAAGAGATAACAAGGGGTGTTCCAATATTTGACACAATACAAAATTGCAAAATCAATAAAAACAAAAAAGGAAGACATTCCTTGACATAAACATGAAATTATTAATTGTGTTTGATTTGTAATATATATTGATTTTGCAGATTAAAGTTGAACCAAAAGAAGAGGGCTTTGTAATCGAGGTGATGAGTGAAAAGAGATGTCAAGGATTGCTAGTGTTCATATTGGAAGCCATTGAAGAGCTGGGTCTTGAAGTGCTCGACGCTAGGGTTTCTTGTGTTGATAACTTCTCCTTAGAGGCTGTTGGGAACAAAGTAATTGCTAAACACATAAAATTACTCACATATGATACATACATACAGCTGCAACTGCAGTTGTATGTAATGTTGTTACAAAGACCTATAAAACCTTCAAATTGCAATTTAGAACTAAGTAATGATTTTTTTTCACGAAATCACTTATCTTTGAAACATATTTTTAAGGTATCACTGACGCAGGTAATTTTATATATTGTAGCAGGAGAAGAATGAAGATACTTGTCCTTTGAATGCACAATTAGTTGAACAAGTAGTGTCTCAAGCTATTCAAAACTGGAGGGAAGTTACCCAACAATGA
Protein sequence

>MS.gene38515.t1

MVSKVHKRTAMYRNLHLLRSIIHSTSRSKTSVILDATKYIRDLKQKLEELNPLQVATSTKMVDNDATPKIKVEPKEEGFVIEVMSEKRCQGLLVFILEAIEELGLEVLDARVSCVDNFSLEAVGNKEKNEDTCPLNAQLVEQVVSQAIQNWREVTQQ