AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065079

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065079.t1 MTR_1g111640 92.935 184 8 2 1 179 1 184 1.29e-122 346
MS.gene065079.t1 MTR_7g105780 49.744 195 71 8 1 180 1 183 8.14e-49 160
MS.gene065079.t1 MTR_1g058000 39.894 188 83 6 6 177 1 174 7.53e-31 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065079.t1 AT5G04820 51.923 208 58 9 1 179 1 195 1.35e-51 166
MS.gene065079.t1 AT2G36050 45.833 96 36 5 95 179 66 156 1.84e-17 77.8
MS.gene065079.t1 AT3G52540 49.451 91 40 4 95 179 93 183 4.81e-15 71.6

Find 26 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTATAATGTTCTCTGTT+TGG 0.328276 1.2:+82649744 None:intergenic
AACACAACACTTTCTTTGAA+TGG 0.349626 1.2:+82649536 None:intergenic
CTACAACGACGGCGAATCAT+TGG 0.389604 1.2:-82649651 MS.gene065079:CDS
GATCTCTTAAAATCTTCATA+TGG 0.409145 1.2:+82649494 None:intergenic
AGTCTCATGGTGTGAAAGAT+TGG 0.409364 1.2:-82649454 MS.gene065079:CDS
GATGTTGTGAACCATGATTT+TGG 0.433746 1.2:+82649719 None:intergenic
TGTGAAAGATTGGGAAGGTT+TGG 0.450919 1.2:-82649444 MS.gene065079:CDS
AGCTGGTATTTGAAAGTGAA+TGG 0.468308 1.2:-82649410 MS.gene065079:intron
TGGCAATTCTTACCCTCTTG+TGG 0.498707 1.2:-82649848 MS.gene065079:CDS
TAAGAGATCAATGGAAGAGA+TGG 0.508969 1.2:-82649480 MS.gene065079:CDS
AGAAAGTGTTGTGTTAGCTA+TGG 0.521557 1.2:-82649528 MS.gene065079:CDS
CACGAGTTCGATCTTAGAAA+AGG 0.522622 1.2:-82649576 MS.gene065079:CDS
TGATGATGACATATTCAAAA+CGG 0.538193 1.2:-82649786 MS.gene065079:CDS
TTATAGAAACACCAAAATCA+TGG 0.542649 1.2:-82649730 MS.gene065079:CDS
GTCTCATGGTGTGAAAGATT+GGG 0.558996 1.2:-82649453 MS.gene065079:CDS
TTAGAAAAGGCGAAAGCGAA+TGG 0.571257 1.2:-82649563 MS.gene065079:CDS
CACAAAGAAAACAACATCCA+TGG 0.572198 1.2:-82649868 MS.gene065079:CDS
CGGCGAATCATTGGAGACAT+TGG 0.582049 1.2:-82649642 MS.gene065079:CDS
CAAGAGGGTAAGAATTGCCA+TGG 0.585631 1.2:+82649851 None:intergenic
TGAGAAACTTGCAGATTCAG+AGG 0.589678 1.2:+82649697 None:intergenic
TGTGTTAGCTATGGAGTCAG+AGG 0.627955 1.2:-82649519 MS.gene065079:CDS
GAAGAGATGGTTGAGTCTCA+TGG 0.637125 1.2:-82649467 MS.gene065079:CDS
CATGGTGTGAAAGATTGGGA+AGG 0.649930 1.2:-82649449 MS.gene065079:CDS
ATTGGTACGAGGAGTTAAGT+CGG 0.655000 1.2:-82649624 MS.gene065079:CDS
GATTACTATTGCTACAACGA+CGG 0.655187 1.2:-82649662 MS.gene065079:CDS
TCATTGGAGACATTGGTACG+AGG 0.730029 1.2:-82649635 MS.gene065079:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGTACAACAACTAAAAA+AGG + chr1.2:82649815-82649834 None:intergenic 20.0%
!! GTTAATTAAATTATGATGCA+GGG - chr1.2:82649905-82649924 MS.gene065079:CDS 20.0%
!! TGTTAATTAAATTATGATGC+AGG - chr1.2:82649904-82649923 MS.gene065079:CDS 20.0%
!!! TTTTCTTTGTGAAATTTCTT+TGG + chr1.2:82649085-82649104 None:intergenic 20.0%
! ATAATAATGTAACAGCTTCT+TGG - chr1.2:82649763-82649782 MS.gene065079:CDS 25.0%
! GATCTCTTAAAATCTTCATA+TGG + chr1.2:82649471-82649490 None:intergenic 25.0%
! GTGAATGGTAAAAATAATCA+TGG - chr1.2:82649567-82649586 MS.gene065079:CDS 25.0%
! TTATAGAAACACCAAAATCA+TGG - chr1.2:82649232-82649251 MS.gene065079:intron 25.0%
! TTTCTATAATGTTCTCTGTT+TGG + chr1.2:82649221-82649240 None:intergenic 25.0%
!! TGATGATGACATATTCAAAA+CGG - chr1.2:82649176-82649195 MS.gene065079:intron 25.0%
!!! AATAATCATGGCTTTATTGT+TGG - chr1.2:82649579-82649598 MS.gene065079:CDS 25.0%
!!! TGAAGATTTTAAGAGATCAA+TGG - chr1.2:82649473-82649492 MS.gene065079:CDS 25.0%
AACACAACACTTTCTTTGAA+TGG + chr1.2:82649429-82649448 None:intergenic 30.0%
! ACTCGAAAAGAAAGAGTTTT+TGG + chr1.2:82649144-82649163 None:intergenic 30.0%
!! GAAAAGAAAGAGTTTTTGGA+TGG + chr1.2:82649140-82649159 None:intergenic 30.0%
!!! AAAACTCTTTCTTTTCGAGT+TGG - chr1.2:82649144-82649163 MS.gene065079:intron 30.0%
!!! CTTATAGTGATCTTGTTTTG+TGG - chr1.2:82649875-82649894 MS.gene065079:CDS 30.0%
!!! TCTTTGGTTTTGAAAAGAGA+AGG + chr1.2:82649069-82649088 None:intergenic 30.0%
AGCTGGTATTTGAAAGTGAA+TGG - chr1.2:82649552-82649571 MS.gene065079:CDS 35.0%
CACAAAGAAAACAACATCCA+TGG - chr1.2:82649094-82649113 MS.gene065079:intron 35.0%
GATTACTATTGCTACAACGA+CGG - chr1.2:82649300-82649319 MS.gene065079:intron 35.0%
TAAGAGATCAATGGAAGAGA+TGG - chr1.2:82649482-82649501 MS.gene065079:CDS 35.0%
TAGATACAAAGGTGAAGAAG+AGG + chr1.2:82649703-82649722 None:intergenic 35.0%
TCACCTTTGTATCTATGTGA+GGG - chr1.2:82649708-82649727 MS.gene065079:CDS 35.0%
TTCACCTTTGTATCTATGTG+AGG - chr1.2:82649707-82649726 MS.gene065079:CDS 35.0%
! GATGTTGTGAACCATGATTT+TGG + chr1.2:82649246-82649265 None:intergenic 35.0%
!! AGAAAGTGTTGTGTTAGCTA+TGG - chr1.2:82649434-82649453 MS.gene065079:CDS 35.0%
AGTCTCATGGTGTGAAAGAT+TGG - chr1.2:82649508-82649527 MS.gene065079:CDS 40.0%
ATTGGTACGAGGAGTTAAGT+CGG - chr1.2:82649338-82649357 MS.gene065079:intron 40.0%
CACGAGTTCGATCTTAGAAA+AGG - chr1.2:82649386-82649405 MS.gene065079:intron 40.0%
GTCTCATGGTGTGAAAGATT+GGG - chr1.2:82649509-82649528 MS.gene065079:CDS 40.0%
TGAGAAACTTGCAGATTCAG+AGG + chr1.2:82649268-82649287 None:intergenic 40.0%
TGTCCCTCACATAGATACAA+AGG + chr1.2:82649714-82649733 None:intergenic 40.0%
TGTGAAAGATTGGGAAGGTT+TGG - chr1.2:82649518-82649537 MS.gene065079:CDS 40.0%
TTAGAAAAGGCGAAAGCGAA+TGG - chr1.2:82649399-82649418 MS.gene065079:intron 40.0%
!!! ACTCTTTCTTTTCGAGTTGG+TGG - chr1.2:82649147-82649166 MS.gene065079:intron 40.0%
CAAGAGGGTAAGAATTGCCA+TGG + chr1.2:82649114-82649133 None:intergenic 45.0%
CATGGTGTGAAAGATTGGGA+AGG - chr1.2:82649513-82649532 MS.gene065079:CDS 45.0%
GAAGAGATGGTTGAGTCTCA+TGG - chr1.2:82649495-82649514 MS.gene065079:CDS 45.0%
TCATTGGAGACATTGGTACG+AGG - chr1.2:82649327-82649346 MS.gene065079:intron 45.0%
TGGCAATTCTTACCCTCTTG+TGG - chr1.2:82649114-82649133 MS.gene065079:intron 45.0%
TGTGTTAGCTATGGAGTCAG+AGG - chr1.2:82649443-82649462 MS.gene065079:CDS 45.0%
! GTTTGGAAGAGCTTTTGAGC+TGG - chr1.2:82649535-82649554 MS.gene065079:CDS 45.0%
!! AGTTTTTGGATGGCCACAAG+AGG + chr1.2:82649130-82649149 None:intergenic 45.0%
!! GTTTTTGGATGGCCACAAGA+GGG + chr1.2:82649129-82649148 None:intergenic 45.0%
CGGCGAATCATTGGAGACAT+TGG - chr1.2:82649320-82649339 MS.gene065079:intron 50.0%
CTACAACGACGGCGAATCAT+TGG - chr1.2:82649311-82649330 MS.gene065079:intron 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 82649042 82649942 82649042 ID=MS.gene065079
chr1.2 mRNA 82649042 82649942 82649042 ID=MS.gene065079.t1;Parent=MS.gene065079
chr1.2 exon 82649411 82649942 82649411 ID=MS.gene065079.t1.exon1;Parent=MS.gene065079.t1
chr1.2 CDS 82649411 82649942 82649411 ID=cds.MS.gene065079.t1;Parent=MS.gene065079.t1
chr1.2 exon 82649042 82649058 82649042 ID=MS.gene065079.t1.exon2;Parent=MS.gene065079.t1
chr1.2 CDS 82649042 82649058 82649042 ID=cds.MS.gene065079.t1;Parent=MS.gene065079.t1
Gene Sequence

>MS.gene065079

ATGGGAAAGAAAAATTTGAAACTACCTTCTCTTTTCAAAACCAAAGAAATTTCACAAAGAAAACAACATCCATGGCAATTCTTACCCTCTTGTGGCCATCCAAAAACTCTTTCTTTTCGAGTTGGTGGTACTACTGATGATGACATATTCAAAACGGTTAATTCTGTGTTTTTTGACCAAACAGAGAACATTATAGAAACACCAAAATCATGGTTCACAACATCCTCTGAATCTGCAAGTTTCTCAACAGAATCAGAAGATTACTATTGCTACAACGACGGCGAATCATTGGAGACATTGGTACGAGGAGTTAAGTCGGAGAGATTGTTTTTCGAAGCAGAAGACACGAGTTCGATCTTAGAAAAGGCGAAAGCGAATGGTTTTCCATTCAAAGAAAGTGTTGTGTTAGCTATGGAGTCAGAGGATCCATATGAAGATTTTAAGAGATCAATGGAAGAGATGGTTGAGTCTCATGGTGTGAAAGATTGGGAAGGTTTGGAAGAGCTTTTGAGCTGGTATTTGAAAGTGAATGGTAAAAATAATCATGGCTTTATTGTTGGTGCTTTTGTTGATTTGTTGATTAGTTTAGCAGCTTCTAATCATTCTAATAACTCTTGTTCTAATTTAACGTTATATTCTTCTGCTGTTTCTTCTTTTGCCTCTTCTTCACCTTTGTATCTATGTGAGGGACAGAATGAGATTACTGAGATTGAAGATGATAATAATAATGTAACAGCTTCTTGGTATTAATTAGATGTAGCTAGTTTTAACCTTTTTTAGTTGTTGTACATTTTGTAGATTGAAAGAATATTTAATGAAAATTAAGTTATAGACTTATAGTGATCTTGTTTTGTGGTTTTGTTGTTAATTAAATTATGATGCAGGGCGAATCATAACTTAA
Protein sequence

>MS.gene065079.t1

MGKKNLKLPSLFKTKEISQRKQHPWQFLPSCGHPKTLSFRVGGTTDDDIFKTVNSVFFDQTENIIETPKSWFTTSSESASFSTESEDYYCYNDGESLETLVRGVKSERLFFEAEDTSSILEKAKANGFPFKESVVLAMESEDPYEDFKRSMEEMVESHGVKDWEGLEELLSWYLKVNGRIIT