AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21827

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21827.t1 MTR_5g006520 92.632 190 14 0 1 190 1719 1908 2.70e-120 374
MS.gene21827.t1 MTR_5g006450 80.000 190 38 0 1 190 1 190 8.52e-108 306
MS.gene21827.t1 MTR_5g006470 78.421 190 39 1 1 190 1 188 9.27e-107 304
MS.gene21827.t1 MTR_5g006460 74.359 195 43 5 1 190 1 193 1.90e-96 278
MS.gene21827.t1 MTR_5g006510 72.778 180 46 2 12 190 14 191 1.02e-90 263
MS.gene21827.t1 MTR_1g103110 63.542 192 66 2 1 190 1 190 8.99e-84 246
MS.gene21827.t1 MTR_1g103150 59.375 192 74 2 1 190 1 190 5.65e-78 231
MS.gene21827.t1 MTR_7g114410 43.860 171 93 1 17 187 4 171 7.39e-48 154
MS.gene21827.t1 MTR_3g463610 41.279 172 101 0 16 187 2 173 2.85e-46 151
MS.gene21827.t1 MTR_7g114410 43.590 156 85 1 17 172 4 156 9.54e-43 140
MS.gene21827.t1 MTR_7g024780 40.230 174 94 3 17 187 4 170 1.07e-37 128
MS.gene21827.t1 MTR_7g024760 41.667 168 93 3 20 187 7 169 1.26e-37 128
MS.gene21827.t1 MTR_7g024765 40.476 168 95 3 20 187 7 169 1.69e-34 120
MS.gene21827.t1 MTR_1g103320 54.321 81 35 1 51 131 11 89 1.52e-21 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21827.t1 AT2G32030 48.634 183 79 4 6 187 17 185 3.91e-57 178
MS.gene21827.t1 AT2G32020 48.521 169 80 2 20 187 18 180 1.65e-53 169
MS.gene21827.t1 AT3G22560 42.012 169 93 2 21 187 7 172 3.81e-38 129

Find 38 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATCAATGCTCTCTTCTT+TGG 0.193418 5.2:+1250703 None:intergenic
TCCTAAGAATTCCTTCCTTC+TGG 0.242611 5.2:+1250261 None:intergenic
CTCTTCTTTGGCACATGGTT+TGG 0.246122 5.2:+1250715 None:intergenic
GTTGATGCCTTGTTCTTTGC+TGG 0.260002 5.2:+1250577 None:intergenic
TCCTTTACCCCAGTATTTAG+AGG 0.284343 5.2:+1250412 None:intergenic
ATGTTCTAGCCTCTAAATAC+TGG 0.304005 5.2:-1250421 MS.gene21827:CDS
CCTTGTTCTTTGCTGGTGTA+TGG 0.318147 5.2:+1250584 None:intergenic
TGCCTTAATGATCGTGCTAT+TGG 0.357294 5.2:-1250509 MS.gene21827:CDS
ATATACCAAACAAATTTCTA+TGG 0.388477 5.2:-1250544 MS.gene21827:CDS
TCCAGAAGGAAGGAATTCTT+AGG 0.397920 5.2:-1250262 MS.gene21827:CDS
GGCCAATAGCACGATCATTA+AGG 0.403869 5.2:+1250507 None:intergenic
TTGCACCATAGAAATTTGTT+TGG 0.404833 5.2:+1250539 None:intergenic
TTGTTGATGTTGAAAATGTT+GGG 0.408191 5.2:-1250313 MS.gene21827:CDS
TTCTGACCTTGATGATCTCC+TGG 0.414515 5.2:-1250651 MS.gene21827:CDS
CCAAACAAATAAATCATAGT+TGG 0.419913 5.2:+1250174 None:intergenic
TGTTGTGAAACAAGCAGTTA+AGG 0.427234 5.2:-1250378 MS.gene21827:CDS
GCCTCTAAATACTGGGGTAA+AGG 0.441976 5.2:-1250413 MS.gene21827:CDS
TTTGTTGATGTTGAAAATGT+TGG 0.442167 5.2:-1250314 MS.gene21827:CDS
AGTGGCCAAGTTCTGCTCTT+GGG 0.462852 5.2:-1250609 MS.gene21827:CDS
AAGTGGCCAAGTTCTGCTCT+TGG 0.474319 5.2:-1250610 MS.gene21827:CDS
AGGAAGTATTTGTTCATGAA+AGG 0.475944 5.2:-1250242 MS.gene21827:CDS
TTTCATCAGTTCTCCATACC+AGG 0.488119 5.2:+1250633 None:intergenic
CAAAGAGTGTTGGAGAAAGC+TGG 0.497277 5.2:-1250287 MS.gene21827:CDS
ATGCTCTCTTCTTTGGCACA+TGG 0.504425 5.2:+1250710 None:intergenic
TGCTTGTTTCACAACATATG+TGG 0.509570 5.2:+1250385 None:intergenic
GTATTTAGAGGCTAGAACAT+AGG 0.521725 5.2:+1250424 None:intergenic
TGTTCTAGCCTCTAAATACT+GGG 0.523419 5.2:-1250420 MS.gene21827:CDS
ACCTTGATGATCTCCTGGTA+TGG 0.538483 5.2:-1250646 MS.gene21827:CDS
ATTCAGTGAGTTGTCACACT+TGG 0.554731 5.2:-1250351 MS.gene21827:CDS
GATCACCTCATGATAAAAGC+AGG 0.555612 5.2:-1250466 MS.gene21827:CDS
TGTTGGGTCTCAAAGAGTGT+TGG 0.566749 5.2:-1250297 MS.gene21827:CDS
TGGTTCCCAAGAGCAGAACT+TGG 0.574822 5.2:+1250604 None:intergenic
CCATACACCAGCAAAGAACA+AGG 0.601334 5.2:-1250584 MS.gene21827:CDS
GGAGAAAGCTGGTTTCCAGA+AGG 0.617484 5.2:-1250276 MS.gene21827:CDS
AAAGCTGGTTTCCAGAAGGA+AGG 0.623258 5.2:-1250272 MS.gene21827:CDS
TCCATACCAGGAGATCATCA+AGG 0.624213 5.2:+1250645 None:intergenic
GTTCTAGCCTCTAAATACTG+GGG 0.689247 5.2:-1250419 MS.gene21827:CDS
ATCTTGATTTCAGAGAAACA+CGG 0.706701 5.2:+1250486 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATACCAAACAAATTTCTA+TGG - chr5.2:1250380-1250399 MS.gene21827:CDS 20.0%
! TTGTTGATGTTGAAAATGTT+GGG - chr5.2:1250611-1250630 MS.gene21827:CDS 25.0%
! TTTGTTGATGTTGAAAATGT+TGG - chr5.2:1250610-1250629 MS.gene21827:CDS 25.0%
ATCTTGATTTCAGAGAAACA+CGG + chr5.2:1250441-1250460 None:intergenic 30.0%
! TTGCACCATAGAAATTTGTT+TGG + chr5.2:1250388-1250407 None:intergenic 30.0%
!! AGGAAGTATTTGTTCATGAA+AGG - chr5.2:1250682-1250701 MS.gene21827:CDS 30.0%
ATGGAGAACTGATGAAAAAG+TGG - chr5.2:1250297-1250316 MS.gene21827:CDS 35.0%
ATGTTCTAGCCTCTAAATAC+TGG - chr5.2:1250503-1250522 MS.gene21827:CDS 35.0%
CAAATCAATGCTCTCTTCTT+TGG + chr5.2:1250224-1250243 None:intergenic 35.0%
GGTCAGAAAGATGAAAAAGT+CGG + chr5.2:1250261-1250280 None:intergenic 35.0%
GTATTTAGAGGCTAGAACAT+AGG + chr5.2:1250503-1250522 None:intergenic 35.0%
TGCTTGTTTCACAACATATG+TGG + chr5.2:1250542-1250561 None:intergenic 35.0%
TGTTCTAGCCTCTAAATACT+GGG - chr5.2:1250504-1250523 MS.gene21827:CDS 35.0%
TGTTGTGAAACAAGCAGTTA+AGG - chr5.2:1250546-1250565 MS.gene21827:CDS 35.0%
!! TTGTTCCTGCTTTTATCATG+AGG + chr5.2:1250466-1250485 None:intergenic 35.0%
ATTCAGTGAGTTGTCACACT+TGG - chr5.2:1250573-1250592 MS.gene21827:CDS 40.0%
GAAAAAGTCGGAGTGTGATT+TGG + chr5.2:1250249-1250268 None:intergenic 40.0%
GATCACCTCATGATAAAAGC+AGG - chr5.2:1250458-1250477 MS.gene21827:CDS 40.0%
GTTCTAGCCTCTAAATACTG+GGG - chr5.2:1250505-1250524 MS.gene21827:CDS 40.0%
TCCAGAAGGAAGGAATTCTT+AGG - chr5.2:1250662-1250681 MS.gene21827:CDS 40.0%
TCCTAAGAATTCCTTCCTTC+TGG + chr5.2:1250666-1250685 None:intergenic 40.0%
TCCTTTACCCCAGTATTTAG+AGG + chr5.2:1250515-1250534 None:intergenic 40.0%
TGCCTTAATGATCGTGCTAT+TGG - chr5.2:1250415-1250434 MS.gene21827:CDS 40.0%
TTTCATCAGTTCTCCATACC+AGG + chr5.2:1250294-1250313 None:intergenic 40.0%
ATGCTCTCTTCTTTGGCACA+TGG + chr5.2:1250217-1250236 None:intergenic 45.0%
CCATACACCAGCAAAGAACA+AGG - chr5.2:1250340-1250359 MS.gene21827:CDS 45.0%
CCTTGTTCTTTGCTGGTGTA+TGG + chr5.2:1250343-1250362 None:intergenic 45.0%
CTCTTCTTTGGCACATGGTT+TGG + chr5.2:1250212-1250231 None:intergenic 45.0%
GCCTCTAAATACTGGGGTAA+AGG - chr5.2:1250511-1250530 MS.gene21827:CDS 45.0%
GGCCAATAGCACGATCATTA+AGG + chr5.2:1250420-1250439 None:intergenic 45.0%
TCCATACCAGGAGATCATCA+AGG + chr5.2:1250282-1250301 None:intergenic 45.0%
! AAAGCTGGTTTCCAGAAGGA+AGG - chr5.2:1250652-1250671 MS.gene21827:CDS 45.0%
! ACCTTGATGATCTCCTGGTA+TGG - chr5.2:1250278-1250297 MS.gene21827:CDS 45.0%
! GTTGATGCCTTGTTCTTTGC+TGG + chr5.2:1250350-1250369 None:intergenic 45.0%
! TGTTGGGTCTCAAAGAGTGT+TGG - chr5.2:1250627-1250646 MS.gene21827:CDS 45.0%
! TTCTGACCTTGATGATCTCC+TGG - chr5.2:1250273-1250292 MS.gene21827:CDS 45.0%
!! CAAAGAGTGTTGGAGAAAGC+TGG - chr5.2:1250637-1250656 MS.gene21827:CDS 45.0%
AAGTGGCCAAGTTCTGCTCT+TGG - chr5.2:1250314-1250333 MS.gene21827:CDS 50.0%
AGTGGCCAAGTTCTGCTCTT+GGG - chr5.2:1250315-1250334 MS.gene21827:CDS 50.0%
TGGTTCCCAAGAGCAGAACT+TGG + chr5.2:1250323-1250342 None:intergenic 50.0%
! GGAGAAAGCTGGTTTCCAGA+AGG - chr5.2:1250648-1250667 MS.gene21827:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 1250187 1250759 1250187 ID=MS.gene21827
chr5.2 mRNA 1250187 1250759 1250187 ID=MS.gene21827.t1;Parent=MS.gene21827
chr5.2 exon 1250187 1250759 1250187 ID=MS.gene21827.t1.exon1;Parent=MS.gene21827.t1
chr5.2 CDS 1250187 1250759 1250187 ID=cds.MS.gene21827.t1;Parent=MS.gene21827.t1
Gene Sequence

>MS.gene21827

ATGGAGAAAACTTTTATTTCTTCCAAACCATGTGCCAAAGAAGAGAGCATTGATTTGAACCAAATCACACTCCGACTTTTTCATCTTTCTGACCTTGATGATCTCCTGGTATGGAGAACTGATGAAAAAGTGGCCAAGTTCTGCTCTTGGGAACCATACACCAGCAAAGAACAAGGCATCAACTTCATTGAAAATATACCAAACAAATTTCTATGGTGCAAAGCAATATGCCTTAATGATCGTGCTATTGGCCGTGTTTCTCTGAAATCAAGATCACCTCATGATAAAAGCAGGAACAAAACTGCAGAACTTGCCTATGTTCTAGCCTCTAAATACTGGGGTAAAGGAATTGCCACATATGTTGTGAAACAAGCAGTTAAGGTTGCATTCAGTGAGTTGTCACACTTGGAAAGAGTTGAAGCTTTTGTTGATGTTGAAAATGTTGGGTCTCAAAGAGTGTTGGAGAAAGCTGGTTTCCAGAAGGAAGGAATTCTTAGGAAGTATTTGTTCATGAAAGGAAAAAGTAGAGATATGATCATATTCAGTGTTCTTTCTAATGATCTCCAACTATGA
Protein sequence

>MS.gene21827.t1

MEKTFISSKPCAKEESIDLNQITLRLFHLSDLDDLLVWRTDEKVAKFCSWEPYTSKEQGINFIENIPNKFLWCKAICLNDRAIGRVSLKSRSPHDKSRNKTAELAYVLASKYWGKGIATYVVKQAVKVAFSELSHLERVEAFVDVENVGSQRVLEKAGFQKEGILRKYLFMKGKSRDMIIFSVLSNDLQL