AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029778

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029778.t1 MTR_1g063150 60.870 207 22 4 36 240 19 168 2.52e-73 222
MS.gene029778.t1 MTR_1g085590 52.209 249 57 11 6 240 15 215 8.78e-58 185
MS.gene029778.t1 MTR_1g063140 59.603 151 19 4 91 240 1 110 1.54e-44 148
MS.gene029778.t1 MTR_1g046810 43.777 233 68 10 53 240 94 308 5.75e-39 137
MS.gene029778.t1 MTR_1g053530 31.818 176 94 7 72 225 68 239 1.44e-13 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAGAGAAAGAAGGGTATT+TGG 0.170547 1.2:+48321521 None:intergenic
AATGAAGGTGAAACAGAATT+AGG 0.205798 1.2:-48320928 MS.gene029778:CDS
CTTAGCACTTGCCGTTTCTT+AGG 0.240976 1.2:+48321246 None:intergenic
CTCTTCAATACTTTGATTAG+AGG 0.294988 1.2:+48320960 None:intergenic
TGAATCACCGTGGTGCTAAA+AGG 0.300323 1.2:-48321125 MS.gene029778:CDS
AAAGAGAAAGAAGGGTATTT+GGG 0.359789 1.2:+48321522 None:intergenic
ACTTCTAACAAAGCTTTGAA+TGG 0.400226 1.2:-48321339 MS.gene029778:CDS
ACGGTGATTCAAATTGATAT+TGG 0.408428 1.2:+48321137 None:intergenic
TATATCTCGTGGCGGTTTCG+AGG 0.421737 1.2:-48321169 MS.gene029778:CDS
ATGAAGGTGAAACAGAATTA+GGG 0.423059 1.2:-48320927 MS.gene029778:CDS
TATTCAGTTCCTAATGATGC+TGG 0.435072 1.2:-48321405 MS.gene029778:CDS
AAGGGTATTTGGGTTGTTGA+AGG 0.465907 1.2:+48321532 None:intergenic
CTGGAAAACAGAAGATCATA+TGG 0.475072 1.2:-48321437 MS.gene029778:CDS
TGTTCAGCAACTAATGATGC+TGG 0.488263 1.2:-48321456 MS.gene029778:CDS
ATACTTTGATTAGAGGCAGC+AGG 0.495332 1.2:+48320967 None:intergenic
CATCATTAGTTGCTGAACAT+AGG 0.504304 1.2:+48321460 None:intergenic
AGGGTATTTGGGTTGTTGAA+GGG 0.505337 1.2:+48321533 None:intergenic
GAAGAGAAGAAGATTAATGA+AGG 0.510676 1.2:-48320943 MS.gene029778:CDS
TGGGTTGTTGAAGGGAGCTA+TGG 0.513930 1.2:+48321541 None:intergenic
CTCATGTGATGTTTGCAACA+AGG 0.514548 1.2:-48321367 MS.gene029778:CDS
AATCAATGAAAGAGAAAGAA+GGG 0.516168 1.2:+48321514 None:intergenic
ATATCTCGTGGCGGTTTCGA+GGG 0.521594 1.2:-48321168 MS.gene029778:CDS
ATCTTCCTCTGCAAGCTATG+AGG 0.522500 1.2:-48321283 MS.gene029778:CDS
TATGATGGATGCTAATATGA+TGG 0.534594 1.2:-48321085 MS.gene029778:CDS
TGATATTGAGAAGACGAAGA+AGG 0.543732 1.2:-48321061 MS.gene029778:CDS
TAATCAATGAAAGAGAAAGA+AGG 0.544898 1.2:+48321513 None:intergenic
TCATAGCTTGCAGAGGAAGA+TGG 0.548781 1.2:+48321285 None:intergenic
ACTTTCTACCACCTAAGAAA+CGG 0.555851 1.2:-48321257 MS.gene029778:CDS
AAATTCTTCACATCATCACT+TGG 0.564670 1.2:+48320864 None:intergenic
AGCACTTGCCGTTTCTTAGG+TGG 0.568114 1.2:+48321249 None:intergenic
TATTGCAGCTGAAACTCTGT+TGG 0.580874 1.2:-48321193 MS.gene029778:CDS
GTGTTGCTAACAAGTGCCAC+AGG 0.600284 1.2:-48321024 MS.gene029778:CDS
GAGGAAGATGGTGCAACAGT+TGG 0.627306 1.2:+48321297 None:intergenic
ACGAAGAAGGAGAAAGAACA+AGG 0.647791 1.2:-48321048 MS.gene029778:CDS
CTGTTGGATATATCTCGTGG+CGG 0.650335 1.2:-48321177 MS.gene029778:CDS
GTGATCCTCATAGCTTGCAG+AGG 0.672732 1.2:+48321278 None:intergenic
ACTCTGTTGGATATATCTCG+TGG 0.678764 1.2:-48321180 MS.gene029778:CDS
AATATCAATTTGAATCACCG+TGG 0.727003 1.2:-48321135 MS.gene029778:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAGTTTTGTTCTGATTA+GGG + chr1.2:48320980-48320999 None:intergenic 20.0%
!!! TTTTTAGTTTTGTTCTGATT+AGG + chr1.2:48320981-48321000 None:intergenic 20.0%
! AATCAATGAAAGAGAAAGAA+GGG + chr1.2:48320950-48320969 None:intergenic 25.0%
! TAATCAATGAAAGAGAAAGA+AGG + chr1.2:48320951-48320970 None:intergenic 25.0%
!! AAAACTCTTTTGCAATATGA+TGG - chr1.2:48321361-48321380 MS.gene029778:CDS 25.0%
AATATCAATTTGAATCACCG+TGG - chr1.2:48321326-48321345 MS.gene029778:CDS 30.0%
AATGAAGGTGAAACAGAATT+AGG - chr1.2:48321533-48321552 MS.gene029778:CDS 30.0%
ACGGTGATTCAAATTGATAT+TGG + chr1.2:48321327-48321346 None:intergenic 30.0%
ATGAAGGTGAAACAGAATTA+GGG - chr1.2:48321534-48321553 MS.gene029778:CDS 30.0%
CTCTTCAATACTTTGATTAG+AGG + chr1.2:48321504-48321523 None:intergenic 30.0%
GAAGAGAAGAAGATTAATGA+AGG - chr1.2:48321518-48321537 MS.gene029778:CDS 30.0%
!! AAAGAGAAAGAAGGGTATTT+GGG + chr1.2:48320942-48320961 None:intergenic 30.0%
!! ACTTCTAACAAAGCTTTGAA+TGG - chr1.2:48321122-48321141 MS.gene029778:CDS 30.0%
!! TATGATGGATGCTAATATGA+TGG - chr1.2:48321376-48321395 MS.gene029778:CDS 30.0%
!!! TGGTCAACATGATTAGTTTT+TGG + chr1.2:48320903-48320922 None:intergenic 30.0%
!!! TTTTGTTTTCCAGCATCATT+AGG + chr1.2:48321068-48321087 None:intergenic 30.0%
ACTTTCTACCACCTAAGAAA+CGG - chr1.2:48321204-48321223 MS.gene029778:CDS 35.0%
CATCATTAGTTGCTGAACAT+AGG + chr1.2:48321004-48321023 None:intergenic 35.0%
CTGGAAAACAGAAGATCATA+TGG - chr1.2:48321024-48321043 MS.gene029778:CDS 35.0%
TATTCAGTTCCTAATGATGC+TGG - chr1.2:48321056-48321075 MS.gene029778:CDS 35.0%
TGATATTGAGAAGACGAAGA+AGG - chr1.2:48321400-48321419 MS.gene029778:CDS 35.0%
TGTTTGAAAAATCATGCCTG+TGG + chr1.2:48321456-48321475 None:intergenic 35.0%
!! GAAAGAGAAAGAAGGGTATT+TGG + chr1.2:48320943-48320962 None:intergenic 35.0%
ACGAAGAAGGAGAAAGAACA+AGG - chr1.2:48321413-48321432 MS.gene029778:CDS 40.0%
ACTCTGTTGGATATATCTCG+TGG - chr1.2:48321281-48321300 MS.gene029778:CDS 40.0%
ATACTTTGATTAGAGGCAGC+AGG + chr1.2:48321497-48321516 None:intergenic 40.0%
CTCATGTGATGTTTGCAACA+AGG - chr1.2:48321094-48321113 MS.gene029778:CDS 40.0%
TATTGCAGCTGAAACTCTGT+TGG - chr1.2:48321268-48321287 MS.gene029778:CDS 40.0%
TGTTCAGCAACTAATGATGC+TGG - chr1.2:48321005-48321024 MS.gene029778:CDS 40.0%
! GTTTTTGCCTTTTAGCACCA+CGG + chr1.2:48321346-48321365 None:intergenic 40.0%
!! AAGGGTATTTGGGTTGTTGA+AGG + chr1.2:48320932-48320951 None:intergenic 40.0%
!! AGGGTATTTGGGTTGTTGAA+GGG + chr1.2:48320931-48320950 None:intergenic 40.0%
ATCTTCCTCTGCAAGCTATG+AGG - chr1.2:48321178-48321197 MS.gene029778:CDS 45.0%
CTGTTGGATATATCTCGTGG+CGG - chr1.2:48321284-48321303 MS.gene029778:CDS 45.0%
! CTTAGCACTTGCCGTTTCTT+AGG + chr1.2:48321218-48321237 None:intergenic 45.0%
! TCATAGCTTGCAGAGGAAGA+TGG + chr1.2:48321179-48321198 None:intergenic 45.0%
! TGAATCACCGTGGTGCTAAA+AGG - chr1.2:48321336-48321355 MS.gene029778:CDS 45.0%
ATATCTCGTGGCGGTTTCGA+GGG - chr1.2:48321293-48321312 MS.gene029778:CDS 50.0%
GAGGAAGATGGTGCAACAGT+TGG + chr1.2:48321167-48321186 None:intergenic 50.0%
TATATCTCGTGGCGGTTTCG+AGG - chr1.2:48321292-48321311 MS.gene029778:CDS 50.0%
TGGGTTGTTGAAGGGAGCTA+TGG + chr1.2:48320923-48320942 None:intergenic 50.0%
! AGCACTTGCCGTTTCTTAGG+TGG + chr1.2:48321215-48321234 None:intergenic 50.0%
! GTGATCCTCATAGCTTGCAG+AGG + chr1.2:48321186-48321205 None:intergenic 50.0%
! GTGTTGCTAACAAGTGCCAC+AGG - chr1.2:48321437-48321456 MS.gene029778:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 48320879 48321604 48320879 ID=MS.gene029778
chr1.2 mRNA 48320879 48321604 48320879 ID=MS.gene029778.t1;Parent=MS.gene029778
chr1.2 exon 48320879 48321604 48320879 ID=MS.gene029778.t1.exon1;Parent=MS.gene029778.t1
chr1.2 CDS 48320879 48321604 48320879 ID=cds.MS.gene029778.t1;Parent=MS.gene029778.t1
Gene Sequence

>MS.gene029778

ATGTCTTCTTTTGATCATAAACCAAAAACTAATCATGTTGACCATAGCTCCCTTCAACAACCCAAATACCCTTCTTTCTCTTTCATTGATTATTCAAACCCTAATCAGAACAAAACTAAAAACCTATGTTCAGCAACTAATGATGCTGGAAAACAGAAGATCATATGGTTTTTTTCTTATTCAGTTCCTAATGATGCTGGAAAACAAAAGAAACACTCATGTGATGTTTGCAACAAGGTTTTTACTTCTAACAAAGCTTTGAATGGACATATGATATGTCACTCACCAACTGTTGCACCATCTTCCTCTGCAAGCTATGAGGATCACTTTCTACCACCTAAGAAACGGCAAGTGCTAAGAAGAAGTTATATGAATAATGATGATGATGCTATTGCAGCTGAAACTCTGTTGGATATATCTCGTGGCGGTTTCGAGGGATCAACTACCAATATCAATTTGAATCACCGTGGTGCTAAAAGGCAAAAACTCTTTTGCAATATGATGGATGCTAATATGATGGATGATATTGAGAAGACGAAGAAGGAGAAAGAACAAGGTGTGTTGCTAACAAGTGCCACAGGCATGATTTTTCAAACATCACAAGATTGCAAGCAACCTGCTGCCTCTAATCAAAGTATTGAAGAGAAGAAGATTAATGAAGGTGAAACAGAATTAGGGTCAAAAGTTGTGAAGAATTTTGATTTGAACGAGCTAGCTTCCAAGTGA
Protein sequence

>MS.gene029778.t1

MSSFDHKPKTNHVDHSSLQQPKYPSFSFIDYSNPNQNKTKNLCSATNDAGKQKIIWFFSYSVPNDAGKQKKHSCDVCNKVFTSNKALNGHMICHSPTVAPSSSASYEDHFLPPKKRQVLRRSYMNNDDDAIAAETLLDISRGGFEGSTTNINLNHRGAKRQKLFCNMMDANMMDDIEKTKKEKEQGVLLTSATGMIFQTSQDCKQPAASNQSIEEKKINEGETELGSKVVKNFDLNELASK