AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035434

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035434.t1 MTR_8g442330 76.984 126 26 1 2 124 14 139 3.65e-67 200
MS.gene035434.t1 MTR_8g051480 83.333 108 17 1 36 143 16 122 2.60e-59 180
MS.gene035434.t1 MTR_2g076780 42.703 185 63 6 2 143 46 230 9.22e-39 131
MS.gene035434.t1 MTR_8g069080 42.857 189 56 7 2 143 78 261 1.82e-35 124
MS.gene035434.t1 MTR_8g069380 62.500 88 30 2 54 141 22 106 2.00e-29 103
MS.gene035434.t1 MTR_5g020510 29.208 202 77 4 2 149 108 297 1.75e-23 93.6
MS.gene035434.t1 MTR_7g010300 31.915 188 74 4 2 143 97 276 2.46e-22 90.9
MS.gene035434.t1 MTR_3g100650 32.022 178 84 2 3 143 90 267 9.57e-22 88.6
MS.gene035434.t1 MTR_1g077020 30.488 164 91 2 2 143 18 180 1.80e-21 85.9
MS.gene035434.t1 MTR_6g012280 31.383 188 76 5 1 143 99 278 4.18e-20 84.7
MS.gene035434.t1 MTR_6g073013 29.861 144 86 3 2 143 28 158 1.38e-17 75.5
MS.gene035434.t1 MTR_4g134580 57.143 56 24 0 88 143 285 340 2.77e-15 71.6
MS.gene035434.t1 MTR_8g032100 77.273 44 10 0 94 137 125 168 7.31e-15 68.2
MS.gene035434.t1 MTR_5g032600 57.143 56 24 0 88 143 210 265 2.26e-14 68.6
MS.gene035434.t1 MTR_5g032600 63.889 36 13 0 4 39 89 124 8.44e-11 58.5
MS.gene035434.t1 MTR_8g467340 50.000 56 28 0 88 143 272 327 1.44e-12 64.3
MS.gene035434.t1 MTR_8g032050 72.727 44 12 0 94 137 125 168 2.88e-12 61.2
MS.gene035434.t1 MTR_3g039810 60.526 38 15 0 2 39 29 66 7.24e-12 58.2
MS.gene035434.t1 MTR_5g065440 48.214 56 29 0 88 143 206 261 3.13e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035434.t1 AT4G24660 37.037 162 74 3 3 143 59 213 5.63e-26 98.2
MS.gene035434.t1 AT4G24660 37.037 162 74 3 3 143 59 213 7.70e-26 98.2
MS.gene035434.t1 AT5G65410 32.317 164 87 2 3 143 85 247 1.43e-23 93.2
MS.gene035434.t1 AT2G18350 33.898 177 83 4 2 149 91 262 2.31e-23 92.4
MS.gene035434.t1 AT1G14440 32.571 175 84 3 4 144 101 275 2.44e-23 93.2
MS.gene035434.t1 AT1G14440 32.571 175 84 3 4 144 101 275 2.44e-23 93.2
MS.gene035434.t1 AT5G15210 31.977 172 88 4 2 144 65 236 3.57e-21 87.0
MS.gene035434.t1 AT2G02540 28.421 190 81 4 2 143 96 278 3.42e-20 84.7
MS.gene035434.t1 AT2G02540 28.421 190 81 4 2 143 96 278 3.42e-20 84.7
MS.gene035434.t1 AT3G50890 30.000 170 90 4 2 143 69 237 4.62e-18 78.2
MS.gene035434.t1 AT3G28920 30.645 186 83 4 4 143 63 248 7.59e-18 78.6
MS.gene035434.t1 AT5G60480 31.481 162 85 4 3 143 47 203 3.53e-16 72.8
MS.gene035434.t1 AT1G75240 51.667 60 29 0 84 143 237 296 2.90e-14 68.6
MS.gene035434.t1 AT1G74660 63.158 38 14 0 2 39 48 85 4.68e-13 61.6
MS.gene035434.t1 AT1G74660 63.158 38 14 0 2 39 48 85 6.96e-13 61.2

Find 27 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAATTCGAATAAGAGGTTT+TGG 0.293267 8.2:-51873088 MS.gene035434:CDS
AAGAGAGTAGCCTCCAATAT+TGG 0.357209 8.2:+51873334 None:intergenic
TTGGATCTTGCTATGACATT+AGG 0.384999 8.2:-51873032 MS.gene035434:CDS
ATTGGAGGCTACTCTCTTGA+TGG 0.400758 8.2:-51873329 MS.gene035434:CDS
CCAGCACCATCACCATTGAT+AGG 0.458035 8.2:+51873122 None:intergenic
GGACGTCGAATTCGAATAAG+AGG 0.459103 8.2:-51873094 MS.gene035434:CDS
AGGTTTGGATGTATAACAAA+AGG 0.464637 8.2:-51872932 MS.gene035434:intron
GTGGTACCTTCCGCTCCAAC+GGG 0.471679 8.2:+51873290 None:intergenic
CCTATCAATGGTGATGGTGC+TGG 0.500146 8.2:-51873122 MS.gene035434:CDS
TGTGGGGATCCACATTTCAA+TGG 0.533396 8.2:-51873183 MS.gene035434:CDS
GGTGGTACCTTCCGCTCCAA+CGG 0.536942 8.2:+51873289 None:intergenic
AGACATATTGAGCCTATCAA+TGG 0.544287 8.2:-51873134 MS.gene035434:CDS
AATGGTGATGGTGCTGGAGA+AGG 0.551509 8.2:-51873116 MS.gene035434:CDS
ATCTTGCTATGACATTAGGT+TGG 0.558400 8.2:-51873028 MS.gene035434:CDS
TGAGCAAAGGAAGAAAATGT+TGG 0.580678 8.2:-51873051 MS.gene035434:CDS
ATGGTGATGGTGCTGGAGAA+GGG 0.586074 8.2:-51873115 MS.gene035434:CDS
TCTTGTCATAACTTCATCTG+TGG 0.590465 8.2:-51873201 MS.gene035434:CDS
AATCACATGTCCAATATTGG+AGG 0.604304 8.2:-51873344 None:intergenic
GTTATGACAAGAGTGGTTGA+AGG 0.607154 8.2:+51873212 None:intergenic
CTTGTCATAACTTCATCTGT+GGG 0.610212 8.2:-51873200 MS.gene035434:CDS
CAAGATCCTCCATTGAAATG+TGG 0.611943 8.2:+51873174 None:intergenic
GAATGATGAGAATGTTGTTG+AGG 0.621829 8.2:-51872994 MS.gene035434:CDS
CAAAGTTTACCCATGAGCAA+AGG 0.627081 8.2:-51873064 MS.gene035434:CDS
ATTGAGCCTATCAATGGTGA+TGG 0.658220 8.2:-51873128 MS.gene035434:CDS
GGGGATCCACATTTCAATGG+AGG 0.659887 8.2:-51873180 MS.gene035434:CDS
AGATGAAGTTATGACAAGAG+TGG 0.686011 8.2:+51873205 None:intergenic
TTGTCATAACTTCATCTGTG+GGG 0.706690 8.2:-51873199 MS.gene035434:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATGCTAAAAAATGAAT+AGG - chr8.2:51873311-51873330 MS.gene035434:CDS 15.0%
!!! AATGAATTAGGATGATTTTT+TGG + chr8.2:51873032-51873051 None:intergenic 20.0%
!!! ATTTTGATGCTTTTTATTGT+AGG - chr8.2:51873160-51873179 MS.gene035434:CDS 20.0%
!!! TACAATAAAAAGCATCAAAA+TGG + chr8.2:51873161-51873180 None:intergenic 20.0%
! AGCAACATCTTAAATGAATT+AGG + chr8.2:51873044-51873063 None:intergenic 25.0%
! AGCACAATTAAAAAAAATGG+TGG + chr8.2:51872260-51872279 None:intergenic 25.0%
! AGCAGCACAATTAAAAAAAA+TGG + chr8.2:51872263-51872282 None:intergenic 25.0%
!! AAAAGCATGTTAAGCATAAA+TGG + chr8.2:51873227-51873246 None:intergenic 25.0%
!!! CTTTATTCTGAAATGTTTGT+TGG - chr8.2:51872799-51872818 MS.gene035434:intron 25.0%
!!! CTTTTGATGCTTTTTATTGT+AGG - chr8.2:51873242-51873261 MS.gene035434:CDS 25.0%
!!! GAATAAAGCATGTTTGTTTT+CGG + chr8.2:51872787-51872806 None:intergenic 25.0%
!!! GTTTGTTTAGCTTTTCAAAT+AGG - chr8.2:51873278-51873297 MS.gene035434:CDS 25.0%
!!! TATCATCTACTTTTTTCCAT+GGG + chr8.2:51872626-51872645 None:intergenic 25.0%
!!! TTATCATCTACTTTTTTCCA+TGG + chr8.2:51872627-51872646 None:intergenic 25.0%
AGGTTTGGATGTATAACAAA+AGG - chr8.2:51872596-51872615 MS.gene035434:intron 30.0%
AGTGACACAATCTAATGTTA+AGG - chr8.2:51873134-51873153 MS.gene035434:CDS 30.0%
! TATAACAAAAGGTATACCCA+TGG - chr8.2:51872607-51872626 MS.gene035434:intron 30.0%
!! ATTCTGAAATGTTTGTTGGA+AGG - chr8.2:51872803-51872822 MS.gene035434:intron 30.0%
!! TAATGACACGTTGATTTACT+TGG - chr8.2:51873096-51873115 MS.gene035434:CDS 30.0%
AAATTCCCTGACTTTCTTTC+AGG + chr8.2:51872920-51872939 None:intergenic 35.0%
AGACATATTGAGCCTATCAA+TGG - chr8.2:51872394-51872413 MS.gene035434:intron 35.0%
AGATGAAGTTATGACAAGAG+TGG + chr8.2:51872326-51872345 None:intergenic 35.0%
AGATGACGTGTTAAGAATGT+TGG + chr8.2:51873193-51873212 None:intergenic 35.0%
CTTGTCATAACTTCATCTGT+GGG - chr8.2:51872328-51872347 MS.gene035434:intron 35.0%
GAATGATGAGAATGTTGTTG+AGG - chr8.2:51872534-51872553 MS.gene035434:intron 35.0%
GATGACGTGTTAAGAATGTT+GGG + chr8.2:51873192-51873211 None:intergenic 35.0%
TCTTGTCATAACTTCATCTG+TGG - chr8.2:51872327-51872346 MS.gene035434:intron 35.0%
TGAGCAAAGGAAGAAAATGT+TGG - chr8.2:51872477-51872496 MS.gene035434:intron 35.0%
TGCTTACAACTGAACAAGTT+TGG - chr8.2:51873071-51873090 MS.gene035434:CDS 35.0%
TTGTCATAACTTCATCTGTG+GGG - chr8.2:51872329-51872348 MS.gene035434:intron 35.0%
! ACATTTTCTTCCTTTGCTCA+TGG + chr8.2:51872477-51872496 None:intergenic 35.0%
! ATCTTGCTATGACATTAGGT+TGG - chr8.2:51872500-51872519 MS.gene035434:intron 35.0%
! CATTTTCTTCCTTTGCTCAT+GGG + chr8.2:51872476-51872495 None:intergenic 35.0%
! CGAATTCGAATAAGAGGTTT+TGG - chr8.2:51872440-51872459 MS.gene035434:intron 35.0%
! CTATTGTCTGTTTTGTGTGT+TGG - chr8.2:51872998-51873017 MS.gene035434:CDS 35.0%
! TTGGATCTTGCTATGACATT+AGG - chr8.2:51872496-51872515 MS.gene035434:intron 35.0%
!! GGAGTTTTATAACGAGATAG+AGG - chr8.2:51872555-51872574 MS.gene035434:intron 35.0%
!!! AGCATCGTGTTTTTAAGGTT+TGG - chr8.2:51872581-51872600 MS.gene035434:intron 35.0%
AAGAGAGTAGCCTCCAATAT+TGG + chr8.2:51872197-51872216 None:intergenic 40.0%
ATTGAGCCTATCAATGGTGA+TGG - chr8.2:51872400-51872419 MS.gene035434:intron 40.0%
CAAAGTTTACCCATGAGCAA+AGG - chr8.2:51872464-51872483 MS.gene035434:intron 40.0%
CAAGATCCTCCATTGAAATG+TGG + chr8.2:51872357-51872376 None:intergenic 40.0%
GTTATGACAAGAGTGGTTGA+AGG + chr8.2:51872319-51872338 None:intergenic 40.0%
! CTGAAATGTTTGTTGGAAGG+AGG - chr8.2:51872806-51872825 MS.gene035434:intron 40.0%
!!! GGTGAAGCATCGTGTTTTTA+AGG - chr8.2:51872576-51872595 MS.gene035434:intron 40.0%
ATTGGAGGCTACTCTCTTGA+TGG - chr8.2:51872199-51872218 MS.gene035434:intron 45.0%
CACTGCCTGAAAGAAAGTCA+GGG - chr8.2:51872912-51872931 MS.gene035434:intron 45.0%
CTGACTTTCTTTCAGGCAGT+GGG + chr8.2:51872913-51872932 None:intergenic 45.0%
GGACGTCGAATTCGAATAAG+AGG - chr8.2:51872434-51872453 MS.gene035434:intron 45.0%
TGTGGGGATCCACATTTCAA+TGG - chr8.2:51872345-51872364 MS.gene035434:intron 45.0%
! TGAGTTTTTACCCGTTGGAG+CGG - chr8.2:51872228-51872247 MS.gene035434:intron 45.0%
! TGTCGTGAGTTTTTACCCGT+TGG - chr8.2:51872223-51872242 MS.gene035434:intron 45.0%
CCACTGCCTGAAAGAAAGTC+AGG - chr8.2:51872911-51872930 MS.gene035434:intron 50.0%
CCAGCACCATCACCATTGAT+AGG + chr8.2:51872409-51872428 None:intergenic 50.0%
CCTGACTTTCTTTCAGGCAG+TGG + chr8.2:51872914-51872933 None:intergenic 50.0%
GGGGATCCACATTTCAATGG+AGG - chr8.2:51872348-51872367 MS.gene035434:intron 50.0%
! TTTTTACCCGTTGGAGCGGA+AGG - chr8.2:51872232-51872251 MS.gene035434:intron 50.0%
!! AATGGTGATGGTGCTGGAGA+AGG - chr8.2:51872412-51872431 MS.gene035434:intron 50.0%
!! ATGGTGATGGTGCTGGAGAA+GGG - chr8.2:51872413-51872432 MS.gene035434:intron 50.0%
!! CCTATCAATGGTGATGGTGC+TGG - chr8.2:51872406-51872425 MS.gene035434:intron 50.0%
GGTGGTACCTTCCGCTCCAA+CGG + chr8.2:51872242-51872261 None:intergenic 60.0%
GTGGTACCTTCCGCTCCAAC+GGG + chr8.2:51872241-51872260 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 51872190 51873360 51872190 ID=MS.gene035434
chr8.2 mRNA 51872190 51873360 51872190 ID=MS.gene035434.t1;Parent=MS.gene035434
chr8.2 exon 51872933 51873360 51872933 ID=MS.gene035434.t1.exon1;Parent=MS.gene035434.t1
chr8.2 CDS 51872933 51873360 51872933 ID=cds.MS.gene035434.t1;Parent=MS.gene035434.t1
chr8.2 exon 51872190 51872217 51872190 ID=MS.gene035434.t1.exon2;Parent=MS.gene035434.t1
chr8.2 CDS 51872190 51872217 51872190 ID=cds.MS.gene035434.t1;Parent=MS.gene035434.t1
Gene Sequence

>MS.gene035434

ATGTCCAATATTGGAGGCTACTCTCTTGATGGTTGTCGTGAGTTTTTACCCGTTGGAGCGGAAGGTACCACCATTTTTTTTAATTGTGCTGCTTGTGAATGTCACAGAAACTTGCATTGTATTGTACCTTCAACCACTCTTGTCATAACTTCATCTGTGGGGATCCACATTTCAATGGAGGATCTTGAAGAAAATGTTCATGTTAGACATATTGAGCCTATCAATGGTGATGGTGCTGGAGAAGGGACGTCGAATTCGAATAAGAGGTTTTGGACAAAGTTTACCCATGAGCAAAGGAAGAAAATGTTGGATCTTGCTATGACATTAGGTTGGAAGAATAAAAAGAATGATGAGAATGTTGTTGAGGAGTTTTATAACGAGATAGAGGTGAAGCATCGTGTTTTTAAGGTTTGGATGTATAACAAAAGGTATACCCATGGAAAAAAGTAGATGATAATGACGAAGATGAAGATTACGATGATGATGATAAGATGTATGTTTATGAGTTCTTGCAACAATTTGTAATCTAATAATTTTTTCTATGTTTAAAATCAATATTTATGTTATCTCAAAAGTATGCTTAATTCTATTCTACCGAAAACAAACATGCTTTATTCTGAAATGTTTGTTGGAAGGAGGATAGTTTCTTCATAGCATCAACTTTTTCTTGCTATTACATTTTCTGAATTTTAATGTCTTTTTATTATATGTTTAGCTTTTCCCACTGCCTGAAAGAAAGTCAGGGAATTTCATGTTCTCTAATGTTGTGTATACTTTATCTTATGTTCATATGTTCTGTATACTTTTTCTATTGTCTGTTTTGTGTGTTGGTTCAAACGCCAAAAAATCATCCTAATTCATTTAAGATGTTGCTACAAAATTGCTTACAACTGAACAAGTTTGGTCTAATGACACGTTGATTTACTTGGTGATTTGACACGTTGAGTGACACAATCTAATGTTAAGGACCATTTTGATGCTTTTTATTGTAGGTGTATACCCAACATTCTTAACACGTCATCTGATATTATAGACCATTTATGCTTAACATGCTTTTGATGCTTTTTATTGTAGGATTATATGAGCTTGTTTGTTTAGCTTTTCAAATAGGTTTAAATTACATTTATGCTAAAAAATGAATAGGTTGAAGAAGATTGATCTGAATAATTGA
Protein sequence

>MS.gene035434.t1

MSNIGGYSLDGCREFLPVGAEGTTIFFNCAACECHRNLHCIVPSTTLVITSSVGIHISMEDLEENVHVRHIEPINGDGAGEGTSNSNKRFWTKFTHEQRKKMLDLAMTLGWKNKKNDENVVEEFYNEIEVKHRVFKVWMYNKRLKKIDLNN