AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31313

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31313.t1 MTR_2g093980 94.872 273 8 3 1 269 14 284 0.0 498
MS.gene31313.t1 MTR_4g059780 65.399 263 79 4 14 269 46 303 6.03e-92 274
MS.gene31313.t1 MTR_2g017970 56.808 213 87 2 51 263 67 274 2.69e-77 236
MS.gene31313.t1 MTR_2g017960 55.607 214 90 2 51 264 67 275 1.35e-75 231
MS.gene31313.t1 MTR_4g059840 48.227 282 124 8 1 266 15 290 3.55e-74 228
MS.gene31313.t1 MTR_4g053380 51.867 241 103 5 16 244 34 273 2.13e-71 221
MS.gene31313.t1 MTR_4g059790 50.206 243 102 7 38 267 53 289 3.36e-71 221
MS.gene31313.t1 MTR_8g087450 48.540 274 113 5 14 266 22 288 8.71e-71 219
MS.gene31313.t1 MTR_2g093970 44.765 277 130 5 4 263 17 287 1.31e-65 206
MS.gene31313.t1 MTR_8g087460 53.306 242 90 7 7 237 52 281 5.16e-63 201
MS.gene31313.t1 MTR_8g087470 49.818 275 108 9 8 264 53 315 1.35e-62 199
MS.gene31313.t1 MTR_2g017950 48.163 245 106 7 4 232 19 258 5.76e-62 197
MS.gene31313.t1 MTR_4g059720 55.975 159 69 1 45 203 35 192 1.42e-57 184
MS.gene31313.t1 MTR_2g093990 61.074 149 57 1 52 200 41 188 6.38e-55 177
MS.gene31313.t1 MTR_7g101080 47.742 155 79 2 48 201 36 189 6.35e-43 147
MS.gene31313.t1 MTR_2g090765 35.455 220 138 2 43 259 29 247 1.07e-27 107
MS.gene31313.t1 MTR_5g098060 33.140 172 108 4 52 220 48 215 9.28e-18 80.9
MS.gene31313.t1 MTR_2g437700 29.870 154 101 3 52 201 195 345 2.46e-14 72.8
MS.gene31313.t1 MTR_7g075453 30.994 171 102 4 52 217 184 343 7.76e-13 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31313.t1 AT5G03170 50.296 169 82 2 43 209 27 195 6.82e-49 162
MS.gene31313.t1 AT5G60490 47.333 150 77 2 52 200 39 187 4.55e-43 147
MS.gene31313.t1 AT5G44130 38.624 189 103 4 52 238 36 213 1.53e-30 114
MS.gene31313.t1 AT2G20520 35.238 210 130 5 40 244 25 233 5.54e-29 110
MS.gene31313.t1 AT1G03870 34.010 197 115 5 52 242 39 226 2.52e-25 100
MS.gene31313.t1 AT3G46550 28.415 183 120 5 26 200 178 357 1.78e-13 70.1
MS.gene31313.t1 AT3G60900 28.866 194 128 4 37 227 175 361 2.61e-12 66.6

Find 50 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTCCTCTTGATTTCTT+TGG 0.151087 2.3:+7747285 MS.gene31313:CDS
TGCTTCCTCTTGATTTCTTT+GGG 0.217030 2.3:+7747286 MS.gene31313:CDS
ATGTTCAATGGAAGCTTTAA+AGG 0.264173 2.3:-7747153 None:intergenic
GTTGCTGTTGCTGCCGCGTT+GGG 0.332898 2.3:-7746727 None:intergenic
TTACCAGCCACTGTCTCAAC+AGG 0.354909 2.3:-7747126 None:intergenic
GTGAAATGAGTTGTGAGTTT+AGG 0.360618 2.3:-7746939 None:intergenic
CAAGCTTGCTATATATCGTT+TGG 0.363154 2.3:+7747254 MS.gene31313:CDS
TCTTGATTTCTTTGGGACTA+AGG 0.372078 2.3:+7747293 MS.gene31313:CDS
TTGTTGCAGTAGCAATGTTA+TGG 0.375151 2.3:+7747487 MS.gene31313:CDS
CCTGGTAATGTCGGGACTAA+TGG 0.381878 2.3:-7746814 None:intergenic
GGAACAACTTATATATCTAT+TGG 0.386014 2.3:+7747456 MS.gene31313:CDS
GCTATTGCTTCCGCAGCAAC+AGG 0.394680 2.3:-7747330 None:intergenic
TTTGGTGCCGGGGCATGTTT+CGG 0.395055 2.3:-7746766 None:intergenic
TCCGGAGCAGTGAGTTTACT+TGG 0.396599 2.3:+7747426 MS.gene31313:CDS
GATGTTGGTGATGCTGCTTT+TGG 0.401270 2.3:-7746784 None:intergenic
TGCTATATATCGTTTGGATA+AGG 0.401381 2.3:+7747260 MS.gene31313:CDS
TGTTGCTGTTGCTGCCGCGT+TGG 0.413271 2.3:-7746728 None:intergenic
GCAGCAACAGGAGCAGCAGC+AGG 0.428213 2.3:-7747318 None:intergenic
ACCAGTGTTAGTCTTTCAAC+TGG 0.433716 2.3:+7747189 MS.gene31313:CDS
GTGGTTAATGCTACTGTTAC+CGG 0.444157 2.3:+7747213 MS.gene31313:CDS
GTGAGTTTACTTGGAATTCA+AGG 0.448721 2.3:+7747435 MS.gene31313:CDS
GCTTTCTCACATCTCAAAGC+AGG 0.456572 2.3:+7747003 MS.gene31313:CDS
TGTTCAATGGAAGCTTTAAA+GGG 0.463949 2.3:-7747152 None:intergenic
CCATTGAACATCGAATCGTT+TGG 0.477903 2.3:+7747165 MS.gene31313:CDS
CCATTAGTCCCGACATTACC+AGG 0.482861 2.3:+7746814 MS.gene31313:CDS
GCATGTTTCGGTGACGCTGC+TGG 0.495698 2.3:-7746754 None:intergenic
TGTTAGTCTTTCAACTGGTG+TGG 0.520094 2.3:+7747194 MS.gene31313:CDS
TGTGAGAAAGCTGAGTCATC+CGG 0.520744 2.3:-7746991 None:intergenic
TGCTGCTGCTCCTGTTGCTG+CGG 0.526125 2.3:+7747320 MS.gene31313:CDS
CAGAAGTGCCTGGTAATGTC+GGG 0.526324 2.3:-7746822 None:intergenic
TCCAAGTAAACTCACTGCTC+CGG 0.532738 2.3:-7747427 None:intergenic
CCAAACGATTCGATGTTCAA+TGG 0.533393 2.3:-7747165 None:intergenic
TCAGAAGTGCCTGGTAATGT+CGG 0.535783 2.3:-7746823 None:intergenic
CAACAAACTGTGGAAGAATG+TGG 0.559737 2.3:-7747074 None:intergenic
ATCTTCTTCTGAAGAAGATG+AGG 0.562976 2.3:+7747374 MS.gene31313:CDS
AACCCTGTTGAGACAGTGGC+TGG 0.569511 2.3:+7747123 MS.gene31313:CDS
CTTTCTCACATCTCAAAGCA+GGG 0.577178 2.3:+7747004 MS.gene31313:CDS
AGCGTCACCGAAACATGCCC+CGG 0.581778 2.3:+7746759 MS.gene31313:CDS
GTTATCTTGATAAACTACTC+CGG 0.598934 2.3:-7747232 None:intergenic
ACCAGTTGAAAGACTAACAC+TGG 0.603639 2.3:-7747190 None:intergenic
CGGATTAACAATCTTAGCAC+CGG 0.603845 2.3:+7746972 MS.gene31313:CDS
TAGTAACCCTGTTGAGACAG+TGG 0.611903 2.3:+7747119 MS.gene31313:CDS
TTAGTCCCAAAGAAATCAAG+AGG 0.616533 2.3:-7747291 None:intergenic
GGGGTGGAATCAGAAGTGCC+TGG 0.646474 2.3:-7746832 None:intergenic
TGAGGATGATACAACAACAC+AGG 0.648105 2.3:+7747392 MS.gene31313:CDS
TACCAGCCACTGTCTCAACA+GGG 0.663127 2.3:-7747125 None:intergenic
CTCATTGTATTCTCCCAACG+CGG 0.668766 2.3:+7746714 MS.gene31313:CDS
TTATTGCTATCAACAAACTG+TGG 0.684733 2.3:-7747084 None:intergenic
CGCGTTGGGAGAATACAATG+AGG 0.706376 2.3:-7746713 None:intergenic
AGGCACTTCTGATTCCACCC+CGG 0.729635 2.3:+7746834 MS.gene31313:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CATAACAAAAATCCTCAAAA+AGG + chr2.3:7746861-7746880 MS.gene31313:CDS 25.0%
! GGAACAACTTATATATCTAT+TGG + chr2.3:7747456-7747475 MS.gene31313:CDS 25.0%
ACACAGGATAAAAAAAGTTC+CGG + chr2.3:7747408-7747427 MS.gene31313:CDS 30.0%
GTTATCTTGATAAACTACTC+CGG - chr2.3:7747235-7747254 None:intergenic 30.0%
TGCTATATATCGTTTGGATA+AGG + chr2.3:7747260-7747279 MS.gene31313:CDS 30.0%
TTATTGCTATCAACAAACTG+TGG - chr2.3:7747087-7747106 None:intergenic 30.0%
! ATGTTCAATGGAAGCTTTAA+AGG - chr2.3:7747156-7747175 None:intergenic 30.0%
! GATTTTGTCTTATCAGCTTT+CGG - chr2.3:7747357-7747376 None:intergenic 30.0%
!! TGTTCAATGGAAGCTTTAAA+GGG - chr2.3:7747155-7747174 None:intergenic 30.0%
!!! TTTGTGTTGTTTTTAGGAGA+CGG - chr2.3:7746909-7746928 None:intergenic 30.0%
CAACTCATTTCACCAAAAAG+CGG + chr2.3:7746949-7746968 MS.gene31313:CDS 35.0%
CCTAAAAACAACACAAATCG+TGG + chr2.3:7746912-7746931 MS.gene31313:CDS 35.0%
GTGAAATGAGTTGTGAGTTT+AGG - chr2.3:7746942-7746961 None:intergenic 35.0%
GTGAGTTTACTTGGAATTCA+AGG + chr2.3:7747435-7747454 MS.gene31313:CDS 35.0%
TGCTTCCTCTTGATTTCTTT+GGG + chr2.3:7747286-7747305 MS.gene31313:CDS 35.0%
TTAGTCCCAAAGAAATCAAG+AGG - chr2.3:7747294-7747313 None:intergenic 35.0%
TTGCTTCCTCTTGATTTCTT+TGG + chr2.3:7747285-7747304 MS.gene31313:CDS 35.0%
TTGTTGCAGTAGCAATGTTA+TGG + chr2.3:7747487-7747506 MS.gene31313:CDS 35.0%
! ATCTTCTTCTGAAGAAGATG+AGG + chr2.3:7747374-7747393 MS.gene31313:CDS 35.0%
! TGAATGTTTTCGCCTTTTTG+AGG - chr2.3:7746876-7746895 None:intergenic 35.0%
!! AGGATTTTTGTTATGTCGTC+CGG - chr2.3:7746856-7746875 None:intergenic 35.0%
!! CAAGCTTGCTATATATCGTT+TGG + chr2.3:7747254-7747273 MS.gene31313:CDS 35.0%
!! TCTTGATTTCTTTGGGACTA+AGG + chr2.3:7747293-7747312 MS.gene31313:CDS 35.0%
!!! ACTAATGGTTTTGTCGATGT+TGG - chr2.3:7746802-7746821 None:intergenic 35.0%
!!! CCACGATTTGTGTTGTTTTT+AGG - chr2.3:7746915-7746934 None:intergenic 35.0%
!!! TTGTGTTGTTTTTAGGAGAC+GGG - chr2.3:7746908-7746927 None:intergenic 35.0%
ACCAGTTGAAAGACTAACAC+TGG - chr2.3:7747193-7747212 None:intergenic 40.0%
CAACAAACTGTGGAAGAATG+TGG - chr2.3:7747077-7747096 None:intergenic 40.0%
CCAAACGATTCGATGTTCAA+TGG - chr2.3:7747168-7747187 None:intergenic 40.0%
CCATTGAACATCGAATCGTT+TGG + chr2.3:7747165-7747184 MS.gene31313:CDS 40.0%
CGGATTAACAATCTTAGCAC+CGG + chr2.3:7746972-7746991 MS.gene31313:CDS 40.0%
CTTTCTCACATCTCAAAGCA+GGG + chr2.3:7747004-7747023 MS.gene31313:CDS 40.0%
GTGGTTAATGCTACTGTTAC+CGG + chr2.3:7747213-7747232 MS.gene31313:CDS 40.0%
TGAGGATGATACAACAACAC+AGG + chr2.3:7747392-7747411 MS.gene31313:CDS 40.0%
!! ACCAGTGTTAGTCTTTCAAC+TGG + chr2.3:7747189-7747208 MS.gene31313:CDS 40.0%
!! GATTTTTGTTATGTCGTCCG+GGG - chr2.3:7746854-7746873 None:intergenic 40.0%
!! GGATTTTTGTTATGTCGTCC+GGG - chr2.3:7746855-7746874 None:intergenic 40.0%
!! TGTTAGTCTTTCAACTGGTG+TGG + chr2.3:7747194-7747213 MS.gene31313:CDS 40.0%
!!! ATTGTTAATCCGCCGCTTTT+TGG - chr2.3:7746964-7746983 None:intergenic 40.0%
!!! TTGTTTTTAGGAGACGGGTT+AGG - chr2.3:7746903-7746922 None:intergenic 40.0%
CTCATTGTATTCTCCCAACG+CGG + chr2.3:7746714-7746733 MS.gene31313:CDS 45.0%
CTCATTTCACCAAAAAGCGG+CGG + chr2.3:7746952-7746971 MS.gene31313:CDS 45.0%
GCTTTCTCACATCTCAAAGC+AGG + chr2.3:7747003-7747022 MS.gene31313:CDS 45.0%
TAGTAACCCTGTTGAGACAG+TGG + chr2.3:7747119-7747138 MS.gene31313:CDS 45.0%
TCCAAGTAAACTCACTGCTC+CGG - chr2.3:7747430-7747449 None:intergenic 45.0%
TGTGAGAAAGCTGAGTCATC+CGG - chr2.3:7746994-7747013 None:intergenic 45.0%
!! TCAGAAGTGCCTGGTAATGT+CGG - chr2.3:7746826-7746845 None:intergenic 45.0%
!!! GATGTTGGTGATGCTGCTTT+TGG - chr2.3:7746787-7746806 None:intergenic 45.0%
CCATTAGTCCCGACATTACC+AGG + chr2.3:7746814-7746833 MS.gene31313:CDS 50.0%
CGCGTTGGGAGAATACAATG+AGG - chr2.3:7746716-7746735 None:intergenic 50.0%
TACCAGCCACTGTCTCAACA+GGG - chr2.3:7747128-7747147 None:intergenic 50.0%
TCCGGAGCAGTGAGTTTACT+TGG + chr2.3:7747426-7747445 MS.gene31313:CDS 50.0%
TTACCAGCCACTGTCTCAAC+AGG - chr2.3:7747129-7747148 None:intergenic 50.0%
! CCTGGTAATGTCGGGACTAA+TGG - chr2.3:7746817-7746836 None:intergenic 50.0%
!! CAGAAGTGCCTGGTAATGTC+GGG - chr2.3:7746825-7746844 None:intergenic 50.0%
!! TTTTGTTATGTCGTCCGGGG+TGG - chr2.3:7746851-7746870 None:intergenic 50.0%
AACCCTGTTGAGACAGTGGC+TGG + chr2.3:7747123-7747142 MS.gene31313:CDS 55.0%
AGGCACTTCTGATTCCACCC+CGG + chr2.3:7746834-7746853 MS.gene31313:CDS 55.0%
GCTATTGCTTCCGCAGCAAC+AGG - chr2.3:7747333-7747352 None:intergenic 55.0%
!! TTTGGTGCCGGGGCATGTTT+CGG - chr2.3:7746769-7746788 None:intergenic 55.0%
!!! GGTGATGCTGCTTTTGGTGC+CGG - chr2.3:7746781-7746800 None:intergenic 55.0%
!!! GTGATGCTGCTTTTGGTGCC+GGG - chr2.3:7746780-7746799 None:intergenic 55.0%
!!! TGATGCTGCTTTTGGTGCCG+GGG - chr2.3:7746779-7746798 None:intergenic 55.0%
AGCGTCACCGAAACATGCCC+CGG + chr2.3:7746759-7746778 MS.gene31313:CDS 60.0%
GCATGTTTCGGTGACGCTGC+TGG - chr2.3:7746757-7746776 None:intergenic 60.0%
TGCTGCTGCTCCTGTTGCTG+CGG + chr2.3:7747320-7747339 MS.gene31313:CDS 60.0%
! GTTGCTGTTGCTGCCGCGTT+GGG - chr2.3:7746730-7746749 None:intergenic 60.0%
! TGTTGCTGTTGCTGCCGCGT+TGG - chr2.3:7746731-7746750 None:intergenic 60.0%
!! GGGGTGGAATCAGAAGTGCC+TGG - chr2.3:7746835-7746854 None:intergenic 60.0%
GCAGCAACAGGAGCAGCAGC+AGG - chr2.3:7747321-7747340 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 7746706 7747515 7746706 ID=MS.gene31313
chr2.3 mRNA 7746706 7747515 7746706 ID=MS.gene31313.t1;Parent=MS.gene31313
chr2.3 exon 7746706 7747515 7746706 ID=MS.gene31313.t1.exon1;Parent=MS.gene31313.t1
chr2.3 CDS 7746706 7747515 7746706 ID=cds.MS.gene31313.t1;Parent=MS.gene31313.t1
Gene Sequence

>MS.gene31313

ATGTTCTCCTCATTGTATTCTCCCAACGCGGCAGCAACAGCAACAGCACCAGCAGCGTCACCGAAACATGCCCCGGCACCAAAAGCAGCATCACCAACATCGACAAAACCATTAGTCCCGACATTACCAGGCACTTCTGATTCCACCCCGGACGACATAACAAAAATCCTCAAAAAGGCGAAAACATTCACAATCCTAACCCGTCTCCTAAAAACAACACAAATCGTGGACAACCTAAACTCACAACTCATTTCACCAAAAAGCGGCGGATTAACAATCTTAGCACCGGATGACTCAGCTTTCTCACATCTCAAAGCAGGGTTCTTCAACTCGCTAAATGAAAACAAAAAAATCGAACTATTACAATTCCACATTCTTCCACAGTTTGTTGATAGCAATAACTTTGATTCTCTTAGTAACCCTGTTGAGACAGTGGCTGGTAAAGACCCTTTAAAGCTTCCATTGAACATCGAATCGTTTGGTACCAGTGTTAGTCTTTCAACTGGTGTGGTTAATGCTACTGTTACCGGAGTAGTTTATCAAGATAACAAGCTTGCTATATATCGTTTGGATAAGGTTTTGCTTCCTCTTGATTTCTTTGGGACTAAGGCACCTGCTGCTGCTCCTGTTGCTGCGGAAGCAATAGCACCGAAAGCTGATAAGACAAAATCTTCTTCTGAAGAAGATGAGGATGATACAACAACACAGGATAAAAAAAGTTCCGGAGCAGTGAGTTTACTTGGAATTCAAGGAACAACTTATATATCTATTGGAGTAGCTTTTGTTGCAGTAGCAATGTTATGGAGTTGA
Protein sequence

>MS.gene31313.t1

MFSSLYSPNAAATATAPAASPKHAPAPKAASPTSTKPLVPTLPGTSDSTPDDITKILKKAKTFTILTRLLKTTQIVDNLNSQLISPKSGGLTILAPDDSAFSHLKAGFFNSLNENKKIELLQFHILPQFVDSNNFDSLSNPVETVAGKDPLKLPLNIESFGTSVSLSTGVVNATVTGVVYQDNKLAIYRLDKVLLPLDFFGTKAPAAAPVAAEAIAPKADKTKSSSEEDEDDTTTQDKKSSGAVSLLGIQGTTYISIGVAFVAVAMLWS