AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88588

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88588.t1 MTR_1g038650 95.378 238 8 1 1 238 1 235 3.81e-166 458
MS.gene88588.t1 MTR_1g114380 59.449 254 54 6 16 236 18 255 5.57e-83 248
MS.gene88588.t1 MTR_2g006150 75.000 84 18 1 20 100 115 198 1.37e-36 134
MS.gene88588.t1 MTR_5g039600 78.205 78 12 1 28 100 58 135 1.38e-36 133
MS.gene88588.t1 MTR_2g006150 75.000 84 18 1 20 100 115 198 1.73e-36 134
MS.gene88588.t1 MTR_7g028160 54.400 125 53 1 1 121 15 139 3.48e-36 129
MS.gene88588.t1 MTR_4g108370 70.930 86 21 1 19 100 80 165 7.88e-36 132
MS.gene88588.t1 MTR_1g063870 78.082 73 13 1 25 94 39 111 5.22e-35 124
MS.gene88588.t1 MTR_1g101810 65.934 91 30 1 5 94 36 126 1.17e-32 121
MS.gene88588.t1 MTR_1g101810 65.934 91 30 1 5 94 66 156 2.74e-32 121
MS.gene88588.t1 MTR_8g033070 72.603 73 20 0 28 100 76 148 2.24e-31 118
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88588.t1 AT5G23280 55.253 257 62 6 10 238 19 250 8.39e-74 224
MS.gene88588.t1 AT5G08330 57.143 231 57 7 27 236 26 235 3.47e-62 195
MS.gene88588.t1 AT1G72010 81.944 72 13 0 29 100 60 131 4.48e-37 134
MS.gene88588.t1 AT1G69690 68.889 90 23 1 16 100 31 120 4.94e-37 132
MS.gene88588.t1 AT3G47620 75.610 82 15 1 24 100 104 185 1.35e-36 134
MS.gene88588.t1 AT1G58100 84.058 69 11 0 32 100 60 128 6.20e-36 131
MS.gene88588.t1 AT1G35560 83.333 72 12 0 29 100 52 123 9.38e-35 127
MS.gene88588.t1 AT3G27010 63.000 100 28 2 3 93 40 139 1.70e-33 123
MS.gene88588.t1 AT3G27010 63.000 100 28 2 3 93 40 139 1.70e-33 123
MS.gene88588.t1 AT5G51910 67.059 85 28 0 28 112 53 137 3.57e-32 119
MS.gene88588.t1 AT5G51910 67.059 85 28 0 28 112 53 137 3.57e-32 119
MS.gene88588.t1 AT2G45680 76.471 68 16 0 27 94 70 137 1.02e-31 119
MS.gene88588.t1 AT5G41030 67.164 67 22 0 28 94 64 130 3.88e-28 107
MS.gene88588.t1 AT2G37000 75.000 60 15 0 32 91 43 102 4.21e-27 103
MS.gene88588.t1 AT3G45150 52.055 73 35 0 33 105 18 90 7.46e-20 83.6
MS.gene88588.t1 AT1G58100 55.072 69 7 1 32 100 60 104 4.77e-15 73.9

Find 61 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACGTGCGGCGCAGATTAT+AGG 0.250067 1.4:+23364426 None:intergenic
CTACTGCTCCGCCGGGGTTT+TGG 0.252668 1.4:-23364182 MS.gene88588:CDS
CAACCTTCTCCGTTTATTCT+TGG 0.258658 1.4:-23364252 MS.gene88588:CDS
AATTTGTTGGCTTCATTGTC+TGG 0.298075 1.4:-23363919 MS.gene88588:CDS
GCTGCTGGTGGTGCTGGTGC+TGG 0.299192 1.4:+23364013 None:intergenic
GTTGATGCTGCTGGTGGTGC+TGG 0.308604 1.4:+23364007 None:intergenic
GAAGCTTCCGCGGCGAGGTT+AGG 0.328795 1.4:-23363964 MS.gene88588:CDS
GACCAAGCTCACGTGTTAAC+TGG 0.329708 1.4:+23364400 None:intergenic
GGTGGTGCTGGTGCTGGTGC+TGG 0.354651 1.4:+23364019 None:intergenic
TCCTGGTCATCTGAATTTGT+TGG 0.361921 1.4:-23363932 MS.gene88588:CDS
CTTGTTGCTGTTGATGCTGC+TGG 0.390685 1.4:+23363998 None:intergenic
TGCTGCACCTACTGCTCCGC+CGG 0.410157 1.4:-23364190 MS.gene88588:CDS
GAAAGAAGCAGGTGTAGTTC+CGG 0.413992 1.4:+23364305 None:intergenic
AAGCTTCCGCGGCGAGGTTA+GGG 0.415378 1.4:-23363963 MS.gene88588:CDS
TGATGATGGTGATGCTGTTT+CGG 0.418538 1.4:-23364214 MS.gene88588:CDS
TCTGGTGGGAATGGAAATTC+TGG 0.419287 1.4:-23363901 MS.gene88588:CDS
AACGGAGAAGGTTGAAGAAA+AGG 0.424552 1.4:+23364261 None:intergenic
TGCTGCTGCTCAACCGCCGC+CGG 0.429682 1.4:-23364127 MS.gene88588:CDS
GCTGCTCAACCGCCGCCGGA+AGG 0.449544 1.4:-23364123 MS.gene88588:CDS
CTCCAAAGCTGAGCAAAATC+CGG 0.465288 1.4:+23364156 None:intergenic
AAACGTTTACCAAGAATAAA+CGG 0.469719 1.4:+23364243 None:intergenic
TCAACAGCAACAAGGTTCAA+TGG 0.473044 1.4:-23363989 MS.gene88588:CDS
ATCATCGCCGCCACCGGTAC+CGG 0.476622 1.4:-23364324 MS.gene88588:CDS
TGTAGTTCCGGTACCGGTGG+CGG 0.480445 1.4:+23364317 None:intergenic
GCTGCACCTACTGCTCCGCC+GGG 0.481411 1.4:-23364189 MS.gene88588:CDS
GCTTCATTGTCTGGTGGGAA+TGG 0.484637 1.4:-23363910 MS.gene88588:CDS
CAACAGCAACAAGGTTCAAT+GGG 0.485127 1.4:-23363988 MS.gene88588:CDS
AGGTTAGGGAATTATCTTCC+TGG 0.487752 1.4:-23363949 MS.gene88588:CDS
AGCAGGTGTAGTTCCGGTAC+CGG 0.496500 1.4:+23364311 None:intergenic
AGAAGTGGGTTCTACTAGAT+CGG 0.502592 1.4:+23364530 None:intergenic
GAAAGAGAAGAGAAAGAAGC+AGG 0.509335 1.4:+23364294 None:intergenic
TGATCGACGGTTCAGCTTGA+CGG 0.511819 1.4:+23364343 None:intergenic
TTCCAGTTAACACGTGAGCT+TGG 0.518020 1.4:-23364402 MS.gene88588:CDS
TTCCGTCTACTTTACTGTGA+CGG 0.524053 1.4:+23364469 None:intergenic
AAATCCGGCCGCCAAAACCC+CGG 0.528380 1.4:+23364171 None:intergenic
TGTTGGCTTCATTGTCTGGT+GGG 0.531348 1.4:-23363915 MS.gene88588:CDS
CCGTCGATCATCGCCGCCAC+CGG 0.537613 1.4:-23364330 MS.gene88588:CDS
CACAGTAAAGTAGACGGAAG+AGG 0.537838 1.4:-23364465 MS.gene88588:CDS
CAAAACCCCGGCGGAGCAGT+AGG 0.540114 1.4:+23364183 None:intergenic
TTGTTGGCTTCATTGTCTGG+TGG 0.543932 1.4:-23363916 MS.gene88588:CDS
GGGAATGGAAATTCTGGTCG+TGG 0.548380 1.4:-23363895 MS.gene88588:CDS
TTCTACTAGATCGGTTGTTG+TGG 0.553500 1.4:+23364539 None:intergenic
GCCAACAAATTCAGATGACC+AGG 0.560326 1.4:+23363931 None:intergenic
CCGGTGGCGGCGATGATCGA+CGG 0.572268 1.4:+23364330 None:intergenic
TGATAGTTGTTGTTTCCTTG+TGG 0.582444 1.4:+23364562 None:intergenic
GTTGCTGTTGATGCTGCTGG+TGG 0.588478 1.4:+23364001 None:intergenic
TTCAATGGGTGAAGCTTCCG+CGG 0.595814 1.4:-23363974 MS.gene88588:CDS
TTACCAAGAATAAACGGAGA+AGG 0.605589 1.4:+23364249 None:intergenic
AGGTGTAGTTCCGGTACCGG+TGG 0.608264 1.4:+23364314 None:intergenic
CCATTCGATAGTTTGACCGT+CGG 0.631339 1.4:+23364371 None:intergenic
ACCTCAAATGTCTAACCACA+AGG 0.638869 1.4:-23364577 None:intergenic
GACCGTCACAGTAAAGTAGA+CGG 0.641647 1.4:-23364471 MS.gene88588:CDS
CAGCAGCATCAACAGCAACA+AGG 0.643976 1.4:-23363997 MS.gene88588:CDS
CCGACGGTCAAACTATCGAA+TGG 0.646959 1.4:-23364371 MS.gene88588:CDS
AAACGTTTACGTGATGATGA+TGG 0.660458 1.4:-23364228 MS.gene88588:CDS
GAGCTTGGTCATAAATCCGA+CGG 0.680249 1.4:-23364387 MS.gene88588:CDS
CTGCACCTACTGCTCCGCCG+GGG 0.682389 1.4:-23364188 MS.gene88588:CDS
TGGGTGAAGCTTCCGCGGCG+AGG 0.688189 1.4:-23363969 MS.gene88588:CDS
TCCGGCCGCCAAAACCCCGG+CGG 0.699527 1.4:+23364174 None:intergenic
TGTTAACTGGAAAACACGTG+CGG 0.728936 1.4:+23364413 None:intergenic
ATAATTCCCTAACCTCGCCG+CGG 0.758456 1.4:+23363957 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAACGTTTACCAAGAATAAA+CGG + chr1.4:23364206-23364225 None:intergenic 25.0%
TGAGAAACAGAAAAACCTTC+CGG + chr1.4:23364341-23364360 None:intergenic 35.0%
TTACCAAGAATAAACGGAGA+AGG + chr1.4:23364200-23364219 None:intergenic 35.0%
! AAACGTTTACGTGATGATGA+TGG - chr1.4:23364218-23364237 MS.gene88588:CDS 35.0%
!! AATTTGTTGGCTTCATTGTC+TGG - chr1.4:23364527-23364546 MS.gene88588:CDS 35.0%
!! TGATAGTTGTTGTTTCCTTG+TGG + chr1.4:23363887-23363906 None:intergenic 35.0%
!!! GTTAGAGTGTTTTGAGAAGT+GGG + chr1.4:23363933-23363952 None:intergenic 35.0%
!!! TGTTAGAGTGTTTTGAGAAG+TGG + chr1.4:23363934-23363953 None:intergenic 35.0%
AACGGAGAAGGTTGAAGAAA+AGG + chr1.4:23364188-23364207 None:intergenic 40.0%
AGGTTAGGGAATTATCTTCC+TGG - chr1.4:23364497-23364516 MS.gene88588:CDS 40.0%
CAACAGCAACAAGGTTCAAT+GGG - chr1.4:23364458-23364477 MS.gene88588:CDS 40.0%
CAACCTTCTCCGTTTATTCT+TGG - chr1.4:23364194-23364213 MS.gene88588:CDS 40.0%
GAAAGAGAAGAGAAAGAAGC+AGG + chr1.4:23364155-23364174 None:intergenic 40.0%
TCAACAGCAACAAGGTTCAA+TGG - chr1.4:23364457-23364476 MS.gene88588:CDS 40.0%
TCCTGGTCATCTGAATTTGT+TGG - chr1.4:23364514-23364533 MS.gene88588:CDS 40.0%
TGTTAACTGGAAAACACGTG+CGG + chr1.4:23364036-23364055 None:intergenic 40.0%
TTCCGTCTACTTTACTGTGA+CGG + chr1.4:23363980-23363999 None:intergenic 40.0%
TTCTACTAGATCGGTTGTTG+TGG + chr1.4:23363910-23363929 None:intergenic 40.0%
! AGAAGTGGGTTCTACTAGAT+CGG + chr1.4:23363919-23363938 None:intergenic 40.0%
! TTACTGTGACGGTCTTTTGA+CGG + chr1.4:23363969-23363988 None:intergenic 40.0%
!! TGATGATGGTGATGCTGTTT+CGG - chr1.4:23364232-23364251 MS.gene88588:CDS 40.0%
CACAGTAAAGTAGACGGAAG+AGG - chr1.4:23363981-23364000 MS.gene88588:CDS 45.0%
CCATTCGATAGTTTGACCGT+CGG + chr1.4:23364078-23364097 None:intergenic 45.0%
CTCCAAAGCTGAGCAAAATC+CGG + chr1.4:23364293-23364312 None:intergenic 45.0%
GAAACAGAAAAACCTTCCGG+CGG + chr1.4:23364338-23364357 None:intergenic 45.0%
GAAAGAAGCAGGTGTAGTTC+CGG + chr1.4:23364144-23364163 None:intergenic 45.0%
GACCGTCACAGTAAAGTAGA+CGG - chr1.4:23363975-23363994 MS.gene88588:CDS 45.0%
GAGCTTGGTCATAAATCCGA+CGG - chr1.4:23364059-23364078 MS.gene88588:CDS 45.0%
GCCAACAAATTCAGATGACC+AGG + chr1.4:23364518-23364537 None:intergenic 45.0%
TCTGGTGGGAATGGAAATTC+TGG - chr1.4:23364545-23364564 MS.gene88588:CDS 45.0%
TTCCAGTTAACACGTGAGCT+TGG - chr1.4:23364044-23364063 MS.gene88588:CDS 45.0%
!! TGTTGGCTTCATTGTCTGGT+GGG - chr1.4:23364531-23364550 MS.gene88588:CDS 45.0%
!! TTGTTGGCTTCATTGTCTGG+TGG - chr1.4:23364530-23364549 MS.gene88588:CDS 45.0%
ATAATTCCCTAACCTCGCCG+CGG + chr1.4:23364492-23364511 None:intergenic 50.0%
CAGCAGCATCAACAGCAACA+AGG - chr1.4:23364449-23364468 MS.gene88588:CDS 50.0%
CCGACGGTCAAACTATCGAA+TGG - chr1.4:23364075-23364094 MS.gene88588:CDS 50.0%
GACCAAGCTCACGTGTTAAC+TGG + chr1.4:23364049-23364068 None:intergenic 50.0%
GCTTCATTGTCTGGTGGGAA+TGG - chr1.4:23364536-23364555 MS.gene88588:CDS 50.0%
GGGAATGGAAATTCTGGTCG+TGG - chr1.4:23364551-23364570 MS.gene88588:CDS 50.0%
TGATCGACGGTTCAGCTTGA+CGG + chr1.4:23364106-23364125 None:intergenic 50.0%
TTCAATGGGTGAAGCTTCCG+CGG - chr1.4:23364472-23364491 MS.gene88588:CDS 50.0%
! CTTGTTGCTGTTGATGCTGC+TGG + chr1.4:23364451-23364470 None:intergenic 50.0%
ACACGTGCGGCGCAGATTAT+AGG + chr1.4:23364023-23364042 None:intergenic 55.0%
ACAGAAAAACCTTCCGGCGG+CGG + chr1.4:23364335-23364354 None:intergenic 55.0%
AGCAGGTGTAGTTCCGGTAC+CGG + chr1.4:23364138-23364157 None:intergenic 55.0%
! CTGTGACGGTCTTTTGACGG+CGG + chr1.4:23363966-23363985 None:intergenic 55.0%
! GGCCGGATTTTGCTCAGCTT+TGG - chr1.4:23364288-23364307 MS.gene88588:CDS 55.0%
! GTTGCTGTTGATGCTGCTGG+TGG + chr1.4:23364448-23364467 None:intergenic 55.0%
AAATCCGGCCGCCAAAACCC+CGG + chr1.4:23364278-23364297 None:intergenic 60.0%
AAGCTTCCGCGGCGAGGTTA+GGG - chr1.4:23364483-23364502 MS.gene88588:CDS 60.0%
! AGGTGTAGTTCCGGTACCGG+TGG + chr1.4:23364135-23364154 None:intergenic 60.0%
! GTTGATGCTGCTGGTGGTGC+TGG + chr1.4:23364442-23364461 None:intergenic 60.0%
!! TGTAGTTCCGGTACCGGTGG+CGG + chr1.4:23364132-23364151 None:intergenic 60.0%
ATCATCGCCGCCACCGGTAC+CGG - chr1.4:23364122-23364141 MS.gene88588:CDS 65.0%
CAAAACCCCGGCGGAGCAGT+AGG + chr1.4:23364266-23364285 None:intergenic 65.0%
GAAGCTTCCGCGGCGAGGTT+AGG - chr1.4:23364482-23364501 MS.gene88588:CDS 65.0%
TGCTGCACCTACTGCTCCGC+CGG - chr1.4:23364256-23364275 MS.gene88588:CDS 65.0%
! CTACTGCTCCGCCGGGGTTT+TGG - chr1.4:23364264-23364283 MS.gene88588:CDS 65.0%
CCGTCGATCATCGCCGCCAC+CGG - chr1.4:23364116-23364135 MS.gene88588:CDS 70.0%
CTGCACCTACTGCTCCGCCG+GGG - chr1.4:23364258-23364277 MS.gene88588:CDS 70.0%
GCTGCACCTACTGCTCCGCC+GGG - chr1.4:23364257-23364276 MS.gene88588:CDS 70.0%
TGCTGCTGCTCAACCGCCGC+CGG - chr1.4:23364319-23364338 MS.gene88588:CDS 70.0%
TGGGTGAAGCTTCCGCGGCG+AGG - chr1.4:23364477-23364496 MS.gene88588:CDS 70.0%
! CCGGTGGCGGCGATGATCGA+CGG + chr1.4:23364119-23364138 None:intergenic 70.0%
!! CTGCTCCGCCGGGGTTTTGG+CGG - chr1.4:23364267-23364286 MS.gene88588:CDS 70.0%
!! GCTGCTGGTGGTGCTGGTGC+TGG + chr1.4:23364436-23364455 None:intergenic 70.0%
!! GGTGGTGCTGGTGCTGGTGC+TGG + chr1.4:23364430-23364449 None:intergenic 70.0%
GCTGCTCAACCGCCGCCGGA+AGG - chr1.4:23364323-23364342 MS.gene88588:CDS 75.0%
TCCGGCCGCCAAAACCCCGG+CGG + chr1.4:23364275-23364294 None:intergenic 75.0%
!! TCCGCCGGGGTTTTGGCGGC+CGG - chr1.4:23364271-23364290 MS.gene88588:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 23363876 23364592 23363876 ID=MS.gene88588
chr1.4 mRNA 23363876 23364592 23363876 ID=MS.gene88588.t1;Parent=MS.gene88588
chr1.4 exon 23363876 23364592 23363876 ID=MS.gene88588.t1.exon1;Parent=MS.gene88588.t1
chr1.4 CDS 23363876 23364592 23363876 ID=cds.MS.gene88588.t1;Parent=MS.gene88588.t1
Gene Sequence

>MS.gene88588

ATGTCTAACCACAAGGAAACAACAACTATCACCACAACAACCGATCTAGTAGAACCCACTTCTCAAAACACTCTAACAGTAAAAAAACCGCCGTCAAAAGACCGTCACAGTAAAGTAGACGGAAGAGGAAGACGCATAAGAATGCCTATAATCTGCGCCGCACGTGTTTTCCAGTTAACACGTGAGCTTGGTCATAAATCCGACGGTCAAACTATCGAATGGCTTCTCCGTCAAGCTGAACCGTCGATCATCGCCGCCACCGGTACCGGAACTACACCTGCTTCTTTCTCTTCTCTTTCTGAGCATAAACCTTTTCTTCAACCTTCTCCGTTTATTCTTGGTAAACGTTTACGTGATGATGATGGTGATGCTGTTTCGGTTGCTGCACCTACTGCTCCGCCGGGGTTTTGGCGGCCGGATTTTGCTCAGCTTTGGAGCTTTGCTGCTGCTGCTCAACCGCCGCCGGAAGGTTTTTCTGTTTCTCAGCATAATTCATTGTTTCATCATCAACAGCAACAACAACAACAACAACAACAACAGCAGCAACAACACCAGCACCAGCACCAGCACCACCAGCAGCATCAACAGCAACAAGGTTCAATGGGTGAAGCTTCCGCGGCGAGGTTAGGGAATTATCTTCCTGGTCATCTGAATTTGTTGGCTTCATTGTCTGGTGGGAATGGAAATTCTGGTCGTGGAGATGACGAAGATCGTTGA
Protein sequence

>MS.gene88588.t1

MSNHKETTTITTTTDLVEPTSQNTLTVKKPPSKDRHSKVDGRGRRIRMPIICAARVFQLTRELGHKSDGQTIEWLLRQAEPSIIAATGTGTTPASFSSLSEHKPFLQPSPFILGKRLRDDDGDAVSVAAPTAPPGFWRPDFAQLWSFAAAAQPPPEGFSVSQHNSLFHHQQQQQQQQQQQQQQHQHQHQHHQQHQQQQGSMGEASAARLGNYLPGHLNLLASLSGGNGNSGRGDDEDR