AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034254

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034254.t1 MTR_4g006575 97.333 225 5 1 1 225 1 224 6.60e-162 446
MS.gene034254.t1 MTR_4g006600 97.333 225 5 1 1 225 1 224 6.60e-162 446
MS.gene034254.t1 MTR_2g104900 52.083 240 81 11 9 225 19 247 8.38e-60 188
MS.gene034254.t1 MTR_1g013130 38.136 236 96 10 21 225 46 262 1.99e-34 124
MS.gene034254.t1 MTR_3g106230 35.610 205 99 6 24 198 25 226 5.44e-27 103
MS.gene034254.t1 MTR_5g077370 49.580 119 50 3 16 127 38 153 4.98e-21 88.2
MS.gene034254.t1 MTR_1g107055 44.231 104 55 1 32 132 29 132 2.38e-19 82.8
MS.gene034254.t1 MTR_1g033340 56.944 72 24 2 67 131 97 168 6.14e-19 82.8
MS.gene034254.t1 MTR_3g065020 60.274 73 21 3 62 127 80 151 2.60e-18 80.9
MS.gene034254.t1 MTR_4g128340 65.385 52 16 1 64 115 42 91 4.85e-16 73.2
MS.gene034254.t1 MTR_5g008280 40.909 110 41 3 46 137 25 128 8.14e-16 75.9
MS.gene034254.t1 MTR_5g008320 35.294 136 54 5 59 178 64 181 9.13e-15 72.4
MS.gene034254.t1 MTR_5g008390 46.753 77 38 1 61 137 8 81 1.21e-14 67.4
MS.gene034254.t1 MTR_8g466760 41.346 104 47 4 46 137 76 177 5.21e-14 70.1
MS.gene034254.t1 MTR_3g011990 42.157 102 49 3 46 137 76 177 7.43e-14 69.3
MS.gene034254.t1 MTR_5g008310 41.935 93 34 3 61 137 66 154 1.50e-13 68.9
MS.gene034254.t1 MTR_3g012010 40.000 110 44 3 47 137 77 183 4.50e-13 67.4
MS.gene034254.t1 MTR_7g086860 76.471 34 8 0 67 100 30 63 3.93e-12 62.4
MS.gene034254.t1 MTR_7g083210 75.758 33 8 0 67 99 39 71 4.27e-12 63.2
MS.gene034254.t1 MTR_3g011970 40.909 88 37 2 65 137 96 183 1.14e-11 63.2
MS.gene034254.t1 MTR_7g022960 28.436 211 106 10 6 185 27 223 5.19e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034254.t1 AT1G80730 38.428 229 92 7 24 225 22 228 4.36e-33 119
MS.gene034254.t1 AT5G25160 42.593 216 87 10 36 225 31 235 1.68e-31 115
MS.gene034254.t1 AT5G10970 39.726 219 113 8 22 225 58 272 3.12e-31 115
MS.gene034254.t1 AT1G24625 62.121 66 24 1 63 127 53 118 3.76e-20 85.1
MS.gene034254.t1 AT1G66140 48.485 99 23 3 67 137 83 181 1.95e-17 79.0
MS.gene034254.t1 AT5G57520 70.833 48 14 0 66 113 49 96 2.72e-16 73.6
MS.gene034254.t1 AT5G14010 79.412 34 7 0 67 100 36 69 2.25e-13 65.9
MS.gene034254.t1 AT5G01860 62.222 45 17 0 56 100 54 98 7.95e-13 65.5

Find 34 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTTCACTACCTTCTTA+TGG 0.229495 4.1:+88731160 MS.gene034254:CDS
GGGTAGCCATGTTTCCTAAA+AGG 0.278959 4.1:+88731389 MS.gene034254:CDS
TTTCGCGCTTGTGTGCATTC+TGG 0.297005 4.1:-88731099 None:intergenic
GAGAACTATAAAACTTTCTT+TGG 0.300653 4.1:-88731060 None:intergenic
TTGTTTCCATGCAAATTTAT+CGG 0.310453 4.1:+88730973 MS.gene034254:CDS
AGGACTTGGAGGTTACTTAT+TGG 0.313639 4.1:+88731423 MS.gene034254:CDS
TCAATGCCTAAAACCTTCTA+TGG 0.314982 4.1:+88730847 MS.gene034254:CDS
AATGGAAGCTTTCCAATTGC+TGG 0.323356 4.1:-88731310 None:intergenic
TTTGATTCACAACCAGCAAT+TGG 0.384518 4.1:+88731298 MS.gene034254:CDS
AAAACGGGTGTTTGATAAGA+AGG 0.401545 4.1:-88731232 None:intergenic
CTCACATGAAAATTTCCTAA+TGG 0.404461 4.1:-88731328 None:intergenic
GCAATTGGAAAGCTTCCATT+AGG 0.416438 4.1:+88731313 MS.gene034254:CDS
CCTTTGGTGGTAGCATTTCA+AGG 0.427189 4.1:+88731368 MS.gene034254:CDS
CCTAAAAGGCTTGCAAATGA+AGG 0.436826 4.1:+88731403 MS.gene034254:CDS
GATGAAGTTGAATCATCCTT+TGG 0.437021 4.1:+88731352 MS.gene034254:CDS
AGGCTTGCAAATGAAGGACT+TGG 0.478799 4.1:+88731409 MS.gene034254:CDS
GTTCAAATGGACAAAATGGA+TGG 0.492994 4.1:+88731263 MS.gene034254:CDS
TTGTTACACAAGCCATAAGA+AGG 0.503153 4.1:-88731172 None:intergenic
CTTGCAAATGAAGGACTTGG+AGG 0.517674 4.1:+88731412 MS.gene034254:CDS
TATAGTTCTCAAGCACTTGG+AGG 0.518487 4.1:+88731073 MS.gene034254:CDS
AATTTGCATGGAAACAATTG+AGG 0.530917 4.1:-88730967 None:intergenic
GGCTTGTGTAACAAATCACT+TGG 0.540135 4.1:+88731181 MS.gene034254:CDS
ACACAAGCGCGAAAGAACTT+TGG 0.541231 4.1:+88731108 MS.gene034254:CDS
AGCTTTCCGATAAATTTGCA+TGG 0.561003 4.1:-88730979 None:intergenic
CCTTGAAATGCTACCACCAA+AGG 0.566032 4.1:-88731368 None:intergenic
TCTGACTTTGAATCACTACA+TGG 0.579513 4.1:-88730935 None:intergenic
AAATTTATCGGAAAGCTCCT+CGG 0.581574 4.1:+88730985 MS.gene034254:CDS
TTGCATGGAAACAATTGAGG+AGG 0.582251 4.1:-88730964 None:intergenic
GAAAGAACTTTGGCGAGAAG+AGG 0.587899 4.1:+88731118 MS.gene034254:CDS
TGATCTAAGTCTCTCTAGCA+AGG 0.597107 4.1:+88730910 MS.gene034254:CDS
CTTTGGTGGTAGCATTTCAA+GGG 0.599828 4.1:+88731369 MS.gene034254:CDS
GAAGTTGAATCATCCTTTGG+TGG 0.613485 4.1:+88731355 MS.gene034254:CDS
AAGAGGCTATACAACTAGCA+TGG 0.636438 4.1:+88731135 MS.gene034254:CDS
ATTCTCATGACTAGATTCCG+AGG 0.661115 4.1:-88731002 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTGAACAAAATCCAAAAA+CGG - chr4.1:88731251-88731270 None:intergenic 20.0%
! GAGAACTATAAAACTTTCTT+TGG - chr4.1:88731063-88731082 None:intergenic 25.0%
! TTGTTTCCATGCAAATTTAT+CGG + chr4.1:88730973-88730992 MS.gene034254:CDS 25.0%
! TTTGAACAAAATCCAAAAAC+GGG - chr4.1:88731250-88731269 None:intergenic 25.0%
!! ATTAGGAAATTTTCATGTGA+GGG + chr4.1:88731330-88731349 MS.gene034254:CDS 25.0%
!! TTTTGTTCAAATGGACAAAA+TGG + chr4.1:88731259-88731278 MS.gene034254:CDS 25.0%
!!! GTTTTTGGATTTTGTTCAAA+TGG + chr4.1:88731250-88731269 MS.gene034254:CDS 25.0%
AATTTGCATGGAAACAATTG+AGG - chr4.1:88730970-88730989 None:intergenic 30.0%
CTCACATGAAAATTTCCTAA+TGG - chr4.1:88731331-88731350 None:intergenic 30.0%
TAGTTGCATGAAAAAACTCT+CGG - chr4.1:88731037-88731056 None:intergenic 30.0%
! CATTAGGAAATTTTCATGTG+AGG + chr4.1:88731329-88731348 MS.gene034254:CDS 30.0%
! TTCTATCCATAGAAGGTTTT+AGG - chr4.1:88730856-88730875 None:intergenic 30.0%
! TTGTGTTTTCTATCCATAGA+AGG - chr4.1:88730863-88730882 None:intergenic 30.0%
! TTTTATAGTTCTCAAGCACT+TGG + chr4.1:88731070-88731089 MS.gene034254:CDS 30.0%
AAAACGGGTGTTTGATAAGA+AGG - chr4.1:88731235-88731254 None:intergenic 35.0%
AAATTTATCGGAAAGCTCCT+CGG + chr4.1:88730985-88731004 MS.gene034254:CDS 35.0%
AGCTTTCCGATAAATTTGCA+TGG - chr4.1:88730982-88731001 None:intergenic 35.0%
GATGAAGTTGAATCATCCTT+TGG + chr4.1:88731352-88731371 MS.gene034254:CDS 35.0%
GTTCAAATGGACAAAATGGA+TGG + chr4.1:88731263-88731282 MS.gene034254:CDS 35.0%
TCAATGCCTAAAACCTTCTA+TGG + chr4.1:88730847-88730866 MS.gene034254:CDS 35.0%
TCTGACTTTGAATCACTACA+TGG - chr4.1:88730938-88730957 None:intergenic 35.0%
TCTTCTTCACTACCTTCTTA+TGG + chr4.1:88731160-88731179 MS.gene034254:CDS 35.0%
TTGTTACACAAGCCATAAGA+AGG - chr4.1:88731175-88731194 None:intergenic 35.0%
TTTGATTCACAACCAGCAAT+TGG + chr4.1:88731298-88731317 MS.gene034254:CDS 35.0%
! TCTTATCAAACACCCGTTTT+TGG + chr4.1:88731235-88731254 MS.gene034254:CDS 35.0%
AAGAGGCTATACAACTAGCA+TGG + chr4.1:88731135-88731154 MS.gene034254:CDS 40.0%
AATGGAAGCTTTCCAATTGC+TGG - chr4.1:88731313-88731332 None:intergenic 40.0%
AGGACTTGGAGGTTACTTAT+TGG + chr4.1:88731423-88731442 MS.gene034254:CDS 40.0%
ATTCTCATGACTAGATTCCG+AGG - chr4.1:88731005-88731024 None:intergenic 40.0%
CCTAAAAGGCTTGCAAATGA+AGG + chr4.1:88731403-88731422 MS.gene034254:CDS 40.0%
GAAGTTGAATCATCCTTTGG+TGG + chr4.1:88731355-88731374 MS.gene034254:CDS 40.0%
GCAATTGGAAAGCTTCCATT+AGG + chr4.1:88731313-88731332 MS.gene034254:CDS 40.0%
GGCTTGTGTAACAAATCACT+TGG + chr4.1:88731181-88731200 MS.gene034254:CDS 40.0%
TATAGTTCTCAAGCACTTGG+AGG + chr4.1:88731073-88731092 MS.gene034254:CDS 40.0%
TGATCTAAGTCTCTCTAGCA+AGG + chr4.1:88730910-88730929 MS.gene034254:CDS 40.0%
TTGCATGGAAACAATTGAGG+AGG - chr4.1:88730967-88730986 None:intergenic 40.0%
! CCTTCATTTGCAAGCCTTTT+AGG - chr4.1:88731406-88731425 None:intergenic 40.0%
! CTTTGGTGGTAGCATTTCAA+GGG + chr4.1:88731369-88731388 MS.gene034254:CDS 40.0%
!! TGCAAGCCTTTTAGGAAACA+TGG - chr4.1:88731398-88731417 None:intergenic 40.0%
ACACAAGCGCGAAAGAACTT+TGG + chr4.1:88731108-88731127 MS.gene034254:CDS 45.0%
AGGCTTGCAAATGAAGGACT+TGG + chr4.1:88731409-88731428 MS.gene034254:CDS 45.0%
CCTTGAAATGCTACCACCAA+AGG - chr4.1:88731371-88731390 None:intergenic 45.0%
CTTGCAAATGAAGGACTTGG+AGG + chr4.1:88731412-88731431 MS.gene034254:CDS 45.0%
GAAAGAACTTTGGCGAGAAG+AGG + chr4.1:88731118-88731137 MS.gene034254:CDS 45.0%
GGGTAGCCATGTTTCCTAAA+AGG + chr4.1:88731389-88731408 MS.gene034254:CDS 45.0%
! CCTTTGGTGGTAGCATTTCA+AGG + chr4.1:88731368-88731387 MS.gene034254:CDS 45.0%
TTTCGCGCTTGTGTGCATTC+TGG - chr4.1:88731102-88731121 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 88730839 88731516 88730839 ID=MS.gene034254
chr4.1 mRNA 88730839 88731516 88730839 ID=MS.gene034254.t1;Parent=MS.gene034254
chr4.1 exon 88730839 88731516 88730839 ID=MS.gene034254.t1.exon1;Parent=MS.gene034254.t1
chr4.1 CDS 88730839 88731516 88730839 ID=cds.MS.gene034254.t1;Parent=MS.gene034254.t1
Gene Sequence

>MS.gene034254

ATGAATCTTCAATGCCTAAAACCTTCTATGGATAGAAAACACAAAAATGATTCATCTTCTCAACTTGTACTTGATCTAAGTCTCTCTAGCAAGGATCCATGTAGTGATTCAAAGTCAGAACTTAACCTCCTCAATTGTTTCCATGCAAATTTATCGGAAAGCTCCTCGGAATCTAGTCATGAGAATGAACTTGATCCGAGAGTTTTTTCATGCAACTACTGCCAAAGAAAGTTTTATAGTTCTCAAGCACTTGGAGGACACCAGAATGCACACAAGCGCGAAAGAACTTTGGCGAGAAGAGGCTATACAACTAGCATGGCTTCTTCTTCACTACCTTCTTATGGCTTGTGTAACAAATCACTTGGCATTCAAGTGCATTCTATGATTAACAAACCTTCTTATCAAACACCCGTTTTTGGATTTTGTTCAAATGGACAAAATGGATGGAGAAGACAAAACTTTGATTCACAACCAGCAATTGGAAAGCTTCCATTAGGAAATTTTCATGTGAGGGATGAAGTTGAATCATCCTTTGGTGGTAGCATTTCAAGGGTAGCCATGTTTCCTAAAAGGCTTGCAAATGAAGGACTTGGAGGTTACTTATTGGATAGTAACACTTCTCATTTGCAGTCTAAACAAGAGAAGTTGCAAAAACTTGACTTATCTCTTAAGCTCTAA
Protein sequence

>MS.gene034254.t1

MNLQCLKPSMDRKHKNDSSSQLVLDLSLSSKDPCSDSKSELNLLNCFHANLSESSSESSHENELDPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLARRGYTTSMASSSLPSYGLCNKSLGIQVHSMINKPSYQTPVFGFCSNGQNGWRRQNFDSQPAIGKLPLGNFHVRDEVESSFGGSISRVAMFPKRLANEGLGGYLLDSNTSHLQSKQEKLQKLDLSLKL