AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0700440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0700440 MtrunA17_Chr8g0377781 55.714 210 52 2 4 172 167 376 1.06e-66 207
Msa0700440 MtrunA17_Chr8g0377801 54.502 211 55 4 3 172 179 389 5.45e-66 206
Msa0700440 MtrunA17_Chr2g0296251 31.544 149 92 1 32 170 250 398 1.05e-15 73.6
Msa0700440 MtrunA17_Chr2g0295731 31.298 131 90 0 41 171 248 378 2.54e-15 72.4
Msa0700440 MtrunA17_Chr2g0296191 30.464 151 95 1 32 172 362 512 3.86e-15 72.4
Msa0700440 MtrunA17_Chr2g0296191 34.454 119 78 0 49 167 876 994 1.71e-13 67.4
Msa0700440 MtrunA17_Chr2g0296211 30.872 149 95 2 30 170 210 358 7.63e-15 70.9
Msa0700440 MtrunA17_Chr2g0296171 34.426 122 80 0 49 170 274 395 2.07e-14 70.1
Msa0700440 MtrunA17_Chr2g0296751 30.328 122 85 0 49 170 8 129 2.81e-14 67.0
Msa0700440 MtrunA17_Chr2g0315731 31.169 154 98 2 22 167 247 400 3.08e-14 69.3
Msa0700440 MtrunA17_Chr2g0296551 32.787 122 82 0 49 170 63 184 3.63e-14 67.4
Msa0700440 MtrunA17_Chr4g0067121 31.298 131 90 0 40 170 250 380 7.65e-14 68.2
Msa0700440 MtrunA17_Chr2g0296151 31.507 146 90 1 35 170 225 370 7.85e-14 68.2
Msa0700440 MtrunA17_Chr2g0296741 31.148 122 84 0 49 170 282 403 8.72e-14 68.2
Msa0700440 MtrunA17_Chr2g0296701 29.932 147 95 2 32 170 10 156 1.36e-13 65.5
Msa0700440 MtrunA17_Chr2g0296121 31.298 131 85 1 45 170 326 456 1.86e-13 67.4
Msa0700440 MtrunA17_Chr2g0286221 30.894 123 84 1 48 170 48 169 2.05e-13 65.1
Msa0700440 MtrunA17_Chr2g0295761 32.743 113 76 0 55 167 274 386 1.05e-12 65.1
Msa0700440 MtrunA17_Chr2g0296721 28.049 164 110 2 15 170 219 382 4.69e-12 63.2
Msa0700440 MtrunA17_Chr8g0339041 35.714 126 76 3 46 168 225 348 7.20e-12 62.4
Msa0700440 MtrunA17_Chr2g0296131 29.752 121 85 0 48 168 40 160 7.79e-12 60.5
Msa0700440 MtrunA17_Chr2g0296711 29.508 122 86 0 49 170 265 386 8.35e-12 62.4
Msa0700440 MtrunA17_Chr2g0296291 33.607 122 81 0 49 170 277 398 8.57e-12 62.4
Msa0700440 MtrunA17_Chr2g0296221 31.148 122 84 0 49 170 293 414 2.13e-11 61.2
Msa0700440 MtrunA17_Chr2g0286191 30.328 122 84 1 49 170 239 359 3.40e-11 60.5
Msa0700440 MtrunA17_Chr4g0067141 31.667 120 82 0 50 169 252 371 3.97e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0700440 AT5G64950.1 36.957 138 77 3 40 172 248 380 1.62e-20 87.4
Msa0700440 AT1G21150.3 33.099 142 86 3 32 164 206 347 1.00e-16 76.6
Msa0700440 AT1G21150.1 33.099 142 86 3 32 164 242 383 1.06e-16 76.6
Msa0700440 AT1G21150.2 33.099 142 86 3 32 164 306 447 1.36e-16 76.6
Msa0700440 AT5G07900.1 32.174 115 78 0 55 169 287 401 7.22e-14 68.6
Msa0700440 AT1G61970.2 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61970.7 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61970.6 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61970.3 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61970.5 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61970.4 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61970.1 31.250 144 88 4 21 153 256 399 1.15e-12 65.5
Msa0700440 AT1G61990.2 28.662 157 74 3 46 164 249 405 3.17e-12 63.9
Msa0700440 AT1G61990.1 28.662 157 74 3 46 164 249 405 3.17e-12 63.9
Msa0700440 AT1G61960.1 29.323 133 88 2 44 170 322 454 2.46e-11 61.6
Msa0700440 AT1G56380.1 31.967 122 74 3 47 159 253 374 4.96e-11 60.5
Msa0700440 AT1G56380.2 31.967 122 74 3 47 159 264 385 5.22e-11 60.5

Find 29 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGATACCCTAAGCAAATT+TGG 0.167535 4_4:+71489646 None:intergenic
CTTGATTTCATTCAGCGTTT+TGG 0.212498 4_4:-71489709 Msa0700440:CDS
AACAATGCCACAACTCTCTA+AGG 0.240848 4_4:+71489906 None:intergenic
GAGCTTGCAAATGTTCAAAA+AGG 0.301950 4_4:-71489671 Msa0700440:CDS
TAGAGAGTTGTGGCATTGTT+GGG 0.304274 4_4:-71489903 Msa0700440:CDS
TTTATCTGAGGACACGTTCT+TGG 0.315238 4_4:-71489434 Msa0700440:CDS
TTGTGGCATTGTTGGGGATC+AGG 0.331357 4_4:-71489896 Msa0700440:CDS
AAAAGGTTCCAAATTTGCTT+AGG 0.354562 4_4:-71489654 Msa0700440:CDS
GGTATCAGAGAAGAAGATAA+AGG 0.405797 4_4:-71489632 Msa0700440:CDS
CAAAGTCAGCATTGGTTACT+CGG 0.409355 4_4:-71489573 Msa0700440:CDS
TTAGAGAGTTGTGGCATTGT+TGG 0.418272 4_4:-71489904 Msa0700440:CDS
CTCTAAGGGCAACAAATGTT+TGG 0.420557 4_4:+71489921 None:intergenic
AAAGGTTCCAAATTTGCTTA+GGG 0.440166 4_4:-71489653 Msa0700440:CDS
CGAGTAACCAATGCTGACTT+TGG 0.457799 4_4:+71489574 None:intergenic
TTTAACACATAAAGAAAGCT+TGG 0.468094 4_4:+71489457 None:intergenic
TCAGAGAAGAAGATAAAGGT+TGG 0.472055 4_4:-71489628 Msa0700440:CDS
GGCATTATTGATAGCTTACA+AGG 0.499504 4_4:-71489377 Msa0700440:CDS
ATCACAAAATCTATGTAAGA+AGG 0.510006 4_4:-71489482 Msa0700440:CDS
AGAGAGTTGTGGCATTGTTG+GGG 0.519144 4_4:-71489902 Msa0700440:CDS
GCAACAAATGTTTGGTACAC+TGG 0.546385 4_4:+71489929 None:intergenic
TTATGTGTTAAATTTATCTG+AGG 0.573104 4_4:-71489446 Msa0700440:CDS
TATGCTGCCAAAGTCAGCAT+TGG 0.579046 4_4:-71489581 Msa0700440:CDS
TTGTTGCCCTTAGAGAGTTG+TGG 0.581308 4_4:-71489913 Msa0700440:CDS
ACAATGCCACAACTCTCTAA+GGG 0.616141 4_4:+71489907 None:intergenic
TAGTTTCTAATACGAGATTG+TGG 0.627705 4_4:+71489835 None:intergenic
ATGCTATACATCAAAATCAG+AGG 0.630674 4_4:+71489550 None:intergenic
CATTATTGATAGCTTACAAG+GGG 0.646556 4_4:-71489375 Msa0700440:CDS
GCATTATTGATAGCTTACAA+GGG 0.653907 4_4:-71489376 Msa0700440:CDS
AAAGTTTAAAGAAAATGCAG+AGG 0.668498 4_4:-71489398 Msa0700440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGTGTTAAATTTATCTG+AGG - chr4_4:71489885-71489904 Msa0700440:CDS 20.0%
!!! GCTTTTTCCTAAATGTTTTA+TGG + chr4_4:71489603-71489622 None:intergenic 25.0%
! AAAGCTGAAAAACTCTAAAT+CGG + chr4_4:71489825-71489844 None:intergenic 25.0%
! ATCACAAAATCTATGTAAGA+AGG - chr4_4:71489849-71489868 Msa0700440:CDS 25.0%
! TTTAACACATAAAGAAAGCT+TGG + chr4_4:71489877-71489896 None:intergenic 25.0%
!! TCTGCATTTTCTTTAAACTT+TGG + chr4_4:71489934-71489953 None:intergenic 25.0%
! AAAGTTTAAAGAAAATGCAG+AGG - chr4_4:71489933-71489952 Msa0700440:CDS 25.0%
TAGTTTCTAATACGAGATTG+TGG + chr4_4:71489499-71489518 None:intergenic 30.0%
! TGTTTTGCAAGCTGAAAAAT+TGG - chr4_4:71489519-71489538 Msa0700440:CDS 30.0%
! GTTTTGCAAGCTGAAAAATT+GGG - chr4_4:71489520-71489539 Msa0700440:CDS 30.0%
! CAAGCATTCTTGAATTTTGA+TGG + chr4_4:71489549-71489568 None:intergenic 30.0%
GTTTGAGCCATAAAACATTT+AGG - chr4_4:71489593-71489612 Msa0700440:CDS 30.0%
! TTGATTTCATTCAGCGTTTT+GGG - chr4_4:71489623-71489642 Msa0700440:CDS 30.0%
! AAAAGGTTCCAAATTTGCTT+AGG - chr4_4:71489677-71489696 Msa0700440:CDS 30.0%
! AAAGGTTCCAAATTTGCTTA+GGG - chr4_4:71489678-71489697 Msa0700440:CDS 30.0%
ATGCTATACATCAAAATCAG+AGG + chr4_4:71489784-71489803 None:intergenic 30.0%
!! TCTGATTTTGATGTATAGCA+TGG - chr4_4:71489783-71489802 Msa0700440:intron 30.0%
AAGCTGAAAAACTCTAAATC+GGG + chr4_4:71489824-71489843 None:intergenic 30.0%
! GCATTATTGATAGCTTACAA+GGG - chr4_4:71489955-71489974 Msa0700440:CDS 30.0%
! CATTATTGATAGCTTACAAG+GGG - chr4_4:71489956-71489975 Msa0700440:CDS 30.0%
!!! AATCAAGTTTTGAGCTACTG+TGG - chr4_4:71489369-71489388 Msa0700440:CDS 35.0%
! CTTGATTTCATTCAGCGTTT+TGG - chr4_4:71489622-71489641 Msa0700440:CDS 35.0%
GAGCTTGCAAATGTTCAAAA+AGG - chr4_4:71489660-71489679 Msa0700440:CDS 35.0%
TCTGATACCCTAAGCAAATT+TGG + chr4_4:71489688-71489707 None:intergenic 35.0%
GGTATCAGAGAAGAAGATAA+AGG - chr4_4:71489699-71489718 Msa0700440:CDS 35.0%
TCAGAGAAGAAGATAAAGGT+TGG - chr4_4:71489703-71489722 Msa0700440:CDS 35.0%
!! GATTTTGATGTATAGCATGG+AGG - chr4_4:71489786-71489805 Msa0700440:intron 35.0%
AGCTGAAAAACTCTAAATCG+GGG + chr4_4:71489823-71489842 None:intergenic 35.0%
! GGCATTATTGATAGCTTACA+AGG - chr4_4:71489954-71489973 Msa0700440:CDS 35.0%
GCAACAAATGTTTGGTACAC+TGG + chr4_4:71489405-71489424 None:intergenic 40.0%
! CTCTAAGGGCAACAAATGTT+TGG + chr4_4:71489413-71489432 None:intergenic 40.0%
ACAATGCCACAACTCTCTAA+GGG + chr4_4:71489427-71489446 None:intergenic 40.0%
AACAATGCCACAACTCTCTA+AGG + chr4_4:71489428-71489447 None:intergenic 40.0%
TTAGAGAGTTGTGGCATTGT+TGG - chr4_4:71489427-71489446 Msa0700440:CDS 40.0%
TAGAGAGTTGTGGCATTGTT+GGG - chr4_4:71489428-71489447 Msa0700440:CDS 40.0%
!! CAAAGTCAGCATTGGTTACT+CGG - chr4_4:71489758-71489777 Msa0700440:intron 40.0%
TTTATCTGAGGACACGTTCT+TGG - chr4_4:71489897-71489916 Msa0700440:CDS 40.0%
!!! AAGTTTTGAGCTACTGTGGC+TGG - chr4_4:71489373-71489392 Msa0700440:CDS 45.0%
TTGTTGCCCTTAGAGAGTTG+TGG - chr4_4:71489418-71489437 Msa0700440:CDS 45.0%
AGAGAGTTGTGGCATTGTTG+GGG - chr4_4:71489429-71489448 Msa0700440:CDS 45.0%
TATGCTGCCAAAGTCAGCAT+TGG - chr4_4:71489750-71489769 Msa0700440:intron 45.0%
!! CGAGTAACCAATGCTGACTT+TGG + chr4_4:71489760-71489779 None:intergenic 45.0%
TTGTGGCATTGTTGGGGATC+AGG - chr4_4:71489435-71489454 Msa0700440:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 71489363 71489990 71489363 ID=Msa0700440;Name=Msa0700440
chr4_4 mRNA 71489363 71489990 71489363 ID=Msa0700440-mRNA-1;Parent=Msa0700440;Name=Msa0700440-mRNA-1;_AED=0.44;_eAED=0.45;_QI=0|0|0|1|0|0|2|0|172
chr4_4 exon 71489848 71489990 71489848 ID=Msa0700440-mRNA-1:exon:21815;Parent=Msa0700440-mRNA-1
chr4_4 exon 71489363 71489738 71489363 ID=Msa0700440-mRNA-1:exon:21814;Parent=Msa0700440-mRNA-1
chr4_4 CDS 71489848 71489990 71489848 ID=Msa0700440-mRNA-1:cds;Parent=Msa0700440-mRNA-1
chr4_4 CDS 71489363 71489738 71489363 ID=Msa0700440-mRNA-1:cds;Parent=Msa0700440-mRNA-1
Gene Sequence

>Msa0700440

ATGAGAAATCAAGTTTTGAGCTACTGTGGCTGGCTACTACCAGTGTACCAAACATTTGTTGCCCTTAGAGAGTTGTGGCATTGTTGGGGATCAGGTTTTGATTTTAATCAAACATTCAAGACTTTTGACTGCACCACAATCTCGAAAAAGCTTGATTTCATTCAGCGTTTTGGGTTTTCTAAAGATGAGAGCTTGCAAATGTTCAAAAAGGTTCCAAATTTGCTTAGGGTATCAGAGAAGAAGATAAAGGTTGGAATTAAGTTCTTCTTAGATACAGTTATGCTGCCAAAGTCAGCATTGGTTACTCGGCCTCTGATTTTGATGTATAGCATGGAGGATCGAGTGTTTCCCCGATTTAGAGTTTTTCAGCTTTTGAAATCACAAAATCTATGTAAGAAGGTTCCAAGCTTTCTTTATGTGTTAAATTTATCTGAGGACACGTTCTTGGACAAGTTTATACCAAAGTTTAAAGAAAATGCAGAGGCATTATTGATAGCTTACAAGGGGCGTTGTCTATAA
Protein sequence

>Msa0700440

MRNQVLSYCGWLLPVYQTFVALRELWHCWGSGFDFNQTFKTFDCTTISKKLDFIQRFGFSKDESLQMFKKVPNLLRVSEKKIKVGIKFFLDTVMLPKSALVTRPLILMYSMEDRVFPRFRVFQLLKSQNLCKKVPSFLYVLNLSEDTFLDKFIPKFKENAEALLIAYKGRCL*