AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69258

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69258.t1 MTR_3g070110 92.593 216 16 0 30 245 1 216 5.09e-140 391
MS.gene69258.t1 MTR_5g081860 40.764 157 79 6 50 200 48 196 2.76e-19 84.7
MS.gene69258.t1 MTR_5g088010 57.143 77 27 4 121 196 57 128 1.17e-16 77.0
MS.gene69258.t1 MTR_5g069710 36.434 129 69 2 78 200 80 201 4.92e-16 76.3
MS.gene69258.t1 MTR_3g462790 32.967 182 99 4 19 200 58 216 1.02e-15 75.5
MS.gene69258.t1 MTR_5g027570 37.778 135 72 5 67 196 32 159 2.82e-15 73.2
MS.gene69258.t1 MTR_8g063600 33.133 166 95 6 38 196 17 173 3.49e-15 73.6
MS.gene69258.t1 MTR_5g027550 44.828 87 40 4 90 169 37 122 6.31e-15 72.0
MS.gene69258.t1 MTR_7g067080 39.823 113 54 3 88 200 111 209 1.51e-14 72.0
MS.gene69258.t1 MTR_5g088060 57.534 73 25 4 125 196 273 340 5.93e-14 71.2
MS.gene69258.t1 MTR_5g488160 57.534 73 25 4 125 196 273 340 5.93e-14 71.2
MS.gene69258.t1 MTR_8g063870 38.298 141 65 6 61 199 42 162 1.30e-13 68.9
MS.gene69258.t1 MTR_3g104370 37.607 117 57 2 79 195 58 158 1.91e-13 67.8
MS.gene69258.t1 MTR_1g048660 57.407 54 23 0 116 169 4 57 2.89e-13 64.3
MS.gene69258.t1 MTR_1g111830 28.655 171 95 4 29 199 49 192 2.19e-12 65.1
MS.gene69258.t1 MTR_4g107230 32.479 117 67 2 53 169 25 129 4.04e-12 65.1
MS.gene69258.t1 MTR_6g092540 36.923 130 58 6 112 241 87 192 3.61e-11 62.0
MS.gene69258.t1 MTR_2g090305 45.333 75 34 2 123 197 27 94 5.63e-11 60.5
MS.gene69258.t1 MTR_4g100630 35.714 112 53 2 88 199 71 163 7.71e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69258.t1 AT5G05790 40.625 128 64 3 78 201 82 201 1.72e-18 82.8
MS.gene69258.t1 AT5G05790 40.625 128 64 3 78 201 82 201 1.72e-18 82.8
MS.gene69258.t1 AT3G11280 35.326 184 91 9 25 201 35 197 1.17e-17 80.1
MS.gene69258.t1 AT3G11280 35.326 184 91 9 25 201 35 197 1.17e-17 80.1
MS.gene69258.t1 AT5G01200 44.444 117 51 4 85 200 112 215 6.95e-17 78.2
MS.gene69258.t1 AT2G38090 36.207 116 64 2 88 200 102 210 3.21e-15 73.9
MS.gene69258.t1 AT5G58900 43.617 94 46 1 107 200 124 210 7.97e-15 72.8
MS.gene69258.t1 AT5G08520 36.571 175 82 11 41 198 23 185 2.12e-14 71.6
MS.gene69258.t1 AT4G09450 39.024 123 62 4 99 215 66 181 7.50e-13 65.9
MS.gene69258.t1 AT5G04760 48.101 79 34 2 121 199 96 167 3.96e-12 63.9
MS.gene69258.t1 AT1G19000 49.123 57 29 0 113 169 91 147 9.11e-12 63.9
MS.gene69258.t1 AT1G19000 49.123 57 29 0 113 169 91 147 9.11e-12 63.9
MS.gene69258.t1 AT5G47390 35.115 131 67 3 115 245 87 199 1.36e-11 63.9
MS.gene69258.t1 AT1G70000 39.726 73 42 1 99 169 71 143 2.66e-11 62.4
MS.gene69258.t1 AT1G70000 39.726 73 42 1 99 169 71 143 2.66e-11 62.4
MS.gene69258.t1 AT3G10580 45.570 79 34 1 121 199 92 161 5.80e-11 61.6
MS.gene69258.t1 AT3G10580 45.570 79 34 1 121 199 92 161 6.03e-11 61.2
MS.gene69258.t1 AT1G49010 44.304 79 37 2 121 199 131 202 9.00e-11 61.2

Find 34 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGATCTTGATCACATTCT+TGG 0.190525 3.2:-63854856 None:intergenic
TCAACCAATAATCATCTTCT+TGG 0.216049 3.2:-63854189 None:intergenic
AGTTCTATTGTTATTGTTAT+CGG 0.227795 3.2:-63854356 None:intergenic
ATTTCCAAGAAGATGATTAT+TGG 0.238910 3.2:+63854185 MS.gene69258:CDS
GACTCATATGCGTGGTTATT+TGG 0.243758 3.2:+63854773 MS.gene69258:CDS
ATAACTACTCTTGATCTTCT+TGG 0.251399 3.2:+63854743 MS.gene69258:CDS
TTTGAGCATGGCTTGCTACT+TGG 0.356659 3.2:-63854640 None:intergenic
AAAATATCAAAAGGAAACTT+AGG 0.373972 3.2:+63854705 MS.gene69258:CDS
AGAATGGTAGAGAATATTCT+AGG 0.388611 3.2:+63854136 MS.gene69258:CDS
TTGAGCATGGCTTGCTACTT+GGG 0.417939 3.2:-63854639 None:intergenic
TATTTGTAGGCGTTTCTTGA+AGG 0.450413 3.2:+63854547 MS.gene69258:intron
AAAGTGGAAAGAAATCTCTA+AGG 0.460560 3.2:+63854592 MS.gene69258:CDS
TCAAACTCAAATAATAGTTA+TGG 0.460594 3.2:+63854082 MS.gene69258:CDS
AAATATCAAAAGGAAACTTA+GGG 0.461487 3.2:+63854706 MS.gene69258:CDS
AGATGATTATTGGTTGATGA+AGG 0.467158 3.2:+63854195 MS.gene69258:CDS
AAAGAAATCATTCAAGAAAG+TGG 0.476326 3.2:+63854399 MS.gene69258:CDS
ATTTGTAGGCGTTTCTTGAA+GGG 0.494586 3.2:+63854548 MS.gene69258:intron
GATCAAGAGTAGTTATATCA+TGG 0.499404 3.2:-63854736 None:intergenic
GCATGGCTTGCTACTTGGGA+TGG 0.505418 3.2:-63854635 None:intergenic
TACACGGCAAAGACAGAAAG+TGG 0.505479 3.2:+63854576 MS.gene69258:CDS
TGTTGTCGTCTTCAATCACT+TGG 0.511632 3.2:-63854799 None:intergenic
CATTCAAGAAAGTGGTCCAT+TGG 0.520016 3.2:+63854407 MS.gene69258:CDS
CATCGAAGAAAGTAGTAGAA+TGG 0.523965 3.2:+63854120 MS.gene69258:CDS
CAATAGAACTACGAATATTG+TGG 0.554412 3.2:+63854369 MS.gene69258:CDS
TGTGTTCATCACGTGACCAA+TGG 0.573216 3.2:-63854423 None:intergenic
GCTCAGCATTAACAATGGAA+TGG 0.581833 3.2:+63854038 None:intergenic
ATACATATGAACATATCAAG+TGG 0.590413 3.2:-63854891 None:intergenic
TTCTTGAAGGGACTTCTACA+CGG 0.594579 3.2:+63854560 MS.gene69258:CDS
GAAGACGACAACAATAACAA+TGG 0.605151 3.2:+63854809 MS.gene69258:CDS
TCAGCACAACATCGATGAAG+TGG 0.609150 3.2:+63854249 MS.gene69258:CDS
TTATTGTTATCGGTTGCATG+AGG 0.640753 3.2:-63854346 None:intergenic
GCACAACATCGATGAAGTGG+TGG 0.668571 3.2:+63854252 MS.gene69258:CDS
AATATCAAAAGGAAACTTAG+GGG 0.670754 3.2:+63854707 MS.gene69258:CDS
GAAGTGATGACTCATATGCG+TGG 0.764866 3.2:+63854765 MS.gene69258:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATATCAAAAGGAAACTT+AGG + chr3.2:63854705-63854724 MS.gene69258:CDS 20.0%
!! AAATATCAAAAGGAAACTTA+GGG + chr3.2:63854706-63854725 MS.gene69258:CDS 20.0%
!! ATGATAGCAAAAATATCAAA+AGG + chr3.2:63854696-63854715 MS.gene69258:CDS 20.0%
!! TCAAACTCAAATAATAGTTA+TGG + chr3.2:63854082-63854101 MS.gene69258:CDS 20.0%
!!! AGTTCTATTGTTATTGTTAT+CGG - chr3.2:63854359-63854378 None:intergenic 20.0%
!!! TTTCTTGAATGATTTCTTTT+TGG - chr3.2:63854398-63854417 None:intergenic 20.0%
! AAAGAAATCATTCAAGAAAG+TGG + chr3.2:63854399-63854418 MS.gene69258:CDS 25.0%
! AATATCAAAAGGAAACTTAG+GGG + chr3.2:63854707-63854726 MS.gene69258:CDS 25.0%
! ATTTCCAAGAAGATGATTAT+TGG + chr3.2:63854185-63854204 MS.gene69258:CDS 25.0%
! GAAACAATAAACGATGAAAA+AGG - chr3.2:63854456-63854475 None:intergenic 25.0%
!!! GACATGGATTTTTTATTTGT+AGG + chr3.2:63854534-63854553 MS.gene69258:intron 25.0%
AAAGTGGAAAGAAATCTCTA+AGG + chr3.2:63854592-63854611 MS.gene69258:CDS 30.0%
AGAATGGTAGAGAATATTCT+AGG + chr3.2:63854136-63854155 MS.gene69258:CDS 30.0%
ATAACTACTCTTGATCTTCT+TGG + chr3.2:63854743-63854762 MS.gene69258:CDS 30.0%
CAATAGAACTACGAATATTG+TGG + chr3.2:63854369-63854388 MS.gene69258:CDS 30.0%
GATCAAGAGTAGTTATATCA+TGG - chr3.2:63854739-63854758 None:intergenic 30.0%
TCAACCAATAATCATCTTCT+TGG - chr3.2:63854192-63854211 None:intergenic 30.0%
! ATGCTCAAAAGTACGAAAAA+AGG + chr3.2:63854654-63854673 MS.gene69258:CDS 30.0%
!! AGATGATTATTGGTTGATGA+AGG + chr3.2:63854195-63854214 MS.gene69258:CDS 30.0%
!!! TTTTTTCGTACTTTTGAGCA+TGG - chr3.2:63854655-63854674 None:intergenic 30.0%
ATTTGTAGGCGTTTCTTGAA+GGG + chr3.2:63854548-63854567 MS.gene69258:intron 35.0%
CATCGAAGAAAGTAGTAGAA+TGG + chr3.2:63854120-63854139 MS.gene69258:CDS 35.0%
CATGATCTTGATCACATTCT+TGG - chr3.2:63854859-63854878 None:intergenic 35.0%
GAAGACGACAACAATAACAA+TGG + chr3.2:63854809-63854828 MS.gene69258:CDS 35.0%
TATTTGTAGGCGTTTCTTGA+AGG + chr3.2:63854547-63854566 MS.gene69258:intron 35.0%
! TTATTGTTATCGGTTGCATG+AGG - chr3.2:63854349-63854368 None:intergenic 35.0%
CATTCAAGAAAGTGGTCCAT+TGG + chr3.2:63854407-63854426 MS.gene69258:CDS 40.0%
GACTCATATGCGTGGTTATT+TGG + chr3.2:63854773-63854792 MS.gene69258:CDS 40.0%
TGTTGTCGTCTTCAATCACT+TGG - chr3.2:63854802-63854821 None:intergenic 40.0%
TTCTTGAAGGGACTTCTACA+CGG + chr3.2:63854560-63854579 MS.gene69258:CDS 40.0%
GAAGTGATGACTCATATGCG+TGG + chr3.2:63854765-63854784 MS.gene69258:CDS 45.0%
TACACGGCAAAGACAGAAAG+TGG + chr3.2:63854576-63854595 MS.gene69258:CDS 45.0%
TCAGCACAACATCGATGAAG+TGG + chr3.2:63854249-63854268 MS.gene69258:CDS 45.0%
TGTGTTCATCACGTGACCAA+TGG - chr3.2:63854426-63854445 None:intergenic 45.0%
!! TCGACGAGCGTTTCACTTTT+TGG + chr3.2:63854292-63854311 MS.gene69258:CDS 45.0%
!! TTGAGCATGGCTTGCTACTT+GGG - chr3.2:63854642-63854661 None:intergenic 45.0%
!! TTTGAGCATGGCTTGCTACT+TGG - chr3.2:63854643-63854662 None:intergenic 45.0%
GCACAACATCGATGAAGTGG+TGG + chr3.2:63854252-63854271 MS.gene69258:CDS 50.0%
GCGCACACATGTGTTTGACA+TGG + chr3.2:63854518-63854537 MS.gene69258:intron 50.0%
!! GCATGGCTTGCTACTTGGGA+TGG - chr3.2:63854638-63854657 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 63854052 63854898 63854052 ID=MS.gene69258
chr3.2 mRNA 63854052 63854898 63854052 ID=MS.gene69258.t1;Parent=MS.gene69258
chr3.2 exon 63854052 63854446 63854052 ID=MS.gene69258.t1.exon1;Parent=MS.gene69258.t1
chr3.2 CDS 63854052 63854446 63854052 ID=cds.MS.gene69258.t1;Parent=MS.gene69258.t1
chr3.2 exon 63854556 63854898 63854556 ID=MS.gene69258.t1.exon2;Parent=MS.gene69258.t1
chr3.2 CDS 63854556 63854898 63854556 ID=cds.MS.gene69258.t1;Parent=MS.gene69258.t1
Gene Sequence

>MS.gene69258

ATGGAATGGATGAATTCTTGTTTGAACTCGTCAAACTCAAATAATAGTTATGGCTACATATATGACAGCATCGAAGAAAGTAGTAGAATGGTAGAGAATATTCTAGGTTACAGTCTTCATAGCATGATGAATAATTTCCAAGAAGATGATTATTGGTTGATGAAGGAAACTATGCTATGTAGTGTTGATCAAATCAATCAGCACAACATCGATGAAGTGGTGGTAGAAAATAATATTGCATCGACGAGCGTTTCACTTTTTGGATATGATTCAGTTGATTCTTTCAACTTCTCTCCTCATGCAACCGATAACAATAACAATAGAACTACGAATATTGTGGAATCCAAAAAGAAATCATTCAAGAAAGTGGTCCATTGGTCACGTGATGAACACATGTAAGTCCTTTTTCATCGTTTATTGTTTCATGTAGTTTGAATTATATCTCTCTTTATATATACACTCGTGCGCGCACACATGTGTTTGACATGGATTTTTTATTTGTAGGCGTTTCTTGAAGGGACTTCTACACGGCAAAGACAGAAAGTGGAAAGAAATCTCTAAGGACTATGTAAAAACAAAGACTCCATCCCAAGTAGCAAGCCATGCTCAAAAGTACGAAAAAAGGCAAAAGCAAAGACTTGATGATGATAGCAAAAATATCAAAAGGAAACTTAGGGGTAGCATCCATGATATAACTACTCTTGATCTTCTTGGAAGTGATGACTCATATGCGTGGTTATTTGGTGACCAAGTGATTGAAGACGACAACAATAACAATGGATCACTCTCAGTCACAACTTTCAACCAAGAATGTGATCAAGATCATGAAGTTGTTGCTTCCACTTGA
Protein sequence

>MS.gene69258.t1

MEWMNSCLNSSNSNNSYGYIYDSIEESSRMVENILGYSLHSMMNNFQEDDYWLMKETMLCSVDQINQHNIDEVVVENNIASTSVSLFGYDSVDSFNFSPHATDNNNNRTTNIVESKKKSFKKVVHWSRDEHMRFLKGLLHGKDRKWKEISKDYVKTKTPSQVASHAQKYEKRQKQRLDDDSKNIKRKLRGSIHDITTLDLLGSDDSYAWLFGDQVIEDDNNNNGSLSVTTFNQECDQDHEVVAST