AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene072838

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072838.t1 MTR_3g106230 85.532 235 27 3 1 235 1 228 2.29e-140 393
MS.gene072838.t1 MTR_1g013130 48.361 244 106 10 5 240 24 255 2.51e-58 186
MS.gene072838.t1 MTR_2g104900 37.449 243 114 14 12 242 20 236 1.33e-28 108
MS.gene072838.t1 MTR_4g006575 37.654 162 69 5 75 233 65 197 1.57e-22 92.4
MS.gene072838.t1 MTR_4g006600 37.654 162 69 5 75 233 65 197 1.57e-22 92.4
MS.gene072838.t1 MTR_1g033340 44.068 118 42 6 54 165 69 168 5.14e-19 83.6
MS.gene072838.t1 MTR_5g077370 50.538 93 26 3 76 167 86 159 3.83e-18 80.9
MS.gene072838.t1 MTR_3g065020 48.913 92 26 4 77 167 86 157 2.71e-17 78.6
MS.gene072838.t1 MTR_1g107055 41.584 101 29 4 71 166 57 132 2.04e-14 69.7
MS.gene072838.t1 MTR_4g128340 73.684 38 10 0 75 112 43 80 6.20e-14 68.2
MS.gene072838.t1 MTR_3g011970 41.837 98 48 4 69 166 90 178 1.77e-13 68.9
MS.gene072838.t1 MTR_8g466760 35.075 134 65 6 51 184 75 186 2.41e-12 65.5
MS.gene072838.t1 MTR_3g009410 35.398 113 52 4 74 176 95 196 3.43e-11 62.4
MS.gene072838.t1 MTR_3g011990 36.364 110 50 4 71 176 92 185 5.19e-11 61.6
MS.gene072838.t1 MTR_5g008280 34.454 119 62 4 77 195 46 148 5.58e-11 62.0
MS.gene072838.t1 MTR_7g022980 35.088 114 56 5 75 184 64 163 8.58e-11 60.8
MS.gene072838.t1 MTR_7g086860 61.538 39 15 0 77 115 30 68 9.34e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072838.t1 AT5G25160 43.871 155 59 8 48 201 37 164 1.12e-26 103
MS.gene072838.t1 AT5G10970 41.558 154 63 6 48 201 79 205 8.23e-24 96.7
MS.gene072838.t1 AT1G80730 40.580 138 73 4 36 166 19 154 5.62e-22 90.9
MS.gene072838.t1 AT1G66140 46.739 92 37 3 77 161 83 169 6.22e-16 75.1
MS.gene072838.t1 AT1G24625 76.316 38 9 0 74 111 54 91 3.36e-15 72.4
MS.gene072838.t1 AT5G57520 65.909 44 15 0 75 118 48 91 1.54e-14 69.3
MS.gene072838.t1 AT5G14010 73.529 34 9 0 77 110 36 69 2.04e-12 63.5
MS.gene072838.t1 AT1G67030 44.944 89 44 3 44 132 7 90 6.58e-11 60.5
MS.gene072838.t1 AT3G58070 64.444 45 16 0 72 116 84 128 6.83e-11 61.2

Find 44 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAATTGAAAGCAATTATTA+TGG 0.211258 3.3:+87195637 MS.gene072838:CDS
TATGAGACCATTTGCAATTA+AGG 0.217801 3.3:+87195564 MS.gene072838:CDS
TCACAACCGTTATGCAAATA+TGG 0.314680 3.3:+87195504 MS.gene072838:CDS
TAGATTCGGAAAGGTTAAAA+AGG 0.319744 3.3:+87195765 MS.gene072838:CDS
GCTACTGATGCAAACTTTCC+AGG 0.343879 3.3:+87195711 MS.gene072838:CDS
CCTAACGATGATTGTGATCT+TGG 0.347148 3.3:+87195214 MS.gene072838:CDS
TTCCAGATTGTTGATTCATA+AGG 0.348814 3.3:-87195681 None:intergenic
TCCAGATTGTTGATTCATAA+GGG 0.359823 3.3:-87195680 None:intergenic
ATTGCAGAATCCACATGAAT+TGG 0.369569 3.3:+87195123 MS.gene072838:CDS
GAATTGAAAGCAATTATTAT+GGG 0.373275 3.3:+87195638 MS.gene072838:CDS
AGAATTATCTATGTCTAAAC+AGG 0.387114 3.3:-87195263 None:intergenic
ATGCAAACTTTCCAGGAAAC+AGG 0.389355 3.3:+87195718 MS.gene072838:CDS
GTGATGGTAATCCTGTTTCC+TGG 0.396510 3.3:-87195729 None:intergenic
TTGGATGAAAATTTATGAAA+AGG 0.404264 3.3:-87195607 None:intergenic
CAAAGTAGTGTTGGTAGATT+CGG 0.411274 3.3:+87195751 MS.gene072838:CDS
AGCAATTATTATGGGTATCA+TGG 0.430203 3.3:+87195646 MS.gene072838:CDS
CCCCTTATGAATCAACAATC+TGG 0.432563 3.3:+87195679 MS.gene072838:CDS
GACATGCTCAATTCAGGAAC+TGG 0.435799 3.3:+87195787 MS.gene072838:CDS
AGAACGATGTTCTCAGCAAC+AGG 0.459446 3.3:+87195448 MS.gene072838:CDS
TTCTTCAGTTCACAAGCACT+TGG 0.470251 3.3:+87195373 MS.gene072838:CDS
CTAACGATGATTGTGATCTT+GGG 0.483992 3.3:+87195215 MS.gene072838:CDS
GCTTTCAATTCCAAAGCCAT+TGG 0.496119 3.3:-87195626 None:intergenic
TCTTCAGTTCACAAGCACTT+GGG 0.508835 3.3:+87195374 MS.gene072838:CDS
CTTCAGTTCACAAGCACTTG+GGG 0.514360 3.3:+87195375 MS.gene072838:CDS
GAGTGTGCCTTAATTGCAAA+TGG 0.520506 3.3:-87195571 None:intergenic
TGCAATTAAGGCACACTCGA+TGG 0.523345 3.3:+87195576 MS.gene072838:CDS
CCAAGATCACAATCATCGTT+AGG 0.527605 3.3:-87195214 None:intergenic
GGAAGAAGAAAAGGAAGCAA+AGG 0.530366 3.3:+87195165 MS.gene072838:CDS
ATGAATCAACAATCTGGAAG+AGG 0.552126 3.3:+87195685 MS.gene072838:CDS
ATGATATTTATGAAGAAATG+AGG 0.554191 3.3:-87195479 None:intergenic
GAGATGCCATATTTGCATAA+CGG 0.557005 3.3:-87195510 None:intergenic
ATTATTATGGGTATCATGGA+TGG 0.573211 3.3:+87195650 MS.gene072838:CDS
TTATGTTTCTCCAATTCATG+TGG 0.577273 3.3:-87195133 None:intergenic
CCAGATTGTTGATTCATAAG+GGG 0.580761 3.3:-87195679 None:intergenic
TAGTGTTGGTAGATTCGGAA+AGG 0.588233 3.3:+87195756 MS.gene072838:CDS
CTCGAAGAGTAATCAACAAG+AGG 0.595525 3.3:+87195816 MS.gene072838:CDS
CTACCAACACTACTTTGTGA+TGG 0.596720 3.3:-87195745 None:intergenic
TTACCATCACAAAGTAGTGT+TGG 0.606864 3.3:+87195742 MS.gene072838:CDS
TCATCAGAAAACTTCACTTG+TGG 0.611490 3.3:+87195295 MS.gene072838:CDS
AAAATGCTCACAAGAGAGAG+AGG 0.643637 3.3:+87195404 MS.gene072838:CDS
TTCAGTTCACAAGCACTTGG+GGG 0.644584 3.3:+87195376 MS.gene072838:CDS
ATATTTATGAAGAAATGAGG+TGG 0.662714 3.3:-87195476 None:intergenic
TTACTATTAGCACAGAAGAG+TGG 0.684083 3.3:-87195538 None:intergenic
ACGATGTTCTCAGCAACAGG+AGG 0.689396 3.3:+87195451 MS.gene072838:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGATATTTATGAAGAAATG+AGG - chr3.3:87195482-87195501 None:intergenic 20.0%
!! GAATTGAAAGCAATTATTAT+GGG + chr3.3:87195638-87195657 MS.gene072838:CDS 20.0%
!! TTGGATGAAAATTTATGAAA+AGG - chr3.3:87195610-87195629 None:intergenic 20.0%
!!! TTTCATAAATTTTCATCCAA+TGG + chr3.3:87195610-87195629 MS.gene072838:CDS 20.0%
! AGAATTATCTATGTCTAAAC+AGG - chr3.3:87195266-87195285 None:intergenic 25.0%
! ATATTTATGAAGAAATGAGG+TGG - chr3.3:87195479-87195498 None:intergenic 25.0%
! GGAATTGAAAGCAATTATTA+TGG + chr3.3:87195637-87195656 MS.gene072838:CDS 25.0%
AGCAATTATTATGGGTATCA+TGG + chr3.3:87195646-87195665 MS.gene072838:CDS 30.0%
ATTATTATGGGTATCATGGA+TGG + chr3.3:87195650-87195669 MS.gene072838:CDS 30.0%
TAGATTCGGAAAGGTTAAAA+AGG + chr3.3:87195765-87195784 MS.gene072838:CDS 30.0%
TATGAGACCATTTGCAATTA+AGG + chr3.3:87195564-87195583 MS.gene072838:CDS 30.0%
TTATGTTTCTCCAATTCATG+TGG - chr3.3:87195136-87195155 None:intergenic 30.0%
! AAATTTTCATCCAATGGCTT+TGG + chr3.3:87195616-87195635 MS.gene072838:CDS 30.0%
! GGAGAAACATAAAACTTTTG+AGG + chr3.3:87195144-87195163 MS.gene072838:CDS 30.0%
!! AACTTTTGAGGAAGAAGAAA+AGG + chr3.3:87195156-87195175 MS.gene072838:CDS 30.0%
!! TCCAGATTGTTGATTCATAA+GGG - chr3.3:87195683-87195702 None:intergenic 30.0%
!! TTCCAGATTGTTGATTCATA+AGG - chr3.3:87195684-87195703 None:intergenic 30.0%
AAAAAGGACATGCTCAATTC+AGG + chr3.3:87195781-87195800 MS.gene072838:CDS 35.0%
ATGAATCAACAATCTGGAAG+AGG + chr3.3:87195685-87195704 MS.gene072838:CDS 35.0%
ATTGCAGAATCCACATGAAT+TGG + chr3.3:87195123-87195142 MS.gene072838:CDS 35.0%
CTAACGATGATTGTGATCTT+GGG + chr3.3:87195215-87195234 MS.gene072838:CDS 35.0%
GAGATGCCATATTTGCATAA+CGG - chr3.3:87195513-87195532 None:intergenic 35.0%
TAGTTGCAAGTGAAAAATCG+TGG - chr3.3:87195340-87195359 None:intergenic 35.0%
TCACAACCGTTATGCAAATA+TGG + chr3.3:87195504-87195523 MS.gene072838:CDS 35.0%
TCATCAGAAAACTTCACTTG+TGG + chr3.3:87195295-87195314 MS.gene072838:CDS 35.0%
TTACCATCACAAAGTAGTGT+TGG + chr3.3:87195742-87195761 MS.gene072838:CDS 35.0%
TTACTATTAGCACAGAAGAG+TGG - chr3.3:87195541-87195560 None:intergenic 35.0%
!! CAAAGTAGTGTTGGTAGATT+CGG + chr3.3:87195751-87195770 MS.gene072838:CDS 35.0%
!! CCAGATTGTTGATTCATAAG+GGG - chr3.3:87195682-87195701 None:intergenic 35.0%
AAAATGCTCACAAGAGAGAG+AGG + chr3.3:87195404-87195423 MS.gene072838:CDS 40.0%
ATGCAAACTTTCCAGGAAAC+AGG + chr3.3:87195718-87195737 MS.gene072838:CDS 40.0%
CCAAGATCACAATCATCGTT+AGG - chr3.3:87195217-87195236 None:intergenic 40.0%
CCCCTTATGAATCAACAATC+TGG + chr3.3:87195679-87195698 MS.gene072838:CDS 40.0%
CCTAACGATGATTGTGATCT+TGG + chr3.3:87195214-87195233 MS.gene072838:CDS 40.0%
CTACCAACACTACTTTGTGA+TGG - chr3.3:87195748-87195767 None:intergenic 40.0%
GAGAGGTCAATTGCAAAAAG+AGG + chr3.3:87195421-87195440 MS.gene072838:CDS 40.0%
GAGTGTGCCTTAATTGCAAA+TGG - chr3.3:87195574-87195593 None:intergenic 40.0%
GCTTTCAATTCCAAAGCCAT+TGG - chr3.3:87195629-87195648 None:intergenic 40.0%
GGAAGAAGAAAAGGAAGCAA+AGG + chr3.3:87195165-87195184 MS.gene072838:CDS 40.0%
GGTCAATTGCAAAAAGAGGA+CGG + chr3.3:87195425-87195444 MS.gene072838:CDS 40.0%
TCTTCAGTTCACAAGCACTT+GGG + chr3.3:87195374-87195393 MS.gene072838:CDS 40.0%
TTCTTCAGTTCACAAGCACT+TGG + chr3.3:87195373-87195392 MS.gene072838:CDS 40.0%
!! TAGTGTTGGTAGATTCGGAA+AGG + chr3.3:87195756-87195775 MS.gene072838:CDS 40.0%
AGAACGATGTTCTCAGCAAC+AGG + chr3.3:87195448-87195467 MS.gene072838:CDS 45.0%
CTTCAGTTCACAAGCACTTG+GGG + chr3.3:87195375-87195394 MS.gene072838:CDS 45.0%
GACATGCTCAATTCAGGAAC+TGG + chr3.3:87195787-87195806 MS.gene072838:CDS 45.0%
GCTACTGATGCAAACTTTCC+AGG + chr3.3:87195711-87195730 MS.gene072838:CDS 45.0%
GTGATGGTAATCCTGTTTCC+TGG - chr3.3:87195732-87195751 None:intergenic 45.0%
TGCAATTAAGGCACACTCGA+TGG + chr3.3:87195576-87195595 MS.gene072838:CDS 45.0%
TTCAGTTCACAAGCACTTGG+GGG + chr3.3:87195376-87195395 MS.gene072838:CDS 45.0%
ACGATGTTCTCAGCAACAGG+AGG + chr3.3:87195451-87195470 MS.gene072838:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 87195112 87195837 87195112 ID=MS.gene072838
chr3.3 mRNA 87195112 87195837 87195112 ID=MS.gene072838.t1;Parent=MS.gene072838
chr3.3 exon 87195112 87195837 87195112 ID=MS.gene072838.t1.exon1;Parent=MS.gene072838.t1
chr3.3 CDS 87195112 87195837 87195112 ID=cds.MS.gene072838.t1;Parent=MS.gene072838.t1
Gene Sequence

>MS.gene072838

ATGGAAATATCATTGCAGAATCCACATGAATTGGAGAAACATAAAACTTTTGAGGAAGAAGAAAAGGAAGCAAAGGTAGACACTTCATTTGATCTGAATGTTCCTAACGATGATTGTGATCTTGGGTGCAGTTTAAAGTCAAATTTAGTTACCTGTTTAGACATAGATAATTCTTCTAAAACATCATCAGAAAACTTCACTTGTGGCTCTGAATCAACTTCAGAGCCACGATTTTTCACTTGCAACTACTGCAAGAGAAAATTCTTCAGTTCACAAGCACTTGGGGGACATCAAAATGCTCACAAGAGAGAGAGGTCAATTGCAAAAAGAGGACGGAGAACGATGTTCTCAGCAACAGGAGGAACCACCTCATTTCTTCATAAATATCATCTTCACAACCGTTATGCAAATATGGCATCTCTACTACCACTCTTCTGTGCTAATAGTAATAGTATGAGACCATTTGCAATTAAGGCACACTCGATGGTTCAGAAGCCTTTTCATAAATTTTCATCCAATGGCTTTGGAATTGAAAGCAATTATTATGGGTATCATGGATGGTCAAGACCCCTTATGAATCAACAATCTGGAAGAGGAAAGCTACTGATGCAAACTTTCCAGGAAACAGGATTACCATCACAAAGTAGTGTTGGTAGATTCGGAAAGGTTAAAAAGGACATGCTCAATTCAGGAACTGGTTTGAACTCGAAGAGTAATCAACAAGAG
Protein sequence

>MS.gene072838.t1

MEISLQNPHELEKHKTFEEEEKEAKVDTSFDLNVPNDDCDLGCSLKSNLVTCLDIDNSSKTSSENFTCGSESTSEPRFFTCNYCKRKFFSSQALGGHQNAHKRERSIAKRGRRTMFSATGGTTSFLHKYHLHNRYANMASLLPLFCANSNSMRPFAIKAHSMVQKPFHKFSSNGFGIESNYYGYHGWSRPLMNQQSGRGKLLMQTFQETGLPSQSSVGRFGKVKKDMLNSGTGLNSKSNQQE