AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044458

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044458.t1 MTR_4g109660 98.148 162 2 1 1 161 1 162 6.34e-103 301
MS.gene044458.t1 MTR_4g109660 90.476 84 8 0 161 244 222 305 5.53e-45 153
MS.gene044458.t1 MTR_3g026050 70.455 132 35 3 4 132 3 133 8.66e-55 181
MS.gene044458.t1 MTR_7g015010 60.504 119 44 2 1 117 1 118 1.75e-43 150
MS.gene044458.t1 MTR_6g015350 71.429 84 24 0 38 121 31 114 7.75e-38 135
MS.gene044458.t1 MTR_8g463380 52.809 89 42 0 29 117 27 115 1.60e-22 95.9
MS.gene044458.t1 MTR_4g079580 54.321 81 37 0 49 129 15 95 2.69e-22 94.0
MS.gene044458.t1 MTR_2g090960 60.870 69 27 0 49 117 17 85 1.37e-21 92.0
MS.gene044458.t1 MTR_2g078200 58.824 68 28 0 50 117 14 81 2.05e-20 88.2
MS.gene044458.t1 MTR_1g103380 50.000 60 30 0 55 114 200 259 1.39e-12 67.0
MS.gene044458.t1 MTR_7g018500 49.123 57 29 0 58 114 122 178 1.91e-12 66.6
MS.gene044458.t1 MTR_6g017055 48.276 58 30 0 57 114 127 184 2.48e-12 66.2
MS.gene044458.t1 MTR_4g111935 48.276 58 30 0 57 114 133 190 5.25e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044458.t1 AT5G60970 80.682 88 16 1 39 125 45 132 1.26e-46 159
MS.gene044458.t1 AT3G02150 48.171 164 75 4 10 163 28 191 1.39e-41 144
MS.gene044458.t1 AT3G02150 48.780 164 74 4 10 163 28 191 5.01e-41 144
MS.gene044458.t1 AT5G08070 75.610 82 20 0 44 125 21 102 3.46e-40 139
MS.gene044458.t1 AT5G08070 75.610 82 20 0 44 125 21 102 3.46e-40 139
MS.gene044458.t1 AT1G30210 55.752 113 44 3 8 118 4 112 1.31e-30 116
MS.gene044458.t1 AT1G30210 55.752 113 44 3 8 118 4 112 1.31e-30 116
MS.gene044458.t1 AT4G18390 68.493 73 23 0 46 118 32 104 1.03e-28 112
MS.gene044458.t1 AT4G18390 68.493 73 23 0 46 118 32 104 1.03e-28 112
MS.gene044458.t1 AT1G53230 56.790 81 32 1 49 126 42 122 1.80e-23 98.2
MS.gene044458.t1 AT1G53230 56.790 81 32 1 49 126 42 122 1.80e-23 98.2
MS.gene044458.t1 AT3G15030 60.870 69 27 0 49 117 38 106 2.59e-22 95.1
MS.gene044458.t1 AT3G15030 60.870 69 27 0 49 117 38 106 2.59e-22 95.1
MS.gene044458.t1 AT3G15030 60.870 69 27 0 49 117 38 106 2.59e-22 95.1
MS.gene044458.t1 AT3G15030 60.870 69 27 0 49 117 38 106 2.59e-22 95.1
MS.gene044458.t1 AT2G31070 60.606 66 26 0 49 114 22 87 1.08e-20 90.1
MS.gene044458.t1 AT1G68800 46.269 67 36 0 48 114 104 170 8.68e-15 73.2
MS.gene044458.t1 AT1G68800 46.269 67 36 0 48 114 104 170 9.31e-15 73.2
MS.gene044458.t1 AT1G67260 41.429 70 41 0 45 114 76 145 6.43e-14 70.9
MS.gene044458.t1 AT1G67260 41.429 70 41 0 45 114 76 145 6.43e-14 70.9
MS.gene044458.t1 AT1G67260 41.429 70 41 0 45 114 76 145 7.71e-14 70.5
MS.gene044458.t1 AT3G18550 39.024 82 49 1 33 114 126 206 2.17e-12 66.6
MS.gene044458.t1 AT3G18550 39.024 82 49 1 33 114 126 206 2.42e-12 66.2
MS.gene044458.t1 AT3G18550 39.024 82 49 1 33 114 126 206 2.42e-12 66.2
MS.gene044458.t1 AT3G18550 39.024 82 49 1 33 114 126 206 2.90e-12 66.2

Find 45 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCTAAACGGCGAATTTAT+TGG 0.202116 8.1:+16009119 None:intergenic
CGTGACACTCTCACTATTCT+TGG 0.252002 8.1:+16009830 None:intergenic
TACTACCTGGTTGCTGAAAT+AGG 0.258592 8.1:+16009579 None:intergenic
CTACCATAACTACCCATTTC+TGG 0.267833 8.1:+16009046 None:intergenic
AGCAAAGTTTGCACAATTAG+AGG 0.305586 8.1:-16009782 MS.gene044458:CDS
TGATGTAGCTATTGCTTTGT+TGG 0.307657 8.1:+16009877 None:intergenic
GTGAGAGTGTCACGTTCTTT+AGG 0.317533 8.1:-16009821 MS.gene044458:CDS
GATGATAATAACACCAGAAA+TGG 0.330153 8.1:-16009059 MS.gene044458:CDS
AATTCACTACTTTCCATTGA+TGG 0.341892 8.1:+16009215 None:intergenic
TGTGAATTACAAGATGAATT+AGG 0.346372 8.1:+16009299 None:intergenic
GATTAAGAGACCGTAGGATT+AGG 0.348209 8.1:-16009760 MS.gene044458:CDS
ACTACCTGGTTGCTGAAATA+GGG 0.363637 8.1:+16009580 None:intergenic
TTTATTGGAAGATGAATAGT+TGG 0.406511 8.1:+16009134 None:intergenic
AGAAGCTGAAAGTTCAGAAA+AGG 0.433467 8.1:-16009504 MS.gene044458:CDS
TACTCTGAATGCTCCATCAA+TGG 0.441615 8.1:-16009228 MS.gene044458:CDS
GTTCAAGATTTGAACATGGT+TGG 0.449373 8.1:+16009181 None:intergenic
TATGGTATGAATCAAACTAA+AGG 0.451228 8.1:-16009530 MS.gene044458:CDS
AACCTAGCAAAGTTGTTGAA+TGG 0.462940 8.1:-16009679 MS.gene044458:CDS
AGTGTTGGATGGCGTCTAAA+CGG 0.463809 8.1:+16009107 None:intergenic
ATCATCTGAATCAAGAAGCT+TGG 0.472188 8.1:+16009076 None:intergenic
TGAACATGGTTGGATTGTCT+TGG 0.473682 8.1:+16009191 None:intergenic
ATGATAATAACACCAGAAAT+GGG 0.506853 8.1:-16009058 MS.gene044458:CDS
ATGAAAGAACCATTACTTGA+GGG 0.508573 8.1:+16009158 None:intergenic
AGAAGGTGAACATGGAAGAA+TGG 0.508923 8.1:-16009915 MS.gene044458:CDS
TGTTGTTGAGTGAAACTTTG+AGG 0.510713 8.1:+16009605 None:intergenic
AACCATTCAACAACTTTGCT+AGG 0.525009 8.1:+16009677 None:intergenic
GAAGCTGAAAGTTCAGAAAA+GGG 0.530447 8.1:-16009503 MS.gene044458:intron
AGCTTGGAACTAAACAGTGT+TGG 0.544286 8.1:+16009092 None:intergenic
TATGATCTTCAAGACAGACT+TGG 0.562288 8.1:-16009710 MS.gene044458:CDS
ATCTTGAACCCCTCAAGTAA+TGG 0.568276 8.1:-16009167 MS.gene044458:CDS
AGAGTGTCACGTTCTTTAGG+AGG 0.573587 8.1:-16009818 MS.gene044458:CDS
TCATATAGCTGAATTGCTGT+TGG 0.578184 8.1:+16009728 None:intergenic
AATGAAAGAACCATTACTTG+AGG 0.584582 8.1:+16009157 None:intergenic
ACAAAACAAGAAGGTGAACA+TGG 0.590894 8.1:-16009923 MS.gene044458:CDS
AAAGAAGCAACAAAACAAGA+AGG 0.599775 8.1:-16009932 MS.gene044458:CDS
GTACAGACAACCTAATCCTA+CGG 0.604529 8.1:+16009750 None:intergenic
TGAAAGAACCATTACTTGAG+GGG 0.615132 8.1:+16009159 None:intergenic
GATGGCAATGGCATAACAGA+AGG 0.624451 8.1:+16009263 None:intergenic
TGGAACTAAACAGTGTTGGA+TGG 0.631286 8.1:+16009096 None:intergenic
AAACTTTGAGGAATATCAAG+TGG 0.636206 8.1:+16009617 None:intergenic
CAATAGCTACATCAAGACAA+TGG 0.639730 8.1:-16009868 MS.gene044458:CDS
CTTTGAGGAATATCAAGTGG+TGG 0.640320 8.1:+16009620 None:intergenic
CAAACCCTATTTCAGCAACC+AGG 0.642234 8.1:-16009584 MS.gene044458:CDS
TTAGAGGATTAAGAGACCGT+AGG 0.643012 8.1:-16009766 MS.gene044458:CDS
AGGGGTTCAAGATTTGAACA+TGG 0.658690 8.1:+16009177 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATACTAATTATTCATCAAA+TGG - chr8.1:16009547-16009566 MS.gene044458:CDS 15.0%
!! GAAATAAATTACCATGATTA+TGG + chr8.1:16009633-16009652 None:intergenic 20.0%
!!! TTTTCCTTTTCCATATAAAT+TGG - chr8.1:16009570-16009589 MS.gene044458:CDS 20.0%
! ACTCTATCTTTATCACAATT+TGG - chr8.1:16009604-16009623 MS.gene044458:CDS 25.0%
! ATGATAATAACACCAGAAAT+GGG - chr8.1:16009959-16009978 MS.gene044458:CDS 25.0%
! CTAGTACTTATTTGATAAGA+AGG + chr8.1:16009655-16009674 None:intergenic 25.0%
! TATGGTATGAATCAAACTAA+AGG - chr8.1:16009487-16009506 MS.gene044458:intron 25.0%
! TCTTATCAAATAAGTACTAG+TGG - chr8.1:16009655-16009674 MS.gene044458:CDS 25.0%
! TGTGAATTACAAGATGAATT+AGG + chr8.1:16009721-16009740 None:intergenic 25.0%
! TTTATTGGAAGATGAATAGT+TGG + chr8.1:16009886-16009905 None:intergenic 25.0%
AAAGAAGCAACAAAACAAGA+AGG - chr8.1:16009085-16009104 MS.gene044458:CDS 30.0%
AATGAAAGAACCATTACTTG+AGG + chr8.1:16009863-16009882 None:intergenic 30.0%
AATTCACTACTTTCCATTGA+TGG + chr8.1:16009805-16009824 None:intergenic 30.0%
ATGAAAGAACCATTACTTGA+GGG + chr8.1:16009862-16009881 None:intergenic 30.0%
CTTGAAGGATCCAATTTATA+TGG + chr8.1:16009583-16009602 None:intergenic 30.0%
GATGATAATAACACCAGAAA+TGG - chr8.1:16009958-16009977 MS.gene044458:CDS 30.0%
GGATCCAATTTATATGGAAA+AGG + chr8.1:16009577-16009596 None:intergenic 30.0%
! AAACTTTGAGGAATATCAAG+TGG + chr8.1:16009403-16009422 None:intergenic 30.0%
! AGAGTACTAGTAAAAAGTGA+TGG + chr8.1:16009775-16009794 None:intergenic 30.0%
! GATAAAGATAGAGTACTTGA+AGG + chr8.1:16009598-16009617 None:intergenic 30.0%
AACCATTCAACAACTTTGCT+AGG + chr8.1:16009343-16009362 None:intergenic 35.0%
AACCTAGCAAAGTTGTTGAA+TGG - chr8.1:16009338-16009357 MS.gene044458:intron 35.0%
ACAAAACAAGAAGGTGAACA+TGG - chr8.1:16009094-16009113 MS.gene044458:CDS 35.0%
AGAAGCTGAAAGTTCAGAAA+AGG - chr8.1:16009513-16009532 MS.gene044458:CDS 35.0%
AGAGAAAAACAAGTACTACC+TGG + chr8.1:16009454-16009473 None:intergenic 35.0%
AGCAAAGTTTGCACAATTAG+AGG - chr8.1:16009235-16009254 MS.gene044458:CDS 35.0%
ATCATCTGAATCAAGAAGCT+TGG + chr8.1:16009944-16009963 None:intergenic 35.0%
CAATAGCTACATCAAGACAA+TGG - chr8.1:16009149-16009168 MS.gene044458:CDS 35.0%
CAATTTGGAAGCCATAATCA+TGG - chr8.1:16009619-16009638 MS.gene044458:CDS 35.0%
CTAGTAAAAAGTGATGGCAA+TGG + chr8.1:16009769-16009788 None:intergenic 35.0%
GAAGCTGAAAGTTCAGAAAA+GGG - chr8.1:16009514-16009533 MS.gene044458:CDS 35.0%
GTTCAAGATTTGAACATGGT+TGG + chr8.1:16009839-16009858 None:intergenic 35.0%
TATGATCTTCAAGACAGACT+TGG - chr8.1:16009307-16009326 MS.gene044458:intron 35.0%
TCATATAGCTGAATTGCTGT+TGG + chr8.1:16009292-16009311 None:intergenic 35.0%
TGAAAGAACCATTACTTGAG+GGG + chr8.1:16009861-16009880 None:intergenic 35.0%
TGATGTAGCTATTGCTTTGT+TGG + chr8.1:16009143-16009162 None:intergenic 35.0%
TGTTGTTGAGTGAAACTTTG+AGG + chr8.1:16009415-16009434 None:intergenic 35.0%
!! AGTACTTGTTTTTCTCTTGG+AGG - chr8.1:16009457-16009476 MS.gene044458:intron 35.0%
!! GGTAGTACTTGTTTTTCTCT+TGG - chr8.1:16009454-16009473 MS.gene044458:intron 35.0%
ACTACCTGGTTGCTGAAATA+GGG + chr8.1:16009440-16009459 None:intergenic 40.0%
AGAAGGTGAACATGGAAGAA+TGG - chr8.1:16009102-16009121 MS.gene044458:CDS 40.0%
AGCTTGGAACTAAACAGTGT+TGG + chr8.1:16009928-16009947 None:intergenic 40.0%
AGGGGTTCAAGATTTGAACA+TGG + chr8.1:16009843-16009862 None:intergenic 40.0%
ATCTTGAACCCCTCAAGTAA+TGG - chr8.1:16009850-16009869 MS.gene044458:CDS 40.0%
CGTCTAAACGGCGAATTTAT+TGG + chr8.1:16009901-16009920 None:intergenic 40.0%
GATTAAGAGACCGTAGGATT+AGG - chr8.1:16009257-16009276 MS.gene044458:CDS 40.0%
GTACAGACAACCTAATCCTA+CGG + chr8.1:16009270-16009289 None:intergenic 40.0%
TACTACCTGGTTGCTGAAAT+AGG + chr8.1:16009441-16009460 None:intergenic 40.0%
TACTCTGAATGCTCCATCAA+TGG - chr8.1:16009789-16009808 MS.gene044458:CDS 40.0%
TGAACATGGTTGGATTGTCT+TGG + chr8.1:16009829-16009848 None:intergenic 40.0%
TTAGAGGATTAAGAGACCGT+AGG - chr8.1:16009251-16009270 MS.gene044458:CDS 40.0%
! CTTTGAGGAATATCAAGTGG+TGG + chr8.1:16009400-16009419 None:intergenic 40.0%
! TCTCTTGGAGGTGGTTTTTA+TGG - chr8.1:16009469-16009488 MS.gene044458:intron 40.0%
! TGGAACTAAACAGTGTTGGA+TGG + chr8.1:16009924-16009943 None:intergenic 40.0%
!! ACTTGTTTTTCTCTTGGAGG+TGG - chr8.1:16009460-16009479 MS.gene044458:intron 40.0%
CAAACCCTATTTCAGCAACC+AGG - chr8.1:16009433-16009452 MS.gene044458:intron 45.0%
CGTGACACTCTCACTATTCT+TGG + chr8.1:16009190-16009209 None:intergenic 45.0%
GATGGCAATGGCATAACAGA+AGG + chr8.1:16009757-16009776 None:intergenic 45.0%
! AGAGTGTCACGTTCTTTAGG+AGG - chr8.1:16009199-16009218 MS.gene044458:CDS 45.0%
! AGTGTTGGATGGCGTCTAAA+CGG + chr8.1:16009913-16009932 None:intergenic 45.0%
!! GTGAGAGTGTCACGTTCTTT+AGG - chr8.1:16009196-16009215 MS.gene044458:CDS 45.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 16009055 16009984 16009055 ID=MS.gene044458
chr8.1 mRNA 16009055 16009984 16009055 ID=MS.gene044458.t1;Parent=MS.gene044458
chr8.1 exon 16009504 16009984 16009504 ID=MS.gene044458.t1.exon1;Parent=MS.gene044458.t1
chr8.1 CDS 16009504 16009984 16009504 ID=cds.MS.gene044458.t1;Parent=MS.gene044458.t1
chr8.1 exon 16009055 16009323 16009055 ID=MS.gene044458.t1.exon2;Parent=MS.gene044458.t1
chr8.1 CDS 16009055 16009323 16009055 ID=cds.MS.gene044458.t1;Parent=MS.gene044458.t1
Gene Sequence

>MS.gene044458

ATGATAGAAAGTTCAAGTAAAGATTATAACAAAGAAGCAACAAAACAAGAAGGTGAACATGGAAGAATGGAATCAGAGAAATTCTCCAACAAAGCAATAGCTACATCAAGACAATGGACATCATTAAGAAATCCAAGAATAGTGAGAGTGTCACGTTCTTTAGGAGGAAAAGACAGACACAGCAAAGTTTGCACAATTAGAGGATTAAGAGACCGTAGGATTAGGTTGTCTGTACCAACAGCAATTCAGCTATATGATCTTCAAGACAGACTTGGTTTAAGTCAACCTAGCAAAGTTGTTGAATGGTTAATTGAAGCAACTCAATCTGATATTGATAAATTACCACCACTTGATATTCCTCAAAGTTTCACTCAACAACAAACCCTATTTCAGCAACCAGGTAGTACTTGTTTTTCTCTTGGAGGTGGTTTTTATGGTATGAATCAAACTAAAGGTAAAGAAGCTGAAAGTTCAGAAAAGGGTAATTATTATAATACTAATTATTCATCAAATGGTTTTCCTTTTCCATATAAATTGGATCCTTCAAGTACTCTATCTTTATCACAATTTGGAAGCCATAATCATGGTAATTTATTTCCTTCTTATCAAATAAGTACTAGTGGCAGTGATATGCAATTTTCATCATCTTCAAATTTGACAGCACCTAATTCATCTTGTAATTCACAGTTACTTTTGTGTCCTTCTGTTATGCCATTGCCATCACTTTTTACTAGTACTCTGAATGCTCCATCAATGGAAAGTAGTGAATTTCCAAGACAATCCAACCATGTTCAAATCTTGAACCCCTCAAGTAATGGTTCTTTCATTCCAACTATTCATCTTCCAATAAATTCGCCGTTTAGACGCCATCCAACACTGTTTAGTTCCAAGCTTCTTGATTCAGATGATAATAACACCAGAAATGGGTAG
Protein sequence

>MS.gene044458.t1

MIESSSKDYNKEATKQEGEHGRMESEKFSNKAIATSRQWTSLRNPRIVRVSRSLGGKDRHSKVCTIRGLRDRRIRLSVPTAIQLYDLQDRLGLSQPSKVVEWLIEATQSDIDKLPPLDIPQSFTQQQTLFQQPGSTCFSLGGGFYGMNQTKGKEAESSEKAPNSSCNSQLLLCPSVMPLPSLFTSTLNAPSMESSEFPRQSNHVQILNPSSNGSFIPTIHLPINSPFRRHPTLFSSKLLDSDDNNTRNG