AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38449

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38449.t1 MTR_3g466830 94.410 161 9 0 1 161 1 161 4.68e-110 310
MS.gene38449.t1 MTR_3g466890 75.625 160 39 0 1 160 1 160 6.48e-85 246
MS.gene38449.t1 MTR_3g466930 77.692 130 29 0 31 160 2 131 6.00e-72 213
MS.gene38449.t1 MTR_3g466900 73.077 130 35 0 31 160 2 131 2.30e-67 201
MS.gene38449.t1 MTR_3g466980 47.059 153 81 0 2 154 3 155 6.73e-49 157
MS.gene38449.t1 MTR_3g065100 53.247 154 72 0 2 155 3 156 1.63e-48 157
MS.gene38449.t1 MTR_8g036130 47.853 163 82 2 2 161 3 165 7.74e-48 155
MS.gene38449.t1 MTR_4g032620 42.593 162 90 2 2 161 3 163 5.57e-44 145
MS.gene38449.t1 MTR_4g031910 47.205 161 84 1 2 161 3 163 5.12e-41 137
MS.gene38449.t1 MTR_2g035610 53.782 119 55 0 2 120 3 121 2.49e-39 129
MS.gene38449.t1 MTR_3g031240 42.500 160 89 2 2 159 3 161 4.43e-39 131
MS.gene38449.t1 MTR_1g090697 43.226 155 87 1 2 156 3 156 7.99e-39 129
MS.gene38449.t1 MTR_1g090783 43.312 157 88 1 1 157 1 156 3.59e-38 128
MS.gene38449.t1 MTR_4g032260 49.020 153 77 1 1 152 2 154 1.47e-37 126
MS.gene38449.t1 MTR_4g032290 46.914 162 85 1 1 161 2 163 1.83e-37 128
MS.gene38449.t1 MTR_5g075380 43.506 154 87 0 3 156 4 157 2.46e-36 123
MS.gene38449.t1 MTR_5g047580 43.506 154 86 1 2 155 3 155 1.11e-35 121
MS.gene38449.t1 MTR_1g077390 44.737 152 83 1 1 152 2 152 4.05e-34 117
MS.gene38449.t1 MTR_1g090710 39.744 156 92 2 2 156 3 157 8.84e-33 114
MS.gene38449.t1 MTR_2g016210 41.497 147 85 1 3 148 4 150 1.07e-31 114
MS.gene38449.t1 MTR_3g031100 37.736 159 98 1 2 159 3 161 1.88e-30 110
MS.gene38449.t1 MTR_7g011950 45.223 157 85 1 2 158 3 158 2.00e-30 108
MS.gene38449.t1 MTR_3g467080 36.842 152 95 1 2 152 3 154 3.12e-29 105
MS.gene38449.t1 MTR_1g077320 45.223 157 85 1 2 158 3 158 3.12e-29 105
MS.gene38449.t1 MTR_1g084950 44.156 154 85 1 2 155 3 155 4.03e-29 105
MS.gene38449.t1 MTR_4g063790 36.129 155 98 1 2 155 3 157 6.06e-28 102
MS.gene38449.t1 MTR_4g028720 42.038 157 90 1 2 158 3 158 8.01e-28 101
MS.gene38449.t1 MTR_1g077300 43.671 158 86 2 1 158 2 156 1.03e-25 96.3
MS.gene38449.t1 MTR_4g028800 60.000 70 26 1 3 72 4 71 5.85e-25 91.7
MS.gene38449.t1 MTR_2g035580 38.667 150 92 0 3 152 4 153 1.10e-24 93.6
MS.gene38449.t1 MTR_4g019670 31.788 151 102 1 2 152 6 155 5.46e-19 83.2
MS.gene38449.t1 MTR_5g047560 34.416 154 84 2 2 155 3 139 2.36e-18 77.0
MS.gene38449.t1 MTR_3g465410 32.558 129 86 1 28 155 1 129 8.12e-18 75.5
MS.gene38449.t1 MTR_7g106510 30.921 152 104 1 2 153 6 156 1.20e-17 79.3
MS.gene38449.t1 MTR_7g055800 35.043 117 48 2 2 118 3 91 7.69e-17 71.6
MS.gene38449.t1 MTR_3g093900 27.389 157 114 0 2 158 6 162 1.33e-15 73.6
MS.gene38449.t1 MTR_7g055790 41.667 108 45 2 2 109 61 150 1.27e-14 67.4
MS.gene38449.t1 MTR_6g018920 35.455 110 64 3 2 105 3 111 3.15e-13 66.2
MS.gene38449.t1 MTR_7g055940 33.654 104 41 2 2 105 3 78 1.07e-12 60.5
MS.gene38449.t1 MTR_6g005450 33.636 110 66 3 2 105 3 111 3.46e-12 63.2
MS.gene38449.t1 MTR_6g005440 35.714 112 61 4 2 105 3 111 5.50e-12 62.8
MS.gene38449.t1 MTR_1g114730 32.727 110 67 3 2 105 3 111 1.35e-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.gene38449.t1 AT5G48670 44.654 159 88 0 2 160 3 161 2.13e-37 130
MS.gene38449.t1 AT1G65300 39.474 152 92 0 1 152 1 152 2.16e-33 119
MS.gene38449.t1 AT1G65330 40.789 152 90 0 1 152 1 152 2.54e-33 119
MS.gene38449.t1 AT3G05860 38.776 147 90 0 2 148 3 149 9.15e-29 105
MS.gene38449.t1 AT3G05860 38.158 152 94 0 2 153 3 154 3.12e-28 105
MS.gene38449.t1 AT3G05860 38.158 152 94 0 2 153 3 154 4.32e-28 105
MS.gene38449.t1 AT5G26650 35.333 150 97 0 3 152 2 151 1.58e-25 100
MS.gene38449.t1 AT5G27960 39.831 118 71 0 3 120 2 119 4.71e-25 98.6
MS.gene38449.t1 AT5G27810 44.681 94 52 0 28 121 1 94 6.62e-25 93.2
MS.gene38449.t1 AT5G26630 38.411 151 93 0 2 152 3 153 6.96e-25 95.9
MS.gene38449.t1 AT1G31630 30.921 152 104 1 1 152 1 151 5.97e-22 90.5
MS.gene38449.t1 AT2G28700 36.975 119 75 0 2 120 3 121 2.84e-21 88.6
MS.gene38449.t1 AT1G31640 31.788 151 102 1 1 151 1 150 4.27e-21 89.0
MS.gene38449.t1 AT1G22590 29.747 158 108 1 2 159 3 157 4.57e-20 82.0
MS.gene38449.t1 AT5G26580 37.815 119 58 2 3 120 4 107 3.07e-18 80.5
MS.gene38449.t1 AT2G40210 39.394 99 60 0 2 100 3 101 6.09e-14 68.6
MS.gene38449.t1 AT5G55690 31.847 157 85 3 2 151 3 144 1.99e-13 66.2
MS.gene38449.t1 AT5G55690 31.847 157 85 3 2 151 3 144 1.99e-13 66.2
MS.gene38449.t1 AT5G06500 29.661 118 83 0 2 119 3 120 2.76e-11 60.1

Find 33 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTTCATCAATTGCTCTT+TGG 0.234493 3.4:+63198466 None:intergenic
CAAAGAGCAATTGATGAAAT+TGG 0.277019 3.4:-63198465 MS.gene38449:CDS
TGGTAATCATAATCTCTAAT+TGG 0.297332 3.4:+63198274 None:intergenic
GAAGGTGAAACTTGCATTCA+TGG 0.348876 3.4:-63198744 MS.gene38449:CDS
TGAAATTGGAGAAGAACAAT+TGG 0.354245 3.4:-63198451 MS.gene38449:CDS
CTGAGGTTTGGCCTTCTCCA+TGG 0.412577 3.4:-63198592 MS.gene38449:CDS
TTAACTTTGTGAGAACCCTT+TGG 0.427011 3.4:+63198564 None:intergenic
TTCATTCAGAGCCTGAGGTT+TGG 0.430822 3.4:-63198604 MS.gene38449:CDS
TCTCCCTCAAATAGCTCTCT+TGG 0.434445 3.4:+63198501 None:intergenic
CTTCTCCATGGGAGGTCCAA+AGG 0.434530 3.4:-63198580 MS.gene38449:CDS
ACCACCCTATGTGGGATTGA+TGG 0.443138 3.4:-63198650 MS.gene38449:CDS
TGAGGTTTGGCCTTCTCCAT+GGG 0.458648 3.4:-63198591 MS.gene38449:CDS
TTCTCCATGGGAGGTCCAAA+GGG 0.475139 3.4:-63198579 MS.gene38449:CDS
GAAATTGGAGAAGAACAATT+GGG 0.477120 3.4:-63198450 MS.gene38449:CDS
AAGAGAGCTATTTGAGGGAG+AGG 0.486973 3.4:-63198499 MS.gene38449:CDS
CATGGAGAAGGCCAAACCTC+AGG 0.496084 3.4:+63198593 None:intergenic
AATGAACTCACCACCCTATG+TGG 0.505218 3.4:-63198659 MS.gene38449:CDS
GATGAAGGAGATTACTTCAA+AGG 0.505350 3.4:-63198321 MS.gene38449:CDS
GGAAATTAATGAGAAGATGA+AGG 0.515316 3.4:-63198336 MS.gene38449:CDS
AATTATTCAGAATTCGAGCT+AGG 0.540322 3.4:-63198539 MS.gene38449:CDS
GCATCCATCAATCCCACATA+GGG 0.545713 3.4:+63198646 None:intergenic
GAACCAAGAGAGCTATTTGA+GGG 0.547706 3.4:-63198504 MS.gene38449:CDS
AGAACCCTTTGGACCTCCCA+TGG 0.549154 3.4:+63198575 None:intergenic
AAGACATTGAAACAAGATCA+AGG 0.553196 3.4:+63198415 None:intergenic
TGAACCAAGAGAGCTATTTG+AGG 0.555069 3.4:-63198505 MS.gene38449:CDS
CTTTGGACCTCCCATGGAGA+AGG 0.564387 3.4:+63198581 None:intergenic
CACACTGACTATGAGAAAGA+AGG 0.564705 3.4:-63198762 None:intergenic
CGAATTTCATTCAGAGCCTG+AGG 0.566026 3.4:-63198609 MS.gene38449:CDS
CGCATCCATCAATCCCACAT+AGG 0.580138 3.4:+63198645 None:intergenic
GGTTTGGCCTTCTCCATGGG+AGG 0.605628 3.4:-63198588 MS.gene38449:CDS
TCCATCAATCCCACATAGGG+TGG 0.620094 3.4:+63198649 None:intergenic
ATGAACTCACCACCCTATGT+GGG 0.624743 3.4:-63198658 MS.gene38449:CDS
TCATGGTCAGTGATTCCGCA+AGG 0.658742 3.4:-63198727 MS.gene38449:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAAAAGAGTTTGATCAAGA+AGG - chr3.4:63198357-63198376 MS.gene38449:CDS 25.0%
AAGACATTGAAACAAGATCA+AGG + chr3.4:63198629-63198648 None:intergenic 30.0%
AATTATTCAGAATTCGAGCT+AGG - chr3.4:63198502-63198521 MS.gene38449:CDS 30.0%
CAAAGAGCAATTGATGAAAT+TGG - chr3.4:63198576-63198595 MS.gene38449:CDS 30.0%
CAATTTCATCAATTGCTCTT+TGG + chr3.4:63198578-63198597 None:intergenic 30.0%
GAAATTGGAGAAGAACAATT+GGG - chr3.4:63198591-63198610 MS.gene38449:CDS 30.0%
GGAAATTAATGAGAAGATGA+AGG - chr3.4:63198705-63198724 MS.gene38449:CDS 30.0%
TGAAATTGGAGAAGAACAAT+TGG - chr3.4:63198590-63198609 MS.gene38449:CDS 30.0%
!! GTTGTAAGTTATTTTCCTTG+CGG + chr3.4:63198332-63198351 None:intergenic 30.0%
GATGAAGGAGATTACTTCAA+AGG - chr3.4:63198720-63198739 MS.gene38449:CDS 35.0%
TTAACTTTGTGAGAACCCTT+TGG + chr3.4:63198480-63198499 None:intergenic 35.0%
!! ATGTTTTGAATGATCTCGCA+TGG - chr3.4:63198683-63198702 MS.gene38449:CDS 35.0%
!! TGTTTTGAATGATCTCGCAT+GGG - chr3.4:63198684-63198703 MS.gene38449:CDS 35.0%
GAACCAAGAGAGCTATTTGA+GGG - chr3.4:63198537-63198556 MS.gene38449:CDS 40.0%
GAAGGTGAAACTTGCATTCA+TGG - chr3.4:63198297-63198316 MS.gene38449:CDS 40.0%
TGAACCAAGAGAGCTATTTG+AGG - chr3.4:63198536-63198555 MS.gene38449:CDS 40.0%
AAGAGAGCTATTTGAGGGAG+AGG - chr3.4:63198542-63198561 MS.gene38449:CDS 45.0%
AATGAACTCACCACCCTATG+TGG - chr3.4:63198382-63198401 MS.gene38449:CDS 45.0%
ATGAACTCACCACCCTATGT+GGG - chr3.4:63198383-63198402 MS.gene38449:CDS 45.0%
CGAATTTCATTCAGAGCCTG+AGG - chr3.4:63198432-63198451 MS.gene38449:CDS 45.0%
GCATCCATCAATCCCACATA+GGG + chr3.4:63198398-63198417 None:intergenic 45.0%
TCTCCCTCAAATAGCTCTCT+TGG + chr3.4:63198543-63198562 None:intergenic 45.0%
TTCATTCAGAGCCTGAGGTT+TGG - chr3.4:63198437-63198456 MS.gene38449:CDS 45.0%
ACCACCCTATGTGGGATTGA+TGG - chr3.4:63198391-63198410 MS.gene38449:CDS 50.0%
CGCATCCATCAATCCCACAT+AGG + chr3.4:63198399-63198418 None:intergenic 50.0%
TCATGGTCAGTGATTCCGCA+AGG - chr3.4:63198314-63198333 MS.gene38449:CDS 50.0%
TCCATCAATCCCACATAGGG+TGG + chr3.4:63198395-63198414 None:intergenic 50.0%
TTCTCCATGGGAGGTCCAAA+GGG - chr3.4:63198462-63198481 MS.gene38449:CDS 50.0%
! TGAGGTTTGGCCTTCTCCAT+GGG - chr3.4:63198450-63198469 MS.gene38449:CDS 50.0%
AGAACCCTTTGGACCTCCCA+TGG + chr3.4:63198469-63198488 None:intergenic 55.0%
CATGGAGAAGGCCAAACCTC+AGG + chr3.4:63198451-63198470 None:intergenic 55.0%
CTTCTCCATGGGAGGTCCAA+AGG - chr3.4:63198461-63198480 MS.gene38449:CDS 55.0%
CTTTGGACCTCCCATGGAGA+AGG + chr3.4:63198463-63198482 None:intergenic 55.0%
! CTGAGGTTTGGCCTTCTCCA+TGG - chr3.4:63198449-63198468 MS.gene38449:CDS 55.0%
! GGTTTGGCCTTCTCCATGGG+AGG - chr3.4:63198453-63198472 MS.gene38449:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 63198289 63198774 63198289 ID=MS.gene38449
chr3.4 mRNA 63198289 63198774 63198289 ID=MS.gene38449.t1;Parent=MS.gene38449
chr3.4 exon 63198289 63198774 63198289 ID=MS.gene38449.t1.exon1;Parent=MS.gene38449.t1
chr3.4 CDS 63198289 63198774 63198289 ID=cds.MS.gene38449.t1;Parent=MS.gene38449.t1
Gene Sequence

>MS.gene38449

ATGAGAAAGAAGGTGAAACTTGCATTCATGGTCAGTGATTCCGCAAGGAAAATAACTTACAACAAAAGAAAAAAGAGTTTGATCAAGAAGGTTAATGAACTCACCACCCTATGTGGGATTGATGGATGCGCTATAGTTTATAGCGAATTTCATTCAGAGCCTGAGGTTTGGCCTTCTCCATGGGAGGTCCAAAGGGTTCTCACAAAGTTAAAAAATTATTCAGAATTCGAGCTAGGAAAGAAGAAGCTGAACCAAGAGAGCTATTTGAGGGAGAGGATTATGAAGTCCAAAGAGCAATTGATGAAATTGGAGAAGAACAATTGGGAGACAGAGAAGTCCTTGATCTTGTTTCAATGTCTTGTCAAAGAAAATTTTGTTGACACTTTGAACACAAATGTTTTGAATGATCTCGCATGGGAAATTAATGAGAAGATGAAGGAGATTACTTCAAAGGTCAATGAACTAGACACAAGTGCAACCAATTAG
Protein sequence

>MS.gene38449.t1

MRKKVKLAFMVSDSARKITYNKRKKSLIKKVNELTTLCGIDGCAIVYSEFHSEPEVWPSPWEVQRVLTKLKNYSEFELGKKKLNQESYLRERIMKSKEQLMKLEKNNWETEKSLILFQCLVKENFVDTLNTNVLNDLAWEINEKMKEITSKVNELDTSATN