AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004246

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004246.t1 MTR_2g016030 96.273 161 5 1 1 160 1 161 1.63e-113 318
MS.gene004246.t1 MTR_6g012450 69.136 81 24 1 19 99 110 189 5.72e-36 130
MS.gene004246.t1 MTR_7g010950 70.667 75 22 0 25 99 114 188 2.23e-35 128
MS.gene004246.t1 MTR_4g082060 67.500 80 26 0 20 99 96 175 3.39e-35 127
MS.gene004246.t1 MTR_8g044220 61.628 86 32 1 25 109 96 181 3.09e-34 124
MS.gene004246.t1 MTR_7g086780 71.233 73 20 1 28 99 80 152 1.45e-32 120
MS.gene004246.t1 MTR_5g041380 58.065 93 37 1 18 108 97 189 4.00e-32 117
MS.gene004246.t1 MTR_6g027460 67.105 76 24 1 24 99 75 149 2.97e-31 115
MS.gene004246.t1 MTR_3g435480 57.778 90 29 1 19 99 100 189 8.66e-31 115
MS.gene004246.t1 MTR_5g041530 70.423 71 18 1 32 99 123 193 1.70e-30 114
MS.gene004246.t1 MTR_5g041400 62.338 77 29 0 32 108 105 181 4.61e-30 112
MS.gene004246.t1 MTR_6g027450 63.158 76 27 1 24 99 68 142 5.76e-30 111
MS.gene004246.t1 MTR_5g041420 71.667 60 17 0 40 99 132 191 9.31e-30 110
MS.gene004246.t1 MTR_2g096740 55.263 76 34 0 24 99 40 115 4.06e-27 103
MS.gene004246.t1 MTR_2g096740 55.263 76 34 0 24 99 55 130 4.28e-27 103
MS.gene004246.t1 MTR_8g015840 59.155 71 23 1 34 98 2 72 4.60e-26 99.0
MS.gene004246.t1 MTR_8g068210 47.059 102 48 3 24 123 12 109 5.71e-26 100
MS.gene004246.t1 MTR_8g479350 48.000 100 41 2 48 138 70 167 9.96e-26 100
MS.gene004246.t1 MTR_4g022370 70.175 57 17 0 43 99 79 135 1.52e-25 100
MS.gene004246.t1 MTR_8g027295 56.098 82 32 2 36 113 12 93 3.76e-25 97.4
MS.gene004246.t1 MTR_8g079060 51.250 80 39 0 46 125 29 108 4.58e-25 96.7
MS.gene004246.t1 MTR_4g063780 64.286 70 24 1 43 111 72 141 1.31e-24 97.4
MS.gene004246.t1 MTR_4g109980 69.811 53 16 0 44 96 38 90 1.93e-24 96.7
MS.gene004246.t1 MTR_3g091820 64.912 57 20 0 43 99 40 96 2.10e-24 96.3
MS.gene004246.t1 MTR_2g093220 55.263 76 34 0 24 99 18 93 2.35e-24 95.9
MS.gene004246.t1 MTR_2g059540 73.469 49 13 0 46 94 31 79 3.06e-24 94.0
MS.gene004246.t1 MTR_7g024670 76.000 50 12 0 48 97 79 128 4.75e-24 96.3
MS.gene004246.t1 MTR_7g059400 68.421 57 18 0 43 99 73 129 1.07e-23 95.1
MS.gene004246.t1 MTR_1g077600 63.636 55 20 0 43 97 40 94 1.29e-23 93.6
MS.gene004246.t1 MTR_1g077600 63.636 55 20 0 43 97 40 94 1.48e-23 94.0
MS.gene004246.t1 MTR_5g031440 68.519 54 17 0 43 96 40 93 1.97e-23 94.4
MS.gene004246.t1 MTR_4g088580 73.077 52 14 0 48 99 57 108 2.25e-23 94.7
MS.gene004246.t1 MTR_4g089095 67.308 52 17 0 48 99 52 103 4.43e-23 92.8
MS.gene004246.t1 MTR_4g089095 67.308 52 17 0 48 99 18 69 5.17e-23 92.0
MS.gene004246.t1 MTR_1g056810 64.516 62 21 1 39 99 4 65 1.24e-22 91.3
MS.gene004246.t1 MTR_4g461080 54.054 74 34 0 24 97 7 80 1.24e-22 91.3
MS.gene004246.t1 MTR_3g090430 65.517 58 20 0 42 99 47 104 1.46e-22 91.7
MS.gene004246.t1 MTR_2g014060 49.351 77 39 0 22 98 1 77 1.59e-22 91.7
MS.gene004246.t1 MTR_2g014170 71.429 49 14 0 46 94 45 93 1.69e-22 91.3
MS.gene004246.t1 MTR_2g013370 62.963 54 20 0 46 99 46 99 2.68e-22 90.1
MS.gene004246.t1 MTR_3g077750 66.667 51 17 0 46 96 61 111 1.43e-21 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004246.t1 AT1G29160 61.404 114 24 1 8 101 4 117 1.40e-45 147
MS.gene004246.t1 AT2G34140 62.727 110 25 1 8 101 4 113 2.61e-44 144
MS.gene004246.t1 AT5G62430 59.000 100 29 2 12 99 8 107 1.21e-35 125
MS.gene004246.t1 AT3G47500 58.252 103 43 0 20 122 84 186 7.53e-35 126
MS.gene004246.t1 AT5G39660 82.540 63 11 0 40 102 132 194 1.86e-34 125
MS.gene004246.t1 AT5G39660 82.540 63 11 0 40 102 132 194 1.86e-34 125
MS.gene004246.t1 AT5G39660 82.540 63 11 0 40 102 132 194 1.86e-34 125
MS.gene004246.t1 AT1G26790 56.311 103 38 1 23 125 88 183 4.75e-34 123
MS.gene004246.t1 AT1G69570 60.440 91 29 1 34 124 120 203 7.12e-33 120
MS.gene004246.t1 AT5G60850 57.692 78 33 0 46 123 51 128 3.05e-27 103
MS.gene004246.t1 AT1G51700 71.698 53 15 0 46 98 33 85 4.53e-26 98.2
MS.gene004246.t1 AT3G21270 76.923 52 12 0 46 97 29 80 8.99e-26 97.8
MS.gene004246.t1 AT2G28810 72.727 55 15 0 43 97 74 128 1.75e-25 99.8
MS.gene004246.t1 AT4G38000 60.294 68 26 1 43 109 38 105 2.21e-25 97.8
MS.gene004246.t1 AT3G50410 71.698 53 15 0 46 98 30 82 2.46e-25 97.8
MS.gene004246.t1 AT2G28810 72.727 55 15 0 43 97 91 145 3.23e-25 99.0
MS.gene004246.t1 AT3G55370 68.421 57 18 0 43 99 73 129 8.44e-25 97.8
MS.gene004246.t1 AT2G37590 68.421 57 18 0 43 99 86 142 8.47e-25 97.8
MS.gene004246.t1 AT3G55370 68.421 57 18 0 43 99 73 129 9.48e-25 98.2
MS.gene004246.t1 AT3G55370 68.421 57 18 0 43 99 118 174 1.22e-24 97.8
MS.gene004246.t1 AT5G65590 68.421 57 18 0 43 99 38 94 1.34e-24 97.1
MS.gene004246.t1 AT1G07640 52.500 80 38 0 18 97 49 128 3.07e-24 96.3
MS.gene004246.t1 AT1G07640 76.000 50 12 0 48 97 23 72 3.24e-24 95.5
MS.gene004246.t1 AT1G07640 52.500 80 38 0 18 97 57 136 3.63e-24 96.3
MS.gene004246.t1 AT5G66940 67.925 53 17 0 46 98 32 84 9.05e-24 93.2
MS.gene004246.t1 AT5G60200 66.667 57 19 0 43 99 52 108 1.12e-23 93.6
MS.gene004246.t1 AT5G02460 68.421 57 18 0 43 99 92 148 1.61e-23 95.1
MS.gene004246.t1 AT3G45610 63.158 57 21 0 43 99 37 93 2.17e-23 92.4
MS.gene004246.t1 AT4G24060 63.158 57 21 0 43 99 50 106 2.29e-23 94.4
MS.gene004246.t1 AT1G47655 64.815 54 19 0 41 94 24 77 3.39e-23 91.3
MS.gene004246.t1 AT3G52440 66.102 59 19 1 44 101 22 80 3.90e-23 92.0
MS.gene004246.t1 AT3G52440 66.102 59 19 1 44 101 41 99 3.96e-23 92.4
MS.gene004246.t1 AT1G28310 68.519 54 17 0 46 99 27 80 4.05e-23 93.2
MS.gene004246.t1 AT3G61850 57.812 64 27 0 36 99 52 115 4.19e-23 92.4
MS.gene004246.t1 AT3G61850 57.812 64 27 0 36 99 52 115 4.19e-23 92.4
MS.gene004246.t1 AT3G61850 57.812 64 27 0 36 99 64 127 4.64e-23 92.8
MS.gene004246.t1 AT1G28310 68.519 54 17 0 46 99 51 104 5.82e-23 92.8
MS.gene004246.t1 AT3G61850 57.812 64 27 0 36 99 52 115 6.82e-23 92.4
MS.gene004246.t1 AT3G61850 57.812 64 27 0 36 99 64 127 7.36e-23 92.4
MS.gene004246.t1 AT2G28510 71.154 52 15 0 48 99 50 101 1.12e-22 91.7
MS.gene004246.t1 AT1G64620 65.385 52 18 0 43 94 46 97 1.12e-22 92.4
MS.gene004246.t1 AT4G00940 71.154 52 15 0 48 99 70 121 1.73e-22 91.3
MS.gene004246.t1 AT4G00940 71.154 52 15 0 48 99 70 121 1.73e-22 91.3
MS.gene004246.t1 AT4G00940 71.154 52 15 0 48 99 70 121 1.73e-22 91.3
MS.gene004246.t1 AT1G21340 70.000 50 15 0 48 97 40 89 2.11e-22 90.1
MS.gene004246.t1 AT5G62940 69.388 49 15 0 48 96 75 123 1.16e-21 89.7
MS.gene004246.t1 AT4G21050 58.730 63 26 0 48 110 26 88 1.89e-21 86.7
MS.gene004246.t1 AT2G46590 68.750 48 15 0 46 93 68 115 5.83e-21 87.8
MS.gene004246.t1 AT2G46590 68.750 48 15 0 46 93 80 127 6.60e-21 87.8
MS.gene004246.t1 AT4G21040 48.101 79 37 1 29 103 8 86 1.52e-19 82.0
MS.gene004246.t1 AT4G21080 44.828 87 44 1 29 111 8 94 5.34e-19 80.9
MS.gene004246.t1 AT4G21030 45.588 68 37 0 48 115 23 90 2.17e-14 67.8

Find 45 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATACAAGGGATTAAGCTATT+TGG 0.296201 2.4:+68959048 MS.gene004246:CDS
GGTCTTCCTCCGCCGCTTGC+CGG 0.325640 2.4:-68959448 None:intergenic
GCTTCATAGACACAACTTTC+CGG 0.327262 2.4:-68959345 None:intergenic
GTAAGAGCTGTCAAAGATAC+TGG 0.350596 2.4:+68959238 MS.gene004246:CDS
ATGTCCAAGATGCAAGAGTA+TGG 0.357770 2.4:+68959161 MS.gene004246:CDS
GATGATGGCCATAACTACTT+AGG 0.390058 2.4:+68959378 MS.gene004246:CDS
GTTCTAACCCTAAGTAGTTA+TGG 0.403963 2.4:-68959386 None:intergenic
GTTTCCATACTCTTGCATCT+TGG 0.414049 2.4:-68959165 None:intergenic
TGGGGCCCTCCGTAACGTTC+CGG 0.432988 2.4:+68959269 MS.gene004246:CDS
TTCCGACGACCTGCTCCAAC+CGG 0.436863 2.4:-68959288 None:intergenic
ATCCTCAAGACTTGGCGGCT+TGG 0.465996 2.4:-68959313 None:intergenic
CGTAACGTTCCGGTTGGAGC+AGG 0.491556 2.4:+68959279 MS.gene004246:CDS
CAAAGATACTGGACGGCTGG+TGG 0.496439 2.4:+68959249 MS.gene004246:CDS
ATGATGGCCATAACTACTTA+GGG 0.502994 2.4:+68959379 MS.gene004246:CDS
CTGCTCCAACCGGAACGTTA+CGG 0.518351 2.4:-68959278 None:intergenic
GCCCTCCGTAACGTTCCGGT+TGG 0.526190 2.4:+68959273 MS.gene004246:CDS
AAAAGAAAATGAAGATCAAA+CGG 0.528108 2.4:+68959110 MS.gene004246:CDS
AAAGATACTGGACGGCTGGT+GGG 0.536772 2.4:+68959250 MS.gene004246:CDS
TTGCATGAGGAATTAAAAGA+AGG 0.537463 2.4:+68959084 MS.gene004246:CDS
TCTTGAGGATAGCGGTTCAC+CGG 0.541063 2.4:+68959326 MS.gene004246:CDS
TGTCAAAGATACTGGACGGC+TGG 0.542444 2.4:+68959246 MS.gene004246:CDS
AGAAAAGGTGAAGAGATACA+AGG 0.544735 2.4:+68959033 MS.gene004246:CDS
ATACTCTTGCATCTTGGACA+TGG 0.546078 2.4:-68959159 None:intergenic
GGCCAAGCCGCCAAGTCTTG+AGG 0.555303 2.4:+68959311 MS.gene004246:CDS
TTCCGGTTGGAGCAGGTCGT+CGG 0.558411 2.4:+68959286 MS.gene004246:CDS
AAGCGGCGGAGGAAGACCTC+AGG 0.572311 2.4:+68959453 MS.gene004246:CDS
AAAATGGCTGAAGTGAGAAA+AGG 0.579551 2.4:+68959018 None:intergenic
AAGATACTGGACGGCTGGTG+GGG 0.581078 2.4:+68959251 MS.gene004246:CDS
CCGCTATCCTCAAGACTTGG+CGG 0.597183 2.4:-68959318 None:intergenic
GAACCGCTATCCTCAAGACT+TGG 0.599554 2.4:-68959321 None:intergenic
GAAAAGGTGAAGAGATACAA+GGG 0.603099 2.4:+68959034 MS.gene004246:CDS
GGTTGGAGCAGGTCGTCGGA+AGG 0.608139 2.4:+68959290 MS.gene004246:CDS
CACAACAATAAAATTGCATG+AGG 0.620119 2.4:+68959071 MS.gene004246:CDS
GAAGCTGCTAGTTCTGATGA+TGG 0.628789 2.4:+68959363 MS.gene004246:CDS
CGGCGGAGGAAGACCTCAGG+TGG 0.630380 2.4:+68959456 MS.gene004246:CDS
TGCTAATGAATAACCACCTG+AGG 0.631649 2.4:-68959469 None:intergenic
GAGCTGTCAAAGATACTGGA+CGG 0.644495 2.4:+68959242 MS.gene004246:CDS
TCCAACCGGAACGTTACGGA+GGG 0.647718 2.4:-68959274 None:intergenic
TCCCGAAAATCACTCTGAGG+AGG 0.648141 2.4:-68959417 None:intergenic
CTCCAACCGGAACGTTACGG+AGG 0.649811 2.4:-68959275 None:intergenic
ACTTCCCGAAAATCACTCTG+AGG 0.686816 2.4:-68959420 None:intergenic
GTAAAGAACAAGAAATCACA+AGG 0.691544 2.4:-68959496 None:intergenic
AGAAAATGAAGATCAAACGG+TGG 0.696077 2.4:+68959113 MS.gene004246:CDS
CCGCCAAGTCTTGAGGATAG+CGG 0.704408 2.4:+68959318 MS.gene004246:CDS
AAGAACAAGAAATCACAAGG+AGG 0.761754 2.4:-68959493 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAATGAAGATCAAA+CGG + chr2.4:68959110-68959129 MS.gene004246:CDS 20.0%
ATACAAGGGATTAAGCTATT+TGG + chr2.4:68959048-68959067 MS.gene004246:CDS 30.0%
CACAACAATAAAATTGCATG+AGG + chr2.4:68959071-68959090 MS.gene004246:CDS 30.0%
TTGCATGAGGAATTAAAAGA+AGG + chr2.4:68959084-68959103 MS.gene004246:CDS 30.0%
AGAAAAGGTGAAGAGATACA+AGG + chr2.4:68959033-68959052 MS.gene004246:CDS 35.0%
AGAAAATGAAGATCAAACGG+TGG + chr2.4:68959113-68959132 MS.gene004246:CDS 35.0%
ATGATGGCCATAACTACTTA+GGG + chr2.4:68959379-68959398 MS.gene004246:CDS 35.0%
CAGCTCTTACAAAAATGTCT+TGG - chr2.4:68959228-68959247 None:intergenic 35.0%
GAAAAGGTGAAGAGATACAA+GGG + chr2.4:68959034-68959053 MS.gene004246:CDS 35.0%
GTTCTAACCCTAAGTAGTTA+TGG - chr2.4:68959389-68959408 None:intergenic 35.0%
!!! GATTTTCGGGAAGTATTTTC+CGG + chr2.4:68959429-68959448 MS.gene004246:CDS 35.0%
ATACTCTTGCATCTTGGACA+TGG - chr2.4:68959162-68959181 None:intergenic 40.0%
ATGTCCAAGATGCAAGAGTA+TGG + chr2.4:68959161-68959180 MS.gene004246:CDS 40.0%
GCTTCATAGACACAACTTTC+CGG - chr2.4:68959348-68959367 None:intergenic 40.0%
GTAAGAGCTGTCAAAGATAC+TGG + chr2.4:68959238-68959257 MS.gene004246:CDS 40.0%
GTTTCCATACTCTTGCATCT+TGG - chr2.4:68959168-68959187 None:intergenic 40.0%
TGCTAATGAATAACCACCTG+AGG - chr2.4:68959472-68959491 None:intergenic 40.0%
! GATGATGGCCATAACTACTT+AGG + chr2.4:68959378-68959397 MS.gene004246:CDS 40.0%
ACTTCCCGAAAATCACTCTG+AGG - chr2.4:68959423-68959442 None:intergenic 45.0%
GAGCTGTCAAAGATACTGGA+CGG + chr2.4:68959242-68959261 MS.gene004246:CDS 45.0%
! TGCCTCCTCAGAGTGATTTT+CGG + chr2.4:68959415-68959434 MS.gene004246:CDS 45.0%
!! GAAGCTGCTAGTTCTGATGA+TGG + chr2.4:68959363-68959382 MS.gene004246:CDS 45.0%
AAAGATACTGGACGGCTGGT+GGG + chr2.4:68959250-68959269 MS.gene004246:CDS 50.0%
GAACCGCTATCCTCAAGACT+TGG - chr2.4:68959324-68959343 None:intergenic 50.0%
TGTCAAAGATACTGGACGGC+TGG + chr2.4:68959246-68959265 MS.gene004246:CDS 50.0%
! AAGTATTTTCCGGCAAGCGG+CGG + chr2.4:68959439-68959458 MS.gene004246:CDS 50.0%
! GCCTCCTCAGAGTGATTTTC+GGG + chr2.4:68959416-68959435 MS.gene004246:CDS 50.0%
! TCCCGAAAATCACTCTGAGG+AGG - chr2.4:68959420-68959439 None:intergenic 50.0%
! TCTTGAGGATAGCGGTTCAC+CGG + chr2.4:68959326-68959345 MS.gene004246:CDS 50.0%
!!! GGGAAGTATTTTCCGGCAAG+CGG + chr2.4:68959436-68959455 MS.gene004246:CDS 50.0%
AAGATACTGGACGGCTGGTG+GGG + chr2.4:68959251-68959270 MS.gene004246:CDS 55.0%
ATCCTCAAGACTTGGCGGCT+TGG - chr2.4:68959316-68959335 None:intergenic 55.0%
CAAAGATACTGGACGGCTGG+TGG + chr2.4:68959249-68959268 MS.gene004246:CDS 55.0%
CCGCCAAGTCTTGAGGATAG+CGG + chr2.4:68959318-68959337 MS.gene004246:CDS 55.0%
CCGCTATCCTCAAGACTTGG+CGG - chr2.4:68959321-68959340 None:intergenic 55.0%
CTGCTCCAACCGGAACGTTA+CGG - chr2.4:68959281-68959300 None:intergenic 55.0%
TCCAACCGGAACGTTACGGA+GGG - chr2.4:68959277-68959296 None:intergenic 55.0%
CGTAACGTTCCGGTTGGAGC+AGG + chr2.4:68959279-68959298 MS.gene004246:CDS 60.0%
CTCCAACCGGAACGTTACGG+AGG - chr2.4:68959278-68959297 None:intergenic 60.0%
TTCCGACGACCTGCTCCAAC+CGG - chr2.4:68959291-68959310 None:intergenic 60.0%
TTCCGGTTGGAGCAGGTCGT+CGG + chr2.4:68959286-68959305 MS.gene004246:CDS 60.0%
! TATTTTCCGGCAAGCGGCGG+AGG + chr2.4:68959442-68959461 MS.gene004246:CDS 60.0%
AAGCGGCGGAGGAAGACCTC+AGG + chr2.4:68959453-68959472 MS.gene004246:CDS 65.0%
GCCCTCCGTAACGTTCCGGT+TGG + chr2.4:68959273-68959292 MS.gene004246:CDS 65.0%
GGCCAAGCCGCCAAGTCTTG+AGG + chr2.4:68959311-68959330 MS.gene004246:CDS 65.0%
GGTTGGAGCAGGTCGTCGGA+AGG + chr2.4:68959290-68959309 MS.gene004246:CDS 65.0%
TGGGGCCCTCCGTAACGTTC+CGG + chr2.4:68959269-68959288 MS.gene004246:CDS 65.0%
CGGCGGAGGAAGACCTCAGG+TGG + chr2.4:68959456-68959475 MS.gene004246:CDS 70.0%
GGTCTTCCTCCGCCGCTTGC+CGG - chr2.4:68959451-68959470 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 68959021 68959503 68959021 ID=MS.gene004246
chr2.4 mRNA 68959021 68959503 68959021 ID=MS.gene004246.t1;Parent=MS.gene004246
chr2.4 exon 68959021 68959503 68959021 ID=MS.gene004246.t1.exon1;Parent=MS.gene004246.t1
chr2.4 CDS 68959021 68959503 68959021 ID=cds.MS.gene004246.t1;Parent=MS.gene004246.t1
Gene Sequence

>MS.gene004246

ATGGCTGAAGTGAGAAAAGGTGAAGAGATACAAGGGATTAAGCTATTTGGCACAACAATAAAATTGCATGAGGAATTAAAAGAAGGTGAAAAAGAAAATGAAGATCAAACGGTGGAGAAGAAGATAGAAAAGATCATACCATGTCCAAGATGCAAGAGTATGGAAACTAAATTTTGTTATTTCAATAATTATAACGTTAATCAACCAAGACATTTTTGTAAGAGCTGTCAAAGATACTGGACGGCTGGTGGGGCCCTCCGTAACGTTCCGGTTGGAGCAGGTCGTCGGAAGGCCAAGCCGCCAAGTCTTGAGGATAGCGGTTCACCGGAAAGTTGTGTCTATGAAGCTGCTAGTTCTGATGATGGCCATAACTACTTAGGGTTAGAACAATTTATGCCTCCTCAGAGTGATTTTCGGGAAGTATTTTCCGGCAAGCGGCGGAGGAAGACCTCAGGTGGTTATTCATTAGCATCCTCCTTGTGA
Protein sequence

>MS.gene004246.t1

MAEVRKGEEIQGIKLFGTTIKLHEELKEGEKENEDQTVEKKIEKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKSCQRYWTAGGALRNVPVGAGRRKAKPPSLEDSGSPESCVYEAASSDDGHNYLGLEQFMPPQSDFREVFSGKRRRKTSGGYSLASSL