AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29228

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29228.t1 MTR_1g039040 97.895 190 3 1 1 189 1 190 1.43e-140 389
MS.gene29228.t1 MTR_4g133952 81.188 101 19 0 4 104 56 156 2.25e-58 183
MS.gene29228.t1 MTR_7g061270 65.625 96 33 0 4 99 24 119 2.94e-47 152
MS.gene29228.t1 MTR_2g026710 62.745 102 38 0 2 103 13 114 4.60e-47 152
MS.gene29228.t1 MTR_7g100650 65.625 96 33 0 4 99 24 119 5.36e-47 152
MS.gene29228.t1 MTR_5g095740 62.037 108 41 0 5 112 22 129 6.18e-47 152
MS.gene29228.t1 MTR_3g058980 68.421 95 30 0 5 99 26 120 1.58e-46 151
MS.gene29228.t1 MTR_8g091720 62.745 102 38 0 5 106 27 128 4.15e-45 148
MS.gene29228.t1 MTR_1g072790 60.194 103 41 0 5 107 28 130 1.40e-44 146
MS.gene29228.t1 MTR_8g093920 60.606 99 39 0 5 103 39 137 8.40e-44 145
MS.gene29228.t1 MTR_0392s0020 62.500 96 36 0 2 97 14 109 1.41e-42 139
MS.gene29228.t1 MTR_4g119500 63.830 94 34 0 4 97 20 113 2.62e-42 138
MS.gene29228.t1 MTR_1g088860 62.500 96 36 0 4 99 34 129 5.97e-42 140
MS.gene29228.t1 MTR_4g133938 57.426 101 41 1 2 100 13 113 1.12e-39 132
MS.gene29228.t1 MTR_1g083070 51.087 92 45 0 6 97 4 95 1.53e-31 111
MS.gene29228.t1 MTR_1g029070 51.579 95 46 0 5 99 51 145 2.92e-31 112
MS.gene29228.t1 MTR_5g095900 47.917 96 47 1 2 94 9 104 1.62e-24 94.7
MS.gene29228.t1 MTR_1g028480 57.353 68 29 0 36 103 19 86 7.37e-23 88.6
MS.gene29228.t1 MTR_1g029100 43.421 76 43 0 11 86 7 82 7.01e-19 77.8
MS.gene29228.t1 MTR_2g056000 30.337 89 62 0 6 94 41 129 6.73e-16 72.4
MS.gene29228.t1 MTR_4g112380 31.395 86 59 0 1 86 6 91 7.26e-15 68.9
MS.gene29228.t1 MTR_5g095860 39.024 82 40 1 12 93 22 93 8.63e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29228.t1 AT5G47670 84.375 96 15 0 4 99 27 122 4.33e-58 181
MS.gene29228.t1 AT5G47670 84.375 96 15 0 4 99 56 151 7.57e-58 181
MS.gene29228.t1 AT5G47670 84.375 96 15 0 4 99 56 151 7.57e-58 181
MS.gene29228.t1 AT1G21970 69.231 130 22 2 5 116 58 187 3.59e-57 180
MS.gene29228.t1 AT4G14540 65.686 102 35 0 2 103 17 118 8.56e-49 156
MS.gene29228.t1 AT2G38880 64.583 96 34 0 4 99 19 114 1.74e-46 149
MS.gene29228.t1 AT2G38880 64.583 96 34 0 4 99 19 114 2.09e-46 149
MS.gene29228.t1 AT2G38880 64.583 96 34 0 4 99 19 114 2.09e-46 149
MS.gene29228.t1 AT2G38880 64.583 96 34 0 4 99 19 114 2.09e-46 149
MS.gene29228.t1 AT5G47640 64.356 101 36 0 5 105 26 126 5.18e-46 150
MS.gene29228.t1 AT3G53340 64.583 96 34 0 4 99 27 122 8.89e-46 149
MS.gene29228.t1 AT3G53340 64.583 96 34 0 4 99 27 122 8.89e-46 149
MS.gene29228.t1 AT2G37060 63.542 96 35 0 4 99 28 123 1.46e-45 148
MS.gene29228.t1 AT2G37060 63.542 96 35 0 4 99 28 123 1.46e-45 148
MS.gene29228.t1 AT2G37060 63.542 96 35 0 4 99 28 123 1.46e-45 148
MS.gene29228.t1 AT2G38880 63.830 94 34 0 4 97 19 112 2.41e-45 147
MS.gene29228.t1 AT2G38880 48.344 151 65 2 4 154 19 156 3.89e-45 147
MS.gene29228.t1 AT2G38880 48.344 151 65 2 4 154 19 156 3.89e-45 147
MS.gene29228.t1 AT2G38880 65.217 92 32 0 4 95 19 110 1.75e-44 143
MS.gene29228.t1 AT3G53340 63.366 101 35 1 4 102 27 127 2.29e-44 144
MS.gene29228.t1 AT3G53340 63.366 101 35 1 4 102 27 127 2.29e-44 144
MS.gene29228.t1 AT3G53340 65.217 92 32 0 4 95 27 118 4.65e-44 143
MS.gene29228.t1 AT2G38880 65.217 92 32 0 4 95 19 110 9.08e-44 143
MS.gene29228.t1 AT2G38880 65.217 92 32 0 4 95 19 110 9.08e-44 143
MS.gene29228.t1 AT2G38880 65.217 92 32 0 4 95 19 110 9.08e-44 143
MS.gene29228.t1 AT2G13570 63.158 95 35 0 5 99 35 129 1.64e-43 144
MS.gene29228.t1 AT2G47810 62.500 96 36 0 4 99 49 144 2.24e-41 137
MS.gene29228.t1 AT1G09030 53.191 94 44 0 6 99 3 96 4.37e-35 120
MS.gene29228.t1 AT5G08190 31.481 108 73 1 1 107 6 113 1.04e-15 71.2
MS.gene29228.t1 AT5G08190 32.558 86 58 0 1 86 6 91 1.25e-15 71.2
MS.gene29228.t1 AT5G23090 28.723 94 67 0 1 94 6 99 2.30e-15 70.5
MS.gene29228.t1 AT5G23090 28.723 94 67 0 1 94 6 99 2.66e-15 70.1
MS.gene29228.t1 AT5G23090 28.723 94 67 0 1 94 6 99 2.66e-15 70.1
MS.gene29228.t1 AT5G23090 28.723 94 67 0 1 94 6 99 2.66e-15 70.1
MS.gene29228.t1 AT5G23090 30.986 71 49 0 24 94 16 86 7.22e-11 58.2

Find 30 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGAATGCTGCTGCATTAA+TGG 0.212560 1.1:+23413366 None:intergenic
TTGAATCAATGGCTGGAATA+AGG 0.233634 1.1:-23413719 None:intergenic
AATGGTTATGGTCATGGTTA+TGG 0.317428 1.1:-23413294 MS.gene29228:CDS
ATACGAATCACGTTTGCTAT+TGG 0.343423 1.1:+23413678 None:intergenic
TGTTATGAAGCTTATGTATT+CGG 0.344608 1.1:+23413584 None:intergenic
CGTTGAAGGTAAAATGTTAA+AGG 0.361813 1.1:+23413459 None:intergenic
TTACAGCAGAAGATATACTA+TGG 0.368505 1.1:-23413518 MS.gene29228:CDS
TTATAATTATTATTAATTAG+AGG 0.371549 1.1:+23413321 None:intergenic
TGAATCAATGGCTGGAATAA+GGG 0.407117 1.1:-23413718 None:intergenic
CACTTTCACGGTAACGTTGA+AGG 0.420587 1.1:+23413445 None:intergenic
GAAGATATACTATGGGCAAT+GGG 0.428461 1.1:-23413510 MS.gene29228:CDS
CGTTTGCTATTGGCATGTAT+TGG 0.431652 1.1:+23413688 None:intergenic
CAGGTTCACCTTCACTTTCA+CGG 0.431684 1.1:+23413433 None:intergenic
AATTATAATAGCAATGGTTA+TGG 0.433619 1.1:-23413306 MS.gene29228:CDS
AGAAAACTACAATCAAAGTT+TGG 0.434642 1.1:+23413201 None:intergenic
TTCGGATACACATTCTTGAA+TGG 0.445869 1.1:+23413602 None:intergenic
TTATTATTAATTAGAGGAAG+TGG 0.469233 1.1:+23413327 None:intergenic
CTATGGGCAATGGGGAAACT+AGG 0.473445 1.1:-23413501 MS.gene29228:CDS
TGCTGCATTAATGGAAAAGA+AGG 0.476955 1.1:+23413375 None:intergenic
AGGTAACTTGAATCAATGGC+TGG 0.500850 1.1:-23413726 None:intergenic
GAAGTGCGTCGAACAGAAGC+AGG 0.501979 1.1:+23413414 None:intergenic
AATAGCAATGGTTATGGTCA+TGG 0.503506 1.1:-23413300 MS.gene29228:CDS
AATAATAATTATAATAGCAA+TGG 0.511458 1.1:-23413312 MS.gene29228:CDS
AGAAGATATACTATGGGCAA+TGG 0.533910 1.1:-23413511 MS.gene29228:CDS
GGTACAAAACTAGAGGAAGA+AGG 0.581984 1.1:+23413222 None:intergenic
AAAGTTTGGTACAAAACTAG+AGG 0.609583 1.1:+23413215 None:intergenic
TACAGCAGAAGATATACTAT+GGG 0.616567 1.1:-23413517 MS.gene29228:CDS
CAACGTTACCGTGAAAGTGA+AGG 0.630890 1.1:-23413441 MS.gene29228:CDS
TGCATTAATGGAAAAGAAGG+AGG 0.643868 1.1:+23413378 None:intergenic
AAGATATACTATGGGCAATG+GGG 0.655865 1.1:-23413509 MS.gene29228:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATAATTATAATAGCAA+TGG - chr1.1:23413563-23413582 MS.gene29228:CDS 10.0%
!! AATTATAATAGCAATGGTTA+TGG - chr1.1:23413569-23413588 MS.gene29228:CDS 20.0%
!! TTATTATTAATTAGAGGAAG+TGG + chr1.1:23413551-23413570 None:intergenic 20.0%
! AGAAAACTACAATCAAAGTT+TGG + chr1.1:23413677-23413696 None:intergenic 25.0%
! TGTTATGAAGCTTATGTATT+CGG + chr1.1:23413294-23413313 None:intergenic 25.0%
!!! ATGGTTTTGATTTTGATCAA+GGG - chr1.1:23413600-23413619 MS.gene29228:CDS 25.0%
!!! TATGGTTTTGATTTTGATCA+AGG - chr1.1:23413599-23413618 MS.gene29228:CDS 25.0%
AAAGTTTGGTACAAAACTAG+AGG + chr1.1:23413663-23413682 None:intergenic 30.0%
CGTTGAAGGTAAAATGTTAA+AGG + chr1.1:23413419-23413438 None:intergenic 30.0%
TACAGCAGAAGATATACTAT+GGG - chr1.1:23413358-23413377 MS.gene29228:CDS 30.0%
TTACAGCAGAAGATATACTA+TGG - chr1.1:23413357-23413376 MS.gene29228:CDS 30.0%
!! CTGTTTTTCTTTGTTCTCTT+TGG + chr1.1:23413337-23413356 None:intergenic 30.0%
AAGATATACTATGGGCAATG+GGG - chr1.1:23413366-23413385 MS.gene29228:CDS 35.0%
AATAGCAATGGTTATGGTCA+TGG - chr1.1:23413575-23413594 MS.gene29228:CDS 35.0%
AATGGTTATGGTCATGGTTA+TGG - chr1.1:23413581-23413600 MS.gene29228:CDS 35.0%
AGAAGATATACTATGGGCAA+TGG - chr1.1:23413364-23413383 MS.gene29228:CDS 35.0%
GAAGATATACTATGGGCAAT+GGG - chr1.1:23413365-23413384 MS.gene29228:CDS 35.0%
TGCATTAATGGAAAAGAAGG+AGG + chr1.1:23413500-23413519 None:intergenic 35.0%
TGCTGCATTAATGGAAAAGA+AGG + chr1.1:23413503-23413522 None:intergenic 35.0%
TTCGGATACACATTCTTGAA+TGG + chr1.1:23413276-23413295 None:intergenic 35.0%
!! ATACGAATCACGTTTGCTAT+TGG + chr1.1:23413200-23413219 None:intergenic 35.0%
!! GATCAAGGGTTTTATAGAGA+TGG - chr1.1:23413614-23413633 MS.gene29228:CDS 35.0%
GAAGAATGCTGCTGCATTAA+TGG + chr1.1:23413512-23413531 None:intergenic 40.0%
GGTACAAAACTAGAGGAAGA+AGG + chr1.1:23413656-23413675 None:intergenic 40.0%
! AATGGTTTCTTTTGCGTCGT+CGG + chr1.1:23413258-23413277 None:intergenic 40.0%
!! CAAGGGTTTTATAGAGATGG+TGG - chr1.1:23413617-23413636 MS.gene29228:CDS 40.0%
!! CGTTTGCTATTGGCATGTAT+TGG + chr1.1:23413190-23413209 None:intergenic 40.0%
CAACGTTACCGTGAAAGTGA+AGG - chr1.1:23413434-23413453 MS.gene29228:CDS 45.0%
CACTTTCACGGTAACGTTGA+AGG + chr1.1:23413433-23413452 None:intergenic 45.0%
CAGGTTCACCTTCACTTTCA+CGG + chr1.1:23413445-23413464 None:intergenic 45.0%
! TCGGAGATTTTTGCATGCGA+CGG + chr1.1:23413239-23413258 None:intergenic 45.0%
!! TTATAATTATTATTAATTAG+AGG + chr1.1:23413557-23413576 None:intergenic 5.0%
CTATGGGCAATGGGGAAACT+AGG - chr1.1:23413374-23413393 MS.gene29228:CDS 50.0%
GAAGTGCGTCGAACAGAAGC+AGG + chr1.1:23413464-23413483 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 23413164 23413733 23413164 ID=MS.gene29228
chr1.1 mRNA 23413164 23413733 23413164 ID=MS.gene29228.t1;Parent=MS.gene29228
chr1.1 exon 23413164 23413733 23413164 ID=MS.gene29228.t1.exon1;Parent=MS.gene29228.t1
chr1.1 CDS 23413164 23413733 23413164 ID=cds.MS.gene29228.t1;Parent=MS.gene29228.t1
Gene Sequence

>MS.gene29228

ATGGCTGGAATAAGGGAACAAGACCAATACATGCCAATAGCAAACGTGATTCGTATAATGCGACGAATTCTTCCGTCGCATGCAAAAATCTCCGACGACGCAAAAGAAACCATTCAAGAATGTGTATCCGAATACATAAGCTTCATAACATCTGAAGCAAACGATCGTTGCCAAAGAGAACAAAGAAAAACAGTTACAGCAGAAGATATACTATGGGCAATGGGGAAACTAGGTTTTGATGATTATGTTCATCCTTTAACATTTTACCTTCAACGTTACCGTGAAAGTGAAGGTGAACCTGCTTCTGTTCGACGCACTTCTTCTCTTGCTTTGCCTCCTTCTTTTCCATTAATGCAGCAGCATTCTTCATCATTTTCATCAATGCCACTTCCTCTAATTAATAATAATTATAATAGCAATGGTTATGGTCATGGTTATGGTTTTGATTTTGATCAAGGGTTTTATAGAGATGGTGGTGATGATGCTGCTCCTTCTTCCTCTAGTTTTGTACCAAACTTTGATTGTAGTTTTCTTCATCTCAAACGTGATAATCATAATAATAATATGTGA
Protein sequence

>MS.gene29228.t1

MAGIREQDQYMPIANVIRIMRRILPSHAKISDDAKETIQECVSEYISFITSEANDRCQREQRKTVTAEDILWAMGKLGFDDYVHPLTFYLQRYRESEGEPASVRRTSSLALPPSFPLMQQHSSSFSSMPLPLINNNYNSNGYGHGYGFDFDQGFYRDGGDDAAPSSSSFVPNFDCSFLHLKRDNHNNNM