AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040472

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040472.t1 MTR_5g093010 76.433 157 25 1 1 157 1 145 2.08e-86 249
MS.gene040472.t1 MTR_7g028905 96.552 116 4 0 1 116 1 116 3.12e-83 240
MS.gene040472.t1 MTR_2g068760 50.467 107 53 0 4 110 12 118 1.06e-38 129
MS.gene040472.t1 MTR_5g083230 51.351 111 54 0 4 114 5 115 4.48e-38 128
MS.gene040472.t1 MTR_5g083960 46.970 132 70 0 6 137 40 171 9.93e-38 128
MS.gene040472.t1 MTR_4g083680 50.926 108 53 0 4 111 14 121 5.65e-37 125
MS.gene040472.t1 MTR_3g031660 48.182 110 57 0 4 113 6 115 1.82e-36 124
MS.gene040472.t1 MTR_3g094690 52.830 106 50 0 6 111 48 153 3.03e-36 125
MS.gene040472.t1 MTR_4g105170 51.376 109 53 0 4 112 10 118 6.50e-36 123
MS.gene040472.t1 MTR_3g071590 52.941 102 48 0 4 105 7 108 9.00e-36 122
MS.gene040472.t1 MTR_7g033800 46.825 126 58 1 4 120 10 135 2.55e-35 121
MS.gene040472.t1 MTR_4g060950 47.321 112 58 1 1 111 20 131 5.15e-35 120
MS.gene040472.t1 MTR_3g077240 56.842 95 41 0 4 98 9 103 8.20e-35 120
MS.gene040472.t1 MTR_2g093310 45.045 111 61 0 1 111 29 139 2.37e-34 119
MS.gene040472.t1 MTR_3g452660 49.558 113 57 0 4 116 6 118 3.10e-34 121
MS.gene040472.t1 MTR_3g094690 52.830 106 49 1 6 111 48 152 3.76e-34 120
MS.gene040472.t1 MTR_3g073690 47.619 105 55 0 4 108 8 112 4.82e-34 119
MS.gene040472.t1 MTR_6g005070 43.182 132 75 0 4 135 8 139 4.56e-33 114
MS.gene040472.t1 MTR_5g017950 48.571 105 54 0 4 108 7 111 1.33e-32 118
MS.gene040472.t1 MTR_5g075020 45.865 133 68 1 6 138 44 172 1.67e-32 115
MS.gene040472.t1 MTR_5g075020 45.865 133 68 1 6 138 48 176 1.98e-32 115
MS.gene040472.t1 MTR_1g095850 40.845 142 76 1 6 147 73 206 2.37e-32 115
MS.gene040472.t1 MTR_8g040900 50.459 109 52 1 4 112 6 112 3.92e-32 114
MS.gene040472.t1 MTR_6g005080 48.039 102 53 0 4 105 9 110 6.62e-31 108
MS.gene040472.t1 MTR_3g071420 46.465 99 53 0 4 102 13 111 1.91e-30 108
MS.gene040472.t1 MTR_5g083010 44.660 103 57 0 4 106 10 112 3.41e-30 108
MS.gene040472.t1 MTR_7g096530 46.667 105 55 1 4 107 13 117 6.57e-30 108
MS.gene040472.t1 MTR_6g011250 36.620 142 89 1 6 146 10 151 1.66e-28 103
MS.gene040472.t1 MTR_1g070220 48.000 100 51 1 6 104 16 115 3.40e-28 103
MS.gene040472.t1 MTR_6g027710 41.818 110 63 1 2 110 37 146 4.52e-28 103
MS.gene040472.t1 MTR_7g096610 39.161 143 84 2 4 143 7 149 3.85e-26 99.0
MS.gene040472.t1 MTR_6g011230 42.268 97 56 0 6 102 12 108 8.92e-26 97.4
MS.gene040472.t1 MTR_8g079660 40.000 105 63 0 2 106 5 109 1.05e-25 99.0
MS.gene040472.t1 MTR_8g036085 41.509 106 61 1 6 110 24 129 1.10e-25 98.2
MS.gene040472.t1 MTR_1g070205 44.118 102 56 1 6 106 13 114 2.17e-25 97.4
MS.gene040472.t1 MTR_7g074990 44.554 101 55 1 6 105 21 121 2.65e-25 97.1
MS.gene040472.t1 MTR_6g011200 37.963 108 66 1 6 112 10 117 4.76e-24 94.4
MS.gene040472.t1 MTR_5g080470 41.346 104 60 1 4 106 6 109 6.93e-24 92.4
MS.gene040472.t1 MTR_8g079580 42.857 105 59 1 2 105 5 109 1.87e-23 92.0
MS.gene040472.t1 MTR_6g027700 37.405 131 69 3 6 123 8 138 4.23e-23 90.9
MS.gene040472.t1 MTR_8g036105 41.176 102 59 1 6 106 19 120 5.70e-23 90.5
MS.gene040472.t1 MTR_4g099230 37.037 108 67 1 6 112 3 110 1.11e-22 88.2
MS.gene040472.t1 MTR_8g079620 36.190 105 67 0 2 106 5 109 4.01e-22 89.0
MS.gene040472.t1 MTR_8g017090 39.604 101 61 0 6 106 13 113 5.63e-22 89.7
MS.gene040472.t1 MTR_4g107450 42.000 100 58 0 6 105 11 110 8.94e-22 89.0
MS.gene040472.t1 MTR_7g075230 39.423 104 60 2 6 106 13 116 6.72e-21 84.7
MS.gene040472.t1 MTR_5g085390 36.937 111 68 2 6 114 10 120 1.00e-20 85.1
MS.gene040472.t1 MTR_2g100020 34.653 101 66 0 6 106 20 120 3.35e-19 82.0
MS.gene040472.t1 MTR_4g088035 32.955 88 59 0 4 91 5 92 4.68e-14 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040472.t1 AT3G26660 67.647 102 33 0 5 106 5 106 2.67e-48 152
MS.gene040472.t1 AT3G26620 67.647 102 33 0 5 106 5 106 3.05e-48 152
MS.gene040472.t1 AT2G30130 52.727 110 52 0 4 113 7 116 5.00e-39 131
MS.gene040472.t1 AT1G31320 63.636 88 32 0 4 91 12 99 1.87e-36 124
MS.gene040472.t1 AT1G07900 42.969 128 68 1 1 128 29 151 1.13e-35 122
MS.gene040472.t1 AT2G30340 50.943 106 52 0 6 111 53 158 2.90e-35 124
MS.gene040472.t1 AT2G30340 50.943 106 52 0 6 111 54 159 2.93e-35 124
MS.gene040472.t1 AT2G28500 46.847 111 59 0 1 111 51 161 4.10e-35 122
MS.gene040472.t1 AT5G63090 47.009 117 62 0 4 120 10 126 5.16e-35 120
MS.gene040472.t1 AT5G63090 47.009 117 62 0 4 120 10 126 5.16e-35 120
MS.gene040472.t1 AT5G63090 47.009 117 62 0 4 120 10 126 5.16e-35 120
MS.gene040472.t1 AT5G63090 47.009 117 62 0 4 120 10 126 5.16e-35 120
MS.gene040472.t1 AT3G27650 50.000 102 51 0 4 105 38 139 1.12e-33 116
MS.gene040472.t1 AT5G66870 48.544 103 53 0 4 106 6 108 4.56e-33 119
MS.gene040472.t1 AT2G40470 52.885 104 49 0 6 109 21 124 1.11e-32 115
MS.gene040472.t1 AT2G40470 52.885 104 49 0 6 109 46 149 1.93e-32 115
MS.gene040472.t1 AT2G23660 47.170 106 56 0 1 106 1 106 2.20e-32 117
MS.gene040472.t1 AT2G23660 47.170 106 56 0 1 106 1 106 2.20e-32 117
MS.gene040472.t1 AT2G23660 47.170 106 56 0 1 106 1 106 2.20e-32 117
MS.gene040472.t1 AT1G16530 50.476 105 51 1 4 107 13 117 3.29e-32 113
MS.gene040472.t1 AT1G65620 48.113 106 55 0 4 109 8 113 3.79e-32 114
MS.gene040472.t1 AT1G65620 48.113 106 55 0 4 109 8 113 3.79e-32 114
MS.gene040472.t1 AT1G65620 48.113 106 55 0 4 109 8 113 3.79e-32 114
MS.gene040472.t1 AT1G65620 48.113 106 55 0 4 109 8 113 3.79e-32 114
MS.gene040472.t1 AT1G65620 48.113 106 55 0 4 109 8 113 3.79e-32 114
MS.gene040472.t1 AT3G11090 44.762 105 58 0 4 108 10 114 8.73e-32 112
MS.gene040472.t1 AT4G00210 37.500 144 80 3 6 139 12 155 1.85e-27 102
MS.gene040472.t1 AT3G50510 34.641 153 84 2 2 154 9 145 2.83e-27 101
MS.gene040472.t1 AT3G50510 34.641 153 84 2 2 154 9 145 2.83e-27 101
MS.gene040472.t1 AT2G42430 44.860 107 58 1 4 109 14 120 4.80e-27 102
MS.gene040472.t1 AT3G03760 44.554 101 55 1 6 105 52 152 7.39e-27 102
MS.gene040472.t1 AT2G42440 45.098 102 55 1 4 104 6 107 1.12e-25 98.2
MS.gene040472.t1 AT5G06080 43.243 111 62 1 4 113 6 116 1.67e-25 96.3
MS.gene040472.t1 AT3G58190 44.118 102 56 1 6 106 12 113 2.81e-25 96.7
MS.gene040472.t1 AT3G13850 35.714 154 91 2 6 151 37 190 4.66e-25 97.4
MS.gene040472.t1 AT4G00220 42.308 104 59 1 8 110 20 123 4.25e-24 94.0
MS.gene040472.t1 AT2G45420 42.308 104 59 1 8 110 40 143 1.37e-23 93.2
MS.gene040472.t1 AT2G45410 42.000 100 57 1 8 106 19 118 1.94e-23 91.3
MS.gene040472.t1 AT5G35900 37.624 101 63 0 6 106 6 106 5.41e-22 87.8
MS.gene040472.t1 AT3G47870 37.500 104 65 0 6 109 37 140 7.00e-22 89.7
MS.gene040472.t1 AT2G31310 34.615 104 67 1 4 106 6 109 3.26e-20 82.8
MS.gene040472.t1 AT1G06280 37.931 87 54 0 6 92 25 111 4.49e-18 77.8
MS.gene040472.t1 AT1G72980 36.000 100 64 0 6 105 14 113 6.84e-18 77.4
MS.gene040472.t1 AT2G19820 34.043 94 61 1 6 98 13 106 1.67e-15 68.9
MS.gene040472.t1 AT4G22700 33.043 115 71 3 1 110 1 114 1.59e-13 65.5
MS.gene040472.t1 AT5G15060 43.243 74 38 2 6 76 18 90 7.99e-13 62.4
MS.gene040472.t1 AT1G36000 30.233 86 60 0 6 91 10 95 7.40e-12 59.3

Find 31 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCTTCAAATTGTTGATTT+TGG 0.080390 7.3:+71520938 None:intergenic
AGGATTCAAGATCCTGTTTA+TGG 0.232394 7.3:-71521054 MS.gene040472:CDS
GGCCTAGTCAAACTCCTAAT+TGG 0.295938 7.3:-71520825 MS.gene040472:CDS
GGATCATTGGGAGGGAAATA+TGG 0.321654 7.3:+71521558 None:intergenic
GCTTCTGTTCACCGAATCTA+TGG 0.327300 7.3:-71521525 MS.gene040472:CDS
AGCAAATCTTTGAGGATCAT+TGG 0.352548 7.3:+71521545 None:intergenic
AACTCCTAATTGGTTCAATT+AGG 0.365498 7.3:-71520815 None:intergenic
AAGTCCTAATTGAACCAATT+AGG 0.385923 7.3:+71520811 None:intergenic
TTAACATCATGATTTATAGT+AGG 0.409376 7.3:-71521635 None:intergenic
ATCCCAACACATCCATAAAC+AGG 0.432009 7.3:+71521042 None:intergenic
GCAAATCTTTGAGGATCATT+GGG 0.442273 7.3:+71521546 None:intergenic
CTCCAAAATCAACAATTTGA+AGG 0.458414 7.3:-71520940 MS.gene040472:CDS
ATCTATGGTGGTAGCAATGT+TGG 0.480363 7.3:-71521510 MS.gene040472:CDS
TGTATTTAGAAGCACAATGT+AGG 0.497154 7.3:-71521074 MS.gene040472:CDS
ATCCTGTTTATGGATGTGTT+GGG 0.518295 7.3:-71521044 MS.gene040472:CDS
TCAAGATACAGAAGTTGAGT+TGG 0.518830 7.3:-71520995 MS.gene040472:CDS
TATGGAGAGAAAATGCAATC+AGG 0.521384 7.3:+71521576 None:intergenic
ACAACATGGAGCAGATTCAA+TGG 0.528352 7.3:-71520846 MS.gene040472:CDS
CATTGCTACCACCATAGATT+CGG 0.528587 7.3:+71521514 None:intergenic
GATCCTGTTTATGGATGTGT+TGG 0.530554 7.3:-71521045 MS.gene040472:CDS
TGAACAGAAGCAAATCTTTG+AGG 0.534397 7.3:+71521537 None:intergenic
AATACATAGAATTTGCAGCT+TGG 0.550687 7.3:+71521091 None:intergenic
CTTGCAAGAGTCAAAGAAGA+AGG 0.562843 7.3:-71521605 MS.gene040472:CDS
ATCTTTGAGGATCATTGGGA+GGG 0.584186 7.3:+71521550 None:intergenic
AATCTTTGAGGATCATTGGG+AGG 0.604113 7.3:+71521549 None:intergenic
TCTGTTCACCGAATCTATGG+TGG 0.619615 7.3:-71521522 MS.gene040472:CDS
AACCAATTAGGAGTTTGACT+AGG 0.647531 7.3:+71520823 None:intergenic
TCCATGTTGTTACTATGTAG+TGG 0.647940 7.3:+71520859 None:intergenic
GCCACTACATAGTAACAACA+TGG 0.651155 7.3:-71520860 MS.gene040472:CDS
GCTTGGTGTCGTACATAGTG+AGG 0.654586 7.3:+71521108 None:intergenic
GGAGAGAAAATGCAATCAGG+AGG 0.655607 7.3:+71521579 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAAAATAATCTTATTG+TGG - chr7.3:71521290-71521309 MS.gene040472:intron 10.0%
!! AACATTATATAATTATAGCA+TGG - chr7.3:71521199-71521218 MS.gene040472:intron 15.0%
!! TACTATGTAATATATTATTG+TGG - chr7.3:71521055-71521074 MS.gene040472:CDS 15.0%
!! TCAATGTAAGAATCAATATT+TGG - chr7.3:71521098-71521117 MS.gene040472:CDS 20.0%
AATACATAGAATTTGCAGCT+TGG + chr7.3:71521355-71521374 None:intergenic 30.0%
CTCCAAAATCAACAATTTGA+AGG - chr7.3:71521503-71521522 MS.gene040472:CDS 30.0%
! TGTATTTAGAAGCACAATGT+AGG - chr7.3:71521369-71521388 MS.gene040472:intron 30.0%
!!! CACCTTCAAATTGTTGATTT+TGG + chr7.3:71521508-71521527 None:intergenic 30.0%
AACCAATTAGGAGTTTGACT+AGG + chr7.3:71521623-71521642 None:intergenic 35.0%
AGGATTCAAGATCCTGTTTA+TGG - chr7.3:71521389-71521408 MS.gene040472:intron 35.0%
ATCCTGTTTATGGATGTGTT+GGG - chr7.3:71521399-71521418 MS.gene040472:intron 35.0%
CAATGTTGGAAAAATGCTTC+AGG - chr7.3:71520947-71520966 MS.gene040472:CDS 35.0%
TATGGAGAGAAAATGCAATC+AGG + chr7.3:71520870-71520889 None:intergenic 35.0%
TCAAGATACAGAAGTTGAGT+TGG - chr7.3:71521448-71521467 MS.gene040472:intron 35.0%
TCCATGTTGTTACTATGTAG+TGG + chr7.3:71521587-71521606 None:intergenic 35.0%
TGAACAGAAGCAAATCTTTG+AGG + chr7.3:71520909-71520928 None:intergenic 35.0%
! AGCAAATCTTTGAGGATCAT+TGG + chr7.3:71520901-71520920 None:intergenic 35.0%
! GCAAATCTTTGAGGATCATT+GGG + chr7.3:71520900-71520919 None:intergenic 35.0%
ACAACATGGAGCAGATTCAA+TGG - chr7.3:71521597-71521616 MS.gene040472:CDS 40.0%
ATCCCAACACATCCATAAAC+AGG + chr7.3:71521404-71521423 None:intergenic 40.0%
ATCTATGGTGGTAGCAATGT+TGG - chr7.3:71520933-71520952 MS.gene040472:CDS 40.0%
CATTGCTACCACCATAGATT+CGG + chr7.3:71520932-71520951 None:intergenic 40.0%
CTTGCAAGAGTCAAAGAAGA+AGG - chr7.3:71520838-71520857 MS.gene040472:CDS 40.0%
GATCCTGTTTATGGATGTGT+TGG - chr7.3:71521398-71521417 MS.gene040472:intron 40.0%
GCCACTACATAGTAACAACA+TGG - chr7.3:71521583-71521602 MS.gene040472:CDS 40.0%
! AATCTTTGAGGATCATTGGG+AGG + chr7.3:71520897-71520916 None:intergenic 40.0%
! ATCTTTGAGGATCATTGGGA+GGG + chr7.3:71520896-71520915 None:intergenic 40.0%
GCTTCTGTTCACCGAATCTA+TGG - chr7.3:71520918-71520937 MS.gene040472:CDS 45.0%
GGAGAGAAAATGCAATCAGG+AGG + chr7.3:71520867-71520886 None:intergenic 45.0%
GGATCATTGGGAGGGAAATA+TGG + chr7.3:71520888-71520907 None:intergenic 45.0%
GGCCTAGTCAAACTCCTAAT+TGG - chr7.3:71521618-71521637 MS.gene040472:CDS 45.0%
TCTGTTCACCGAATCTATGG+TGG - chr7.3:71520921-71520940 MS.gene040472:CDS 45.0%
!! GCTTGGTGTCGTACATAGTG+AGG + chr7.3:71521338-71521357 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 71520816 71521649 71520816 ID=MS.gene040472
chr7.3 mRNA 71520816 71521649 71520816 ID=MS.gene040472.t1;Parent=MS.gene040472
chr7.3 exon 71521497 71521649 71521497 ID=MS.gene040472.t1.exon1;Parent=MS.gene040472.t1
chr7.3 CDS 71521497 71521649 71521497 ID=cds.MS.gene040472.t1;Parent=MS.gene040472.t1
chr7.3 exon 71520816 71521136 71520816 ID=MS.gene040472.t1.exon2;Parent=MS.gene040472.t1
chr7.3 CDS 71520816 71521136 71520816 ID=cds.MS.gene040472.t1;Parent=MS.gene040472.t1
Gene Sequence

>MS.gene040472

ATGATTTATAGTAGGTGTGCTGCTTGCAAGAGTCAAAGAAGAAGGTGTCCTCCTGATTGCATTTTCTCTCCATATTTCCCTCCCAATGATCCTCAAAGATTTGCTTCTGTTCACCGAATCTATGGTGGTAGCAATGTTGGAAAAATGCTTCAGGTACTCTTAATAATATAATAAATATATCAATTCAATATTTAGTATTTTTTTTTTGAAATAATCAATATTTAGTATCTAGTATGTATTACTATGTAATATATTATTGTGGAATTTACTTGTAATTTTGTGTCAATGTAAGAATCAATATTTGGTATCTAGATTTCATTAGTGTACTTTTAACTTATAAATTATCAATATCAATATTTAGTATCTAGTATGTATTAGTATGTAACATTATATAATTATAGCATGGACAGAATATAAGAGTTAGAAAAAGTATACTTTTTACTTATAGTTTTTTTTTTTAATGAAAATTTGTATATTTTAAAATAATCTTATTGTGGAATTTTAATGTTGTAGCAATTGCCTCACTATGTACGACACCAAGCTGCAAATTCTATGTATTTAGAAGCACAATGTAGGATTCAAGATCCTGTTTATGGATGTGTTGGGATTATCTCTAAATTATCTCAACAAATTCAAGATACAGAAGTTGAGTTGGCTAAAATCAAAACTCAGATTGCTTATCATAAACTCCAAAATCAACAATTTGAAGGTGAATCAAACTTCAATGTCTTGTCAACAATTGATGCTGAATCAAACTTAAGCTCTTTGCCACTACATAGTAACAACATGGAGCAGATTCAATGGCCTAGTCAAACTCCTAATTGGTTCAATTAG
Protein sequence

>MS.gene040472.t1

MIYSRCAACKSQRRRCPPDCIFSPYFPPNDPQRFASVHRIYGGSNVGKMLQQLPHYVRHQAANSMYLEAQCRIQDPVYGCVGIISKLSQQIQDTEVELAKIKTQIAYHKLQNQQFEGESNFNVLSTIDAESNLSSLPLHSNNMEQIQWPSQTPNWFN